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ECOLOGICAL MODELING

No part of this digital document may be reproduced, stored in a retrieval system or transmitted in any form or

by any means. The publisher has taken reasonable care in the preparation of this digital document, but makes no

expressed or implied warranty of any kind and assumes no responsibility for any errors or omissions. No

liability is assumed for incidental or consequential damages in connection with or arising out of information

contained herein. This digital document is sold with the clear understanding that the publisher is not engaged in

rendering legal, medical or any other professional services.

ENVIRONMENTAL SCIENCE,

ENGINEERING AND TECHNOLOGY

under the Series tab.

ENVIRONMENTAL SCIENCE, ENGINEERING AND TECHNOLOGY

ECOLOGICAL MODELING

WENJUN ZHANG

EDITOR

New York

Copyright © 2012 by Nova Science Publishers, Inc.

All rights reserved. No part of this book may be reproduced, stored in a retrieval system or

transmitted in any form or by any means: electronic, electrostatic, magnetic, tape, mechanical

photocopying, recording or otherwise without the written permission of the Publisher.

For permission to use material from this book please contact us:

Telephone 631-231-7269; Fax 631-231-8175

Web Site: http://www.novapublishers.com

The Publisher has taken reasonable care in the preparation of this book, but makes no expressed or

implied warranty of any kind and assumes no responsibility for any errors or omissions. No

liability is assumed for incidental or consequential damages in connection with or arising out of

information contained in this book. The Publisher shall not be liable for any special,

consequential, or exemplary damages resulting, in whole or in part, from the readers‘ use of, or

reliance upon, this material. Any parts of this book based on government reports are so indicated

and copyright is claimed for those parts to the extent applicable to compilations of such works.

Independent verification should be sought for any data, advice or recommendations contained in

this book. In addition, no responsibility is assumed by the publisher for any injury and/or damage

to persons or property arising from any methods, products, instructions, ideas or otherwise

contained in this publication.

This publication is designed to provide accurate and authoritative information with regard to the

subject matter covered herein. It is sold with the clear understanding that the Publisher is not

engaged in rendering legal or any other professional services. If legal or any other expert

assistance is required, the services of a competent person should be sought. FROM A

DECLARATION OF PARTICIPANTS JOINTLY ADOPTED BY A COMMITTEE OF THE

AMERICAN BAR ASSOCIATION AND A COMMITTEE OF PUBLISHERS.

Additional color graphics may be available in the e-book version of this book.

p. cm.

Includes bibliographical references and index.

ISBN 978-1-62417-275-5 (eBook)

1. Ecology--Simulation methods. I. Zhang, Wen-Jun.

QH541.15.S5E275 2011

577.01'13--dc23

2011013661

CONTENTS

Preface vii

Chapter 1 Artificial Neural Network Simulation of Spatial Distribution of

Arthropods: A Multi-Model Comparison 1

WenJun Zhang and GuangHua Liu

Chapter 2 Multispectral Vegetation Indices in Remote Sensing:

An Overview 15

George P. Petropoulos and

Chariton Kalaitzidis

Chapter 3 Development of a Decision Support System for the Estimation of

Surface Water Pollution Risk From Olive Mill Waste Discharges 41

Anas Altartouri, Kalliope Pediaditi, George P. Petropoulos,

Dimitris Zianis and Nikos Boretos

Chapter 4 Analysis of Green Oak Leaf Roller Population Dynamics

in Various Locations 65

L. V. Nedorezov

Chapter 5 Individual Based Modelling of Planktonic Organisms 83

Daniela Cianelli, Marco Uttieri

and Enrico Zambianchi

Chapter 6 The Effectiveness of Artificial Neural Networks

in Modelling the Nutritional Ecology of a Blowfly Species 97

Michael J. Watts, Andre Bianconi,

Adriane Beatriz S. Serapiao, Jose S. Govone

and Claudio J. Von Zuben

Chapter 7 Development and Utility of an Ecological-based

Decision-Support System for Managing Mixed Coniferous

Forest Stands for Multiple Objectives 115

Peter F. Newton

vi Contents

Past, Present and Future 173

A. Márcia Barbosa, Neftalí Sillero,

Fernando Martínez-Freiría

and Raimundo Real

Chapter 9 Some Aspects of Phytoplankton and Ecosystem Modelling

in Freshwater and Marine Environments: Consideration

of Indirect Interactions, and the Implications for Interpreting

Past and Future Overall Ecosystem Functioning 205

V. Krivtsov and C.F. Jago

Chapter 10 Modeling Population Dynamics, Division of Labor

and Nutrient Economics of Social Insect Colonies 223

Thomas Schmickl and Karl Crailsheim

Chapter 11 Observation and Control in Density-

and Frequency-Dependent Population Models 267

Manuel Gámez

Chapter 12 Environmental Noise and Nonlinear Relaxation

in Biological Systems 289

B. Spagnolo, D. Valenti, S. Spezia, L. Curcio, N. Pizzolato,

A. A. Dubkov, A. Fiasconaro, D. Persano Adorno, P. Lo Bue,

E. Peri and S. Colazza

Chapter 13 Landscape Structural Modeling:

A Multivariate Cartographic Exegesis 325

Alessandro Ferrarini

Chapter 14 Basic Concepts for Modelling in Different and Complementary

Ecological Fields: Plants Canopies Conservation, Thermal

Efficiency in Buildings and Wind Energy Producing 335

Mohamed Habib Sellami

Index 391

PREFACE

Ecological modeling is a fast growing science. More and more innovative methodologies

and theories on ecological modeling are emerging around the world. This book presents

models, methods and theories on ecological modeling. Topics discussed include artificial

neural networks; individual-based modeling; ecological nich models; landscape and GIS

modeling; population dynamics; nutritional ecology; remote sensing and decision support

systems. This book reflects recent achievements of scientists in the study of ecological

modeling.

Chapter 1 - Probability distribution functions have been widely used to model the spatial

distribution of arthropods. Aggregation types (i.e., randomly distributed, uniformly

distributed, aggregately distributed, etc.) of arthropods can be detected based on probability

distribution functions, but the abundance at given location is not able to be predicted by them.

This study aimed to present an artificial neural network to simulate spatial distribution of

arthropods. Response surface model and spline function were compared and evaluated against

the neural network model for their simulation performance.

The results showed that the artificial neural network exhibited good simulation

performance. Simulated spatial distribution was highly in accordant with the observed one.

Overall the neural network performed better in the case of lower total abundance of

arthropods. Response surface model could fit the spatial distribution of arthropods but the

simulation performance was worse than neural network. Cross validation revealed that neural

network performed better than response surface model and spline function in predicting

spatial distribution of arthropods. Confidence interval of predicted abundance could be

obtained using randomized submission of quadrate sequences in the neural network

simulation. It is concluded that artificial neural network is a valuable model to simulate the

spatial distribution of arthropods.

Chapter 2 – Remote sensing has generally demonstrated a great potential in mapping

spatial patterns of vegetation. By employing the amount of reflected radiation at particular

regions of the electromagnetic spectrum, it is possible to make estimates on certain

characteristic of vegetation. The use of radiometric vegetation indices is a fast and efficient

method for vegetation monitoring, exploiting information acquired from remote sensing data.

These indices are dimensionless radiometric measures that generally function as indicators of

relative abundance and activity of green vegetation.

Throughout the years, a large number of multispectral vegetation indices have been

formulated. Each has variable degree of efficiency in estimating one or more vegetation

viii WenJun Zhang

parameters such as, health status, nutrient or water deficiency, crop yield, vegetation cover

fraction, leaf area index, absorbed photosynthetically active radiation, net primary production

and above-ground biomass. Additionally some of them also consider atmospheric effects and/

or the soil background for an enhanced retrieval. The present chapter aims in providing an

overview on the use of radiometric vegetation indices developed over the last few decades,

utilizing spectral information acquired from multispectral optical remote sensing sensors.

This overview is preceded an introduction to some important principles of remote sensing

relevant to the vegetation spectral response is made available, as this was considered

necessary to better understand the context of the present overview.

Chapter 3 – According to the Water Framework Directive (WFD, 2000/60/EC),

Integrated River Basin Management Plans (RBMP) are required at different scales, in order to

prevent amongst other things, water resource deterioration and ensure water pollution

reduction. An integrated river basin management approach underpins a risk-based land

management framework for all activities within a spatial land-use planning framework. To

this end, a risk assessment methodology is required to identify water pollution hazards in

order to set appropriate environmental objectives and in turn design suitable mitigation

measures. Surface water pollution as a result of Olive Mill Waste (OMW) discharge is a

serious hazard in the olive oil producing regions of the Mediterranean. However, there is no

standardised method to assess the risk of water pollution from olive mill waste for any given

river basin. The present chapter shows the results from a study conducted addressing the

above issue by designing a detailed risk assessment methodology, which utilises GIS

modelling to classify within a watershed individual sub-catchment risk of water pollution

occurring from olive mill waste discharges. The chapter presents the proposed criteria and

calculations required to estimate sub-catchment risk significance and comments on the

methods potential for wider application. It combines elements from risk assessment

frameworks, Multi Criteria Analysis (MCA), and Geographic Information Systems (GIS).

MCA is used to aggregate different aspects and elements associated with this environmental

problem, while GIS modeling tools helped in obtaining many criterion values and providing

insight into how different objects interact in nature and how these interactions influence risk

at the watershed level. The proposed method was trialed in the Keritis watershed in Crete,

Greece and the results indicated that this method has the potential to be a useful guide to

prioritise risk management actions and mitigation measures which can subsequently be

incorporated in river basin management plans.

Chapter 4 - Publication is devoted to the problem of population time series analysis with

various discrete time models of population dynamics. Applications of various statistical

criterions, which are normally used for determination of mathematical model parameters, are

under the discussion. With a particular example on green oak leaf roller (Tortrix viridana L.)

population fluctuations, which had been presented in publications by Rubtsov (1992), and

Korzukhin and Semevskiy (1992) for three different locations in Europe, the possibilities of

considering approach to the analysis of population dynamics are demonstrated. For

approximations of empirical datasets the well-known models of population dynamics with a

discrete time (Kostitzin model, Skellam model, Moran – Ricker model, Morris – Varley –

Gradwell model, and discrete logistic model) were applied. For every model the final decision

about the possibility to use the concrete model for approximation of datasets are based on

analyses of deviations between theoretical (model) and empirical trajectories: the

correspondence of distribution of deviations to Normal distribution with zero average was

Preface ix

checked with Kolmogorov – Smirnov and Shapiro – Wilk tests, and existence/absence of

serial correlation was determined with Durbin – Watson criteria. It was shown that for two

experimental trajectories Kostitzin model and discrete logistic model give good

approximations; it means that population dynamics can be explained as a result of influence

of intra-population self-regulative mechanisms only. The third considering empirical

trajectory needs in use more complicated mathematical models for fitting.

Chapter 5 - In the last decades, numerical modelling has gained increasing consensus in

the scientific world, and particularly in the framework of behavioural and population ecology.

Through numerical models it is possible to reconstruct what is observed in the environment or

in the laboratory and to get a more in-depth comprehension of the factors regulating the

phenomena under examination.

Numerous approaches have been developed in this framework, but probably one of the

most promising is the individual-based modelling. With this type of approach it is relatively

straightforward to investigate aspects related to the ecology of a population starting from the

characterisation of processes taking place at the scale of the individual organism.

This contribution is intended to provide a general view of the main features of the

individual-based models and of their peculiarities in comparison to other modelling strategies.

Special emphasis will be given to applications in the field of phyto- and zooplankton ecology

and behaviour, and results from the available literature on this topic will be used as examples.

Chapter 6 - The larval phase of most blowfly species is considered a critical

developmental period in which intense limitation of feeding resources frequently occurs.

Furthermore, such a period is characterised by complex ecological processes occurring at

both individual and population levels. These processes have been analysed by means of

traditional statistical techniques such as simple and multiple linear regression models.

Nonetheless, it has been suggested that some important explanatory variables could well

introduce non-linearity into the modelling of the nutritional ecology of blowflies. In this

context, dynamic aspects of the life history of blowflies could be clarified and detailed by the

deployment of machine learning approaches such as artificial neural networks (ANNs), which

are mathematical tools widely applied to the resolution of complex problems. A

distinguishing feature of neural network models is that their effective implementation is not

precluded by the theoretical distribution of the data used. Therefore, the principal aim of this

investigation was to use neural network models (namely multi-layer perceptrons and fuzzy

neural networks) in order to ascertain whether these tools would be able to outperform a

general quadratic model (that is, a second-order regression model with three predictor

variables) in predicting pupal weight values (outputs) of experimental populations of

Chrysomya megacephala (F.) (Diptera: Calliphoridae), using initial larval density (number of

larvae), amount of available food, and pupal size as input variables. These input variables

may have generated non-linear variation in the output values, and fuzzy neural networks

provided more accurate outcomes than the general quadratic model (i.e. the statistical model).

The superiority of fuzzy neural networks over a regression-based statistical method does

represent an important fact, because more accurate models may well clarify several intricate

aspects regarding the nutritional ecology of blowflies. Additionally, the extraction of fuzzy

rules from the fuzzy neural networks provided an easily comprehensible way of describing

what the networks had learnt.

Chapter 7 - An ecological-based decision-support system and corresponding algorithmic

analogue for managing natural black spruce (Picea mariana (Mill) BSP.) and jack pine (Pinus

x WenJun Zhang

banksiana Lamb.) mixed stands was developed. The integrated hierarchical system consisted

of six sequentially-linked estimation modules. The first module consisted of a key set of

empirical yield-density relationships and theoretically-based functions derived from allometry

and self-thinning theory that were used to describe overall stand dynamics including temporal

size-density interrelationships and expected stand development trajectories. The second

module was comprised of a Weibull-based parameter prediction equation system and an

accompanying composite height-diameter function that were used to recover diameter and

height distributions. The third module included a set of species-specific composite taper

equations that were used to derive log product distributions and volumetric yields. The fourth

module was composed of a set of species-specific allometric-based composite biomass

equations that were used to estimate mass distributions and associated carbon-based

equivalents for each above-ground component (bark, stem, branch and foliage). The fifth

module incorporated a set of species-specific end-product and value equations that were used

to predict chip and lumber volumes and associated monetary equivalents by sawmill type

(stud and randomized length mill configurations). The sixth module encompassed a set of

species-specific composite equations that were used to derive wood and log quality metrics

(specific gravity and mean maximum branch diameter, respectively). The stand dynamic and

structural recovery modules were developed employing 382 stand-level measurements

derived from 155 permanent and temporary sample plots situated throughout the central

portion of the Canadian Boreal Forest Region, the taper and end-product modules were

developed employing published results from taper and sawmill simulation studies, and the

biomass and fibre attribute modules were developed using data from density control

experiments.

The potential of the system in facilitating the transformative change towards the

production of higher value end-products and a broader array of ecosystem services was

exemplified by simultaneously contrasting the consequences of density management regimes

involving commercial thinning treatments in terms of overall productivity, end-product

yields, economic efficiency, and ecological impact. This integration of quantitative

relationships derived from applied ecology, plant population biology and forest science into a

common analytical platform, illustrates the synergy that can be realized through a multi-

disciplinary approach to forest modeling.

Chapter 8 – The authors present a review of the concepts and methods associated to

ecological niche modeling illustrated with the published works on amphibians and reptiles of

the Mediterranean Basin, one of the world's biodiversity hotspots for conservation priorities.

They start by introducing ecological niche models, analyzing the various concepts of niche

and the modeling methods associated to each of them. The authors list some conceptual and

practical steps that should be followed when modeling, and highlight the pitfalls that should

be avoided. The authors then outline the history of ecological modeling of Mediterranean

amphibians and reptiles, including a variety of aspects: identification of the ecological niche;

detection of common distribution areas (chorotypes) and other biogeographical patterns;

analysis and prediction of species richness patterns; analysis of the expansion of native and

invasive species; integration of molecular data with spatial modeling; identification of contact

zones between related taxa; assessment of species' conservation status; and prediction of

future conservation problems, including the effects of global change. They conclude this

review with a discussion of the research that still needs to be developed in this area.

Preface xi

analysis, path analysis, methods of network analysis, and, in particular, simulation modelling)

may be very helpful in investigations of indirect relationships in aquatic ecosystems. Here we

give a brief overview of some examples of the relevant studies, and focus on 1) a case study

of a freshwater eutrophic lake, where statistical analysis of the datasets obtained within a

comprehensive monitoring programme, and sensitivity analysis by a mathematical model

‗Rostherne‘, helped to reveal the previously overlooked relationships between Si and P

biogeochemical cycles coupled through the dynamics of primary producers, and 2) give an

overview of how the coupling of physical, chemical, and biological processes in the marine

ecosystem models offers a basis for investigations of indirect interactions in continental shelf

seas. Complex aquatic ecosystem models provide a numerical simulation of biogeochemical

fluxes underpinned by coupling physical forcing functions with definitions simulating

biological and chemical processes, and offer a potential for quantitative interpretation of

sediment proxies in the stratigraphic record. Combination of models and sediment proxies,

calibrated by training sets, can provide information on water column structure, surface

heating, mixing, and water depth, thus providing a basis for reconstruction of the past, and

predicting the future environmental dynamics.

Chapter 10 - In the evolution of social insects, the colony and not the (often sterile)

individual worker should be considered the major unit of selection. Thus, social insect

colonies are considered to be 'super-organisms', which have – like all other organisms – to

perform behaviors which affect their outside environment and which alter their own future

internal status. The way these behaviors are coordinated is by means of communication,

which is either direct or indirect and which involves information exchange either by

transmitting signals or by exploiting cues. Therefore, social insect colonies perform

information processing in a rather similar way as multicellular organisms do, where behaviors

result from the exchange of information among their sub-modules (cells). In many cases, self-

organization allows a colony to evaluate massive amounts of information in parallel and to

decide about the colony's future behavioral responses. Many feedback systems that govern

self-organization of workers have been investigated empirically and theoretically. Here, the

authors discuss models which have been proposed to explain division of labor and task

selection in social insects. The authors demonstrate how the collective regulation of labor in

eusocial insect colonies is studied by means of top-down modeling and by bottom-up models,

often analyzed with multi-agent computer simulations.

Chapter 11 - The paper is a review of a research line initiated two decades ago. At the

beginning the research was concentrated on basic qualitative properties of ecological and

population-genetic models, such as observability and controllability. For population system,

observability means that, e.g. from partial observation of the system (observing only certain

indicator species), in principle the whole state process can be recovered. Recently, for

different ecosystems, the so-called observer system (or state estimators) have been

constructed that enables us to effectively estimate the whole state process from the

observation. The methodology of observer design can be also applied to estimate unknown

changes in ecological parameters of the system. Clearly, both observation (i.e. monitoring)

and control are important issues in conservation ecology. For an ecological system, in an

appropriate setting, controllability implies that a disturbed ecosystem can be steered beck to

an equilibrium state by an abiotic human intervention. Recent research concern the effective

calculation of such control functions. While the considered ecological models are density-

xii WenJun Zhang

dependent models of population genetics. As for the frequency-dependent case, observation

systems typically occur in case of phenotypic observation of genetic processes; control

systems can be used to model e.g. artificial selection. In this survey, in addition to the basic

methodology and its applications, the recent developments of the field are also reported.

Chapter 12 – The authors analyse the effects of environmental noise in three different

biological systems: (i) mating behavior of individuals of Nezara viridula (L.) (Heteroptera

Pentatomidae); (ii) polymer translocation in crowded solution; (iii) an ecosystem described by

a Verhulst model with a multiplicative Lévy noise. Specifically, they report on experiments

on the behavioral response of N. viridula individuals to sub-threshold deterministic signals in

the presence of noise. The authors analyze the insect response by directionality tests

performed on a group of male individuals at different noise intensities. The percentage of

insects which react to the sub-threshold signal shows a nonmonotonic behavior, characterized

by the presence of a maximum, for increasing values of the noise intensity. This is the

signature of the non-dynamical stochastic resonance phenomenon. By using a ―har d‖

threshold model the authors find that the maximum of the signal-to-noise ratio occurs in the

same range of noise intensity values for which the behavioral activation shows a maximum.

In the second system, the noise driven translocation of short polymers in crowded solutions is

analyzed. An improved version of the Rouse model for a flexible polymer has been adopted

to mimic the molecular dynamics, by taking into account both the interactions between

adjacent monomers and introducing a Lennard-Jones potential between non-adjacent beads. A

bending recoil torque has also been included in our model. The polymer dynamics is

simulated in a two-dimensional domain by numerically solving the Langevin equations of

motion. Thermal fluctuations are taken into account by introducing a Gaussian uncorrelated

noise. The mean first translocation time of the polymer center of inertia shows a minimum as

a function of the frequency of the oscillating forcing field. In the third ecosystem, the

transient dynamics of the Verhulst model perturbed by arbitrary non-Gaussian white noise is

investigated. Based on the infinitely divisible distribution of the Lévy process we study the

nonlinear relaxation of the population density for three cases of white non-Gaussian noise: (i)

shot noise, (ii) noise with a probability density of increments expressed in terms of Gamma

function, and (iii) Cauchy stable noise. The authors obtain exact results for the probability

distribution of the population density in all cases, and for Cauchy stable noise the exact

expression of the nonlinear relaxation time is derived. Moreover starting from an initial delta

function distribution, they find a transition induced by the multiplicative Lévy noise from a

trimodal probability distribution to a bimodal probability distribution in asymptotics. Finally

the authors find a nonmonotonic behavior of the nonlinear relaxation time as a function of the

Cauchy stable noise intensity.

Chapter 13 - Landscape modelling is founded on the idea that the patterning of landscape

elements strongly influences ecological characteristics, thus the ability to quantify landscape

structure is a prerequisite to the study of landscape function and change over time as well. For

this reason, much emphasis has been placed until now on developing methods to quantify

landscape structure.

Unfortunately, on one side landscape (i.e., landcover or landuse) and vegetation maps are

very complex mosaics of thousands of patches, and this makes the interpretation of their

structure very challenging. On the other side, methods developed so far to quantify landscape

structure just return numerical results, that are not linked to cartographic outputs. Last,

Preface xiii

landscape pattern indices are numerous, and the need for a synthetic representation is more

and more impelling.

I provide here the description and application of a novel approach to landscape structural

modelling based on the combined use of GIS (Geographical Information Systems) and

multivariate statistics. First, landscape structure of the study area (Ceno valley, Italy) is

analyzed through 5 patch-based, non-redundant indicators (area, isolation, compactness,

shape complexity, interspersion) with indirect link to functional aspects. Second, PCA

(principal component analysis) is used in order to synthesize structural indicators, and

cartographic output is given. Third, KCA (k-means cluster analysis) is applied in order to

group landscape patches into homogeneous clusters, and again GIS output is supplied. Last,

LDA (linear discriminant analysis) is employed to provide evidence for the differences

among clusters.

This modelling approach provides the chance for a deep and cost-effective exegesis of

landscape structure, with promising consequences on conjecture formulation about functional

aspects as well.

Chapter 14 - Our days, the climatic change, manifested by strong and brutal precipitation,

violent wind and long drought, has as direct consequence to damage the plant canopies

(forests, sylviculture, oasis, pastoral lands and agricultural fields) so menacing the human

feeding either from plants or animals (caprine, ovine, bovine, cameline..), exhausting the

water resources, increasing the need for energy in buildings used for all activities (industrial,

agricultural and services). Which solution the ecological modelling is capable to participate

with, at short and long dated, in order to buffer the climatic change effect and to assume the

need of food and clean energy for human? In this chapter we will present the basic concepts

to model the plant architecture (species, densities, positions and orientation) the most

adaptable to the sudden calamity, the energy use efficiency in building (material of

construction, isolation system, organisation of accessories and apparatus), and the produce of

clean energy from the wind velocity (founding wind sources and evaluating regional wind

potential offshore and inshore, conceptualising wind turbine and testing their efficiencies)

In: Ecological Modeling ISBN: 978-1-61324-567-5

Editor: WenJun Zhang, pp. 1-14 © 2012 Nova Science Publishers, Inc.

Chapter 1

SPATIAL DISTRIBUTION OF ARTHROPODS:

A MULTI-MODEL COMPARISON

1

Research Institute of Entomology, School of Life Sciences,

Sun Yat-sen University, Guangzhou 510275, China.

2

International Academy of Ecology and Environmental Sciences, Hong Kong

3

Guangdong AIB Polytech College, Guangzhou 510507, China.

ABSTRACT

Probability distribution functions have been widely used to model the spatial

distribution of arthropods. Aggregation types (i.e., randomly distributed, uniformly

distributed, aggregately distributed, etc.) of arthropods can be detected based on

probability distribution functions, but the abundance at given location is not able to be

predicted by them. This study aimed to present an artificial neural network to simulate

spatial distribution of arthropods. Response surface model and spline function were

compared and evaluated against the neural network model for their simulation

performance.

The results showed that the artificial neural network exhibited good simulation

performance. Simulated spatial distribution was highly in accordant with the observed

one. Overall the neural network performed better in the case of lower total abundance of

arthropods. Response surface model could fit the spatial distribution of arthropods but the

simulation performance was worse than neural network. Cross validation revealed that

neural network performed better than response surface model and spline function in

predicting spatial distribution of arthropods. Confidence interval of predicted abundance

could be obtained using randomized submission of quadrate sequences in the neural

network simulation. It is concluded that artificial neural network is a valuable model to

simulate the spatial distribution of arthropods.

*

Correspondence: zhwj@mail.sysu.edu.cn.

+

Correspondence: ghliu@gdaib.edu.cn.

2 WenJun Zhang and GuangHua Liu

Keywords: Artificial neural network; response surface model; spline function; arthropods;

spatial distribution; simulation.

1. INTRODUCTION

Arthropods account for 90% of global species. Biomass of arthropods reaches 1,000kg

/ha in a temperate grassland, which is lower than plant (20,000kg/ha) and microorganisms

(7,000kg /ha) but higher than mammals (1.2kg/ha) and birds (0.3kg/ha) (Pimental et al.,

1992). They control the structures and functions of ecosystems (Wilson, 1987).Arthropods

have been used as the sensitive indicators of environment health (Brown, 1991; Kremen et al.,

1993).

In ecological research the spatial distribution means the two-dimensional distribution of

animal or plant individuals in the field. Many methods such as GIS (Dantas et al., 2009) and

probability theory are used in the spatial pattern analysis. In the arthropod researches, a lot of

probability distribution functions have been developed and used to describe spatial

distribution of arthropod individuals (Krebs, 1989; Zhang, 2007b). In such methods the

number of individuals found in a sample (plot, quadrat, etc.) is supposed to be a random

variable and the random variable follows some probability distribution, e.g., binomial

distribution, Poisson distribution, negative binomial distribution, Neyman‘s distribution, etc.

Because lack of spatial variables in the function, it can not be used to predict the abundance at

given location (Krebs, 1989; Zhang, 2007b). This is a substantial problem arisen from the use

of probability distribution functions in spatial distribution researches. However, the spatial

information is not available from those models. Due to the lack of theoretical background it is

also hard to construct a mechanistic model that calculates individual distribution from spatial

information. Questions on spatial distribution are therefore data-driven (Schultz and Wieland,

1997). The relationship between individual distribution and spatial information is usually a

nonlinear relationship (Pastor-Barcenas et al., 2005).

Artificial neural networks are known to be flexible and adaptable function approximators

for nonlinear relationships (Bianconi, 2010; Cereghino et al., 2001; Marchant and Onyango,

2003; Acharya et al., 2006; Filippi and Jensen, 2006; Nour et al., 2006; Zhang, 2007a,b;

Zhang and Barrion, 2006; Zhang et al., 2007; Zhang et al., 2008). They can offer the

advantages of simplified and more automated model synthesis and analytical input-output

models (Abdel-Aal, 2004; Tan et al., 2006). A large number of studies were reported

concerning applications of neural networks. For examples, they are considered to be more

effective in time series prediction than previous procedures based on dynamical system theory

(Ballester et al., 2002). They are used in the forecast of short and middle long-term

concentration levels (Viotti et al., 2002), subsurface modeling (Almasri and Kaluarachchi,

2005), modeling hourly temperature with the alternative abductive networks (Abdel-Aal,

2004), modeling sediment transfer (Abrahart and White, 2001), rule extraction (Drumm et al.,

1999) and subsurface drain outflow and nitrate-nitrogen concentration in tile effluent and

surface ozone (Sharma et al., 2003; Pastor-Barcenas, et al., 2005), and estimation of

endoparasitic load using morphological descriptors (Loot et al., 2002), the uses of BP to

describe nitrogen dioxide dispersion (Nagendra and Khare, 2006), and for reservoir

eutrophication prediction (Kuo et al., 2007). Empirical models regained popularity in recent

Artificial Neural Network Simulation of Spatial Distribution of Arthropods 3

years due to the complexity and nonlinearity of ecosystems (Tan et al., 2006). Various

conventional models, including empirical models, were thus used to compare simulation

performances between neural networks and these models. For instance, it demonstrated that

neural network was superior to linear models, generalized additive models, and classification

and regression trees (Moisen and Frescino, 2002). Neural network was proved to outperform

other models like multiple regression, logistic regression, and multiple discriminant model in

predicting the number of salmonids and community composition (McKenna, 2005; Olden et

al., 2006). In the research areas of arthropods or related taxonomic groups, neural networks

have been used to make simulation and prediction. A stream classification based on

characteristic invertebrate species assemblages was also satisfactorily conducted using self-

organizing map neural network (Cereghino et al., 2001). They were used to explain the

observed structure of functional feeding groups of aquatic macro-invertebrates (Jorgensen et

al., 2002); Self-Organizing Map (SOM) neural network was used to determine pest species

assemblages for global regions (Worner and Gevrey, 2006); BP and RBF (radial basis

function) neural networks were used to simulate and predict species richness of rice

arthropods (Zhang and Barrion, 2006), reconstruct spatial pattern of insects (Zhang et al.,

2007), and simulate survival dynamics of insects (Zhang and Zhang, 2008).

This study aimed to present several models, and evaluate their effectiveness in the

simulation of spatial distribution of arthropods. Arthropods were investigated on the

grassland. A neural network and a partial differential equation were developed to model

above-ground distribution of arthropods (Zhang, 2010). Models were validated and compared

for their power in predictability. Details for developing and using neural network were

discussed.

2.1. Field Investigation

Investigation was conducted on the grassland with 8×8 quadrates. Each quadrate has an

area of 1×1 m2. Arthropods were collected, identified, and counted for every quadrate. Insects

were sorted and identified to order level and the other arthropods were identified to classis

level.

mapping from input space (with the spatial coordinates of quadrate as the element) to output

space (with number of arthropod individuals in the quadrate as the element), U:R2→R and

u(x)=v, where u∈U={u|u:R2→R}. For an input set, xi∈R2, and the output set, vi∈R, there is a

mapping f that satisfies f(xi)=vi, i=1,2,…,n. A mapping u∈U={u|u:R2→R}, represented by

this network, should approximate f(x) and satisfy the following condition:

4 WenJun Zhang and GuangHua Liu

A three-layer neural network was developed for simulating spatial distribution of

arthropods (Figure 1; Zhang, 2010). Both the first and second layers contained thirty neurons,

and bias was used to each layer. Transfer functions for layers 1 to 3 were hyperbolic tangent

sigmoid transfer function:

tansig(x) = 2/(1+exp(-2*x))-1,

logsig(x) =1/(1+exp(-x)),

purelin(x) =x,

respectively. Initialization of network, and weights and bias for each layer, was performed by

a function that initializes each layer i (i=1,2,3) according to its own initialization function

(Hagan et al., 1996; Mathworks, 2002; Fecit, 2003). Network was trained using Levenberg-

Marquardt backpropagation algorithm. Desired performance function was mean squared error

performance function (mse). The first and second layers received inputs from input space and

produced outputs for the third layer. There was a closed loop for the third layer. For each

layer, the net input functions calculated the layer‘s net input by combining its weighted inputs

and biases.

Artificial Neural Network Simulation of Spatial Distribution of Arthropods 5

where

a2(∙)=1/(1+exp(-(ω12 x +ω22 y+b2)))

a3(∙)=∑k=13ωk3 ak(∙)+b3

In eq. (1), x=(x, y) T is the input, u=u(x) is the output; ωi, i=1,2,3; ωij, i,j=1,2; ωi3,

i=1,2,3…, and bi, i=1,2,3, are the parameters.

The artificial neural network was developed using Matlab (Mathworks, 2002). Simulation

performance of the neural network was expressed as mse, Pearson correlation coefficient, and

significance level for the linear regression between the simulated and observed.

The response surface model (He, 2001; Mathworks, 2002), i.e., the trend surface model

(Zhang and Fang, 1982), was also used in present simulation:

where u(x): arthropod abundance (individuals per quadrate); x=(x, y) T: the coordinate of

quadrate; b=(b1,b2)T, c=(c1,c2)T: parametric vectors; a: constant.

Spline interpolation is one of the most efficient interpolation models, among which the

cubic spline interpolation is widely used (Burden and Faires, 2001). The cubic spline function

used in present study was:

x∈[xi,xi+1], i=0,1,…,n-1 (3)

where, xi=i+1, Mi=S’’(xi), i=0,1,…,n; li =xi+1-xi, i=0,1,…,n-1. Mi, i=0,1,…,n, were obtained

from three-bending moment equation (Zhang, 2007b).

were used to train neural network and response surface model. The input space was a

6 WenJun Zhang and GuangHua Liu

two-dimensional space (coordinates of quadrate, e.g., (1,2), (5,7), etc.), and the

output space was a one-dimensional space (arthropod abundance).

2) Cross validation. There are several cross validation methods. I used a widely

applicable method (Olden et al., 2006). Using this method, each quadrate was

separately removed from the input set of 64 quadrates, and the remaining quadrates

were used to train model and to predict the removed quadrates using the trained

model. As a consequence, the cross validation may be conducted within the data set

in the same study. Comparisons between the predicted and observed arthropod

abundances were made and Pearson correlation coefficient (r) and statistic

significance were calculated to validate models.

3) Quadrates were submitted to neural network in two ways, i.e., their fixed sequences,

and randomized sequences of quadrates.

3. RESULTS

Most arthropods found on the grassland were insects, which belong to the orders

Homoptera (523 individuals), Orthoptera (230 individuals), Hymenoptera (110 individuals),

Coleoptera (55 individuals), and Diptera (40 individuals), etc. Other arthropods were sparsely

distributed on the grassland. The spatial distribution of arthropods exhibited a saddle-like

shape, which was similar to the most abundant Homoptera (Figure 2).

Homoptera on the grassland.

Artificial Neural Network Simulation of Spatial Distribution of Arthropods 7

Surface Model

Using the artificial neural network developed above (Figure1, eq.(1)) to simulate spatial

distributions of arthropods and the most abundant orders Orthoptera, Hymenoptera, and

Homoptera. Neural network was trained by 10000 epochs and the desired accuracy (mse) was

0.00001. The results revealed that neural network exhibited excellent simulation performance.

The simulated spatial distribution perfectly coincided with the observed (intercept≈0,

slope≈1, r≈1, p<0.0001), as illustrated by Figure 3.

Using a deviation function, stmse=mse/u2, where u is the averaged individuals per

quadrate, together with Figure 4, it was found that the lower abundance would overall lead

neural network to yield the better simulation performance (Arthropods (stmse=6.39*10-3),

Homoptera (stmse=2.16*10-2), Orthoptera (stmse=5.88*10-7), Hymenoptera

-6

(stmse=1.46*10 )).

Figure 3. Simulating spatial distribution of arthropods using neural network. Quadrates were submitted

to neural network in their fixed sequences.

Response surface model could better fit the spatial distribution of arthropods. However,

its simulation performance was lower than neural network (Figure 4).

8 WenJun Zhang and GuangHua Liu

The cross validation, in which quadrates were submitted to neural network in their fixed

sequences, demonstrated that neural network exhibited much better performance than

response surface model in predicting unknown quadrates (Figure 5). In most cases, response

surface model yielded the negative correlation between the predicted and observed

abundances. As a result, it is not suggested using response surface model to predict spatial

distribution of arthropods.

Different from the situation above, neural network exhibited better prediction

performance in the case of larger abundance than lower abundance on the grassland (Figure

5). This means that compared to simulation the neural network needs more information to

train itself for producing a reasonable extrapolation.

In an additional cross validation of neural network to predict the spatial distribution of

arthropods, quadrates were submitted in randomized sequences and five randomizations were

used. The results showed that neural network yielded the better performance (r=0.5323,

p<0.0001). More than 60% of quadrates were correctly predicted and they fell inside 95%

confidence intervals of the predicted (Figure 6).

Artificial Neural Network Simulation of Spatial Distribution of Arthropods 9

Figure 5. Cross validation of neural network and response surface model for predicting spatial

distribution of arthropods. Quadrates were submitted to neural network in their fixed sequences.

Figure 6. Cross validation of neural network for predicting distribution of arthropods. Quadrates were

submitted to neural network in randomized sequences. Five randomizations were conducted.

10 WenJun Zhang and GuangHua Liu

The cross validation indicated that spline function performed badly than both neural

network and response surface model (Table 1).

Arthropods Orthoptera

Observed=15.6520-0.0041*Simulated Observed=3.8052-0.0545

Hymenoptera Homoptera

Observed=1.7092+0.0067*Simulated Observed=8.3154-0.0148*Simulated

An artificial neural network is developed to model spatial distribution. It exhibits

excellent performance in the simulation of spatial distribution of arthropods. Simulated spatial

distribution would perfectly coincide with the observed one. Lower total abundance would

overall lead neural network to yield the better simulation performance. Response surface

model and spline function can be used to fit the spatial distribution of arthropods. Simulation

performance of response surface model is proved to be lower than neural network. The cross

validation confirms that neural network has much better performance than response surface

model and spline function in predicting unknown quadrates. Submitting quadrates in

randomized sequences helps to yield confidence interval of the result in the neural network

simulation.

There are many kinds of artificial neural networks. More and more new algorithms of

neural networks have been developing in various sciences. Both classic algorithms, like BP,

SOM, RBF (Nagendra and Khare, 2006; Worner and Gevrey, 2006; Zhang and Barrion,

2006), etc., and newly developed algorithms such as the one developed in present study, can

be used in the simulation of spatial distribution of arthropods. New algorithms may be

designed according to the specific requirements and some details should be deliberated, such

as the number of layers, neurons, biases, and targets; transfer functions, training functions;

layer connects, input connects, output connects, bias connects, and target connects; input

delays, input weights, layer weights, and initiate functions, and so on.

In addition to network settings, the quality of input set should also be ensured to obtain a

better neural network. Data quality may be improved through a reasonable experiment or

sampling design, eliminating data redundancy, and randomization procedure, etc (Kilic et al.,

2007). As demonstrated in present study, randomized submission of quadrates helps neural

network eliminate the correlation between inputs in training procedure. A larger number of

randomizations are suggested being used to produce the reliable interval for simulation and

prediction.

Over-learning in neural network simulation should be avoided in order to produce the

best predictive performance. It can be solved by limiting the complexity of the neural network

Artificial Neural Network Simulation of Spatial Distribution of Arthropods 11

(layers, neurons, etc.), by training neural network with noise, and by using techniques as

weight decay, and so on (Ozesmi et al., 2006).

Both spatial information (Euclidean coordinates) and environmental factors like plant

composition, climate conditions, etc., can be considered to be input components. By doing

this, we obtain a more interpretative neural network. This model may be used to interpret

data. Some methods on data interpretation of explore neural network, like sensitivity analysis,

inference rule extraction, randomization approach, neural interpretation diagram, etc., are

available now for this purpose (Bradshaw et al., 2002; Olden and Jackson, 2002; Gevrey et

al., 2006).

Similar to the conclusion from present study, most previous studies showed that neural

networks outperfomed conventional models (Lek et al., 1997; Paruelo and Tomasel, 1997;

Brosse et al., 1999; Abrahart and White, 2001; Yu et al., 2006; Zhang, 2007a,b), although

varied results were also produced in using neural networks (Marchant and Onyango, 2003;

Filippi and Jensen, 2006). This study demonstrates that artificial neural network is more

robust than the conventional model in the modelling of spatial distribution. It can provide a

feasible alternative to more classical spatial statistical techniques (Pearson et al., 2002).

However, researches towards complicate spatial distribution are further desired in the future.

This study used the data set of 64 quadrates to model spatial distribution of arthropods

and a better performance was achieved. As fitting models, their simulation performance is

expected to be improved with the increase of the size of data set. However, more studies with

larger data sets are still needed in the future to further validate these models.

ACKNOWLEDGMENTS

This project was supported by ―N ational Basic Research Program of China‖(973

Program)(No. 2006CB102005). We thank all participants of arthropod investigation, Mr. WG

Zhou, HQ Dai, and undergraduates of ecology 2004, Sun Yat-sen University, China.

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Chapter 2

IN REMOTE SENSING: AN OVERVIEW

1

Department of Natural Resources Development & Agricultural Engineering,

Agricultural University of Athens, 75, Iera Odos St., Athens, Greece, Email:

petropoulos.george@gmail.com

2

Department of Geoinformation, Mediterranean Agronomic Insitute of Chania, Alsyllio

Agrokipiou, Crete, Greece, Email: harry.kalaitzidis@gmail.com

ABSTRACT

Remote sensing has generally demonstrated a great potential in mapping spatial

patterns of vegetation. By employing the amount of reflected radiation at particular

regions of the electromagnetic spectrum, it is possible to make estimates on certain

characteristic of vegetation. The use of radiometric vegetation indices is a fast and

efficient method for vegetation monitoring, exploiting information acquired from remote

sensing data. These indices are dimensionless radiometric measures that generally

function as indicators of relative abundance and activity of green vegetation.

Throughout the years, a large number of multispectral vegetation indices have been

formulated. Each has variable degree of efficiency in estimating one or more vegetation

parameters such as, health status, nutrient or water deficiency, crop yield, vegetation

cover fraction, leaf area index, absorbed photosynthetically active radiation, net primary

production and above-ground biomass. Additionally some of them also consider

atmospheric effects and/ or the soil background for an enhanced retrieval. The present

chapter aims in providing an overview on the use of radiometric vegetation indices

developed over the last few decades, utilizing spectral information acquired from

multispectral optical remote sensing sensors. This overview is preceded an introduction

to some important principles of remote sensing relevant to the vegetation spectral

response is made available, as this was considered necessary to better understand the

context of the present overview.

sensing.

16 George P. Petropoulos and Chariton Kalaitzidis

1. INTRODUCTION

Remote sensing can be generally defined as the technique of gathering information about

an object (or target) without making actual contact with this object. Extraction of information

is done by analyzing the reflected or emitted electromagnetic radiation (EMR) energy of the

object recorded by the sensor of a remote sensing system. The first instances of remote

sensing occured in 1858 with the first aerial photographs, taken from balloons, with the

purpose of being used for mapping and military reconnaissance. Satellite remote sensing

began around 1960‘s with the launch of the first satellite, TIROS-1, which was primarily used

for meteorological purposes. Nowadays, remote sensing data are collected by both

multispectral and hyperspectral sensors operating in both airborne and satellite platforms,

with a very large number of satellite systems operating in orbit over the Earth‘s surface.

The advent of satellite-based remote sensing over the last few decades has lead to a

considerable amount of work being done in determining their potential usefulness in many

disciplines and applications. Among the main advantages of remote sensing include its ability

to provide synoptic views of large areas in a spatially contiguous fashion and in a repetitive

manner, without a disturbing influence on the area to be surveyed and without accessibility

issues to the site to be studied. Remote sensing observations from microwave sensors offer all

weather capability and daytime and nighttime observations, which, combined with their

strong dependence on the dielectric properties of the target, make them potentially very

powerful for the estimation of various parameters, such as of soil moisture content.

Specifically the potential use of remote sensing for mapping vegetation condition and

health has been explored by many scientists over the last decades. A common approach

employed for this purpose involves the use of radiometric vegetation indices computed from

multispectral remote sensing observations. The present chapter aims in providing an overview

of the approaches exploited for the estimation of vegetation health and vigor from the

computation of radiometric vegetation indices from multispectral optical remote sensing

observations. Nevertheless, before that, a discussion to the principles of remote sensing in the

reflective part of the EMR, namely the visible near-infrared (VNIR) and shortwave infrared

(SWIR) is made available. This was deemed necessary, as understanding the characteristics of

EMR and how the latter interacts with land surface targets is crucial in later understanding the

information that is extracted from remote sensing data and subsequently used in the

estimation of vegetation condition by employing these radiometric indices.

REFLECTIVE PART OF EMR

In this section, some basic principles of remote sensing are introduced assisting the reader

in better understanding the basis on which the computation of the different radiometric

vegetation indices has been based on. Here the discussion is focused only on the reflective

part of EMR (0.4 – 2.5 µm), as the overview of the radiometric indices that follows will be

based on the use of remote sensing data from this part of the EMR.

Multispectral Vegetation Indices in Remote Sensing 17

The satellite sensor measures the intensity of the electromagnetic waves reflected by the

surface in different parts of the spectrum. Comparison of the radiometric and spectral

characteristics of the reflected energy to the characteristics of the incident energy derives the

surface reflectivity, which is analyzed to determine the physical and chemical properties of

the surface. However, as the solar waves propagate through a planet‘s atmosphere, they

interact with atmospheric constituents, leading to significant effects on the intensity and

spectral composition of the energy recorded by a remote sensor. These effects are caused

principally through the mechanisms of atmospheric scattering and absorption (e.g. Cambell,

1981). Both these effects are directly related to the atmospheric path length and the

wavelengths involved. Scattering arises when particles of various sizes present in the

atmosphere or large gas molecules interact with the EMR resulting to a redirection of the

radiation from its original path. The magnitude of scattering depends on various factors, most

importantly the wavelength of the radiation, the abundance of particles or gases, and the

distance the radiation travels through the atmosphere (e.g. Verbyla, 1995). The atmospheric

absorption normally involves absorption of EMR energy at particular wavelengths by certain

gases present in the atmosphere. The dominant gases responsible for most of this absorption

are water vapor (H2O), carbon dioxide (CO2) and ozone (O3), and depending on atmospheric

conditions and the amount of radiation emitted from the surface one of these effects will be

dominant. Nevertheless, there are certain spectral domains within the EMR spectrum that are

relatively free from the effects of scattering and absorption, known as atmospheric windows.

Figure 1 illustrates these ―absorption-free‖ regions within the EMR, which are very important

in remote sensing, as in these regions atmospheric effects on radiation minimal in comparison

with other wavelengths.

18 George P. Petropoulos and Chariton Kalaitzidis

All wavelengths shorter than 0.30 µm are unavailable for remote sensing and strong

absorption bands also exist in the near-infrared, particularly around 1.9, 1.4, 1.12, 0.95 and

0.76 µm. The first significant atmospheric window begins at 0.3 μm, providing good

transparency in the visible spectrum, between 0.30-0.75 μm. The atmospheric window

continues but with interruptions in the NIR region (i.e. 0.77-0.91 µm). In the near-infrared

(NIR) part of the EMR spectrum there are several atmospheric windows in narrow wavebands

between 1.0-1.12, 1.19-1.34, 1.55-1.75 and 2.05-2.4 μm. Consequently, it is natural to expect

that correction of these atmospheric effects can be particularly useful for improving the

quality of the remotely sensed data. Description of such atmospheric correction approaches

can be found elsewhere, including Slater (1980) and Rees (2001).

As the solar waves propagate through Earth‘s atmosphere from these atmospheric

windows, radiation that is not absorbed or scattered in the atmosphere can reach and interact

with the Earth's surface. EMR reaching the Earth‘s surface interacts with the Earth‘s surface

objects by the mechanisms of reflection, transmission or absorption. The interrelationship of

these three parameters is expressed by a direct application of the conservation of energy law,

from the equation below:

E I ( ) E R ( ) EA ( ) ET ( ) , (1)

where EI(λ) denotes the incident energy, ER(λ) is the reflected energy, EA(λ) the absorbed

energy and ET(λ) is the transmitted energy.

There are two very important points that should be considered, regarding the

aforementioned equation. The first one is that that the proportions of energy, which is

reflected, absorbed and transmitted, will vary for different Earth surface targets, depending on

their material type and condition. These differences allow the distinguishing of the different

features recorded on a satellite image. In addition, even for a given feature type, the

proportion of the energy reflected, absorbed and transmitted will vary at different

wavelengths (Elachi, 1987). Thus, two features may be possible to be discriminated in one

spectral region but be very different in another wavelength band. Furthermore, another

important consideration accounted in remote sensing is the geometric manner in which an

object is reflecting energy, a function of the surface roughness of the object. Specular

reflectors are flat surfaces that manifest mirror-like reflections, where the angle of reflection

equals the angle of incidence. Diffuse (or Lambertian) reflectors are rough surfaces that

reflect uniformly in all directions.

The satellite sensor records a digital number (DN) for each pixel and spectral band.

However, for the majority of practical applications in remote sensing, the DN values must be

converted in measurements of the amount of energy reaching the sensor in each band, using

an appropriate sensor calibration equation. This energy is expressed by the radiance (L).

Radiance (L) is considered to be the measure of the radiant flux per unit of solid angle leaving

an extended area source in a given direction per unit projected source area in that direction,

and is measured in Wm-2sr-1. This measure of radiance is obviously made in a particular

viewing direction where the perceived surface brightness is considered constant for the entire

hemisphere above the surface. The measure of the amount of energy reflected from the

surface can be related to the amount of energy arriving to the surface, from the Sun, by

Multispectral Vegetation Indices in Remote Sensing 19

introducing the reflectance of the surface term, which is mathematically defined as (e.g.

Lillesand & Kieffer, 1994):

ρλ x100

EI( ) energyof wavelengthλ incident upon the object

where reflectance ρλ is expressed as a percentage whereas all the other parameters defined as

in equation 2, above.

Conventional research in remote sensing has concentrated on the use of spectral response

based on nadir or near-nadir reflectance measurements. However, for remote sensing

applications the spectral response of a target will also depend upon factors such as the

orientation of the Sun (solar azimuth), the height of the Sun in the sky (solar elevation angle),

the direction in which the sensor is pointing relative to nadir (the look angle) and the

wavelength used (Sabins, 1997). All these factors are combined in the bidirectional

reflectance distribution function (BRDF), which is a theoretical concept that describes

directional reflectance phenomena by relating the incident irradiance from one given direction

to its contribution to the reflected radiance in another specific direction (Nicodemus et al.,

1977). The bidirectional reflectance distribution function is normally defined as the ratio of

reflected radiance to incident irradiance at a particular wavelength:

(i; r; ) (3)

dEi(i; )

where the subscripts i and r denote incident and reflected respectively, is the direction of

light propagation, λ is the wavelength of light, L is radiance, and E is irradiance.

Field devices, called ―f ield goniometers‖, which are essentially goniometric radiometric

instruments have been used for a number of years to practically assess the BRDF of natural

and man-made surfaces under natural illumination conditions (e.g Jackson et al., 1990;

Hosgood et al., 1999). Several bidirectional reflectance distribution function (BRDF) models

have been developed to predict the bidirectional reflectance properties (e.g. Verstraete et al.,

1990; Strahler and Jupp, 1991; Qin, 1993; Albuelgasim and Strahler, 1994). Although

detailed reference to these models is beyond the purposes of this discussion it should be

mentioned that essentially the existing approaches to the analytical modelling of the BRDF

are mainly distinguished in two groups; the physical and the statistical models. Physical

models relate the BRDF to various internal properties of the surface relying on physical

parameters (e.g. Myneni et al., 1990; Goel, 1988). On the other hand, statistical models of the

BRDF of the surface characterize the shape of the BRDF function using statistical parameter

(e.g. Kieffer et al., 1977; Pinty & Ramond, 1986).

Studies have addressed the importance of bidirectional effects in remote sensing (e.g.

Holben and Kimes, 1986; Schaaf and Strahler, 1994). Such studies, among others, showed

that correction / normalization of the sun / view angle effects is very important for

quantitative analysis of remotely sensed data. However, it should be taken into consideration

that, in general, most remote sensing applications assume Lambertian reflectance, which is

usually acceptable. Besides, the influence of the atmospheric conditions must also be

20 George P. Petropoulos and Chariton Kalaitzidis

considered for accurate BRDF determination, which practically is constantly changing in the

different viewing angles (Deering and Eck, 1987).

In remote sensing, by measuring the energy that is reflected by targets on the Earth's

surface over a variety of different wavelengths, it is possible to compile a spectral response

for that object. A spectral reflectance curve describes the spectral response of a target as a

function of wavelength, covering the visible to near-infrared region of the electromagnetic

spectrum. The configuration of spectral reflectance curves is particular important in remote

sensing, as it offers an insight into the spectral characteristics of an object and has a strong

influence on the choice of wavelength regions in which remotely sensed data should be

acquired. This important property makes it possible to identify the different substances or

classes and separate them by their spectral signatures denoted by their spectral curves.

The spectral reflectance curves of some typical surface materials are depicted in Figure 2

and their reflectance properties are briefly discussed below. Figure 2 shows reflectance

spectra for three different surface types of terrain cover, i.e. vegetation, soil and water. The

horizontal axis shows the wavelength of the incident energy, whereas the vertical axis shows

the percentage of incident energy reflected at the different wavelengths. Although these lines

for each cover type in Figure 2 represent average reflectance curves, it is prominent how

distinctive the curves are for each surface feature.

Figure 2. Spectral signatures of some terrestrial materials in the reflective part of the EMR (adopted

from http://www.satreponline.org/landsaf/print.htm#page_3.1.0).

Multispectral Vegetation Indices in Remote Sensing 21

generally low in the visible part of the EMR. The vegetation curve shows relatively low

values in the red and the blue regions of the visible spectrum, with a small peak in the green

spectral region. These peaks and troughs are caused by the absorption of blue and red energy

by plant pigments, which are found in the chloroplasts within the leaf mesophyll. The

majority of those pigments use the absorbed energy to power the process of photosynthesis.

The most common of those pigments are chlorophylls, carotenes and xanthophylls. The

chlorophyll molecules exhibit the most dominant absorption in the visible region, particularly

in the blue (400 – 500 nm) and red (600 – 700 nm) regions (Figure 2; Buschmann and Nagel,

1991). Green light is not absorbed for photosynthesis and therefore most plants appear green.

Under the same principle, thicker leaves have lower absorption, due to increased chlorophyll

content, and higher NIR reflectance, due to increased scattering (Gausman and Allen, 1973).

From the vegetation spectral reflectance curve it is also apparent that plants generally

reflect radiation strongly in the NIR region. The area of the sharp increase in reflectance

between the red and NIR region of the spectrum is known as the ―r ed edge‖ region (Filella

and Penuelas, 1994). This slope is known to be affected by the amount of chlorophyll in the

leaves. At high chlorophyll concentrations, energy absorption in the red region increases and

the absorption feature in this part of the spectrum is widening, causing the red edge slope to

shift to longer wavelengths. On the other hand, at low chlorophyll concentrations (in stressed

plants, for example), the red edge is moving towards shorter wavelengths (Gates et. al.,

1965). The high reflectance of vegetation in the NIR region is mainly due to the high air/cell

interface area within leaves, whereas the air gaps in the cells become larger, resulting to a

decrease of multiple scattering and decrease in near-infrared reflectance (Gausman et al.,

1973). This reflectance is independent of wavelength. On the other hand, when light of a

particular wavelength encounters particles of similar size (i.e. chloroplasts) then only the

energy at that particular wavelength is scattered (Buschmann and Nagel, 1991). In general,

the amount of reflected energy in the NIR depends on: 1) the proportion of mesophyll leaf

exposed to intercellular spaces, 2) the presence or absence of leaf bi-colouration (between the

top and bottom leaf surfaces), and 3) the thickness of leaf cuticle (Slaton et. al., 2001).

Because the difference in the refractive index between cell wall and water is smaller than the

one between cell wall and air, when the plant has high water content, the intercellular spaces

fill up with water and the refraction of the NIR energy decreases. As a result, less energy is

reflected upwards and more is transmitted through the leaf (Knipling, 1970; Gausman et. al.,

1974).

Plant reflectance in the range 0.7 to 1.3 μm is primarily dependent on the internal

structure of the plant leaves. Beyond 1.3 μm, energy incident upon vegetation is essentially

absorbed or reflected, with little to no transmittance of energy. Sharp reductions in reflectance

occur at 1.4, 1.9 and 2.7 μm, because water in the leaf absorbs strongly at these wavelengths.

Accordingly, these spectral regions are referred to as water absorption bands. Throughout the

range beyond 1.3 μm, leaf reflectance is inversely related to the total water present in the leaf.

This total is a function of both the moisture content and the thickness of the leaf. Plants with

different internal structure will often vary greatly in NIR reflectance. Figure 2, effectively

illustrates a summary of the dominant factors affecting vegetation reflectance within the

VNIR.

The soil reflectance curve shows considerably less variations in reflectance. The spectral

reflectance curves of soils are generally characterised by a rise in reflectivity as wavelength

22 George P. Petropoulos and Chariton Kalaitzidis

increases. One of the most important parameters controlling reflectance from soil surfaces is

soil moisture content, which inversely related to the reflectance, especially in the mid-infrared

region. Furthermore, dry fine-textured soils (such as clay) will usually have higher reflectance

than dry coarse-textured soils (such as sand) (Verbyla, 2001). In addition, organic matter has

been found to have a strong influence in soil reflectance, where spectral reflectance generally

decreases over the entire shortwave region as organic matter content increases (Stoner and

Baumgardne, 1980). The presence of iron oxide in the soil will also significantly decrease

reflectance, at least in the visible wavelengths (Asrar, 1989). Last but not least, soil particle

size has been found to affect reflectance of particular soil minerals, which is generally

increased and the contrast of the absorption features decrease as the particle size decreases.

Huete (1989) gives a summary of the influences of soil background on measurements of

vegetation spectra.

Finally, the spectral reflectance curve of water shows a general reduction in reflectance

with increasing wavelength, so that in the NIR the reflectance of deep, clear water is

effectively almost zero. Clear water reflects very little in most spectral regions. However,

turbid water reflects significant amounts of radiation, especially in the red and NIR spectral

regions. There is a shift in the spectral reflectance regions, as water increases in turbidity

(Verbyla, 2001). However, the spectral reflectance of water is affected by the presence and

concentration of dissolved and suspended organic and inorganic material, and by the depth of

the water body (Jensen, 2000). Thus, the intensity and distribution of the radiance upwelling

from a water body are indicative of the nature of the dissolved and suspended mater in the

water and of the water depth. The peak of the reflectance curve moves to progressively longer

wavelengths as concentration of these materials increases.

3.1. Indices Linked with Biomass Estimation

Since 1960‘s with the initial attempt by Jordan (1969) scientists have extracted and

modelled various vegetation biophysical variables from remotely sensed data by exploiting

mathematical formulae, referred to as vegetation indices, defined as dimensionless

radiometric measures that function as indicators of relative abundance and activity of green

vegetation (Jensen, 2000). A vegetation index is effectively a numerical value without units,

resulting from the mathematical combination of radiance values at particular wavebands. The

measurements of those radiance values are almost always collected concurrently, and

represent the state of vegetation at that particular moment in time, under the specific

conditions that were in place during the time the data were acquired. Also, comparison of

vegetation indices between different vegetation targets, or the same vegetation target at

different time and conditions can potentially provide information on the differences between

the targets or the effects of the variable conditions to the vegetation.

The remaining part of this chapter provides an overview on the development of

radiometric vegetation indices developed over the past decades which are based on

multispectral remote sensing observations acquired in the reflective part of the EMR. A

summary of the indices reviewed herein is provided in Table 2.

Multispectral Vegetation Indices in Remote Sensing 23

RVI(SR) Ratio VI or Simple Ratio Jordan, 1969

NDVI Normalised Difference VI Rouse et. al., 1974

TVI Transformed Vegetation Index Rouse et. al., 1974

PVI Perpendicular VI Richardson & Wiegand, 1977

SAVI Soil-Adjusted VI Huete, 1988

WDVI Weighted Difference VI Clevers, 1989

SAVI2 2nd version of Soil-Adjusted VI Major et. al., 1990

TSAVI Transformed Soil-Adjusted VI Baret & Guyot, 1991

ARVI Atmospherically Resistent VI Kaufman & Tanre, 1992

GEMI Global Environmental Monotoring Index Pinty & Verstraete, 1992

NDVIc Corrected NDVI Nemani et. al., 1993

SARVI Atmospherically Resistent SAVI Huete et. al., 1994

MSAVI Modified Soil-Adjusted VI Qi, et. al., 1994

EVI Enhanced Vegetation Index Huete et. al., 1997

OSAVI Optimised SAVI Rondeaux, et. al., 1996

GARI Green Atmospherically Resistent VI Gitelson, et. al., 1996

GNDVI Green NDVI Gitelson, et. al., 1996

MGVI MERIS Global Vegetation Index Gobron et. al., 1999

GESAVI Generalised Soil-Adjusted VI Gilabert, et. al., 2002

VARI Visible Atmospericaly Resistant Index Gitelson, et. al., 2002

LVI Linearised Vegetation Index Unsalan & Boywer, 2004

WDRVI Wide Dynamic Range Vegetation Index Gitelson, 2004

MSI Moisture Stress Index Hunt & Rock, 1989

LSWI Land Surface Water Index Xiao et al., 2002

GVMI Global Vegetation Moisture Index Ceccato et al., 2002a,b

The first use of a ratio between NIR and red radiance was reported by Jordan (1969),

when he measured transmittance value at the floor of a tropical forest, to estimate the Leaf

Area Index (LAI). As explained by Knipling (1970), increased Leaf Area Index (LAI) values,

result in lower red and higher NIR reflectance. The cause for the first is the increased amount

of chlorophyll in the sensor‘s field of view, leading to increased absorption and reduced

reflectance. The increase in NIR reflectance is attributed to the increased number of cells

present in the field of view, resulting in an increased amount of scattered NIR radiation

reaching the sensor. The ratio was coined as a vegetation index by Pearson and Miller (1972),

when they introduced the Ratio Vegetation Index (RVI), which is the ratio of the NIR over

the red signal (Eq. 4), in order to estimate grass canopy biomass.

NIR

RVI (4)

RED

The simple ratio of NIR reflectance over red reflectance has been shown on numerous

occasions to be related to crop yield and dry matter accumulation (Markham et. al., 1981;

Tucker et. al., 1981).

24 George P. Petropoulos and Chariton Kalaitzidis

An evolved version of the RVI is the Normalised Difference Vegetation Index (NDVI),

introduced for the first time by Deering et et. al. (1975). This index is a ratio between the

difference and the sum of NIR and red radiation (Eq. 5).

NIR red

NDVI (5)

NIR red

Typically NDVI values can scale between -1 to +1 with water surfaces typically having

an NDVI value less than 0, bare soils between 0 and 0.1, clouds about 0.23, snow and ice

about 0.38 and vegetation over 0.1 (Jensen, 2000). NDVI is considered to be superior of the

RVI. The effectiveness especially of NDVI is because chlorophyll absorbs light in the visible

(0.58-0.68 µm) and foliage reflects light in the NIR part of the EMR (0.72-1.10 µm). The

combination of NIR and red reflectance in one index, succeeded in combining information

regarding the chlorophyll content of the vegetation, as well as information about the leaf

anatomy. Therefore, higher photosynthetic activity would result in lower reflectance in the

red channel and higher reflectance in the NIR channel. Also, the normalisation of the

difference makes the index more robust and less affected by variations in the illumination

intensity, allowing for comparisons of target located at different locations, with data acquired

at different times.

NDVI became very popular and was probably the most broadly used index in many

applications related with vegetation. NDVI has been linked in many studies in a positive

correlation with the amount of green biomass, leaf area index, vegetation percentage cover,

plant vigour and health, plant stress, photosynthetic activity and agricultural crop yield (Asrar

et. al., 1984; Sellers, 1987). However, it should be mentioned here that NDVI values can vary

significantly as a function of sensor calibration (Goward et al., 1991), atmospheric conditions

(Myneni and Asrar, 1994), directional surface reflectance effects (Holben et al., 1986), terrain

relief and soil background effects (Major et al., 1990). What is more, when the vegetation

cover is complete and chlorophyll content reaches a certain level, the relationship between

NDVI and any characteristic that is derived from the amount of chlorophyll is saturated

(Huete et. al., 1997), and further increases in chlorophyll content, do not result in proportional

increases of the NDVI. Last but not least, another important limitation of the NDVI, is its

sensitivity to the contribution of the background beneath the vegetation, when vegetation

cover is not complete. The contribution of soil reflectance to total canopy reflectance in the

NIR is significant (Allen and Richardson, 1968). For a given amount of vegetation and

vegetation cover, darker soils in the background result in higher values of vegetation indices

(Elvidge and Lyon, 1985; Huete et. al., 1985).

The Transformed Vegetation Index proposed by Rouse et. al. (1974), was effectively the

NDVI with the addition of a 0.5 constant and the square-rooting of the sum (Eq. 6). The TVI

was produced in order to avoid the negative values of NDVI, and also to avoid the possibility

that the variances of the ratio would be proportional to the mean values.

When dealing with vegetation canopies, the contribution of the soil reflectance to the total

canopy reflectance is significant, particularly in the NIR region, where there is no pigment

Multispectral Vegetation Indices in Remote Sensing 25

absorption (Allen and Richardson, 1968). In order to discriminate between vegetation and soil

signal, Richardson and Wiegand (1977) proposed the Perpendicular Vegetation Index (PVI;

Eq. 7). The index calculates the difference between the soil and vegetation signals in both the

red (Redsoil, Redveg.) and NIR region (NIRsoil, NIRveg.), and employs those differences.

redveg.) 2 ( NIRsoil NIRveg.) 2 (7)

PVI was one of the first attempts to discriminate vegetation and soil background

reflectance, however it proved to be very sensitive to variable soil brightness and the index

value increased for brighter soils, when vegetation cover remained constant (Elvidge and

Lyon, 1985; Huete, 1988; Baret and Guyot, 1991). Even though the soil line causes the

NIR/red ratio to remain constant, the actual slope and intercept parameters of the soil line

vary depending on the soil properties (Huete et. al., 1984). In addition to soil brightness, other

properties, depending on the soil type, could affect the greenness assessment, even when the

percentage of vegetation cover was as high as 75% (Huete et. al., 1985).

The Soil-Adjusted Vegetation Index (SAVI; Eq. 8) was later introduced by Huete (1988)

as an alternative index dealing with the background signal. This index was employing an L

factor, representing the amount of vegetation present and the extent of vegetation cover. For

total vegetation cover the L receives a value of 0 and the index effectively becomes NDVI,

while for very low vegetation cover, the L acquires a value near 0. When the extent of

vegetation cover is unknown, the author suggested a value of 0.5 as optimal. For this value

and for intermediate vegetation cover, SAVI was found to be superior to both the NDVI and

PVI (Huete, 1988).

NIR red

SAVI (1 L) (8)

NIR red L

The index performs best when the slope of the soil line (a) is equal to 1 and the intercept

(b) equals zero. Deviations from these values tend to reduce the accuracy of SAVI (Baret et.

al., 1989). However, Rondeaux et. al. (1996) suggested that the optimal value of the L factor

for SAVI was 0.16, thus coining the OSAVI index. To address the issue of fixed L values,

another version of the SAVI index was introduced by Baret et. al. (1989). Instead of simply

adding a subjective factor, the NDVI was equipped with information of the soil line, namely

its slope (a) and intercept (b), producing the Transformed Soil-Adjusted Vegetation Index

(TSAVI; Eq. 9). The index ranges from zero for bare soil to a maximum of around 0.7 for

very dense vegetation cover. The index was shown to be able to compensate for changes in

solar elevation and canopy structure (Baret et. al., 1989).

aNIR - a red - b

TSAVI (9)

red a NIR - ab

Another incarnation of the SAVI index was proposed by Major et. al. (1990), employing

once again the soil line slope and intercept. In this instance, instead of using the NDVI as a

basis, the information was added at the denominator of the RVI, producing SAVI2 (Eq. 10).

26 George P. Petropoulos and Chariton Kalaitzidis

NIR

SAVI 2 (10)

red b a

SAVI was derived specifically to reduce the effects due to ground reflectance and

implicitly assumes a linear relationship between red and near-infrared ground reflectances. Qi

et al (1994) suggested that SAVI was significantly less susceptible to changes associated with

soil variations compared to SR an NDVI. On the other hand, Rondeaux et al (1996) compared

NDVI, SAVI and TSAVI and determined that TSAVI was least prone to perturbations

associated with soil changes.

At the time when Huete (1988) was incorporating the soil line to NDVI to produce SAVI,

Clevers (1989) proposed the Weighted Difference Vegetation index (WDVI) stating that this

index could reportedly estimate LAI, with the assumption that red and NIR reflectance was

independent of soil moisture content. However, further studies by Baret and Guyot (1991)

found that the index had no particular advantage over the PVI and shared the same

weaknesses.

Qi et. al. (1994) suggested an iterative process for the determination of the L factor,

through which the initial L value is combining the NDVI and WDVI and is also employing a

primary soil-line parameter γ (a value of 1.06 was used in that study; Eq.11). Each subsequent

L value is calculated by the difference between the resulting MSAVI (Eq. 12) and 1 (Eq. 13).

NIR red

MSAVI (1 L0 ) (12)

0 NIR red L

0

A further attempt to create a more accurate index in the SAVI family, was made by

Gilabert et. al. (2002). They proposed a generalised soil-adjusted vegetation index

(GESAVI), which utilises the red and NIR reflectance, along with the soil parameters a and b,

plus a soil adjustment coefficient (Eq. 14). The difference between this index and the previous

SAVI indices, is the fact that the vegetation isolines in the NIR-red plane, are neither parallel

to the soil line (as required by PVI), nor converging from the same point (as required by the

NDVI), but somewhere in between.

NIR - b Red - a

GESAVI (14)

Red z

The z factor is related to the red reflectance, at the point where the soil line and the

vegetation isolines converge. The authors have suggested the use of a value of 0.35, in case

additional data to derive the actual z value is not available.

A different approach in dealing with partial vegetation cover was followed by Nemani et.

al. (1993), when they introduced a middle infrared band to the traditional NDVI, producing

Multispectral Vegetation Indices in Remote Sensing 27

the corrected NDVI (NDVIc; Eq 15). The middle infrared helped account for understory

effects, when the vegetation cover was partial and the understory vegetation had a

significantly different spectral signature than the tree canopies. As a result the index was

more closely related to the LAI of conifer forests.

NDVI NDVI * (1 ) (15)

c MIR mix - MIR min

In the above equation (Eq. 15), MIR is the middle infrared reflectance of (band 5 of

LANDSAT TM), and MIRmin and MIRmax are the middle infrared reflectance signals from a

completely open and completely closed canopy respectively, from the general study area.

However, atmosphere can affect considerably vegetation indices (Kaufman and Sendra,

1988). As it was discussed earlier, the interference of the atmosphere with the incident solar

radiation affects its intensity and makes it more diffuse, through scattering. The NDVI, like

most vegetation indices, is suffering from those effects. Subsequently, in addition to

minimizing the effect of background, spectral radiance values must be corrected for

atmospheric effects to recover the vegetation signal.

In an attempt to correct these atmospheric effects, Pinty and Verstraete (1992) proposed

the Global Environmental Monitoring Index (GEMI), a complex non-linear polynomial

equation, which combined the red and near-infrared reflectance. The GEMI was shown to be

more useful in comparing observations under variable atmospheric conditions and also more

representative of surface conditions, compared to the simple ratio (SR) and the NDVI. Also

aiming to create an index resistant to atmospheric influence, Kaufman and Tanre (1992) have

developed the Atmospherically Resistant Vegetation Index (ARVI) for the MODIS sensor.

This index is using the blue and red channel to isolate the atmospheric effects and

subsequently apply the corrections on the red and NIR reflectance. Kaufman and Tanre

(1992) showed that ARVI is four times less sensitive to atmospheric changes than NDVI.

The same principle which was applied to SAVI, correcting the red band with the

information contained in the blue band, producing the Soil-adjusted Atmospherically

Resistant Vegetation Index (SARVI; Huete et. al., 1994). Another index which accounts for

residual atmospheric contamination (e.g., aerosols) and variable soil background reflectance,

is the Enhanced Vegetation Index (EVI) developed by Huete et al. (1997; Eq. 16), which

normalizes the reflectance in the red band as a function of the reflectance in the blue band.

Evaluation of radiometric and biophysical performance of EVI implemented from the

Moderate Resolution Imaging Spectroradiometer (MODIS) radiometer revealed that EVI

remained susceptible to canopy variations (Huete et al., 2002).

NIR red

EVI G * (16)

NIR C1red - C 2 blue L

In equation 16, G is a gain factor, C1 and C2 are coefficients to correct aerosol effects and

L is a coefficient do account for canopy background effects. The index was produced for use

with the MODIS sensor.

28 George P. Petropoulos and Chariton Kalaitzidis

Gitelson et. al. (1996) have found the spectral region between 520 and 630 nm (primarily

in the green region of the spectrum) to be more sensitive to chlorophyll fluctuations, even at

very high concentrations. The difference between the red and green bands is that the former is

not affected by the presence of carotenoids. However, the authors have found that the 530 –

570 nm region is not affected by carotenoids absorption either. Instead of using the red band,

they adapted the NDVI and ARVI indices to employ the narrower green band (530 – 570

nm), creating the two ―G reen‖ indices, the Green NDVI (GNDVI) and the Green

Atmospherically Resistant Vegetation Index (GARI).

With the aim of creating an index with the ability to ignore atmospheric effects, while

being sensitive to the fraction of absorbed photosynthetically active radiation (fAPAR) by

vegetation, Gobron et. al. (1999) have formulated a vegetation index to be used the MERIS

sensor data. The MERIS Global Vegetation Index (MGVI) is using a red and NIR band at 681

and 865 nm respectively, in order to estimate the fAPAR. Before the index is calibrated, the

information in the blue band (442 nm) is used, in order to remove the atmospheric effects

present in the red and NIR bands. Comparison of the index with the traditional NDVI has

shown that the MGVI is equally efficient and additionally has a global application. Similarly

to the MGVI, a global vegetation index was designed to be used with SeaWiFS data (Gobron

et. al., 2001). This index also used a red and NIR band combination and was corrected for

atmospheric and geometric effects, before being adjusted to maximise its sensitivity to fAPAR.

Due to the limitations of the use of NIR reflectance, when vegetation canopy cover is not

complete (Colwell, 1974), Gitelson et. al. (2002) have formulated an index that only employs

visible reflectance data. The Visible Atmospherically Resistant Index (VARI) is using the

green and red bands for the estimation of vegetation fraction (VF), as well as the blue band

for the compensation of atmospheric effects in the other two bands (Eq. 17).

R green R red

VARI (17)

R green R red R blue

Despite the fact that the contrast between the bands in the visible region is not as high as

that between red and NIR, the index was found to be more sensitive than NDVI at high VF,

and the error in estimating VF did not exceed 10% (Gitelson et. al., 2002).

The well-known issue of early saturation of many vegetation indices, has also been the

focus of research recently. In their study, Unsalan and Boyer (2004) have analysed the

statistical framework for the NDVI. Subsequently, they represented the index as a slope,

converting its relationship with LAI into a linear form, reducing, in effect, the extend of

saturation. An alternative path was followed by Gitelson (2004), who observed that, while red

reflectance exhibits a flat response once LAI exceeds the value of 2, NIR reflectance

remained sensitive, to LAI values between 2 and 6. On the other hand, the sensitivity of NIR

reflectance was reduced, when its value exceeded 30%. The Wide Dynamic Range

Vegetation Index (WDRVI) is effectively the NDVI, with a factor between 0.1 and 0.2

applied to the NIR reflectance (Eq. 18):

Multispectral Vegetation Indices in Remote Sensing 29

a R NIR R red

WDRVI (18)

a R NIR R red

The value of the a factor is dependent on the vegetation fraction (VF). The new index

was found to be up to three times more sensitive to moderate-to-high LAI values (between 2

and 6). The cause for the increased sensitivity is the effective linearisation of the relationship

with vegetation fraction.

However, in contrast with the numerous studies that use red and NIR spectral bands

discussed so far, a limited number of studies have explored the SWIR spectral bands (e.g., 1.6

and 2.1 µm) for vegetation study. A number of studies have suggested that a combination of

NIR and SWIR bands have the potential for retrieving leaf and canopy water content (e.g.

Hunt & Rock, 1989; Ceccato et al., 2001). One such index is the Moisture Stress Index

(MSI), proposed by Hunt and Rock (1989), which is calculated as a simple ratio between

SWIR (1.6 µm) and NIR (0.82 µm) spectral bands, was proposed to estimate leaf relative

water content (%) and equivalent water thickness (gr cm-2) of different plant species (Eq 19).

SWIR

MSI (19)

NIR

In analyses of the 10-day composite of VGT data another water index was calculated as

the normalized difference between the NIR (0.78–0.89 µm) and SWIR (1.58–1.75 µm)

spectral bands (Xiao et al., 2002), here it is called Land Surface Water Index (LSWI, Eq 20):

NIR SWIR

LSWI (20)

NIR SWIR

More recently, Ceccato et al. (2002 a, b) proposed the Global Vegetation Moisture Index

(GVMI) to retrieve equivalent water thickness (grcm-2) at canopy level, using images from

the SPOT-VGT sensor. This index uses the reflectance values of the rectified NIR band,

which are derived from a complex procedure that involves blue spectral band and uses the

apparent reflectance as seen at the top-of-atmosphere (Gobron et al., 1999), and shown in Eq

21 below:

* *

( pnir 0.1) ( pswir 0.02 )

GVMI (21)

* *

( pnir 0.1) ( pswir 0.02 )

A comparison between GVMI and NDVI showed that the former provided information

related to canopy water content (EWT), while NDVI supplied the information related to

vegetation greenness (Ceccato et al., 2002a).

30 George P. Petropoulos and Chariton Kalaitzidis

The Leaff Area Index (LAI) is a very important plant parameter because its magnitude

affects the amount of radiation that can be absorbed by the canopy. As a result, the LAI has

been related with leaf mass and overall biomass (Wiegand et. al., 1990). Vegetation indices

have been evaluated for their relationship with LAI in many studies, for both forest species

and agricultural crops. Estimation of LAI was found to be possible by the simple ratio of

NIR/red (Asrar et. al., 1985a; Maas, 1993) and the NDVI (Asrar et. al., 1985a) in wheat.

Running et. al. (1986) reached the same conclusion for coniferous forests (r2 = 0.76 for the

simple ratio and r2 = 0.55 for the NDVI). Studying the same area, Peterson et. al. (1987)

improved the relationship of the simple ratio with LAI from r2 of 0.83 to 0.91, by using a log-

linear transformation.

The Normalised Difference Vegetation Index (NDVI) has been the most commonly used

index in studies of estimating LAI and the accuracy of those estimations through this index

have been met with variable results. The highest coefficient of determination between NDVI

and LAI was r2 = 0.95, in a study with corn (Gilabert et. al., 1996). However, the limitations

of using the NDVI for LAI estimations are quite severe. The index has been proven to be very

sensitive to the contribution of soil or background vegetation at low LAI values (Baret and

Guyot, 1991). On the other hand, the NDVI-LAI relationship seems to saturate at high LAI

values, because of the reduced contribution of the lower canopy leaves to the overall canopy

reflectance (Asrar et. al., 1984; Turner et. al., 1999). A corrected version of the NDVI, using

middle-infrared information was shown to improve the estimation of LAI (Nemani et. al.,

1993) and the short-wave infrared reflectance signal has also been suggested as being able to

estimate LAI, taking advantage of the intense water absorption features in that region (Gong

et. al., 2003). However, in addition to the soil sensitivity and saturation issues, the NDVI-LAI

relationship also appears to be affected by leaf orientation (Baret et. al., 1989) and growth

stage (Hatfield et. al., 1984). In particular, Curran et. al. (1992) have shown that the

coefficient of determination between the NDVI and LAI for slash pine is a low r2 = 0.35

during February, increasing to r2 = 0.86 in March and falling to r2 = 0.75 for September data.

Alternative indices have also been evaluated, in an attempt to deal with the issues faced

with the NDVI. The Green Vegetation Index (Jackson, 1983), was evaluated on various fields

of corn and was found to provide accurate estimates of LAI with r2 = 0.78 – 0.93 (Wiegand

et. al., 1990). In order to account for background soil contribution, the PVI was used to

estimate green LAI (Maas, 1988). Wiegand et. al. (1990) evaluated the GVI and PVI on corn

and found that a function of those two indices provided coefficients of determination of r2 =

0.937, higher than those produced by the simple ratio and the NDVI. The introduction of

vegetation indices such as SAVI (Huete, 1988) and TSAVI (Baret et. al., 1989), which tend to

deal better with soil contribution, prompted the comparison with the more traditional PVI and

NDVI indices. The first two indices appeared to be superior to the latter two, due to their

ability to account for soil contribution (Baret and Guyot, 1991). The introduction of

atmospheric resistance employed in the ARVI index (Kaufman and Tanre, 1992) in SAVI,

created a stronger version of the index (SARVI), which appeared to reduce the accuracy error

of estimating LAI in half, in comparison with NDVI (Huete et. al., 1994).

All vegetation indices have an asymptotic relationship with LAI that saturates at high

LAI values (Spanner et. al., 1990; Baret and Guyot, 1991; Turner et. al., 1999). Fassnacht et.

al. (1997) found that a linear relationship was sufficient to connect LAI and a VI, but a log-

Multispectral Vegetation Indices in Remote Sensing 31

Gilabert et. al. (2002) found that the generalised soil-adjusted vegetation index (GESAVI)

was less sensitive to soil contribution and Gitelson (2004) showed that the Wide Dynamic

Range Vegetation Index (WDRVI) was more resistant to saturation, in comparison with the

NDVI. The Enhanced Vegetation Index (EVI; Huete 1997) was shown to be able to make

accurate LAI estimates, in the range of LAI between 0 and 8 (Houborg et. al., 2007). In order

to deal with the saturation issue, Unsalan and Boyer (2004) have suggested representing the

index as a slope and using its inverse tangent, in order to linearise the measure to yield a new

index, the Linearised Vegetation Index (LVI).

The Photosynthetically Active Radiation (PAR) is the spectral range of light that can be

used by vegetation for the process of photosynthesis. This region is between 400 and 700 nm

(the ―v isible‖ region), because in this region the vegetation pigments absorb energy. The

amount of energy that is actually absorbed is known as Absorbed PAR (APAR) and when it

is expressed as a fraction of the total incident radiation it is referred to as the Fraction of

APAR (fAPAR). This energy is very closely related to the primary productivity of plants and

the production of biomass. Dry matter production and the accumulated intercepted

photosynthetically active radiation in the 400-700 nm region of the electromagnetic spectrum

were also shown to be closely related (Biscoe et. al., 1975; Monteith, 1977; Gallagher and

Biscoe, 1978). In addition, a quantitative relationship between dry matter production and

intercepted radiation can be established, as Hodges and Kanemasu (1977) showed for barley

canopies. Hence, it is possible to use remote sensing to estimate the solar radiation that is

intercepted by canopies, and then converted into dry matter (Daughtry et. al., 1983).

Early studies have shown that both the simple ratio (NIR/red) and the NDVI were closely

related to dry matter accumulation (Tucker et. al., 1981). The simple ratio (NIR/red) was used

to derive an empirical relationship with fAPAR on sugarbeet, but that relationship was not

transferable to different crops or different growth stages (Steven et. al., 1983). Christensen

and Gourdiaan (1993) also used the simple ratio to calculate the cumulative PAR and the

result was found to be closely related with the above-ground biomass. The NDVI was also

used in many cases for the estimation of PAR. Asrar et. al. (1985b) found a strong correlation

between the index and PAR, which was then used to calculate above-ground phytomass of

wheat. Steinmetz et. al. (1990) also found a good relationship between NDVI and PAR, but

highlighted the fact that the relationship is affected by nitrogen and water stress and also that

the rate of conversion from PAR to biomass was dependent on growth stage of wheat.

The relationship between the NDVI and fAPAR has a low signal-to-noise ratio (North,

2002) and is linear, but it is only valid during the growth stage of the crops (Ruimy et. al.,

1994). The possible reason is that the canopy continues absorbing radiation at later crop

stages but it contains less photosynthetic pigments, which leads to a decrease in the NDVI

(Hatfield et. al., 1984; Gallo et. al., 1985). On the other hand, when fAPAR is high, NDVI is

less sensitive to fAPAR changes. In those cases the WDRVI (Gitelson, 2004) appears to be

more sensitive, and in cases where hyperspectral data are available (e.g. ESA‘s MERIS or

NASA‘s Hyperion sensors), the red-edge NDVI is the most sensitive index (Vina and

Gitelson, 2005).

32 George P. Petropoulos and Chariton Kalaitzidis

Other indices were also evaluated for their ability to estimate PAR, fAPAR and indirectly,

biomass and in many cases they provided superior results to both the simple ratio and NDVI.

In a study comparing the GVI, PVI, NDVI and RVI, Wiegand et. al. (1990) found that a

combination of GVI and PVI gave the most accurate estimates of f APAR (r2 = 0.94). On the

other hand, a similar study showed that the NDVI and PVI were the most accurate indices in

the estimation of fAPAR in cotton (Wiegand et. al., 1991).Gobron et. al. (1999) evaluated the

MERIS Global Vegetation Index (MGVI) using MERIS data and found that the index

provided more information than the simple NDVI. The WDRVI was used on maize and

soybean plants, employing field spectra, and it was found to be more sensitive than the NDVI

at high fAPAR values (Vina and Gitelson, 2005).

CONCLUSION

In this chapter it was provided an overview of the different radiometric vegetation indices

usilising multispectral remote sensing observations acquired in the reflective part of the EMR

spectrum. In this framework, it was first provided an overview of the main properties of

remote sensing in this part of the EMR, as this was deemed necessary in order to cover the

theoretical background required in understanding the basic principles on which these

radiometric indices have their basis.

As indicated by the overview presented herein, a wide range of radiometric indices have

been developed in order to establish relationships between such data and biomass, or other

vegetation characteristics that can be indirectly linked to the amount of biomass present. As

was also made clear from the overview conducted herein, the factors that affect the efficiency

of vegetation indices are concerned with the characteristics of the recorded signal, which is

affected by bidirectional and atmospheric effects, canopy structure and background

vegetation or soil contribution, scattering, spatial heterogeneity, adjacency effects, non-linear

mixing and topographic effects. These factors are a major concern for the transferability of an

established methodology to a different plant, location, or time. What is more, on many

occasions the proven relationships between vegetation indices and vegetation properties were

empirical in nature, performing well on the particular study, but facing transferability issues

when the same indices were evaluated on a different vegetation type, different location or

even different time of the year.

As was also indicated in the present review, methods of using vegetation indices for the

estimation of the leaf area index (LAI) have had variable results. Canopy structure and

background contribution appear to play a crucial role in the determination of the canopy

reflectance signal, influencing the performance of any VI – LAI relationship. When

vegetation cover is low, the presence of understory vegetation (primarily in the case of

forests) and the spectral characteristics of the underlying soil, affect canopy reflectance and

give erroneous LAI estimates. Soil-adjusted indices that either use information on the soil line

(NIR/red ratio) underneath the canopy, or a factor estimating the vegetation cover, tend to

somewhat deal with the background contribution issue at low LAI values. However, those

indices still present weaknesses that render their operational ability questionable. On the other

hand, when the LAI is high, the multiple layers of leaves within the canopy have a different

contribution to the canopy reflectance signal, causing the VI – LAI relationship to saturate.

Multispectral Vegetation Indices in Remote Sensing 33

through the use of vegetation indices, is another popular method of indirectly assessing the

amount of biomass present. This method is particularly applicable in the case of crops, where

the growth cycle lasts for less than one year. There have been many suggestions on the

optimal period of the growth cycle for the data to be collected, for a variety of crops. It

appears that the best performing method is using integrated series of measurements and

calculations of a vegetation index, in order to account for variability through the growth

season and also to account for the fact that the crops have a different efficiency in biomass

production for a given fAPAR, at different stages of their growth cycle. Initial studies used

integrated NDVI values to estimate biomass production through the fAPAR. However, the

WDRVI was shown to be superior to NDVI, especially at high fAPAR values (Gitelson,

2004).

The recent advancements in remote sensing technology have allowed the development of

a wide range of space-borne multispectral remote sensing systems have been developed

during the last decades, providing a capability for observing land cover at broad spatial scales

and at intervals that previously were not applicable. The recent evolution of remote sensing

technology has also resulted to the development of hyperspectral sensors. Unlike

multispectral sensors, hyperspectral remote sensing systems record spectral information on

land surface targets in numerous narrow continuous spectral bands. This allows to these

systems to provide an enhanced level of information for atmospheric correction and to also

use specific spectral information recorded by selective channels of the sensor accordingly to

the characteristics of the specific problem under analysis (Hansen and Schjoerring, 2003;

Galvao et al., 2005; Dalponte et al., 2009). A number of both airborne and satellite

hyperspectral remote sensing systems have been developed and launched in the recent years,

a review of the most recent ones is made available by Dalaponte et al. (2009). Perhaps the

availability of such rich spectral information context can potentially fosters the development

of new radiometric vegetation indices which will allow overcoming the current limitations

and the same time open up pathways to better map and monitor vegetation health and vigor

conditions and related parameters. Last but not least, if an operational development and

operation of such indices on large scale is in mind, it is required the empirical relationships

between vegetation indices and vegetation variables to be applied on a variety of vegetation

types, locations and conditions, taking also advantage of the recent developments in

spaceborne remote sensors technology.

ACKNOWLEDGMENTS

Part of this work was undertaken within the frame of an FP7 funded programme with the

acronym CEUBIOM, and full title ―Cla ssification of European Biomass Potential for

Bioenergy Using Terrestrial and Earth Observations‖. Authors wish to thank the anonymous

reviewers for the valuable comments which resulted to the improvement of the originally

submitted chapter. Dr. Petropoulos is also grateful to INFOCOSMOS E.E.

(http://www.infocosmos.eu) for supporting his participation to the present work.

34 George P. Petropoulos and Chariton Kalaitzidis

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In: Ecological Modeling ISBN: 978-1-61324-567-5

Editor: WenJun Zhang, pp. 41-64 © 2012 Nova Science Publishers, Inc.

Chapter 3

FOR THE ESTIMATION OF SURFACE WATER

POLLUTION RISK FROM OLIVE MILL

WASTE DISCHARGES

Dimitris Zianis2 and Nikos Boretos5

1

School of Science and Technology, Aalto University, Niemenkatu 73,

15140 Lahti, Finland. Email: anas.altartouri@aalto.fi

2

Department of Environmental Management,

Mediterranean Agronomic Institute Chania,

Alsyllion Agrokepion, Chania, Crete, 73100, Greece.

Email: dzianis_2000@yahoo.com

3

Ministry of Environment, Energy and Climate Change, 17 Amaliados str.,

11523 Athens, Greece. Email: kalliapediaditi@hotmail.com

4

Department of Natural Resources Development & Agricultural Engineering,

Agricultural University of Athens, 75, Iera Odos St., Athens, Greece.

Email: petropoulos.george@gmail.com

5

Department of Information Systems and Technology,

Mediterranean Agronomic Institute Chania,

Alsyllion Agrokepion, Chania, Crete, 73100, Greece.

ABSTRACT

According to the Water Framework Directive (WFD, 2000/60/EC), Integrated River

Basin Management Plans (RBMP) are required at different scales, in order to prevent

amongst other things, water resource deterioration and ensure water pollution reduction.

An integrated river basin management approach underpins a risk-based land management

framework for all activities within a spatial land-use planning framework. To this end, a

risk assessment methodology is required to identify water pollution hazards in order to

set appropriate environmental objectives and in turn design suitable mitigation measures.

42 Anas Altartouri, Kalliope Pediaditi, George P. Petropoulos et al.

Surface water pollution as a result of Olive Mill Waste (OMW) discharge is a serious

hazard in the olive oil producing regions of the Mediterranean. However, there is no

standardised method to assess the risk of water pollution from olive mill waste for any

given river basin. The present chapter shows the results from a study conducted

addressing the above issue by designing a detailed risk assessment methodology, which

utilises GIS modelling to classify within a watershed individual sub-catchment risk of

water pollution occurring from olive mill waste discharges. The chapter presents the

proposed criteria and calculations required to estimate sub-catchment risk significance

and comments on the methods potential for wider application. It combines elements from

risk assessment frameworks, Multi Criteria Analysis (MCA), and Geographic

Information Systems (GIS). MCA is used to aggregate different aspects and elements

associated with this environmental problem, while GIS modeling tools helped in

obtaining many criterion values and providing insight into how different objects interact

in nature and how these interactions influence risk at the watershed level. The proposed

method was trialed in the Keritis watershed in Crete, Greece and the results indicated that

this method has the potential to be a useful guide to prioritise risk management actions

and mitigation measures which can subsequently be incorporated in river basin

management plans.

Keywords: Decision Support Systems (DSS), Geographic Information System (GIS), Multi

Criteria Analysis (MCA), Olive Mill Wastewater (OMW), risk assessment, water

pollution.

1. INTRODUCTION

A major environmental issue in Mediterranean region is the pollution of aquatic

ecosystems through the discharge of industrial and domestic effluents in water bodies

(Karageorgis et al., 2003). One of the main polluting activities is the discharge of effluents

generated from olive mill agricultural industries. Olive mill wastewater (OMW) is the liquid

by-product generated during olive oil production. OMW contains pollutants and hazardous

materials in different concentrations which may cause negative impacts on the natural water

bodies and, consequently, human and environmental health. Indicatively, Paliatziki (2006)

states that 50 m3 of olive oil mill wastewater are equivalent to the waste produced by 30,000

citizens. The dispersed spatial location of a large number of small-sized olive oil mills

together with the concentration and seasonal production of OMW, as the Mediterranean

region accounts for 95% of the global OMW production, are the main reasons for the

environmental degradation caused by OMW (Kapellakis et al., 2002; Niaounakis and

Halvadakis, 2006).

According to Niaounakis and Halvadakis (2006), the OMW composition is: water (80-

83%); organic compounds (15-18%); and inorganic compounds (mainly potassium, salts and

phosphates, 2%). It contains phytotoxic and biotoxic substances and is non-biodegradable. It

has a high organic load and classified among the ‗strongest‘ industrial effluents, with

Chemical Oxygen Demand (COD) up to 220 g/l. The consequence of this is a high

consumption of oxygen dissolved in the water bodies which negatively affects the living

organisms and, thus, an imbalance of the whole ecosystem may be caused (Niaounakis and

Halvadakis, 2006). Similar effects can also result from high phosphorus content in OMW

which accelerate the growth of algae leading to eutrophication. Beside the high number of

Development of a Decision Support System … 43

bacteria and fungi in OMW, the presence of high concentration of nutrients may cause

infection of water bodies since it make perfect medium of pathogens to multiply in these

water bodies. Moreover, OMW has long chain fatty acids and phenolic compounds with high

percentage of dissolved mineral salts (ibid). All these contaminants and their impacts on

natural water bodies can result in significant consequences on the environment and people

who may be in contact with these water bodies (Morrison et al., 2001; Ogunfowokan et al.,

2005, Niaounakis and Halvadakis, 2006).

The EU Water Framework Directive (WFD, 2000/60/EC) aims at harmonizing existing

European water policies and to improve water quality in all aquatic environments within the

community area. It emphasizes the need of new Integrated River Basin Management Plans

(RBMP) at national and regional/local scale resulting in the protection and improvement of

the sustainable use of all waters (Heathwite et al., 2005; Rekolainen et al., 2003). The main

objectives of the RBMP include the prevention of further deterioration of water resources and

the promotion of sustainable water use that ensures the progressive reduction of pollution.

These elements in the EU legislation, policies, and programs underpin the need of including

risk-based land management framework to all activities within a spatial land-use planning

framework (Heathwite et al., 2005). However, there is no standardised method to assess the

risk of water pollution from OMW for any given river basin. Due to the small scale and

dispersed nature of OMW processing and disposal method, regulation using a risk-based

approach which uses planning, for example through RBMP as pollution preventing, rather

than relying on post development or pollution incident mitigation is required. To this end, risk

assessment methodology is needed for this point-source water pollution in order to set

appropriate environmental objectives and risk zones to integrate within RBMP as well as

design suitable mitigation measures.

This chapter presents a risk assessment method based on general frameworks to address

different aspects of the environmental problems associated with the OMW pollution. It

provides an analytical approach based on deep investigation of elements of OMW pollution

risk and linkages between them resulting in a conceptual model to understand and cope with

such problem. This model provides insight into how different objects interact in the nature

and how this interactions influences water resources in a watershed. As number of tools and

techniques are needed for risk assessment process to effectively support decision makers

(Allan et al., 2006), the proposed method combines field and desk-based techniques and

utilizes different tools, such as Geographic Information Systems (GIS) and Multi Criteria

Analysis (MCA). This integration between GIS and MCA in developed risk assessment

method takes advantage of the analytical capabilities of MCA on the one hand. On the other

hand, this method benefits from the information processing and display capabilities of GIS as

risk assessment should involve analysis of spatial variability which consider differences

between locations (Allan et al., 2006; Lapucci et al., 2005). The chapter presents the proposed

approach consisting of all criteria and calculation models required to quantitatively estimate

risk significance at each sub-catchment within the river basin under investigation and

comments on the methods potential for wider application.

44 Anas Altartouri, Kalliope Pediaditi, George P. Petropoulos et al.

MODEL OF OMW POLLUTION

In order to develop a risk assessment process for water pollution from OMW, it is

important to describe the theoretical risk assessment frameworks as well as the conceptual

model of risk generating process of OMW pollution and its controlling factors. Briefly, there

are several risk assessment frameworks which provide a range of definitions of risk (DEFRA

2002; Maltby, 2006; enHealth, 2004; EPA, 1998). Whilst the fundamental processes are

usually similar, slightly different terminologies are used internationally to describe

components of the risk assessment process (Power and McCarrty, 1998). For the purpose of

this research, risk is defined as ―acombination of the probability, or frequency, of occurrence

of a defined hazard and the magnitude of the consequences of the occurrence‖ (DEFRA,

2002, p2). Accordingly, risk can be expressed as: Risk = Probability * Magnitude (Donoghue,

2001; Pediaditi et al., 2005, Billington, 2005).

Component 1: the spatial scale of consequences

Criterion 1 (Cr.1): extent of potentially harmed receptors

Component 2: the temporal scale of consequences

Criterion 2 (Cr.2): possible sedimentation areas

Risk probability components

Component 3: the probability of hazard occurring

Criterion 3 (Cr.3): precipitation

Criterion 4 (Cr.4): waste volume to lagoon capacity ratio

Criterion 5 (Cr.5): lagoon conditions

Component 4: the probability of receptors being exposed to hazard

Criterion 6 (Cr.6): length of the flow path to surface water bodies

Component 5: the probability of harm resulting

Criterion 7 (Cr.7): surface water quality

As this developed surface water OMW pollution risk assessment method has been

designed to be used in RBMP, the method was based on the generic framework of DEFRA

Guidelines for Environmental Risk Assessment and Management (2002) which makes clear

links between risk assessment and risk management focusing on the practical implementation

of risk assessment result to generate risk management solution (Power & McCarty, 1998). In

addition, it provides clear breakdown of risk into basic components upon which several

criteria have been developed (see Box 1). For the determination of these components, the

olive mill waste process was studied from cradle to grave using field observations, expert

opinion, and literature review. Based on the above, the conceptual model, illustrated in Figure

1, was developed which, subsequently, served as the basis for the development of the

quantitative assessment of risk from OMW pollution.

As illustrated in Figure 1, it is essential for risk assessment process to define the three

elements of risk; sources, pathways, and receptors which, subsequently, help developing

quantitative criteria. A source of stressors can be defined as the place where the stressor

Development of a Decision Support System … 45

originates or is released (EPA, 1998), which in this case are the lagoons where OMW is

gathered. These lagoons are the first element of the exposure pathway and the entities where

hazardous events, such as heavy storms or spillage, may occur and, hence, the probability of

hazard occurring is strongly associated with them (Component 3, Box 1).

In the case of OMW pollution risk, the pathway consists of the mechanism by which

receptors are exposed to the water polluted by OMW and, therefore, it controls the probability

of receptors being exposed to hazard (Component 4, Box 1). Water bodies, ground and

surface, are considered as the potential pathways by which receptors may be exposed to the

hazard of OMW. However, it has been noticed that surface water bodies are more likely to

transmit the pollutants released from the lagoons. This is due to the fact that the most

probable hazardous event to cause the lagoon overflowing is the heavy storms during which a

large amount of water is running off to the drainage network, meaning that released OMW is

more likely to be washed away into surface water bodies rather than infiltrated into

groundwater bodies.

The last elements in this chain are the receptors which in this case are people or actual

environmental values to be protected. Studying the probability of adverse effects resulting

46 Anas Altartouri, Kalliope Pediaditi, George P. Petropoulos et al.

requires a clear definition of receptors to be addressed (Allan et al., 2006). For the purpose of

this study, humans and high-value ecological sites (such as NATURA 2000 sites) are

considered as the potential receptors that may be harmed from water pollution from OMW.

The choice of these two generic receptors is underpinned by the fact that they are the most

sensitive and protected according to the EU legislation. As specific dose-response exposure

data is limited in the literature, the use of highly valued and protected by legislation receptors

is the first step in the practical implementation of this method in the context of the WFD and

RBMP.

The developed methodology presented in this chapter to calculate risk of OMW on

human health and protected areas through surface water bodies, using of DEFRA Guidelines

components (Box 1), proposes a number of criteria specific to the risk of OMW pollution.

The process of OMW pollution risk assessment is considered as multi-criteria evaluation

since components of risk depend on several factors which are combined in a specific way

(Mendoza et al., 2002; Eastman, 2003). The criteria have been selected on the basis that they

play a role in the risk generating process considering perspectives of all agents and behaviors

of all the environmental elements playing a part in this process (Lapucci et al., 2005). Below

the rationale behind each criterion is described.

This criterion is proposed to calculate the magnitude of OMW pollution risk at the spatial

scale (Component 1, Box 1). As the main receptor groups of OMW pollution risk are humans

and protected areas, the calculation of this criterion is strongly associated with the spatial

distribution of these receptors and is divided into two directions based on the addressed

receptor group.

Regarding the human receptor group, the magnitude of consequences can be estimated by

the number of affected inhabitants. It can be stated that the larger the population is, the greater

the potential consequences of water pollution in the watershed. Thus, the distribution of

towns and population within sub-catchments in the river basin under investigation should be

drawn. However, the term ‗potentially exposed inhabitants‘ include also all people that may

be exposed to the polluted water in the area regardless their residence place. This may include

people whose drinking water source is located in this area. Also, it may include people who

may have come in contact with the surface water bodies such as tourists or farmers.

However, when addressing the other receptor group, the area of protected areas which

represent a high ecological value should be taken into account in order to calculate the spatial

scale of the magnitude of consequences (Component 1, Box 1). The larger the extension of

these protected areas in the addressed river basin, the greater number of impacted species.

Potentially exposed area within these sites can be delineated by creating a buffer around the

surface water bodies through which the pollutants may be transported. Historical observations

of the heavy storms and floods in the region should take part in determining the extension of

Development of a Decision Support System … 47

the buffer zone. For the EU territories, NATURA 2000 sites can represent these ecologically

valuable areas. NATURA 2000 is a European network of protected sites which represent

areas of the highest environmental value for natural habitats (for several plant and animal

species) which are rare, endangered or vulnerable in the European Community. However,

should designated environmental sites other than NATURA, they should also be included as

receptors1. Ideally, an ecological baseline assessment of areas under consideration should be

undertaken in order to identify areas of potential high ecological value which might not be

designated. However, following discussion with potential end users of this tool, the feasibility

of carrying this out was questioned therefore at a coarser level and, thus as a first step,

calculating the area of potentially exposed protected sites can be used although the first is

preferable.

to the temporal aspect of magnitude of consequences (Component 2, Box 1) for both receptor

groups. Sediments may contain hazardous materials and may expand the time scale of the

consequences for a long period. Therefore, the larger the sedimentation areas in a sub-

catchment, the greater the temporal magnitude of consequences. Sediments may settle in long

flat areas with low velocity of the stream current and, therefore, field investigation of the

topographic nature of the area as well as expert opinion are essential as sediments may not be

applicable in some cases.

Precipitation is one of the factors that may lead to hazard occurrence (Component 3, Box

1). It is important in terms of the potential overflow (hazardous event) of the lagoons where

the waste is deposited. Overflowing, however, causes the pollutants to reach the water bodies

and, therefore, hazard occurs. The greater the precipitation over the area it is, the higher the

probability of overflowing. Records of occasional, heavy storm events should be considered

in estimating the probability of a lagoon to overflow. Alternatively, the maximum monthly

precipitation may substitute in estimating the overflowing probability.

The ratio between generated waste volume and lagoon capacity is another factor which

affects the probability of hazard occurrence, i.e. the probability that OMW lagoons overflow

(Component 3, Box 1). If the amount of produced waste is larger than the lagoon capacity,

then the hazard is more likely to occur. On the contrary, if the lagoons are well designed to

include a buffer margin which can accommodate for excess precipitation, then the probability

1

This is particularly relevant for the application of this method in NON-EU countries which do not belong to

NATRA 2000 network.

48 Anas Altartouri, Kalliope Pediaditi, George P. Petropoulos et al.

of hazard occurrence goes to zero unless of other events like extreme rainstorm occur.

Therefore, the higher the ratio is, the higher the probability of hazard to occur.

The structural conditions of the lagoons where the waste is gathered have to be

considered. It is an essential factor which affects the probability of hazard occurring

(Component 3, Box 1). Infiltration of the pollutants through the basement of lagoons and

spillage through the walls, due to poor lagoon conditions e.g. lack of maintenance, structural

malfunction, etc., lead the hazard occur. Therefore, the better the structural conditions of

lagoons, the lower the probability of pollutants to reach water bodies. In order to calculate

this criterion, site visits to lagoon are required as well as an investigation of their specification

and permits.

3.6. Length of the Flow Path to Surface Water Bodies Criterion (Cr.6)

Water bodies close to lagoons have a higher probability of being contaminated should the

OMW discharge event occur. The longer the flow path is to a sub-catchment, the greater the

probability of pollutants to be diluted before reaching receptors. This criterion plays a main

role in the estimation of probability of stressor and receptor co-occurrence (Component 4,

Box 1). The actual length of the flow paths can be determined using the 3D tools in GIS

associated with the Digital Elevation Model (DEM). Several flow paths can be drawn for a

single lagoon. Each of these flow paths starts from the lagoon and ends at the point where this

flow path joins the water bodies in a receiving sub-catchment.

The probability of receptors to be harmed resulting from exposure to the hazard of water

pollution (Component 5, Box 1) depends on the concentrations of polluting substances in the

water bodies they be in touch with. Water quality parameters are the key factors to estimate

the impact of these pollutants on the receptors. If the concentrations of polluting substances

are within the allowable limits in legislation, then the probability of harm is near to zero. On

the contrary, the probability of harm is very high when the concentrations exceed the

contamination thresholds. For example, if a lagoon is located in a catchment, then iron (Fe)

could be one of the pollutants (hazard) that may be found in the water samples taken from the

water bodies of that catchment. According to the WFD, the guide level and the maximum

admissible concentration for the drinking water are 50µg/l and 200µg/l, respectively.

Therefore, a scale from zero to one is established to express the likelihood of harm resulting.

In this scale, the probability of 0 is assigned for samples with 50µg/l or less iron

concentration, and 1 for those with 200µg/l iron concentration. The intermediate

concentrations are assigned values between 0 and 1 according to the linear equation which

interpolating these two limit values (section 4.2). This should be applied on all the pollutants

associated with the OMW. Table 1 lists the chemicals associated with the OMW (Niaounakis

Development of a Decision Support System … 49

and Halvadakis, 2006) and their preferable and maximum admissible levels according to the

WFD (2000/60/EC).

However, as data about dose-response is available only for human in the WFD, this

method proposes the dilution degree as an alternative approach to calculate its value when

addressing risk of OMW pollution on the protected areas. The degree of pollutants‘

concentrations in the surface water bodies located in the protected areas can be indicated

taking in consideration the pathway by which these pollutants are transported. Pollutants

could be carried by direct surface runoff or, alternatively, by streams. By direct surface

runoff, the concentrations of pollutants remain almost the same as in the origin pollution

source or with a slight dilution degree in the rain water while pollutants carried by streams are

subjected to higher dilution degrees which decrease their concentration before reaching

ecological sites. However, the degree of dilution and its speed depend on stream velocity as

well as the quantity of stream water. These two parameters can be expressed in terms of

stream order. Therefore, the higher the stream order, the faster the dilution and, therefore, the

lower the probability of protected areas to be harmed.

No. Parameter

(mg/l) level (mg/l)

Cr.7.1 Copper (Cu) 0.1 3.0

Cr.7.2 Iron (Fe) 0.05 0.2

Cr.7.3 Lead (Pb) 0 0.05

Cr.7.4 Magnesium (Mg) 30.0 50.0

Cr.7.5 Manganese (Mn) 0.02 0.05

Cr.7.6 Nickel (Ni) 0.0 0.05

Cr.7.7 Nitrogen (N) 0 1.0

Cr.7.8 pH 6.5 8.5

Cr7.9 Phenols 0.0 0.005

Cr.7.10 Phosphorus (P) 0.4 5.0

Cr.7.11 Potassium (K) 10.0 12.0

Cr.7.12 Sodium (Na) 20.0 150.0

Cr.7.13 Zinc (Zn) 0.1 5.0

Cr.7.14 Microbiological contaminants 0 0

This section provides guidelines for applying the developed quantitative risk assessment

method of OMW pollution. As MCA-based approach, the proposed method consists of the

four steps (Mendoza et al., 1999). The initiative step deals mainly with data collection and

database preparation in order to obtain values of every criterion. This is followed by

standardization step which brings criteria of different scales into comparable dimensionless

scale. Then, criteria are weighted based on their relative significance to risk components (Box

1). Finally, standardized criterion values and their weights are aggregated using a calculation

50 Anas Altartouri, Kalliope Pediaditi, George P. Petropoulos et al.

model which consists of a set of formulae. These steps are illustrated in Figure 3, 4, and 5 and

discussed in the following subheadings.

Practically, there are some initiative steps to be performed in order to proceed with this

method. These steps mainly deal with data collection and preparation of appropriate datasets

which serves as an input into the calculation model in order to obtain quantitative values of

risk. This data consists of all the initial values of criteria which result from the application of

a variety of data processing procedures. Such procedures may include hydrological

processing, map derivation, tabular calculations, and other procedures depending on the

available data.

In order to define surface water bodies, namely streams, and determine some criterion

values (Cr.6, Box 1), a hydrological model is needed. As the function of the spatial hydrology

modeling tool is to simulate the water flow and transport on a specified area using GIS data,

a hydrological model is needed in this analysis in order to define the drainage network in the

target watershed, including streams and possible flow paths from the sources of hazard to

surface water bodies. In addition, the hydrological model is essential for dividing the

watershed under investigation into sub-catchments which represent, together with the

lagoons, the analysis units.

Additionally, data from the field is necessary to determine criterion values of water

quality parameters (Cr.7). Samples from surface water bodies in the target watershed should

be collected within a pre-planned sampling strategy and analyzed for the chemicals and

parameters associated with polluting source, namely OMW. The first consideration is the

timing of sampling process. Regarding OMW, water samples should be collected from the

surface water bodies (streams) in the target watershed during the period when lagoons contain

the maximum volume of wastewater and the water is still present in the drainage network.

The proposed sampling strategy consists of collecting samples from the points where possible

flow paths from lagoons join the receiving streams. This sampling strategy is designed in

order that the chemical tests to show the worst case where the pollutants are in the highest

possible concentrations and have not yet been affected by the dilution process. Such an

approach restricts biased sampling and minimizes the bias of one criterion‘s effect to the

other. The concentrations of the analyzed chemicals in each sample should be assigned to the

corresponding lagoon as shown in the analysis below.

Because of the different scales upon which criteria are measured, it is necessary to

standardize them before being combined. There are various standardization procedures,

typically using the minimum and maximum values as scaling points (Eastman, 2003). These

functions transform the values with dimensions to dimensionless values between 0 and 1,

which makes the criteria of different dimensions comparable (Mendoza et al., 1999). The

functions are implemented either as a benefit (the higher the criterion score, the higher the

likelihood or magnitude of risk) or as a cost (the lower the criterion score the higher the

Development of a Decision Support System … 51

for different criteria according to their nature. The first standardization method, which is

applied for all the developed criteria except the waste volume to lagoon capacity ratio

criterion, the lagoon condition criterion, and the water quality criteria, consists of the

following linear scaling functions:

R

ci

Rmax for benefit criteria, and (1)

Rmin

ci

R for cost criteria (2)

where:

ci = the standardized criterion value;R = the origin criterion value; Rmin = the minimum

value of the criterion of all units (lagoons or sub-catchments); and Rmax = the maximum value

of the criterion of all units (lagoons or sub-catchments).

The other standardization method is applied for water quality parameters (Cr.7, Box1).

As the probability of harm resulting is strongly correlated with the amounts of different

OMW hazardous chemical in the water, it can be given as a function of their concentrations.

These functions (see Figure 2) consist of linear multi-segments based on the following linear

scaling functions:

R Rmin

ci

Rmax Rmin for benefit criteria, and (3)

Rmax R

ci

Rmax Rmin for cost criteria (4)

where:

ci = the standardized criterion value; R = the origin criterion value; Rmin = the guide level

according to the WFD (see Table 1) and; and Rmax = the maximum admissible level according

to the WFD (see Table 1).

Finally, as some criteria are assigned dimensionless values, there is no need to

standardize them. These criteria are the ratio between waste volume and lagoon capacity and

the lagoon conditions (see Table 2). The ratio is result of dividing the amount of produced

waste on the volume of the lagoon where it is located which does not exceed the value of one

since the permission of olive mills requires a lagoon size larger than the expected produced

waste. From another side, the lagoon condition criterion is assigned a Boolean value of zero,

where the lagoon has no constructional problems, or one, where obvious construction

problems are detected.

52 Anas Altartouri, Kalliope Pediaditi, George P. Petropoulos et al.

Acknowledging the context specific nature of risk, this method enables through its design

the assignment of weights according to contextual criterion significance. Hence, criteria that

are deemed more significant indicators of risk in the river basin under consideration can be

assigned higher weights thereby giving them greater importance in the estimation of the risk

of OMW pollution (Mendoza et al., 2002). These weights are assigned separately within

every risk component (Box 1) to show the importance of every criterion in relation to that

component. In order to calculate the weights of multiple criteria, the Analytic Hierarchy

Process (AHP) can be used. AHP is a multi-criteria decision support method which uses

paired comparisons in order to calculate the weights of multiple criteria (Saaty, 1990).

Thereafter, the analysis is separated into two directions according to the addressed

receptors. The first direction addresses the hazard of OMW transported by surface water

bodies and affecting population, while the second direction addresses the hazard of OMW

transported by surface water bodies affecting protected areas. This implies producing two risk

Development of a Decision Support System … 53

maps (one for each direction) as a result of this analysis. This separation is due to the slight

differences in the criteria used for each receptor (see Table 3). Assigning the weight for

criteria is a subjective process which results from the pair wise comparisons. The

specifications of every site greatly influence this process. Hence, for more accurate and

unbiased weight assignment, expert opinion should be considered as well as conducting site

visits.

Unit to Direction

Criterion which it is Component (receptors

assigned addressed)

Cr.1 Number of potentially exposed inhabitants Sub-catch. Component 1 (Box 1)

Cr.2 Possible sedimentation areas Sub-catch. Component 2 (Box 1)

Cr.3 Precipitation Lagoon

Cr.4 Waste volume to lagoon capacity ratio Lagoon Component 3 (Box 1)

Cr.5 Lagoon conditions Lagoon

Cr.6 Length of the flow path to surface water bodies Lagoon Component 4 (Box 1)

Cr.7 Copper (Cu) Lagoon

Cr.8 Iron (Fe) Lagoon

Cr.9 Lead (bp) Lagoon

Water quality parameters

Cr.11 Manganese (Mn) Lagoon

Cr.12 Nickel Lagoon

Cr.13 Nitrogen (N) Lagoon Component 5 (Box 1)

Cr.14 ph Lagoon

Cr.15 Phenols Lagoon

Cr.16 Phosphorus (P) Lagoon

Cr.17 Potassium (K) Lagoon

Cr.18 Sodium (Na) Lagoon

Cr.19 Zinc (Zn) Lagoon

Cr.1 Area of potentially exposed NATURA sites Sub-catch. Component 1 (Box 1)

Cr.2 Possible sedimentation areas Sub-catch. Component 2 (Box 1)

Cr.3 Precipitation Lagoon

Cr.4 Waste volume to lagoon capacity ratio Lagoon Component 3 (Box 1) Protected

Cr.5 Lagoon conditions Lagoon areas

Cr.6 Length of the flow path to NATURA sites Lagoon Component 4 (Box 1)

Cr.7 Dilution degree expressed by stream orders Lagoon Component 5 (Box 1)

In order to obtain results about risk in every sub-catchment within the river basin under

investigation, the standardized criterion values have to be combined based on a well-defined

aggregation rule. A set of formulae has been developed in order to arrive at a particular

evaluation of the risk. These formulae are structured in a calculation model which takes into

account the influence of every lagoon on each sub-catchment within the river basin. The

development of the calculation model was based on the comprehension of the relationships

between risk elements (sources, pathways, and receptors) and components (probability and

magnitude, see Box 1) as well as the conceptual model of the problem. Multi-criteria

54 Anas Altartouri, Kalliope Pediaditi, George P. Petropoulos et al.

standardized criteria are combined by mean of a weighted average (Eastman, 2003). The

basic equation of WLC is:

R wi ci (5)

where:

R = the risk value of specific sub-catchment; wi = the weight of criterion I; and ci = the

score of criterion i.

At this point, every criterion has its standardized values assigned either to a lagoon or a

sub-catchment (analysis units) as well as it relative weight. When aggregating these criteria,

every sub-catchment will have a single value which indicates the combined magnitude

components (Component 1 and 2, Box 1). Likewise, every lagoon will have a single value

indicating the first and the third probability components (Component 3 and 5, Box 1).

Differently, every lagoon will have multi values regarding the second probability component

as many as possible receiving sub-catchments. These values are obtained using the formulae

below, which are basically substitutions of the formula of WLC, and they are applied for both

directions (receptor groups).

The first step is to calculate the two components of magnitude of consequences

Component 1 and 2, Box 1). This should be applied for both directions of the analysis using

the following formulae:

where:

catchment y (Component 1, Box 1); 2 magnitudesubcatchment y is the temporal scale of

nd

the value of criterion n of the 2nd magnitude component regarding sub-catchment x;

C M 2 nsubcatchment y is the value of criterion n of the 1st magnitude component regarding sub-

catchment x; WCMmn is the weight of criterion n from the mth magnitude.

The next step is to calculate the three components of probability of risk. The same

formulae are used for both analysis directions with a slight difference in the formula of the 3rd

probability component as shown below:

Development of a Decision Support System … 55

3

1 probabilitylagoon x C P1nlagoon x * WCP1n

st

(8)

n 1

subcatchment y subcatchment y

13

3rd probabilit ylagoon x C P3nlagoon x * WCP 3 n (10.a)

n1

(Receptors: Population)

(10.b)

(Receptors: protected areas)

where:

1st probabilitylagoon x

= the probability of hazard occurring from lagoon x

(Component 3, Box 1);

2 nd probabilit y lagoon x

subcatchment y

= the probability of hazard generated from lagoon x to

reach sub-catchment y (Component 4, Box 1);

3 rd probabilitylagoon x

= the probability of harm resulting from the hazard

generated from lagoon x (Component 5, Box 1),

C P1nlagoon x

= the value of criterion n of the 1st probability

component regarding lagoon x;

C P 2 nlagoon x

subcatchme nt y

= the value of criterion n of the 2nd probability

component regarding lagoon x and sub-catchment y;

C P 3nlagoon x

= the value of criterion n of the 3rd probability component

regarding lagoon x;

WC Pmn

= the weight of criterion n from the mth probability

component.

The next step for both directions is to combine the two magnitude components

(Component 1 and 2, Box 1) into one ‗magnitude‘ component and the three probability

56 Anas Altartouri, Kalliope Pediaditi, George P. Petropoulos et al.

components (Component 3, 4, and 5, Box 1) into one ‗probability‘ component. This can be

done using the following formulae:

sebcatchme nt y subcatchment y

where:

catchment y caused by lagoon x Component 1 and 2, Box 1); and

PROBABILIT Ylagoon x = the overall probability of the risk in sub-catchment y

sebcatchment y

The application of the previously mentioned formulae results in a magnitude of the risk in

a specific sub-catchment and a probability of a specific lagoon to contribute this risk. Hence,

the risk value in a sub-catchment with a contribution probability of all possible lagoons is

determined as the following:

xn

PROBABILIT Y lagoon x

RISK subcatchment y MAGNITUDE subcatchment y * x 1 subcatchment y (13)

xn

PROBABILIT Ylagoon x

x 1 subcatchment y max

where:

x n

PROBABILIT Y

x 1

lagoon x

subcatchment y

= the production of the probabilities of all lagoons

xn

PROBABILIT Ylagoon x = the maximum of all the productions defined

x 1 subcatchment y max

above

The flowchart of the proposed calculation model is illustrated in Figure 3, 4 (a and b),

and 5. Figure 3 illustrates a flowchart of calculations for each ‗sub-catchment‘ unit within the

river basin which results in a value of risk magnitude in that sub-catchment (combination of

component 1 and 3, Box 1). Figure 4 (a and b), however, illustrates a flowchart of

calculations for each ‗lagoon‘ unit located in the river basin which results in multi values of

probabilities (combination of component 3, 4, and 5, Box 1) of the corresponding lagoon to

cause risk in each ‗sub-catchment‘ unit within the river basin regarding humans or protected

Development of a Decision Support System … 57

areas, respectively. Finally, Figure 5 illustrates the flowchart resulting in a risk value for a

‗sub-catchment‘ unit based on aggregation of the magnitude (resulted from the flowchart in

Figure 3 for the corresponding sub-catchment) and probability (resulting from the flowchart

in Figure 4 (a or b) for every lagoon within the river basin).

Figure 3. Flowchart of calculation model at the sub-catchment level (for both receptor groups).

58 Anas Altartouri, Kalliope Pediaditi, George P. Petropoulos et al.

Lagoon x

path to path to path to

subcat. 1 subcat. 2 subcat. y

. . . . . . . . .

. . .

2 nd probabilitylagoon x

sucatchment 1

2 nd probabilitylagoon x

WLC subcatchmnt 2 WLC

. .

2 probabilitylagoon x

nd

subcatchment 1 the risk in sub-catchment 1

x PROBABILIT Ylagoon x

subcatchment 2

the risk in sub-catchment 2

PROBABILIT Ylagoon x the risk in sub-catchment y

subcatchment y

Figure 4a. Flowchart of calculation model at the lagoon level (for humans as receptors).

Development of a Decision Support System … 59

Lagoon x

protected areas protected areas protected areas

in subcat. 1 in subcat. 2 in subcat. y

. . . . . . .

. . .

2 nd probabilitylagoon x

sucatchment 1

2 nd probabilitylagoon x

WLC subcatchmnt 2 WLC

. .

2 probabilitylagoon x

nd

subcatchment 1 the risk in sub-catchment 1

x PROBABILIT Ylagoon x

subcatchment 2

the risk in sub-catchment 2

PROBABILIT Ylagoon x the risk in sub-catchment y

subcatchment y

Figure 4b. Flowchart of calculation model at the lagoon unit (for protected areas as receptors).

60 Anas Altartouri, Kalliope Pediaditi, George P. Petropoulos et al.

The proposed methodology has been implemented in Keritis watershed in western Crete,

Greece (see Figure 6). A 17,855 ha basin, Keritis watershed faces the risk of OMW pollution

as olive mills are the main agricultural industry in the area. Nine sub-catchments have been

delineated and identified within the basin where five OMW lagoons are located (see Figure

6). Having implemented the proposed methodology at a detailed level of analysis, two risk

maps have been produced (see Figure 6). The first map shows the risk of OMW pollution

which may harm the population, while the other map shows the risk of OMW pollution which

may harm the protected areas (NATURA 2000 sites) in the watershed.

The obtained risk maps clearly show that the developed criteria and calculation method

are compatible with risk generating process in the nature. It can be seen from Figure 6 that

some sub-catchments are estimated to have zero-risk value which is due to the absence of

addressed receptors (Figure 6b, sub-catchment 3 and 8), to the absence of connecting

pathways (Figure 6 a and b, sub-catchment 1, 2, and 3), or both (Figure 6b, sub-catchment 8).

Development of a Decision Support System … 61

On the contrary, the study indicated a high risk value in sub-catchments 9 and 6 regarding

population and protected areas, respectively. The reasons behind the former were the

existence of two hazard sources (Component 3, Box1) and their relatively high proximity to

the surface water bodies (Component 4, Box1) as well as the presence of the highest

population (Component 1, Box1), while for the later, the existence of large protected

NATURA sites (Component 1, Box1) as well as the potential of multi sources to contribute to

risk in this sub-catchment (Component 4, Box1).

To conclude, the breakdown of risk into its primary components (Box 1) and the clear

comprehension of risk generating process and its elements (sources, pathways, and receptors)

and controlling factors (represented by the developed criteria) are the main features of this

method resulting in a realistic and unbiased estimation of risk. In other words, not taking into

consideration the aforementioned issues, risk assessment would no longer be an integrated

approach of several components and just a generic description based on a small number of

criteria.

CONCLUSION

This quantitative approach of risk assessment was built based on the risk assessment

framework proposed by DEFRA guidelines. Having analyzed risk elements, components, and

62 Anas Altartouri, Kalliope Pediaditi, George P. Petropoulos et al.

controlling factors as well as the relationships between them, a conceptual model of risk

generating process has been built and a range of criteria has been formulated. This was

followed by MCA which was based on the development of the criteria. The method proposed

different scaling functions in order to standardize the initial raw value of these criteria. Then,

a calculation model, consisting from a set of formulae, was developed in order to obtain a

quantitative assessment of risk in every sub-catchment within the watershed under

investigation. It has been designed in a way to calculate an overall potential risk a sub-

catchment may be exposed to as a result of the contribution of all point-sources, namely

OMW lagoons, located the watershed. This is one of the main strengths of this method as it is

able to estimate risk in every single sub-catchment by considering and analyzing inputs from

all sources of pollution (lagoons) in the whole basin.

This method can be widely applied in the Mediterranean region where water pollution by

OMW is a common environmental problem. It serves as a decision support tools which

inform risk managers and decision makers about the risk assessment results so they can take

the appropriate management measures, e.g. implementing mitigation measures, properly

locating new OMW lagoon, etc. However, site specification should be taken into account in

when applying this approach. The developed method was implemented in the case study of

Keritis watershed (see Section 4). This implementation has shown the applicability of this

method and its potential as a decision supporting tool.

Besides being a replicable method, a strength point of this methodology is its flexibility

to add or remove criteria as well as changing their weights based on the specific needs of

different case studies without affecting the calculation model. This is a very important issue

since the controlling factors of environmental problems are more likely to change spatially

and temporally. In other words, different cases, for the same environmental problem, may be

subjected to different factors which require a modification of the criteria and their weights for

more accurate results. Moreover, this method can be widely applied for other stressor. It can

be effectively refined to address other point-sources of water pollution. In this case, the

calculation model may need some modification in light of the new problem formulation.

However, the generic frame of this method, consisting of the main steps, is still valid. In

addition, this methodology has the potential to be automated and computerized within a GIS

environment. The calculation model can be programmed using a scripting language to be

applied on the related geo-database. This geo-database should contain the layers where

different criteria are assigned and other calculation elements are found.

However, this method has some weaknesses common to all MCA weight assigning

method. In addition, the proposed method does not assess the overall risk on the river basin

under consideration meaning both surface and ground water bodies. Although the risk of

OMW is more likely to be transported via surface water bodies, due to its nature previously

discussed (section 2), investigating its impacts on the groundwater bodies, as a pathway,

would result in more accurate risk map. However, the stated difficulties in modeling the

natural processes associated with the risk generating process needs further investigation

aiming at simulating such processes.

Development of a Decision Support System … 63

ACKNOWLEDGMENTS

This research was carried out within the context of Remotely Accessed Decision Support

System for Transnational Environmental Risk Management, STRiM, INTERREG IIIB

CADSES project which enabled access to the required data and gave the opportunity to

review the research, in its different stages, from experts in several academic and research

institutions within its consortium.

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In: Ecological Modeling ISBN: 978-1-61324-567-5

Editor: WenJun Zhang, pp. 65-81 © 2012 Nova Science Publishers, Inc.

Chapter 4

POPULATION DYNAMICS IN VARIOUS LOCATIONS

L. V. Nedorezov*

The Research Center for Interdisciplinary Environmental Cooperation (INENCO) of

Russian Academy of Sciences, Kutuzov seafront 14, Saint Petersburg 191187, Russia.

ABSTRACT

Publication is devoted to the problem of population time series analysis with various

discrete time models of population dynamics. Applications of various statistical

criterions, which are normally used for determination of mathematical model parameters,

are under the discussion. With a particular example on green oak leaf roller (Tortrix

viridana L.) population fluctuations, which had been presented in publications by

Rubtsov (1992), and Korzukhin and Semevskiy (1992) for three different locations in

Europe, the possibilities of considering approach to the analysis of population dynamics

are demonstrated. For approximations of empirical datasets the well-known models of

population dynamics with a discrete time (Kostitzin model, Skellam model, Moran –

Ricker model, Morris – Varley – Gradwell model, and discrete logistic model) were

applied. For every model the final decision about the possibility to use the concrete

model for approximation of datasets are based on analyses of deviations between

theoretical (model) and empirical trajectories: the correspondence of distribution of

deviations to Normal distribution with zero average was checked with Kolmogorov –

Smirnov and Shapiro – Wilk tests, and existence/absence of serial correlation was

determined with Durbin – Watson criteria. It was shown that for two experimental

trajectories Kostitzin model and discrete logistic model give good approximations; it

means that population dynamics can be explained as a result of influence of intra-

population self-regulative mechanisms only. The third considering empirical trajectory

needs in use more complicated mathematical models for fitting.

time series, green oak leaf roller population dynamics.

*

E-mail address: l.v.nedorezov@gmail.com.

66 L. V. Nedorezov

1. INTRODUCTION

At present in ecological modeling there is a huge number of various mathematical

models, which are used for the description of dynamics of separated populations and

elementary ecosystems with small number of interacting species (Gause, 1934; Kostitzin,

1937; Kot, 2001; Begon, Mortimer, 1981; Varley et al, 1975; Maynard Smith, 1976;

Poluektov et al, 1980; Nedorezov, 1986 and others). At the same time a small number of

models was compared with experimental time series on a quantitative level. In most cases

authors confine themselves by the limits of qualitative comparison of theoretical and real

datasets, which does not allow talking about the adequacy of used models to observations.

Analysis of empirical time series needs in dynamical model using. It is important for

creating forecasts of population size changing in time, for estimation of the probability of pest

population outbreak beginning and so on. It can also be important for finding optimal

methods for population management that leads to the necessity of deep knowledge of all basic

elements of population phase portrait structure (Isaev et al, 1980, 2001, 2009; Nedorezov,

1986, 1999; Berryman, 1981, 1990, 1991).

Abundance of mathematical models, which can be found in modern ecological literature,

leads to appearance of serious problems in selection process – first of all, in finding model,

which gives best fitting for empirical time series. Partly it correlates with absence of the

respective criterions for selection of mathematical expressions, which give adequate

description of one or another biological mechanism affecting population size (Isaev et al,

2001, 2009).

There exists one more important problem in modern ecological modeling – this is the

problem of selection of statistical criteria for estimation values of dynamic model parameters.

In literature there is a big number of various using criterions (Wood, 2001 a, b; Turchin et al.,

2003; Nedorezov, 1986 and others).

But what kind of criteria we have to choose in one or another situation and why – in most

cases this is a puzzle. In current paper we analyze these marked problems – the problem of

selection of mathematical model (and analysis of suitability of selected model to fitting real

trajectories of population dynamics) and the problem of selection the best statistical criteria

for dynamic model parameter estimations. Obtained results are applied to analysis of datasets

on green oak leaf roller (Tortrix viridana L.) population dynamics (Rubtsov, 1992;

Korzukhin, Semevskiy, 1992; Nedorezov, Sadykova, 2005, 2008; Nedorezov, Sadykov,

Sadykova, 2010).

Before creation a new mathematical model of population dynamics for the description of

concrete species fluctuations, it is important to be sure that all existing models (which can be

found in modern ecological literature) are not suitable for the solution of respective problems

(i.e. models cannot be applied for fitting of real trajectories). If it is assumed to construct a

new model in the following form

x k 1 x k F ( x k , ) , (1)

Analysis of Green Oak Leaf Roller Population Dynamics in Various Locations 67

where x k is population size (or population density) in k -th year (or in k -th moment of

observation), F is a population birth rate (Isaev et al, 1980, 2001, 2009),

x k 1

yk F ( xk , ) , (2)

xk

and is a vector of (unknown) model parameters, then the natural question arises – why we

cannot choose and use one of the models from the table 1? It is well-known that among the

recursive equations from this table one can find the models with very rich set of dynamical

regimes. Moreover, part of these models were applied to the description of dynamics of

various natural populations with success (see, for example, May, 1975; Hassell, 1975, 1978;

Varley et al, 1975; Nedorezov, 1986; Nedorezov, Nedorezova, 1995; Kot, 2001). Moreover,

if simple model of type (1) gives us a sufficient good description of population dynamics

(more precisely, applied statistical criterions don‘t allow us to reject the hypothesis about

suitability of model for fitting of considering time series), then we really haven‘t a

background for creating new and more difficult mathematical model, which contains the first

model as a particular case. It is obvious, that for more complicated model we will also have

satisfactory results.

Taking it into account, we have to note that in our opinion at every time we have to start

the process of population dynamics analysis with a group of simplest mathematical models,

which describe the influence on population the minimal set of regulative mechanisms. For

example, we can start with models, which are presented in table 1: all these models describe

the influence on population the intra-population self-regulative mechanisms only. If we can

prove that it is impossible to explain analyzing datasets as a result of influence of these self-

regulative mechanisms only, we have to use more complicated models, which contain

additional equations for population regulator dynamics – for predators, parasites, climatic

factors etc.

Let‘s assume that with the help of any statistical criteria and for given sample the model

parameters were estimated. The following question arises – how can we check the

correspondence between theoretical population values (which can be obtained with the help

of mathematical model) and empirical time series?

There exists a unique way for solution of this problem – we have to analyze the time

series, which is organized by the differences between theoretical (model) and empirical

values. Following the common ideas we‘ll assume that model gives us a good approximation

of empirical sample if the next requirements are truthful: there are no reasons for rejecting the

hypothesis that average for residuals is equal to zero and distribution of residuals is Normal

(that can be checked, for example, by the Kolmogorov – Smirnov test, and Shapiro – Wilk

test etc.; Bolshev, Smirnov, 1983; Shapiro et al, 1968); there is also the absence of serial

correlation in a sequence of residuals (Durbin – Watson test; Draper, Smith, 1986, 1987). If

these conditions are truthful altogether it means that there are no reasons for rejecting a

hypothesis about suitability of considering model for fitting of empirical time series.

If statistical criterions didn‘t allow us to reject the hypothesis about suitability of model

for fitting of analyzing time series we have a possibility to solve another one problem – we

can try to identify a population dynamics regime. We have to note that there are no reasons to

68 L. V. Nedorezov

say that population dynamics corresponds to dynamical regime, which is realized in model

with obtained (estimated) parameters. The initial sample is a sequence of stochastic values,

and, respectively, estimated model parameters are the stochastic values too. These parameters

don‘t equal to real population characteristics. It means that there exists a serious problem in

determination of real population dynamics type. On the other hand, it is possible to estimate

the probabilities that observed trajectory corresponds to population extinction, or to

population asymptotic stabilization at non-zero level etc. In other words, analysis of initial

sample can allow us to obtain a distribution of dynamical regimes, which can be realized for

population.

Estimation of probabilities of realization for population one or another dynamical regime

can be provided by the following way. In a space of model parameters the confidence

domains can be obtained with well-known methods (Draper, Smith, 1986, 1987). In the same

space of model parameters there is a set of bifurcation surfaces that depends on selected

model. These bifurcation surfaces cut confidence domains onto sub-domains, which

correspond to one or another dynamical regime. Respectively, we can estimate desired

probabilities with the help of standard Monte-Carlo methods.

Thus, the general diagram of population dynamics analysis must include the following

basic stages:

number of regulative mechanisms onto population dynamics.

Estimation of parameter‘s values for all selected models.

Analysis of deviations between theoretical and empirical trajectories.

Determination of distribution(s) of dynamical regimes for model(s).

If for all selected models statistical criterions show negative results we have to choose a

group of more complicated mathematical models. These models from a new group may

describe the influence of some additional regulators onto population dynamics (parasites,

quality of food, weather factors etc.), may take into account the existence of time lag in a

reaction of self-regulative mechanisms onto population size changing, or may have additional

variables for sex groups of individuals, age groups or other intra-population structures.

*

Let‘s consider the model (1) and let {x k } , k 1,2,..., N , be an empirical time series of

population size changing in time ( N is a total number of observations). The problem is in

estimation of model (1) parameters with existing time series.

One of very popular criterions is following (see, for example, Berryman, 1991; Turchin et

al., 2003; Nedorezov, Sadykova, 2005, 2008; Tonnang, 2009):

N

Q( ) x k* x k*1 F ( x k*1 , )

2

min

(3)

k 2

Analysis of Green Oak Leaf Roller Population Dynamics in Various Locations 69

It is possible to point out various modifications of criteria (3). For example, when we use

expression (2) for birth rates in (3), the expression for minimizing functional has the

following form:

N

Q( ) y k*1 F ( x k*1 , )

2

min

, (4)

k 2

where y k* are the values of birth rates calculated for empirical time series. When we use log-

transformed values of population size and respective log-transformed expressions in (1)

(sometimes it can lead to strong simplification of final formula) expression (3) can be

presented as follows:

2

N

Q( ) log( xk* ) log( xk*1 ) log(F ( xk*1 , )) min

(5)

k 2

These expressions (3)-(5) have one common property: model (1) is used in these

*

formulas as non-linear regression curve but not as dynamical model. Real trajectory {x k }

compares with set of values, which don‘t belong to any model trajectory altogether (more

precisely, these points belong to one and the same trajectory in unique ideal variant, which is

unrealistic for real datasets). In other words, in expressions (3)-(5) we compare the objects of

two qualitatively different types.

In this situation the following natural question can arise – why we decided to use one-

step ahead regression curve for estimation model parameters? May be, two-step ahead or

three-step ahead can give us better results? What kind of criteria gives us the best results and

why?

Moreover, in expressions (3)-(5) there are the ―doubl e standards‖: if we use (3), (4), or

(5) we assume that elements in initial empirical sample have two qualitatively different

properties. For example, within the limits of first element of sum (3) we assume that x 2* is

any constant, which was measured with Normal distributed error. But in the next element of

sum (3) we assume that expression F ( x2* , ) gives us a theoretical value of population, we

*

have to observe in ecosystem (if amount x 3 was measured without any errors). It means that

in second bracket in sum (3) we assume that amount x 2* was estimated without errors.

These are the reasons we think that criterions of the type (3)-(5) cannot be applied for the

estimation of real population parameters. On the other hand, these criterions can be applied,

for example, for constructing forecasts of population size changing.

One of most perspective ways for model parameter‘s estimations is in using of ―gl obal

fitting‖ (Wood S, 2001a, b), when we try to find the best trajectory (in a set of all model

trajectories), which gives us the best fitting for real trajectory. Let ~

x k ( , x1 ) be a solution of

model (1) for given vector and initial value of population size x1 (we assume that this

70 L. V. Nedorezov

value is unknown model parameter too). Then criteria can be presented in the form (Tonnang

et al., 2009; Nedorezov, Lohr, Sadykova, 2008):

N

Q( , x1 ) ( x k* ~

x k ( , x1 )) 2 min

(6)

, x1

k 1

Note, that in (6) there are no ―doubl e standards‖ and all elements in the sample have the

similar properties. It is possible to point out some other important properties of criteria (6).

For example, if we have the same sample but in model we have more equations (in particular,

for predators, and respective variable in model is invisible) we can use (6) for the estimation

of all model parameters without modification of expression (6). At the same time criteria (3)

needs in additional information and in serious modification.

Below we illustrate this approach to population dynamics analysis on an example of

green oak leaf roller fluctuations (Rubtsov, 1992; Korzukhin, Semevskiy, 1992; Nedorezov,

Sadykova, 2005, 2008; Nedorezov, Sadykov, Sadykova, 2010). Choosing of this object

depends on the existence of several good empirical time series and diversity of biological

opinions about green oak leaf roller dynamics type. Partly it correlates with absence of

common opinion about main population regulators (Hunter et al., 1997; Hassell et al., 1998;

Rubtsov, 1983).

4.1. Phase Portrait of Population Dynamics

A big number of various publications are devoted to the problems of green oak leaf roller

population dynamics and its mathematical models (see, for example, Varley et al., 1975;

Korzukhin, Semevskiy, 1992; Hunter et al., 1997; Rubtsov, 1983, 1992; Rubtsov, Shvytov,

1980 and others). But a set of serious problems (in particular, the problem about main

population regulators) is open up to current moment and under the discussion (Hunter et al.,

1997; Hassell et al., 1998; Nedorezov, Sadykova, 2005, 2008).

Analysis of phase portrait structures, which had been provided in Rubtsov‘s publications

(Rubtsov, 1983, 1992; Rubtsov, Shvytov, 1980), allowed him to describe the basic laws of

population dynamics. In particular, the author had been showed that in some locations tortrix

could realize an outbreak (Isaev et al., 1980, 2001, 2009; pulse eruptive outbreak in

Berryman‘s classification of insect population dynamic types; Berryman, 1990, 1991). This

regime can be realized within the framework of predator – prey system dynamics, and

characterizes by the existence of three non-zero stationary states in a phase space. Following

the basic stages of population dynamics analysis described above, before using difficult

mathematical models including equations for several interacting populations we have to

check the possibilities of simpler models (table 1). First of all, we have to be sure that it is

impossible to explain observed trajectories from the stand point of influence of self-regulative

intra-population mechanisms only.

Analysis of Green Oak Leaf Roller Population Dynamics in Various Locations 71

Models* References and/or used in current

publication)

1 xk 1 axk (1 bxk ) 1 Kostitzin, 1937 Kostitzin** model

Moran, 1950; Ricker,

2 x k 1 axk (b x k ) Discrete logistic model

1954

3 x k 1 a(1 e bxk ) Skellam, 1951 Skellam model

Morris, 1959; Varley, Morris – Varley – Gradwell

4 x k 1 ax1kb Gradwell, 1960, 1970 model

bxk Moran, 1950; Ricker,

5 xk 1 axk e Moran – Ricker model

1954

*

The model‘s numbers are the same in all tables

**

This model is also known in literature as Skellam model (Skellam, 1951) and Beverton – Holt model

(Beverton, Holt, 1957), but for the first time this model was presented in the monograph by V.A.

Kostitzin (1937).

72 L. V. Nedorezov

population size – birth rate‖ in various

locations of European part of Russian Federation. a, b – time series from Rubtsov (1992). Abscissa

axis: number of eggs-laying per 1m of branches in autumn. Point 1 corresponds to 1969. c – time series

from Korzukhin and Semevskiy (1992). Abscissa axis: pupae density per 1000 leafs. Point 1

corresponds to 1962.

Use the models from table 1 means that we a‘priori assume that phase portrait of

population dynamics can be characterized by the existence of one non-zero stationary state (if

population doesn‘t eliminate for every initial values of population size). This stationary state

can be stable or unstable point and in last case we can observe cyclic or chaotic population

fluctuations. In Isaev – Khlebopros classification of insect population dynamics (Isaev et al.,

2001, 2009) such kind of species belong to a group of prodromal species (but not to group of

eruptive species, which can realize an outbreak). This hypothesis will have a good

background if and only if for all analyzed real trajectories (Figure 1) we find at least one

model from the table 1, which gives a good fitting for observed trajectory and all statistical

tests give us positive results.

All models we used for fitting of considering trajectories are presented in table 1.

Parameters of discrete logistic model (table 1) must satisfy the condition ab 4 (Maynard

Smith, 1976; Poluektov et al., 1980; Nedorezov, Nedorezova, 1995). But for fitting of real

time series we have used modified discrete logistic model:

ax (b xk ), xk b

xk 1 k

0, xk b

This model has no additional limits for its non-negative parameters a and b . But the

origin (if ab 4 ) becomes a complicated stationary state.

This additional assumption that product ab can be bigger then 4 can be interpreted as

follows: we assume that population size can intersect the limit level b . But it leads

Analysis of Green Oak Leaf Roller Population Dynamics in Various Locations 73

situation is typical for various outbreak species (Isaev et al., 1980, 2001, 2009; Berryman,

1981, 1990, 1991; Varley et al., 1975).

All other models were used for fitting in the forms they are presented in table 1. All

models have the similar properties: within the framework of every model population

dynamics is determined by the influence of intra-population self-regulative mechanisms only.

Several models (Kostitzin model, Skellam model, and Morris – Varley – Gradwell model)

have a poorest set of dynamical regimes: population can extinct (if a 1, table 1, Kostitzin

model, and Skellam model), or population asymptotically stabilizes at non-zero level (if

a 1 ; for all values of parameter a Morris – Varley – Gradwell model contains the regime

of asymptotic stabilization only). Two other models contain very rich sets of dynamical

regimes, which include cyclic regimes of all lengths and chaos.

If we assume that dynamics of green oak leaf roller on Figure 1a corresponds to pure

stochastic fluctuations near any stationary level x s , then x s 13.671 with SE 2.243

(standard error). Minimum value for functional form (6) is equal to 2324.1. This value is

major for all minimum values of functional form (6) for all models from the table 1 for first

time series. Applications of Kolmogorov – Smirnov test ( d 0.1247 with p 0.2 ) and

Shapiro – Wilk test ( W 0.9145 with p 0.0584) show that there are no reasons for

rejecting the hypothesis about normality (with zero average) of the distribution of residuals

(Bolshev, Smirnov, 1983; Shapiro et al., 1968); Durbin – Watson criteria shows

( d 1.5619; for sample size 22 and for one predictor variable the realization of inequality

d d L 1.24 means that there is a negative serial correlation in a sequence of residuals; if

1.43 d U d 2 there is no serial correlation; critical values d L and d U are presented

for 5% level of significance; for 1% level of significance the values for critical levels are

equal to 1.00 and 1.17 respectively), that there is no serial correlation in a sequence of

residuals (Draper, Smith, 1986, 1987). Thus, there are no reasons for rejecting the hypothesis

that on Figure 1a we have pure stochastic fluctuations near average value.

Realization of last hypothesis means that population regulators are very weak on the

considering interval of population size changing. If we assume, that population dynamics can

be described by the Kostitzin model the value of loss-function Q (6) is less than in previous

case (table 2). At the same time there are no reasons for rejecting the hypothesis that Kostitzin

model is suitable for fitting of experimental time series (table 3). Note that coefficient b ,

which describes in model the influence of self-regulative mechanisms on population size

changing, is small enough.

74 L. V. Nedorezov

Table 2. Model parameter’s estimations and values of functional form Q (6) for all time

series on green oak leaf roller changing in time

Models x0 a b Q

Estimations for first time series (Figure 1a)

1 21.89 1.394 0.032 2190.8

2 15.472 0.174 24.4 1238.0

3 21.636 27.755 0.048 2194.8

4 0.874 40.516 1.467 1476.0

5 8.728 27.04 0.232 1515.6

Estimations for second time series (Figure1b)

1 0.0074 28603.0 1436.2 3571.6

2 2.19 0.116 37.0 1261.6

3 0.682 19.92 3.514 3571.9

4 20.08 1.414 0.119 3940.7

5 0.972 24.26 0.158 3337.6

Estimations for third time series (Figure1c)

1 2.7∙10-12 731489.6 60263.0 6442.3

2 0.103 0.0896 50.8 1310.9

3 0.00014 12.138 8.24 6442.3

4 7.85∙10-258 10.78 0.95 6456.2

5 0.05 147.1 0.708 4578.5

Left Right

Average±SE KS2 SW3 DW4

limit1 limit1

Results for first time series

1 -0.034±2.178 -4.562 4.495 0.1187/p>0.2 0.9311/p=0.129 1.7064

2 0.87±1.626 -2.511 4.252 0.1476/p>0.2 0.9361/p=0.165 1.6634

3 -0.038±2.18 -4.571 4.495 0.1203/p>0.2 0.9302/p=0.124 1.7026

4 0.448±1.785 -3.263 4.16 0.1131/p>0.2 0.9376/p=0.177 0.7935

5 -0.454±1.809 -4.215 3.307 0.1027/p>0.2 0.95/p=0.315 0.7027

Results for second time series

1 0.0042±2.78 -5.778 5.786 0.1673/p>0.2 0.9253/p=0.098 0.995

2 0.7093±1.645 -2.712 4.131 0.1468/p>0.2 0.9793/p=0.905 2.263

3 -0.025±2.781 -5.808 5.757 0.167/p>0.2 0.9259/p=0.101 0.995

4 -0.0005±2.92 -6.074 6.073 0.18/p>0.2 0.9305/p=0.126 0.9972

5 -0.126±2.69 -5.715 5.463 0.136/p>0.2 0.951/p=0.331 1.0197

Results for third time series

1 0.1392±3.148 -6.344 6.622 0.2222/p<0.1 0.7442/p=0.00002 0.935661

2 3.1161±1.276 0.488 5.744 0.2379/p<0.1 0.8524/p=0.0016 1.961968

3 0.1379±3.148 -6.346 6.622 0.2222/p<0.1 0.7441/p=0.00002 0.935704

4 0.1011±3.152 -6.39 6.592 0.2233/p<0.1 0.7426/p=0.00002 0.935025

5 4.06±2.527 -1.144 9.264 0.3405/p<0.01 0.6281/p<10-5 1.824773

1

Limits for 95% confidence interval

2

KS – values and probabilities of Kolmogorov – Smirnov criteria

3

SW – values and probabilities of Shapiro – Wilk criteria

4

DW – values of Durbin – Watson criteria.

Analysis of Green Oak Leaf Roller Population Dynamics in Various Locations 75

The best result is observed for discrete logistic model (table 2); good results are also

observed for Morris – Varley – Gradwell model and Moran – Ricker model. For all models

we can conclude that the estimated values of population parameters belong to ―bi ological‖

zone. From the table 3 we can see that for all models we cannot reject the hypotheses that the

distributions of residuals are Normal with zero averages. At the same time for residuals for

Morris – Varley – Gradwell model and for Moran – Ricker model the negative serial

correlations are observed. It allows us to say that these models cannot be applied for fitting of

considering time series. For other models the Durbin – Watson criteria shows that there are no

serial correlations.

On Figure 2 empirical trajectory of tortrix fluctuations compares with theoretical

trajectories, which were obtained for estimated parameters (table 2) for Kostitzin model and

discrete logistic model. It is important to note that for estimated parameters discrete logistic

model predicts population elimination in 1992; it doesn‘t correspond to reality and can be

interpreted as additional limit for prognostic properties of this model.

On Figure 3 there are the 99% confidence domain for parameters a and b of discrete

logistic model (with fixed value x 0 15.472 ) together with some bifurcation curves.

Taking into account that limits of confidence domain don‘t intersect curve ab 3 we can

conclude that probability of realization of the regime of population stabilization or the regime

of population elimination (within the framework of this model) is less than 0.01 . The

observed minimum for functional (6) is occupied in intersection of straight lines L1

( x 0.174) and L2 ( y 24.4 ) (Figure 3).

Figure 2. Population density changing in time: curve 1 corresponds to empirical time series (Figure 1a),

curve 2 is the trajectory of Kostitzin‘ model, and curve 3 is the trajectory of discrete logistic model.

76 L. V. Nedorezov

Figure 3. Domain on the plane (a, b) where values of functional (6) is less than 2217.3 (with fixed

value x 0 15.472 ) for discrete logistic model. ab 2 , ab 3 , and ab 4 are the bifurcation

curves. Intersection of lines L1 and L2 gives a point of estimated minimum for loss-function (6).

On Figure 4 there are the limits of confidence domains for Kostitzin model parameters on

the plane (a, b) at fixed value of initial population size x 0 ( x 0 21.89 , table 2). As one

can see from this picture, boundaries k of confidence domains intersect bifurcation line

a 1 , but the probability of asymptotic population extinction is very small.

Finally, the provided analysis and comparison of theoretical trajectories with observed

time series (Figure 1a) show that population fluctuations can be explained as a result of

influence of self-regulative intra-population mechanisms only. We have no reasons to reject

the hypothesis that analyzed empirical trajectory corresponds to asymptotic stabilization at

non-zero level (Kostitzin model). Analysis of modified discrete logistic model shows (Figure

3) that with big probability there are the periodic fluctuations in population dynamics.

Figure 4. Curves 1 , 2 3 are the boundaries of confidence domains for 90%, 95% and 99%

and

respectively for Kostitzin‘ model. Bifurcation line a 1 is the boundary for domains of population

extinction ( a 1) and its asymptotic stabilization at non-zero level ( a 1 ).

Analysis of Green Oak Leaf Roller Population Dynamics in Various Locations 77

If we assume that dynamics of green oak leaf roller on Figure 1b corresponds to pure

stochastic fluctuations near any stationary level x s , then x s 18.95 with standard error for

average 2.922. Minimum of functional form (6) is equal to 3943.9. Applications of

Kolmogorov – Smirnov test ( d 0.1861 with p 0.2 ) and Shapiro – Wilk test

( W 0.9197 with p 0.0749) show that there are no reasons for rejecting the hypothesis

about normality of the distribution of the residuals between theoretical and empirical values

(Bolshev, Smirnov, 1983; Shapiro et al., 1968); Durbin – Watson test shows ( d 0.9927 )

that there is the negative serial correlation (Draper, Smith, 1986, 1987) in a sequence of

residuals. Consequently, the hypothesis that on Figure 1b there is the stochastic fluctuations

near average must be rejected.

Note, that obtained estimations for Kostitzin model (table 2) belong to non-biological

zone for population parameters (maximum value of birth rate a is much bigger than

maximum fecundity of individuals). Respectively, it can be one of the reasons for rejecting

the hypothesis about suitability of this model for fitting of empirical time series.

Analysis of the sequence of residuals shows (table 3) that there is no negative serial

correlation for discrete logistic model only. It means that we have reasons for rejecting the

hypotheses about suitability of considering models for fitting of empirical time series. On the

other hand all used tests don‘t allow us to reject the same hypothesis for discrete logistic

model.

Thus, like in previous case population fluctuations can be explained as a result of

influence of self-regulative intra-population mechanisms only. On the other hand, exploitation

of discrete logistic model (table 1) meets with serious problems. In particular, for estimated

values we cannot determine asymptotic regime of population dynamics: model shows that

population must extinct after 14 years (in 2002) that doesn‘t correspond to reality. On Figure

5 real trajectory of tortrix fluctuations compares with theoretical trajectory, which was

obtained for estimated parameters (table 2) for discrete logistic model.

Figure 5. Population density changing in time: curve 1 corresponds to empirical time series (Figure 1b),

and curve 2 is the trajectory of discrete logistic model.

78 L. V. Nedorezov

fluctuations near any stable level x s , then x s 10.927 with SE 3.217 . The minimum

value for functional form (6) is equal to 6997.7. Obviously, this amount is majoring value for

all other values of functional form (6) at the use of models from the table 1 for fitting of third

time series. Applications of Kolmogorov – Smirnov criteria ( d 0.2624 with p 0.05 )

and Shapiro – Wilk criteria ( W 0.6872 with p 105 ) show that the hypothesis about

normality of the distribution of residuals must be rejected (Bolshev, Smirnov, 1983; Shapiro

et al, 1968). Respectively, we have to reject the hypothesis that observed fluctuations are the

stochastic oscillations near average.

Like in previous case, results, which were obtained for Kostitzin model (table 2), belong

to non-biological domain of population parameters. Analyses of deviations (table 3) show that

all considered models did not give us a sufficient approximation of empirical dataset.

Consequently, it can be considered as the background for the following hypothesis: for the

explanation of population fluctuations in third case (Figure 1c) we have to use more

complicated mathematical models, which take into account the influence of external factors

or influence of intra-population effects (Alley effect, group-effect, time lag in reactions of

self-regulative mechanisms etc.) onto population dynamics.

CONCLUSION

In population dynamics analysis it is possible to mark the following important steps:

1) At the beginning we have to select a model or group of models, which have the

similar properties (for example, all models describe the influence of intra-population

self-regulative mechanisms on population size changing only in simplest variant,

there are no time lags in reactions of self-regulative mechanisms etc.), or we must

construct a new model if existing models don‘t describe some important elements of

population structure, regulative mechanisms etc. In other words, we have to construct

a new model if all existing models don‘t correspond to considering situation. During

the selection process it is very important to take into account that every selected

model has its own limits for application to real datasets. In particular, the choosing of

the Kostitzin model means that a‘priory we assume that population size can change

monotonously only. Respectively, all deviations of empirical values from this law

can be (and must be) explained as a result of influence of external stochastic factors

(for example, weather conditions).

2) On the next step we have to select a statistical criterion for determination of model‘s

parameters. If model is only assumed for obtaining forecasts of population size

changing in time it is expedient to use criterions of the type (3)-(5). But if the model

isn‘t assumed for the solution of especially practical problems only, and the main

goal of time series analysis is in determination of population dynamics type, it is

much better to use criterions of the type (6).

Analysis of Green Oak Leaf Roller Population Dynamics in Various Locations 79

characteristics, which cannot be determined in direct experiment. For example, it is

important for estimation of the value of maximum birth rate, coefficient of influence

of intra-population self-regulative mechanisms etc. Taking into account that all

elements of initial sample are the stochastic values, estimations of model parameters

are the stochastic values too. Respectively, for obtaining estimations we have to point

out the confidence domains for selected significance levels (Draper, Smith, 1986,

1987).

3) One of the most important stages in analysis of population dynamics is in finding of

bifurcation structure of confidence domains. It allows estimating the probabilities of

the realization of one or another dynamical regime, which are determined by the

initial sample (particular cases are presented on figures 3 and 4).

4) 4. One of the important elements in analysis of correspondence between model and

empirical datasets is in determination of basic properties of time series, which are

organized by the deviations. If the distribution of deviations doesn‘t correspond to

Normal with zero average, or there is the serial correlation in the sequence of

deviations it gives us a background for the rejecting of hypothesis about the

possibility to use considering model for fitting of the sample.

If all used statistical criterions don‘t allow rejecting the hypothesis about suitability of

considering model for approximation of time series, it gives respectively to present correct

solutions for some other problems. For example, it allows us to solve the problem on

identification of population dynamics type, or at least to describe the set of mechanisms

influenced the population size. Also it can give the solution of the problem of absent

datapoint estimation (―hol es‖ in time series), give a correct (in mathematical sense)

description of the problem of optimal management of population etc.

Application of several mathematical models (table 1) with discrete time for the

approximation of green oak leaf roller population dynamics (Figure 1) showed that in the first

case (Figure 1a) we couldn‘t reject the hypothesis that observed dynamical regime

corresponds to pure stochastic fluctuations near any stationary level. The influence of

regulative mechanisms is considerably weak.

For the second case (Figure 1b) it was obtained that observed fluctuations can be

explained as a result of influence of intra-population self-regulative mechanisms only. In the

last case it was impossible to find good fitting for all models. It gives us a background for the

following hypothesis: in this situation the dynamics of green oak leaf roller population cannot

be explained as a result of influence of self-regulative mechanisms only. It means also that for

fitting of this time series we have to use more difficult mathematical models, which describe

the influence of some other regulators on population dynamics or take into account some

additional intra-population effects.

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In: Ecological Modeling ISBN: 978-1-61324-567-5

Editor: WenJun Zhang, pp. 83-96 © 2012 Nova Science Publishers, Inc.

Chapter 5

OF PLANKTONIC ORGANISMS

1

Department of Environmental Sciences, University of Naples ― Parthenope‖,

Centro Direzionale di Napoli Isola C4, 80143 Naples, Italy.

2

ISPRA – Institute for Environmental Research and Protection,

Via di Casalotti 300, 00166 Rome, Italy.

ABSTRACT

In the last decades, numerical modelling has gained increasing consensus in the

scientific world, and particularly in the framework of behavioural and population

ecology. Through numerical models it is possible to reconstruct what is observed in the

environment or in the laboratory and to get a more in-depth comprehension of the factors

regulating the phenomena under examination.

Numerous approaches have been developed in this framework, but probably one of

the most promising is the individual-based modelling. With this type of approach it is

relatively straightforward to investigate aspects related to the ecology of a population

starting from the characterisation of processes taking place at the scale of the individual

organism.

This contribution is intended to provide a general view of the main features of the

individual-based models and of their peculiarities in comparison to other modelling

strategies. Special emphasis will be given to applications in the field of phyto- and

zooplankton ecology and behaviour, and results from the available literature on this topic

will be used as examples.

behaviour.

84 Daniela Cianelli, Marco Uttieri and Enrico Zambianchi

1. INTRODUCTION

Natural processes are quite often the result of complex and hardly predictable interactions

among the components of a system. Experimental studies, either in situ or in the laboratory,

provide important insights into some of these mechanisms; however, owing to the intrinsic

complexity of these processes and of their interactions, only a few of them can be investigated

at a given time. Numerical modelling often represents an affordable approach to get a more

holistic view of natural systems and of the processes acting in them. As discussed in Mac

Nally (1997), experimental methodology is typically based on the Popperian paradigm of the

hypothesis-deduction approach. Numerical models come to the aid in understanding

ecological processes: in a correct approach, the scope of numerical simulations is to

reproduce natural phenomena and provide new elements to understand their underlying

dynamics, rather than a blind acceptance of model results (Wissel, 1992; Grimm, 1999).

Models are thus ―pur poseful representations‖ (Starfield et al., 1990) and great problem-

solving tools to make the main properties of the considered system emerge and to explain the

observed phenomenon (Grimm, 1999). In a numerical model, the dynamics of several

variables are integrated through interactions of processes (Wroblewski, 1983). As a general

rule of thumb, when modelling a complex system the simplest components should be

identified and the interactions among them and with the environment investigated

(Wroblewski, 1983).

As underlined by Judson (1994), two fundamental aspects make ecology different from

other natural sciences: the lack of first principles but on the other hand the strong presence of

the unifying principle of Darwinian evolution. Since May (1974 and 1976), increasing

awareness has been accumulated about the possible development of chaotic dynamics in even

simple systems. Models of population dynamics are not an exception to this rule (Łomnicki,

1999), and for this reason ecological modelling is still nowadays in a continuous progress.

Over the years several modelling approaches have been developed to address key ecological

topics. Among them, individual-based models (IBMs) have emerged as a promising

framework to relate the individual behaviour with the patterns observed at community and

population levels (Grimm, 1999).

Classically, ecological state-variable models describe a population in terms of bulk

properties averaged over a large number of individuals, without considering the variability

among them, and use continuous functions changing in time and space (Fennel and Osborn,

2005). But within a population individuals are not all the same, and their differences are

reflected in the structure and dynamics of the population itself (Łomnicki, 1999). In an IBM

the focus of the interest is the individual, considered as the central elemental component of

the system (with an approach equivalent to that of experimental biology), and a population is

assumed as made up of individuals differing in their properties (Uchmański and Grimm,

1996). IBMs belong to the family of the agent-based models (or multi agent-based models), a

modelling approach designed to investigate the interactions among numerous components of

a system. These models are a natural extension of the Ising model (Ising, 1925) and of the

cellular-automata like models (Wolfram, 1994). In an IBM the modelled ―agent ‖ is simply an

individual, treated as a unique and discrete entity with at least one property evolving through

time. IBMs explicitly include heterogeneity among individuals (e.g., spatial location, body

size, physiological parameters, etc.), and this makes them particularly suitable to link the

Individual Based Modelling of Planktonic Organisms 85

individual with aggregated levels (e.g., population dynamics, community structure, spatial

distribution, etc.), while at the same time stabilising the model itself (Cope, 2005). By

modelling the probabilistic behaviour of individual organisms and averaging over a

reasonably high number, IBMs use a ―bot tom-up‖ approach (Souissi et al., 2005) and are

capable of delineating population-level dynamics as emergent properties due to the

interactions among the individuals and between the individual and its environment

(Railsback, 2001).

Since the rules governing the individual can account for several processes, IBMs permit

more realistic assumptions than those used for state variable models (Souissi et al., 2004). In

addition, using observed biological entries IBMs do not introduce any mathematical artifact

in the numerical representation (Scheffer et al., 1995). Some IBMs are defined as spatially

explicit, when the individual is associated with a position in space which can be either

continuous or discrete, and may also include mobility if the individual is allowed to move

inside its environment (as for simulations of animal behaviour). IBMs can also be considered

as i-state configuration models (Metz and Diekmann, 1986; Caswell and John, 1992; Maley

and Caswell, 1993), where for each individual a set of i-states (e.g., age, size, weight, etc.) is

defined at each time step.

The first models using individuals as basic units date to the early 1980s (e.g., DeAngelis

et al., 1980; Beyer and Laurence, 1980), but it was only after the work by Huston et al. (1988)

that the IBM approach has been unequivocally defined. The possibility of considering IBMs

as a unifying ecological theory was discussed in Huston et al. (1988) and then reviewed a

decade later by Grimm (1999), while Fennel and Osborn (2005) proposed an alternative

framework to relate state variables and individuals.

In the literature a number of seminal reviews about IBMs are available, focusing on the

potentials and on the applications of this modelling framework to ecological issues (e.g.,

DeAngelis et al., 1990 and 1994; DeAngelis and Gross, 1992; Judson, 1994; Uchmański and

Grimm, 1996; Grimm, 1999; Grimm et al., 1999; Łomnicki, 1999). Of course, all that glitters

ain‘t gold and some proviso must be mentioned. Since IBMs can virtually model all the

individuals of a population, a downside is the costly demand of computational and storage

resources to let the model run fluently. While the computing performances of present personal

computers have made giant leaps and are still evolving very rapidly, some resampling

techniques are commonly adopted. Since realistic numbers of individuals need to be

represented in the model for a reliable representation of natural phenomena, reducing the

number of modelled entries does not represent a suitable solution. This procedure would in

fact decrease the variability in the variables modelled, with possible development of irregular

dynamics (Scheffer et al., 1995). A common procedure consists in assuming the individual

modelled as a group of individuals sharing some common characteristic. This is the root of

the ―L agrangian-ensemble method‖ (Woods and Onken, 1982) and of the ―s uper-individual‖

approach (Scheffer et al., 1995). In this way, every individual represents a varying number of

specimens sharing the same destiny, and for each of them a number of variables and

processes can be simulated and their time-dependent variation be studied. Such methodology

may however modify the spatial and temporal model dynamics, especially when a large

number of individuals is aggregated (Parry and Evans, 2008). Parallel computing can provide

a helpful solution to overcome this limitation maintaining the original model structure (e.g.,

Parry and Evans, 2008).

86 Daniela Cianelli, Marco Uttieri and Enrico Zambianchi

approaches. This criticism prompted the development of the ODD (Overview, Design

concepts, Details) protocol by Grimm et al. (2006 and 2010). This protocol consists of seven

tasks aimed at providing a standard description of individual-based and agent-based models

through a detailed description of the variables used, of their initialisation and of the sub-

model implemented.

It is worth stressing that IBMs are extremely versatile, being capable of representing

animals, plants, human beings or vehicles (e.g., Benenson et al., 2008; Berger et al., 2008).

The focus of this work will be the applications of the IBM approach to the dynamics of

plankton ecosystems. Their components have often been described as continuum fields,

characterized by integrating sets of differential equations parameterizing physical, biological

and chemical processes. While computationally favourable, this approach proved not

exhaustive for plankton ecology (e.g., Woods and Barkmann, 1994) and over the last thirty

years it has been integrated with an individual-based description. The next sections will

provide a synthesis of the studies where the IBM framework has been applied to

phytoplankton and zooplankton organisms, and of the insights gained into the dynamics of

aquatic systems.

2. PHYTOPLANKTON

Phytoplankton is composed by autotrophic, photosynthetic organisms belonging to

different taxa and living in all aquatic ecosystems (Mann and Lazier, 1996). They are moved

by the water currents both horizontally and vertically, even though some species are capable

of some degree of autonomous motility. Most organisms are too small to be seen at naked

eye, they often form large aggregates in the form of blooms. Phytoplankton represents almost

the 1–2 % of the total biomass of the world ocean but at global scale these organisms are able

to fix at least 30-60% of the total organic carbon (Falkowski et al., 1994).

Light and nutrients are the basic resources used by phytoplanktonic organisms as a source

of energy to perform their biosynthetic processes. As light intensity and nutrient

concentration show both diel and seasonal changes, phytoplankton has adapted to these

resource variations that regularly occur in the aquatic environment. In particular

phytoplankton has developed a photosynthetic apparatus, which adapts to the changes in light

intensity frequently observed in the water column. Phytoplanktonic organisms respond to

light variations both by adjusting the rates of biochemical processes and by changing the

organization, composition and functioning of the photosynthetic apparatus (Falkowski and

LaRoche, 1991). Different phytoplankton organisms exposed to the same resource

distributions will show different bio-chemical composition and photosynthetic performances

(Falkowski and LaRoche, 1991). This in turn affects the growth rate of the entire

phytoplankton population in the water column, modulating the species abundances and

altering their distributions and occurrence.

In marine ecosystems the physical-biological conditions continuously change supporting

the wide range of photophysiological responses adopted by phytoplanktonic organisms.

Among the others, the high variability in the light regime and nutrient availability

experienced by the cells as well as the frequent vertical displacements in the water column

Individual Based Modelling of Planktonic Organisms 87

induced by turbulent mixing and convection are crucial factors inducing the different

responses of organisms (e.g., Lewis et al., 1984; Figueiras et al., 1999).

Nevertheless, until recently the phytoplankton community has been frequently described

in the marine ecosystem models through ensemble averages, treating the organisms like a

continuum. For example, using these bulk (Eulerian) models the primary production has been

simulated computing the depth-averaged light intensity experienced by phytoplankton

population and then calculating the growth over time. As showed by Woods and Onken

(1982) such an approach, averaging non-linear equations before integration, causes

inaccuracy in the model results.

In order to reproduce realistic dynamics of phytoplankton populations the individual

physiology and the interactions with other organisms and the environment have to be taken

into account (e.g., DeAngelis and Gross, 1992).

The IBMs currently represents the most suitable tool for reconstructing the time evolution

of a phytoplankton community in terms of temporal and spatial histories of the individual

organisms. The individual-based approach allows treating populations as composed of a large

number of organisms, whose individual histories both determine the physiological response to

environmental conditions and the species composition in the water column.

Modelling the primary production by means of the IBM approach, the light perceived by

each individual is firstly computed, then the growth of each organisms is integrated. The

emergent property of the growth of the entire population produces the primary production

estimate of the water column, which may significantly differ from the estimates obtained

through bulk Eulerian models.

The numerical approach to the study of phytoplankton behaviour in the water column

was first introduced in the late 1970‘s (e.g., Marra, 1978a and 1978b; Kamykowski, 1979;

Falkowski and Wirick, 1981), but it was only after the work by Woods and Onken (1982) that

the IBM description for phytoplankton received wider attention. Here we briefly summarize

some of the most relevant studies applying the IBM approach to simulate a large number of

complex physical-biological processes acting simultaneously and at different scales in the

water column.

The first numerical study conducted by Marra (1978a and 1978b) investigated the

interaction between mixing and light regimes showing the different photophysiological

responses to variable light regime experienced by phytoplankton. Kamykowski (1979) firstly

modelled the interplay between individual phytoplankters and a variable flow field associated

with a semidiurnal internal tide, while the distribution of phytoplanktonic organisms in

Langmuir circulations was simulated by Evans and Taylor (1980). In their paper, Falkowski

and Wirick (1981) analysed the effects of variations in the light regime due to vertical mixing

on primary productivity. Phytoplankton cells were allowed to light-shade adapt on a fixed

time scale by varying their Chla:C ratios in response to variations in the light regime. Their

results showed that despite the physiological adaptation to light, vertical mixing may have

little effect on the integrated water column primary productivity.

However the utility of the IBM approach has been fully recognized only after the

reference paper by Woods and Onken (1982), who developed a Lagrangian ensemble model

coupled with a one-dimensional model of the upper ocean. The authors used a Lagrangian

biological model to study how turbulent transport of cells through the diurnal light gradient

affected the depth distribution and energy uptake of a phytoplankton population. The model

showed that as the surface mixed layer deepened during the night, phytoplankton cells and

88 Daniela Cianelli, Marco Uttieri and Enrico Zambianchi

particles produced in a shallow mixed layer during one day were mixed downward at rates far

larger than their still-water settling rates.

Several additional contributions subsequently appeared in the literature addressing

specific aspects of phytoplankton photophysiology in a rapidly changing environment. Lande

and Lewis (1989) questioned the rationale for using the time consuming Lagrangian approach

as opposed to the traditional Eulerian one, while a more recent attempt to overcome the limit

imposed by handling average quantities within an Eulerian framework has been proposed by

Janowitz and Kamykowski (1999). Yamazaki and Kamykowski (1991) and Kamykowski et

al. (1994) investigated the interactions between vertical swimming and photo-adaptation

response by a random walk representation of dinoflagellates swimming in the surface mixed

layer. The results highlighted the interactions of individual organisms with the simulated

turbulent mixing. Subsequently Kamykowski et al. (1994) also analysed by means of the IBM

approach the effect of the photoinhibition process on primary production estimates. The

model clearly demonstrated that vertical mixing regime strongly determined how the

individual light history affected each population‘s statistical characteristics. More recently

Nagai et al. (2003) coupled the Lagrangian photoresponse model of Kamykowski et al.

(1994) with a 2nd-order turbulence closure model (Mellor and Yamada, 1982). In this study

Nagai et al. (2003) investigated the effects of wind mixing and diurnal photoresponse on the

daily phytoplankton production in a realistic water column. Their results suggested that

intense wind mixing in a lower-transparency water column determined greater phytoplankton

production. Consequently, vertical mixing was not a relevant factor for the photoresponse in

open-ocean water, while in a coastal condition it played a more relevant role.

Cianelli et al. (2004) developed an individual-based model describing the spatial and

temporal evolution of phytoplankton organisms moving in the Antarctic mixed layer during

summer. While previous studies used simplified descriptions of cell photo-response, this

study firstly combined the dynamic photoacclimation of the pigment content with a

mechanistic description of photoinhibition process. Moreover, in order to simulate in detail

the phytoplankton photo-physiology the model explicitly considered the dynamics of organic

carbon (C) and chlorophyll a (Chl a) along with the vertical structure of the water column. As

the paper focused on the role of light variability on phytoplankton growth in the Antarctic

mixed layer, the authors simulated both a nutrient-replete and an iron-replete scenario, thus

reproducing the conditions frequently observed in coastal areas (Martin et al., 1990) or at the

onset of the growth season in Antarctica. The effect of different turbulent regimes and mixed

layer depths on the integrated primary production was investigated using in situ measured

parameters and kinetic constants consistent with the measured photosynthetic rates. The

coupling of different mixing levels with photoacclimation strategies led to a wide range of

photophysiological responses which underlined the role of the individual physiological

histories in determining the growth of the entire population. The results showed that the

highest rate of cell accumulation was reached when the vertical mixing compensated for

photoinhibition, thus suggesting that photoacclimation to low irradiance and strong mixing

regimes represented a crucial factor in the photosynthetic performance of Antarctic

phytoplankton.

In their recent paper Esposito et al. (2009) used the IBM approach to analyse how a

fluctuating light environment may influence the carbon assimilation by phytoplankton cells.

In particular this model included the dynamics of photoacclimation and photodamage-repair

mechanisms. Different light regimes (steady, square wave, sinusoidal light–dark cycles and

Individual Based Modelling of Planktonic Organisms 89

ocean mixed layer, reproduced by a large eddy simulation was also modelled. The results

showed a decrease of carbon assimilation in the light fluctuating scenario, as compared to

steady light regime, due to the temporal delay between light fluctuations and photoresponses.

During the last 15 years few studies have also applied the IBM approach to the

phytoplankton competition dynamics. Dippner (1998) implemented a mixed Lagrangian–

Eulerian model to investigate the nutrient competition of two pelagic phytoplankton species.

The model results suggested that in coastal waters a shift in the composition of functional

groups was due to a phosphate increase and a silicate reduction. Broekhuizen (1999) used a

combination of the Eulerian and Lagrangian method to study the role of motility in promoting

the persistence or the co-existence of dinoflagellates with diatoms. The author described the

nutrient field and the organic matter distributions on an Eulerian grid while the phytoplankton

organisms were modelled using a Lagrangian description. His findings showed that

dinoflagellates were able to coexist with diatoms by means of nutrient storage capacity and by

their great motility.

More recently, Nogueira et al. (2006) used the Lagrangian ensemble method to analyse,

over a three year period, the phytoplankton competition of a size-structured population whose

organisms belonged to the same functional group but differed in size and competed for two

resources (light and nutrient-nitrogen). This one-dimensional IBM was coupled with a NPZD

food-chain plankton ecosystem model, forced by astronomical and climatological conditions

of a subtropical area. The model reproduced the seasonal pattern of the environmental

variables and of the phytoplankton biomass and displayed seasonality in relative demography.

The outcomes also showed that the species co-existence was achieved over the simulated

period despite substantial seasonal variations in competitive advantage.

After Nogueira et al. (2006), Cianelli et al. (2009a) applied the IBM approach to simulate

the dynamics of two coexisting phytoplankton species in the mid-latitude mixed layer. The

model was aimed at investigating whether turbulent mixing affected the dominance of one

species over another on the time scales of maximum abundance of a bloom forming species

(20–30 days). The species were characterized by different photophysiological behaviour and

shared the same resources (light and nutrient) whose availability was determined by the

turbulent mixing. The physiological complexity of the individual organisms was described

explicitly taking into account the time-dependence of biomass and the chemical content of the

cells (carbon, nitrogen and chlorophyll a) in response to variable environmental resources.

The space and time variability of nutrient concentration and turbulent mixing was reproduced

introducing vertical profiles of measured eddy diffusivity. Three case studies were simulated

to analyse the role of environment–individual interactions in determining the outcome of

competition of the selected species. Starting from a low complexity level, where the two

species only shared light and nutrient resources in almost stationary conditions, a further

factor of environmental variability was added for the subsequent simulated scenarios.

In the modelled conditions individual organisms experienced recurrent fluctuations of

light, temperature, and nutrient concentration gradients, due to the turbulent mixing in the

water column. Such a variability of environmental constraints had significant effects on the

growth of the phytoplankton populations as a whole but did not support the prevalence of one

species over the other over the simulated time scale (20 days). The model results showed that

turbulent mixing might favour both species; in particular a stably stratified water column

90 Daniela Cianelli, Marco Uttieri and Enrico Zambianchi

sustained the optimal growth conditions of both populations, while a variable turbulent

mixing limited their growth reducing the photophysiological differences between the species.

Cianelli et al. (2009a) also investigated how the photophysiological responses of an

individual species to the environmental forcings were affected by the concomitant presence of

the other one. The comparison between individual species (each species developing alone in

the same environmental conditions) and coexisting species simulations suggested that the two

species mutually affected their photosynthetic capability in idealized environmental

conditions. On the other hand, in a more realistic scenario the turbulent mixing might support

the diversity of phytoplankton species composition in the water column.

Being aware that an exhaustive review of all the IBM studies applied to phytoplankton

organisms is outside of the aim of the present work, we have here illustrated some of the most

representative IBMs analyzing the influence of individual variance and photosynthetic

responses on the growth of bulk phytoplankton populations.

3. ZOOPLANKTON

Water column ecosystems are populated by a great variety of microscopic metazoans

collectively named zooplankton. They comprise the majority of taxa, covering a wide size

spectrum, from 10-6 m (microzooplankton) to 101 m (megazooplankton) (Sieburth et al.,

1978). In marine environments the most abundant zooplanktonic organisms are copepods,

while in freshwaters cladocerans are the most represented taxon; they both are crustaceans

with an average body length of 0.2-20 mm (mesozooplankton). Besides their numerical and

geographical importance, freely swimming zooplankters are primary actors in the functioning

of pelagic ecosystems. Zooplanktonic organisms are crucial for the transfer of matter and

energy between lower (e.g., phytoplankton) and higher (e.g., fish) trophic levels (Fowler and

Knauer, 1986), as well as for linking the inertial and the viscous realms (Naganuma, 1996).

The predation upon phytoplankton provides the energy for metabolic requirements, but

determines also the egestion of fecal pellets which, by passive sinking, enhance the vertical

fluxes of carbon from the upper layers towards the deep ocean. In addition, these small

inhabitants of aquatic systems can be efficient indicators of global scale climate changes

(Richardson, 2008). For these reason, it is clear that understanding the ecology of these small

organisms can improve the current knowledge of the functioning of aquatic ecosystems and

their criticality with respect to global scale warming issues. The function played by

zooplankton in large-scale dynamics, developing over spatial scale in the order of tens and

hundreds of meters and over time periods of hours and days, is mediated by the behaviour

displayed at the individual level, which instead occurs at millimetre scale and over time scales

in the order of seconds. Despite their gap, these two scales are intimately correlated: small-

scale interactions with other organisms (prey, predators and mates) are regulated by the

individual behaviour and by the environmental abiotic factors (e.g., light, temperature), which

in turn affect the patterns observed at larger scales.

In the last two decades, the use of numerical models in zooplankton ecology has

burgeoned, as summarised by Carlotti et al. (2000). In this framework, models are mainly

used for three objectives (Carlotti et al., 2000):

Individual Based Modelling of Planktonic Organisms 91

2) to study population dynamics as a function of changes in the environmental

properties;

3) to investigate the behaviour of different species.

Depending on the task addressed, different typologies of models can be used (Carlotti et

al., 2000). Despite the great potentialities, IBMs in this research area are still underexploited.

While the number of applications to fisheries research is substantial (as reviewed, e.g., in

Carlotti et al., 2000 and Neuheimer et al., 2010), the use of these models for copepods and

cladocerans is much less developed. In the following we will review applications of the

individual-based approach to copepods only, though several IBMs have been developed for

cladocerans also (e.g., Mooij and Boersma, 1996; Zadereev et al., 2003).

The first application of the individual-based approach to copepods is the work by

Batchelder and Miller (1989), who modelled the growth, development, reproduction and

death of Metridia pacifica over a one-year simulation. This model was subsequently refined

(Batchelder and Williams, 1995) to explain the consequence of the vertical distribution of

food on copepod‘s growth.

IBMs can be coupled with other models, such as water circulation or ecosystem ones.

Miller et al. (1998) modelled the life history and population dynamics of the copepod

Calanus finmarchicus in the Georges Bank region. The IBM included sex- and stage-

dependent biological traits, while the circulation model was used to move the modelled

copepods in the fluid, both horizontally and vertically. Such integrated investigation allowed

the authors to identify aggregative hot-spots in the region and to relate them to possible

restocking mechanisms.

Carlotti and Wolf (1998) implemented an IBM of C. finmarchicus based on the

― Lagrangian-ensemble method‖ (Woods and Onken, 1982) and integrated it with a food

supply deriving from a one-dimensional Eulerian NPZD ecosystem model. The individual-

based part also included a realistic description of individual swimming over the water column

(vertical migrations). The results of this model matched the observed dynamics of C.

finmarchicus in the Norwegian Sea.

Souissi et al. (2004) built an IBM to simulate the whole life cycle of Centropages

abdominalis, while Souissi et al. (2005) used an IBM to study the population dynamics of

Eurytemora affinis. Their results indicated specific space-time patterns to describe the

dynamics of the copepods, with a good match between simulated and in situ observed

blueprints.

Gentleman et al. (2008) compared different model typologies for copepod development

and proposed an alternative approach, the stage-based model of individuals, to represent the

progressive development through stages rather than using growth equations. The benefits of

this approach were demonstrated by replicating the development time for C. finmarchicus as

derived from laboratory trials. This approach was then used by Neuheimer et al. (2009) to

study the time-varying mortality in the nauplii of C. finmarchicus and in Neuheimer et al.

(2010) to model the recruitment of C. finmarchicus in the North-Western Atlantic, evaluating

the effects of temperature and chlorophyll-a on the physiological traits of this species.

Dur et al. (2009) modelled the reproduction of E. affinis using physiological parameters

such as female longevity, clutch size and interclutch duration. The model, validated through

92 Daniela Cianelli, Marco Uttieri and Enrico Zambianchi

parameters, while daily survival was shown to mostly affect the number of clutches produced.

Despite the Greek etymology, zooplanktonic organisms are not passively drifted by the

water currents, but are actually capable of moving on their own through the rhythmic beating

of their swimming appendages. They typically swim in search of food and mates, while at the

same time they use escape strategies to avoid the contact with predators. At the individual

scale, zooplankters exhibit a great variety of swimming repertoires (e.g., Strickler, 1977;

Mazzocchi and Paffenhöfer, 1999; Uttieri et al., 2004 and 2008), with species-specific and

intraspecific stage-dependent differences. The analysis of individual-scale motion contributes

to the comprehension of the adaptations to the varying ambient conditions, while at the same

time casting light on the large-scale behaviour as well as the population dynamics of a target

species (Dodson et al., 1997).

As mentioned above, IBMs are particularly suited to introduce behavioural rules, and

movement may be an important ingredient to stabilise the model and reproduce observed

patterns (Hosseini, 2006). In zooplankton ecology, a preliminary IBM-like approach to

copepod behaviour was used by Tiselius et al. (1993) who modelled the motility of the

copepod Acartia tonsa and of a ciliate of the genus Strombidium as a random walk with three

mobility patterns accounting for different kinetic behaviour. They aimed at verifying the role

of food patchiness and of functional responses on the foraging strategy and the predation risk

in zooplankton, and their results indicated that the risk of being captured must be traded off

with food intake to select an optimal strategy.

Later on, Leising and Franks (2000) implemented a 1D IBM of zooplankton motion in

search of food using a theoretical distribution of phytoplankton. Their simulations showed

that an area-restricted search behaviour increased the foraging efficiency, and indicated that a

model incorporating a behavioural rule was more beneficial than a pure random motion.

These outcomes were then corroborated by successive implementations of the model in a 2D

environment (Leising, 2001 and 2002), supporting the evidence that microscale patches are

critical for copepod growth and for ensuring sufficient energy intake.

Wiggert et al. (2005 and 2008) modelled the swimming behaviour and the foraging mode

of three tropical species (Clausocalanus furcatus, Oithona plumifera and Paracalanus

aculeatus) to evaluate the effects of turbulence, prey-size spectrum and frequency on their

grazing rates. Their simulations indicated that: C. furcatus preferred medium-sized, slowly

moving prey and moderate turbulent intensities; O. plumifera maximised the success of

encounter with large food particles and was favoured by high turbulent intensities; P.

aculeatus was capable of persisting in oligotrophic conditions and capturing smaller cells,

without being significantly affected by turbulence.

The consequences of turbulence upon individual copepod behaviour were also studied by

Mariani et al. (2005 and 2008) through an object-oriented IBM. In these works they focused

on the combined effect of homogeneous isotropic turbulence and contact duration between a

predator and its prey, both from a theoretical perspective (Mariani et al., 2005) and from

applications to real copepods (O. similis: Mariani et al., 2005 – O. davisae: Mariani et al.,

2008). Their simulations indicated that at realistic levels of turbulence the contact duration

was a limiting factor, and increasing intensities of turbulence might be detrimental to copepod

sensitivity. In addition, it was noticed that copepod reactiveness to turbulence was present

only until this stimulus was below a given threshold (approximately one order of magnitude

higher than the typical copepod speed).

Individual Based Modelling of Planktonic Organisms 93

Theoretical IBMs by Uttieri et al. (2007) and Cianelli et al. (2009b) demonstrated the role

of zooplankton motion behaviour and pattern of distribution of resources in determining the

probability of encountering a prey. The results of these works demonstrated that swimming

movement characterised by higher morphological complexity tallied more encounters than

smoother trajectories in uniform (Uttieri et al., 2007) and patchy (Cianelli et al., 2009) prey

distributions. Uttieri et al. (2010) developed an IBM to compare the search strategy and

encounter success of two co-occurring marine copepods (C. furcatus and O. plumifera)

showing different motion rules and sensory performances. This model included the numerical

description of the swimming motion of the two copepods (C. furcatus: Mazzocchi and

Paffenhöfer, 1999; Uttieri et al., 2008 – O. plumifera: Paffenhöfer and Mazzocchi, 2002), as

well as a realistic reconstruction of their perceptive fields (C. furcatus: Uttieri et al., 2008 –

O. plumifera: Paffenhöfer and Mazzocchi, 2002). The encounter success of the two copepods

was tested in homogeneous and patchy distributions of prey, showing that C. furcatus scored

more encounters than O. plumifera which however recorded higher search efficiencies.

CONCLUSION

Plankton populations are composed by microscopic organisms that, even when belonging

to the same species, differ at individual level from each other and interact with the aquatic

environment in a unique way. Planktonic organisms, being a product of evolutionary

processes, have developed adaptation strategies to better exploit the environmental resources.

The inter-individual and individual-environment interactions determine the emergent

properties of the entire population; as a consequence the investigation of the processes taking

place at the level of the individual provides a deeper comprehension of the functioning of

aquatic systems.

An important contribution to the understanding of plankton behaviour and ecology is thus

provided by the individual-based numerical approach (IBMs) which is particularly

appropriate to reproduce the complexity of plankton ecosystems. This promising tool has

been extensively used for a number of applications, revealing important aspects about

population dynamics and behavioural adaptations. In this work we have briefly summarized

the applications of IBMs to the field of phyto- and zooplankton ecology and behaviour. The

results here synthesized highlight that the dynamics of the individual physiological responses

is often non-linear and that extreme behaviour may play a crucial role. In such a framework,

an approach based on individuals is obviously the best candidate for a realistic numerical

description of plankton ecology.

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In: Ecological Modeling ISBN: 978-1-61324-567-5

Editor: WenJun Zhang, pp. 97-114 © 2012 Nova Science Publishers, Inc.

Chapter 6

NETWORKS IN MODELLING THE NUTRITIONAL

ECOLOGY OF A BLOWFLY SPECIES

Jose S. Govone3 and Claudio J. Von Zuben2

1

School of Earth and Environmental Sciences, The University of Adelaide.

2

Departamento de Zoologia, Instituto de Biociências – Unesp – São Paulo

State University, (postcode 13506-900),

Avenida 24-A, 1515, Bela Vista, Rio Claro-SP, Brazil.

3

DEMAC – Unesp – São Paulo State University.

ABSTRACT

The larval phase of most blowfly species is considered a critical developmental

period in which intense limitation of feeding resources frequently occurs. Furthermore,

such a period is characterised by complex ecological processes occurring at both

individual and population levels. These processes have been analysed by means of

traditional statistical techniques such as simple and multiple linear regression models.

Nonetheless, it has been suggested that some important explanatory variables could well

introduce non-linearity into the modelling of the nutritional ecology of blowflies. In this

context, dynamic aspects of the life history of blowflies could be clarified and detailed by

the deployment of machine learning approaches such as artificial neural networks

(ANNs), which are mathematical tools widely applied to the resolution of complex

problems. A distinguishing feature of neural network models is that their effective

implementation is not precluded by the theoretical distribution of the data used.

Therefore, the principal aim of this investigation was to use neural network models

(namely multi-layer perceptrons and fuzzy neural networks) in order to ascertain whether

these tools would be able to outperform a general quadratic model (that is, a second-order

regression model with three predictor variables) in predicting pupal weight values

(outputs) of experimental populations of Chrysomya megacephala (F.) (Diptera:

*

Email address: drebianconi@yahoo.com.br

98 Michael J. Watts, Andre Bianconi, Adriane Beatriz S. Serapiao et al.

Calliphoridae), using initial larval density (number of larvae), amount of available food,

and pupal size as input variables. These input variables may have generated non-linear

variation in the output values, and fuzzy neural networks provided more accurate

outcomes than the general quadratic model (i.e. the statistical model). The superiority of

fuzzy neural networks over a regression-based statistical method does represent an

important fact, because more accurate models may well clarify several intricate aspects

regarding the nutritional ecology of blowflies. Additionally, the extraction of fuzzy rules

from the fuzzy neural networks provided an easily comprehensible way of describing

what the networks had learnt.

Keywords: regression models; life history; neural algorithms; larval phase; pupal mass.

1. INTRODUCTION

It is a well-known fact that several species of blowflies can be mechanical vectors of

pathogenic microorganisms (Zumpt, 1965; Guimarães et al., 1978; Furlanetto et al., 1984;

Laurence, 1986; Lima and Luz, 1991). In addition, blowflies have been increasingly utilised

in forensic studies with the purpose of determining post-mortem intervals (Greenberg, 1991;

Catts and Goff, 1992; Arnaldos et al., 2005; Gomes and Von Zuben, 2005; Shiao and Yeh,

2008; Cammack and Nelder, 2010). From an ecological perspective, detailed studies of the

dynamics of these insects are also very useful because some blowflies may have important

implications for the field of invasion ecology (Cammack and Nelder, 2010). Therefore,

comprehending every developmental stage of blowflies may well be considered essential both

for medico-criminal analyses as well as for ecological research as a whole (Bianconi et al.,

2010a, 2010b).

Chrysomya megacephala (Fabricius) (Diptera: Calliphoridae), for example, represents a

blowfly of well-known medical and veterinary importance that is able to cause facultative

myiasis in humans and animals (Zumpt, 1965; Guimarães et al., 1978; Furlanetto et al., 1984;

Laurence, 1986; Lima and Luz, 1991; Gabre et al., 2005). This species is native to the

Oriental zoogeographic region, but it is now established in parts of South America following

accidental introduction (Guimarães et al., 1978; Laurence, 1981; Wells, 1991). Moreover, in

the field of forensic entomology, the genus Chrysomya has been utilised as a useful biological

indicator (Greenberg, 1991; Catts and Goff, 1992; Arnaldos et al., 2005; Gomes and Von

Zuben, 2005; Shiao and Yeh, 2008; Cammack and Nelder, 2010). Owing to the medico-

criminal, biological, and ecological utility of this species, several studies have been conducted

for analysing its bionomic traits in a detailed manner (e.g. Von Zuben et al., 1993, 2000,

2001; Bianconi et al., 2010a, 2010b; Hu et al., 2010).

With respect to the larval phase of C. megacephala, this developmental stage is

considered a critical period in which intense limitation of resources may well occur (Levot et

al., 1979; Goodbrod and Goff, 1990; Reis et al., 1994). This limitation can lead to dynamic

competitive processes (Shiao and Yeh, 2008), wherein each larva attempts to feed off the

available resources, scrambling to exploit the feeding substrate before the depletion of the

food resource (Ullyett, 1950; de Jong, 1976; Lomnicki, 1988; Von Zuben et al., 2001).

Therefore, such exploitative events are characterised by interrelated processes that take place

at both the individual and population levels (Wijesundara, 1957; Herzog et al., 1992; Von

Zuben et al., 2001; Tammaru et al., 2004). Moreover, it has been suggested that both larval

The Effectiveness of Artificial Neural Networks … 99

density and availability of food affect the competition for food in a concurrent manner.

Hence, it is very useful and important to investigate the crowding level of immature

individuals on the feeding resources by means of simultaneous variations of larval densities

and amounts of food (Von Zuben et al., 2000; Ireland and Turner, 2006).

The outcomes of exploitative competition for food resources may determine population

parameters such as survival, fecundity, weight and size of the resultant adults, so that the

variation of these bionomic features could well be influenced by the immatures‘ population

density (Von Zuben et al., 2000, Ireland and Turner, 2006; Shiao and Yeh, 2008). Von Zuben

et al. (1993), for instance, regard the number of emerging adults as a variable that tends to

decrease with an increase in the number of immature individuals of C. megacephala. Hence,

profitable mass-production techniques usually demand the determination of feasible cost-

benefit relationships between larval density and amount of available food (Papandroulakis et

al., 2000; Von Zuben et al., 2001).

Regarding the analysis of bionomic features of insects, pupal weight is considered to be

an important variable for comprehending potential relationships between larval and pupal

weight of Cochliomyia hominivorax (Coquerel) (Calliphoridae) (Peterson II and Candido,

1987). Investigating the thermal requirements for development of nymphalid species, Bryant

et al. (1997) took pupal weight into consideration with the purpose of determining possible

connections between relative performance and distribution. Tammaru et al. (1996) analysed

the pupal weight of Epirrita autumnata (Borkhausen) (Lepidoptera: Geometridae) in order to

assess the relationship between body size and realised fecundity, and Tammaru et al. (2004)

stated that the pupal weight of this same species could be affected by starvation treatments.

Pupal mass was also utilised in analysing dietary specialisation aspects of a micro-

lepidopteran culture that had been maintained on an artificial diet for approximately 350

generations (Warbrick-Smith et al., 2009). Furthermore, pupal weight has been widely

utilised in several works concerning use of different substrates for rearing dipteran larvae

(Brewer, 1992; Friese, 1992; Chaudhury and Alvarez, 1999; Tachibana and Numata, 2001;

Chang et al., 2004).

Unsuitable or inaccurate predictive models may hinder the effective comprehension of

the underlying principles that govern several biological processes, including the nutritional

ecology of blowflies. For example, mass rearing of larvae and pupae with the purpose of

using these immatures as food or bait for other animals constitutes a process in which

adequate models could effectively ameliorate its implementation (Von Zuben et al., 1993,

2000, 2001). Additionally, the suitable conditions which yield pupae containing higher

concentrations of energy (higher biomass) could be assessed and established, using analytical

tools that permit the implementation of mathematical models with higher prediction

capability (Von Zuben et al., 1993, 2000; Bianconi et al., 2010a, 2010b).

In this context, the complexities of the nutritional ecology of blowflies could be clarified

and detailed by the deployment of appropriate modelling techniques such as artificial neural

networks (ANNs), which are mathematical tools widely applied to the resolution of complex

biological problems. A notable feature of artificial neural networks is their independence

from any assumptions about the theoretical distribution of the data used (Bishop, 1995;

Haykin, 1999; Bryant and Shreeve, 2002; Pearson et al., 2002; Zhang and Barrion, 2006).

Moreover, if the dimensional features of a specific system are too complex for a conventional

regression statistical model, artificial neural networks may represent a more effective

100 Michael J. Watts, Andre Bianconi, Adriane Beatriz S. Serapiao et al.

modelling tool (Schultz and Wieland, 1997; Haykin, 1999; Schultz et al., 2000; Zhang and

Wei, 2009).

Neural network algorithms are founded on the construction of models that may possess a

large number of simple processing units (that is, neurons or nodes) that contain several

connections between them and are usually lined up in layers. The number of neurons in the

input layer represents the variables that will be used to feed the neural network and should be

the most relevant variables for the problem in question (Bishop, 1995; Haykin, 1999). ANNs

were conceived with the aim of imitating the functionality of the human brain (Haykin, 1999;

Huang, 2009; Huang et al., 2010). Thus, part of the terminology used in the area of artificial

neural networks, namely neurons, synapses, learning, layers, etc., is due to such a fact.

However, it is important to emphasise that those terms are only associated with mathematical

functions or the method of implementing them.

Studies of process-based neural network models are not as frequent in ecological and

environmental areas as they are in engineering applications (Zhang and Zhang, 2008; Huang,

2009). However, considerable improvements have been achieved in recent years (Zhang and

Zhang, 2008; Huang, 2009; Zhang and Wei, 2009). In the broader context of ecosystem

dynamics, neural networks have been successfully utilised. For example, the abundance of

selected water insects in a small stream was predicted by means of neural models (Obach et

al., 2001). Environmental data collected as part of a study of microhabitat use by butterflies

were utilised with the aim of evaluating the potential for using neural modelling in developing

predictive models of microhabitat temperature (Bryant and Shreeve, 2002). Furthermore,

other multidisciplinary studies have described the development of scale-independent models,

based on coupling artificial neural networks with climate-hydrological process models in

order to simulate species‘ distribution, including insect species (Pearson et al., 2002; Pearson

and Dawson, 2003; Harrison et al., 2006).

Worner and Gevrey (2006) used a self-organising map, which is an artificial neural

network model, with the purpose of identifying global pest species assemblages and potential

invasive insects, including dipteran species. Zhang and Barrion (2006) conducted function

approximation and documentation on sampling data using neural networks, based on

invertebrate data sampled in an irrigated rice field. Howe et al. (2007) demonstrated the value

of using neural networks to predict body temperature and activity of insects by means of

modelling the body temperature and activity of a widespread butterfly species in relation to

weather. With the purpose of improving the prediction accuracy of potential species invasion,

Watts and Worner (2008) deployed two types of biotic factors in ANN models to predict

global establishment of selected phytophagous insect species, and such predictions were then

combined with those derived from an ANN model based on abiotic (climate) factors.

With respect to mass-production techniques, the adequate development of feasible

automatic feeding devices for rearing larval individuals could well benefit from the use of

neural network-based models (Papandroulakis et al., 2000), and effective control strategies of

insect pests usually rely on the knowledge derived from basic research on oviposition rate,

adult emergence, larval development until pupation, etc (Von Zuben et al., 2000; Köppler et

al., 2009). In this context, neural networks may be useful to establish the best possible cost-

benefit relationships between larval density and amount of food, with the aim of producing

heavier pupae and minimising production costs.

Zhang and Zhang (2008) analysed the effectiveness of neural networks in modelling

survival process and mortality distribution of Spodoptera litura (Fabricius) (Lepidoptera:

The Effectiveness of Artificial Neural Networks … 101

Zhang et al. (2008a) fitted and recognised spatial distribution patterns of grassland insects

using various neural networks, and Zhang et al. (2008b) employed conventional models and

functional link artificial neural networks in modelling the accumulated food intake of larvae

of S. litura. Additionally, the risk of insect species invasion was assessed by means of neural

models (Watts and Worner, 2009). Zhang and Wei (2009) proposed a neural network model

for state space modelling, using data derived from a natural grassland area that contained

dipteran species as well as other arthropods. With respect to blowfly species, the nutritional

ecology of C. megacephala was investigated by Bianconi et al. (2010a, 2010b), using both a

relatively small sample size (Bianconi et al., 2010a), as well as a relatively large data set

(Bianconi et al., 2010b).

The nutritional ecology of blowflies has not been analysed by means of neural models,

and the same is true of other insect species. The two studies which investigated bionomic

features of blowflies (i.e. Bianconi et al., 2010a, 2010b) provided reasonable outcomes.

Nonetheless, these same authors did suggest that their investigation represented only a first

approach to modelling the nutritional ecology of C. megacephala. Specifically, Bianconi et al.

(2010b) utilised three well-known neural networks in order to ascertain whether these tools

would be able to outperform a classical statistical method (i.e. first-order multiple linear

regression) in predicting pupal weight values (i.e. output variable) of experimental

populations of C. megacephala, using larval density (i.e. initial number of larvae), amount of

available food, and pupal size as input data. Therefore, the current investigation is aimed at

implementing more accurate neural models than those utilised by Bianconi et al. (2010b),

using exactly the same input and output data. Owing to the well-known importance of C.

megacephala for forensic and ecological analyses, more accurate outcomes should be derived

from more robust neural network models.

2.1. Chrysomya megacephala Collection and Rearing

Adult blowflies were captured around the campus of the Universidade Estadual de

Campinas-Unicamp in Campinas, São Paulo state, Brazil (22º 49‘ 9.52‖ S and 47º 4‘ 12.54‖

W). The specimens were then identified and kept in nylon net cages (30 x 30 x 48 cm). Prior

to identifying the blowflies, the individuals were anaesthetised in a freezer at -18º C for 30 s.

These insects were provided with water and refined sugar ad libitum and taken as the parental

generation of this investigation. The cages were kept at room temperature (25 + 1º C), 60 +

10% relative humidity, and light:dark regime of 12:12 h. In order to induce the development

of the gonotrophic cycle, females were supplied with beef liver. For the formation of the next

generations, ovipositions were obtained using small pots containing decaying beef that were

put into the cages in order to stimulate egg laying.

Five proportions of larvae to amount of food were considered (i.e. 5, 10, 20, 30, and 40

larvae/g) in the current work, and they were obtained as follows: 75, 150, 300, 450, and 600

larvae were put into pots that contained 15g of food; 150, 300, 600, 900, and 1200 larvae in

pots containing 30g of food; 300, 600, 1200, 1800, and 2400 larvae in pots containing 60g of

102 Michael J. Watts, Andre Bianconi, Adriane Beatriz S. Serapiao et al.

food; and 450, 900, 1800, 2700, and 3600 larvae in pots with 90g of an artificial diet

proposed by Leal et al. (1982). Glass pots (8 cm in height x 7 cm in diameter) containing four

amounts (i.e. 15, 30, 60, and 90g) of the artificial diet were utilised. As to the pupal stage,

pupae were individually weighed, and pupal sizes were taken on the eighth day after the peak

of the larval hatching period. Additional experimental details regarding the formation of the

larval densities and amounts of food are provided in Von Zuben et al. (2000) and Bianconi et

al. (2010a).

2.2. Variables

Pupal weight was the dependent variable (output), and the other three were considered

the independent or explanatory variables (inputs), namely larval density (that is, initial

number of larvae), amount of available food (in grams), and pupal size (in mm). These

variables were chosen based on their biological significance for the comprehension of the

nutritional ecology of blowflies. Combinations of the three input variables provided 1114

output values.

In several practical situations, neural networks and statistical models can both be utilised,

because they may respond to the same question, albeit with important differences in the

accuracy of the outcomes. Therefore, the performance of neural models is usually compared

with that derived from statistical methods (Schultz and Wieland, 1997; Bianconi et al.,

2010b). Hence, a general quadratic regression method was used as the statistical ‗counterpart‘

of the neural models deployed in the current investigation.

Bianconi et al. (2010a; 2010b) utilised a first-order linear regression method in order to

compare the outcomes derived from implementing well-known neural network models to the

results obtained by using the statistical model. Nonetheless, these same authors suggested that

each one of the independent variables might have produced distinct output responses. Overall,

such explanatory attributes might have generated non-linear variation in the output variable

(i.e. pupal weight), and the accuracy of conventional regression methods such as the first-

order regression models may be significantly reduced in the presence of non-linearity (Neter

et al., 1996; Schultz and Wieland, 1997). Therefore, in the present investigation, instead of

using the traditional first-order regression model, we utilised a second-order regression model

(i.e. a general quadratic model) in order to compare the performance of three types of

artificial neural network (ANN) algorithms to that derived from implementing the general

quadratic regression model (i.e. a second-order regression model).

It is important to emphasise that the general quadratic model (GQM) represents a special

case of the traditional linear regression model deployed by Bianconi et al. (2010a, 2010b).

Nonetheless, the term ‗linear model‘ refers to the fact that this model may be linear in the

parameters, but this linearity is not associated with the shape of the response surface. In

simple terms, a general quadratic regression (GQM) may be described in the following form:

ŷ = a + b1x1 + b2x2 + b3x3 + b12x1x2 + b13x1x3 + b23x2x3 + b11x12 + b22x22 + b33x32 (1)

The Effectiveness of Artificial Neural Networks … 103

in which ŷ represents the output (i.e. predicted pupal weight values); x1= initial larval density,

x2= amount of available food (g), x3 = pupal size (mm); a is a constant; and bi, bii, and bij

represent regression coefficients. The regression coefficients bij (i.e. b12, b13, and b23) may be

termed ‗interaction effect coefficients‘ for interactions between pairs of predictor variables. A

general quadratic regression such as (1) is considered to be a second-order regression model

because the input variables may be expressed in the model to the first and second powers

(Kutner et al., 2004). On the other hand, the traditional regression model implemented by

Bianconi et al. (2010a, 2010b) is deemed to be a first-order regression model in which the

effects of the explanatory variables on the mean response of the output variable do represent

additive effects that do not interact with one another (Kutner et al., 2004). Hence, it is

expected that the second-order model described in the present work would be capable of

providing more accurate outcomes than the traditional first-order regression model deployed

by Bianconi et al. (2010b) in predicting pupal weight values.

The entire data set was utilised in implementing the general quadratic model because the

division of the data set into training and test subsets is suitable for neural network modelling.

That is, if entomologists were to deploy this quadratic statistical model in conducting

experiments, they would utilise the entire data set because a general quadratic model is

derived from the whole data set.

In the current paper, the coefficient of determination (R2) and the root mean square error

(RMSE) were utilised in assessing the performance of the statistical and neural network

models. Apart from these metrics, a residual plot (i.e. plot of residuals against fitted values)

was utilised in order to examine the appropriateness of the regression model in relation to the

constancy of the variance of the error terms. The statistical assumptions of the general

quadratic model (GQM) followed the detailed descriptions in Kutner et al. (2004). The ANN

models used in this work will be described in the following section.

Artificial neural networks are able to model complex non-linear systems, even when the

exact nature of any relationships is unknown (Schultz and Wieland, 1997; Schultz et al.,

2000; Bryant and Shreeve, 2002; Howe et al., 2007; Zhang et al., 2008a). The framework for

deploying neural network models is underpinned by the concept of artificial neurons (that is,

processing elements) that are usually laid out in a parallel fashion (Haykin, 1999). On the

whole, interconnected layers in combination with their neurons constitute the architecture of

neural networks, in which each neuron in one specific layer is only fully connected to neurons

of other layers. Neurons are usually interconnected by means of ‗synaptic weights‘ (Cheng

and Titterington, 1994; Haykin, 1999). In outline, the training of a neural network comprises

the act of presenting the neural network model with input and/or output data; the creation and

implementation of connections that are able to recognise patterns; and the learning of such

patterns based on the relationship between input and output data sets via the adaptation of

specific synaptic weights to varying input data (Cheng and Titterington, 1994; Bishop, 1995;

Haykin, 1999).

A widely used ANN is the multi-layer perceptron, or MLP (Crick, 1989). This model

consists of three layers of artificial neurons: an input layer, where there is one neuron for each

input variable; a hidden neuron layer, where each neuron has incoming connections from the

104 Michael J. Watts, Andre Bianconi, Adriane Beatriz S. Serapiao et al.

input layer; and the output layer, where there is one neuron for each output layer, and each

output neuron has incoming connections from the hidden layer neurons. The hidden layer gets

its name from the fact that it is not directly exposed to either the input or output variables: it is

‗hidden‘ from the outside world. Training a MLP involves setting the values of the

connection weights, and the most commonly used method of training MLP is

backpropagation of errors (Rumelhart et al., 1986). This is a gradient-descent error

minimisation algorithm, where errors at the output layer are propagated back through the

structure of the MLP, with the errors at each layer being used to adjust the incoming

connection weights of each neuron.

An alternative method of training MLP is via evolutionary programming (EP) (Fogel et

al., 1965). This is an evolutionary algorithm (Fogel et al., 1997) whereby populations of

solution attempts are evolved over generations; the performance of each solution attempt in

the population is evaluated over the problem, and the solution attempts with the best

performance in each generation are used to generate the next generation. When applied to

training MLP, the populations consist of MLP, the performance of each MLP is evaluated

over the training data, and new solutions are generated by applying normally distributed

changes to the connection weights. We measured the performance of each MLP as the mean

squared error (MSE) over the training data set. For both BP and EP training of MLP, one

hundred trials were carried out over the selected training parameters. The MLP that had the

best performance over the validation data partition was used to predict over the test partition.

For each trial with MLP, the contributions of each input neuron to the output of the

network were also determined. Many methods have been proposed for determining the

importance of each of the input neurons of a MLP. These include the methods of Garson

(1991), Milne (1995), Gevrey et al. (2003) and Olden and Jackson (2002). Since it was

desirable to identify features that negatively affect pupal weight and the methods of Milne

(1995) and Gevrey et al. (2003) return unsigned values, these methods were rejected. Of the

remaining methods, the work of Olden et al. (2004) has shown that the method of Olden and

Jackson (2002) is the least biased, and it has been previously used in ecological modelling

applications (Joy and Death, 2004). Thus, this method was selected.

A more advanced ANN is the Fuzzy Neural Network FuNN (Kasabov et al., 1997).

FuNN was designed to provide an easy method of combining the advantages of fuzzy logic

(Zadeh, 1965) with the advantages of neural networks. FuNN are ANN with fuzzy logic

elements embedded within them, specifically fuzzy membership functions attached to their

input and output variables, and are trained using BP. Fuzzy logic allows concepts that are not

crisply defined, such as ‗Low‘, ‗Medium‘ or ‗High‘, to be expressed in fuzzy rules that are

more easily understood, are more succint and are more robust than rules that rely on crisply

defined concepts. A chief advantage of FuNN is the ability to extract and insert fuzzy rules

from and into a FuNN structure. Fuzzy rules are extracted from a trained FuNN, and are

useful for explaining in a comprehensible manner the knowledge that the network has

captured.

A potential disadvantage of ANN is the network inability to suitably respond to data sets

which were not previously shown (lack of generalisation ability or overfitting). Normally, to

avoid overfitting of the network, the number of neural connections should be lower than the

number of training examples. However, there are not definite rules or methods of establishing

the suitable number of hidden layers and neurons (Watts and Worner, 2008; Zhang and

Zhang, 2008; Huang, 2009; Huang et al., 2010). Therefore, cross-validation (CV) may be a

The Effectiveness of Artificial Neural Networks … 105

useful way of avoiding such drawbacks by means of inserting the cross-validation subset into

the network in order to verify its performance over the training. In regard to the use of neural

modelling in entomology, Zhang and Zhang (2008), for example, utilised cross-validation

procedures.

3. RESULTS

Table 1 shows the coefficients of determination (R2) and root mean square errors that

were derived from the data subsets utilised for testing the neural network models. Regarding

the statistical model (i.e. general quadratic regression), the entire data set (i.e. 1114 examples)

was utilised. The following equation was derived by fitting the entire data set to (1):

0.00000596x12 - 0.0011x22 + 0.7071x32 (2)

in which ŷ represents the estimated quadratic model derived from fitting the entire data set to

(1).

Table 1. Coefficients of determination (R2) and root mean square errors (RMSE)

derived from test subsets of each predictive model. MLP-BP means a multi-layer

perceptron (MLP) ANN trained using backpropagation. MLP-EP means a MLP trained

with evolutionary programming (EP). FuNN is the results of the Fuzzy Neural Network

FuNN. With respect to the statistical model (GQM), the entire data set (n=1114) was

utilised in obtaining the metrics. GQM: general quadratic model

Test

Neural models R2 RMSE

MLP-BP 0.5659 5.8509

MLP-EP 0.5680 6.2415

FuNN 0.6394 5.1099

(n=1114)

GQM 0.5761 7.7530

The training parameters that were found to be the most effective for BP-trained MLP

were 15 hidden neurons, trained for 100 epochs with a learning rate and momentum of 0.5.

The optimal parameters for EP-trained MLP were 12 hidden neurons, a population size of 200

MLP, over 7500 generations. The best 40 MLP of each generation were used as the parents of

the next generation. Finally, for FuNN, the optimal parameters were 15 hidden neurons,

trained for 100 epochs with a learning rate and momentum of 0.5. There were three fuzzy

membership functions attached to each input neuron and the output neuron.

106 Michael J. Watts, Andre Bianconi, Adriane Beatriz S. Serapiao et al.

The mean and standard deviations of the input contributions derived from BP-trained

MLP were x1 = -6.6061±0.5057, x2 = 3.7892±0.4177, and x3 = 12.6191±0.3450. The input

contributions derived from EP-trained MLP were x1 = -8.7523±2.8487, x2 = 4.9177±3.6100,

and x3 = 9.5995±3.9692.

Three fuzzy rules were extracted from the trained FuNN and are presented below. The

numbers following the labels Low, Medium and High are confidence factors:

then y1 is Low 1.81613

then y1 is Medium 2.07653 and y1 is High 2.05552

then y1 is High 1.67556

A threshold value was applied to the rule extraction process, which eliminated rules and

rule elements that did not contribute strongly to the model: thus, not all variables are included

in the rule antecedents.

The R2 obtained by means of the general quadratic model (GQM) was slightly higher (R2

= 0.5761, and RMSE = 7.7530) than that derived from the conventional first-order multiple

linear regression model (i.e. R2 = 0.5720, and RMSE = 7.8320) implemented by Bianconi et

al. (2010b). On the other hand, the fuzzy neural network FuNN provided both a higher R2

(0.6394) and lower RMSE value (5.1099) than the general quadratic model (GQM) utilised in

the present investigation, while the BP-trained MLP and EP-trained MLP both yielded lower

RMSE values (5.8509 and 6.2415 respectively), but slightly lower R2 values (0.5659 and

0.5680).

Figure 1. Residuals (i.e. the difference between predicted and observed values) as a function of the

predicted values. The whole data set is represented (n = 1114). Each point represents the difference

between the observed pupal weight (actual value) and the pupal weight predicted by the general

quadratic model (Equation 2).

The Effectiveness of Artificial Neural Networks … 107

In addition, it is important to note that the residuals derived from the general quadratic

model (Figure 1) are not ‗biased‘. That is, the residuals neither increase nor decrease with the

increase in the predicted output values.

DISCUSSION

Bryant and Shreeve (2002) compared the predictive power of a feed-forward

backpropagation neural network with that provided by a conventional multiple regression

model in estimating microhabitat temperature, and the neural network method was found to

exhibit a higher correlation between predicted and observed values. Howe et al. (2007)

modelled the body temperature and activity of a widespread butterfly species (Polyommatus

icarus) by means of a multilayer feed-forward backpropagation network, and this neural

model was deemed superior to a generalised linear modelling approach to predicting body

temperature.

Similarly, MLP trained using backpropagation and evolutionary programming and the

fuzzy neural network FuNN deployed in the current study exhibited better performances than

a second-order regression-based model (i.e. general quadratic model). Furthermore, Watts and

Worner (2008) successfully used multilayer perceptrons (Cascaded MLP) in order to improve

the prediction accuracy of potential insect species invasions, and improved test accuracy was

obtained through the utilised neural models.

Simple first-order linear regression models (that is, one single output as a function of one

single input variable) have been utilised in studies concerning the nutritional ecology of

blowflies (Von Zuben et al., 1993, 2000). Gomes et al. (2009), for instance, examined the

burrowing behaviour of blowflies in response to different conditions of temperature by means

of a linear regression method in order to determine the relationship between increase in

temperature and decrease in pupal weight. Bianconi et al. (2010a, 2010b) deployed a

conventional multiple linear regression model in analysing the nutritional ecology of C.

megacephala, and this statistical regression technique was less accurate than neural networks.

Bianconi et al. (2010b) suggested that the input variables (i.e. initial number of larvae,

amount of available food, and pupal size) could have introduced some non-linearity into the

output response. Such non-linearity may well hinder the implementation of first-order

multiple linear regression models, because first-order models should be linear both in the

parameters as well as in the response surface. On the other hand, second-order models such as

the general quadratic model utilised in the current work (Equation 1) are not restricted to

linear responses only. Thus, this type of model could be more appropriate for predicting pupal

weight values than the first-order model utilised by Bianconi et al. (2010b).

Nonetheless, the R2 value derived from the general quadratic model implemented in the

current investigation (R2 = 0.5761, Table 1) was slightly higher than that (i.e. R2 = 0.5720)

obtained by means of a traditional first-order regression model (Bianconi et al., 2010b).

Therefore, it could be concluded that traditional multiple regression models such as first- and

second-order models were not capable of incorporating the non-linearity present in the input

variables into the fitted model. Moreover, the RMSE derived from FuNN was lower than all

of the other outcomes (i.e. Bianconi et al., 2010b, and the current investigation).

108 Michael J. Watts, Andre Bianconi, Adriane Beatriz S. Serapiao et al.

The input contribution analysis of both the BP and EP-trained MLP indicated that the

amount of food available (x2) was the least important variable, as this had the lowest

contribution score for both sets of results. This interpretation agrees with the results of the

statistical model, which assigned relatively small coefficients to that variable and from the

fuzzy rules extracted from FuNN, where this variable was included in only one of the three

extracted rules. Pupal size x3 had a large positive contribution, that is, a large value for pupal

size would contribute to a large value for pupal weight (y1). To some extent, this

interpretation agrees with the statistical model, where a relatively large positive coefficient

was assigned to the squared term (i.e. 0.7071, Equation 2), and by the fuzzy rules, as pupal

size was included in each of the three extracted rules. Finally, initial larval density (x1) had a

large negative contribution for MP and EP-trained MLP. This means that a large value for

initial larval density would contribute to a small value for pupal weight. In the statistical

model very small coefficients were assigned to this variable, and in the third extracted fuzzy

rule, a low value of this variable (if x1 is Low) led to a high pupal weight (then y1 is high). In

summary, the neural models utilised in predicting the output variable revealed that a large

value of larval density x1 contributes to a small pupal weight, a large value of pupal size x3

contributes to a high pupal weight, and the amount of food available x2 contributes the least to

the pupal weight.

Zhang et al. (2008a) investigated the spatial distribution pattern of grassland insects by

means of neural models. They concluded from their results that neural networks were more

flexible than a conventional model. Additionally, these authors indicated that further research

based on more complex distribution patterns should be conducted with the aim of obtaining

conclusions that are more reliable. Similarly, neural networks were deemed to be superior to a

conventional model (i.e. general quadratic model) in the current study. Nevertheless, the

present work utilised simple experimental designs and only three explanatory variables

(inputs). Therefore, more complex experimental designs should be implemented in order to

explain the portion of the total variance that was not accounted for by the models.

Furthermore, larger sample sizes are highly desirable, because the number of examples

(sample size) that is usually utilised in nutritional ecology may prevent the full utilisation of

the potential of neural networks (Bianconi et al., 2010a, 2010b).

The sample size used in the present investigation (n = 1114) may be sufficient to conduct

most ecological and biological approaches to analysing the nutritional ecology of blowflies

(Bianconi et al., 2010a, 2010b). Nonetheless, it is important to note that two of the input

variables (i.e. larval density and amount of food available) provided the utilised methods with

few distinct values, because only 11 larval densities and four distinct amounts of available

food were used (see Section 2 for details). Therefore, the larger number of distinct values

measured for the output variable (i.e. pupal weight), using the same combination of values of

those input variables, may have caused a lack of fit between input data and predicted output

values that may have decreased the predictive capability of the statistical and neural network

methods (Bianconi et al., 2010b).

Nonetheless, the number of distinct values of larval densities deployed in the present

work was considerably larger than those widely used in experimental designs on the

nutritional ecology of blowflies (Von Zuben et al., 2000; Bianconi et al., 2010b). Moreover,

such studies would be impractical if an even larger number of larval densities were used (Von

Zuben et al., 1993, 2001; Bianconi et al., 2010a, 2010b). Hence, the utilisation of artificial

The Effectiveness of Artificial Neural Networks … 109

neural networks is justified in this case, since the neural algorithms coped with the lack of fit

better than the general quadratic model (Table 1).

Future studies may consider other complex variables that were not assessed in the current

work. Ambient temperature, for example, was utilised by Zhang et al. (2008b). These authors

deployed neural network algorithms (functional link artificial neural networks) in order to

model the food intake dynamics of larvae of S. litura (Lepidoptera). Six different

temperatures were used for measuring the food intake, and the neural network approach was

deemed accurate. Moreover, temperature is regarded as an important variable in analysing the

dynamics of blowflies (Shiao and Yeh, 2008, Hwang and Turner, 2009; Cammack and

Nelder, 2010; Hu et al., 2010).

The utilisation of a simple linear regression may well require a non-trivial amount of

statistical expertise. The deployment of a multiple non-linear regression model such as a MLP

does require more knowledge and experience (Sarle, 1994). Therefore, it is important to

highlight the usefulness of multidisciplinary studies with the aim of conducting effective

investigations of bionomic parameters, because it is possible that unresolved problems

concerning the bionomics of immature and adult individuals of blowflies could be

disentangled and clarified by the use of neural models (Bianconi et al., 2010a, 2010b).

The employment of these complex analytical tools may well help entomologists to

feasibly schematise the sort of practical situations in which the utilisation of artificial

networks is able to provide new insights into the nutritional ecology of blowflies (Bianconi et

al., 2010a, 2010b). Additionally, the extraction of fuzzy rules from the fuzzy neural networks

provided an easily comprehensible way of describing what the networks had learnt.

Therefore, the outcomes of the present investigation may stimulate the use of artificial neural

networks in entomological research as a whole.

ACKNOWLEDGEMENTS

The Conselho Nacional de Desenvolvimento Científico e Tecnológico provided A.

Bianconi and C.J. Von Zuben with financial support.

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Editor: WenJun Zhang, pp. 115-172 © 2012 Nova Science Publishers, Inc.

Chapter 7

BASED DECISION-SUPPORT SYSTEM FOR MANAGING

MIXED CONIFEROUS FOREST STANDS FOR

MULTIPLE OBJECTIVES

Peter F. Newton1*

1

Canadian Wood Fibre Centre, Canadian Forest Service,

Natural Resources Canada, Sault Ste. Marie, Ontario, Canada, P6A 2E5.

ABSTRACT

An ecological-based decision-support system and corresponding algorithmic

analogue for managing natural black spruce (Picea mariana (Mill) BSP.) and jack pine

(Pinus banksiana Lamb.) mixed stands was developed. The integrated hierarchical system

consisted of six sequentially-linked estimation modules. The first module consisted of a

key set of empirical yield-density relationships and theoretically-based functions derived

from allometry and self-thinning theory that were used to describe overall stand dynamics

including temporal size-density interrelationships and expected stand development

trajectories. The second module was comprised of a Weibull-based parameter prediction

equation system and an accompanying composite height-diameter function that were used

to recover diameter and height distributions. The third module included a set of species-

specific composite taper equations that were used to derive log product distributions and

volumetric yields. The fourth module was composed of a set of species-specific

allometric-based composite biomass equations that were used to estimate mass

distributions and associated carbon-based equivalents for each above-ground component

(bark, stem, branch and foliage). The fifth module incorporated a set of species-specific

end-product and value equations that were used to predict chip and lumber volumes and

associated monetary equivalents by sawmill type (stud and randomized length mill

configurations). The sixth module encompassed a set of species-specific composite

equations that were used to derive wood and log quality metrics (specific gravity and

mean maximum branch diameter, respectively). The stand dynamic and structural

recovery modules were developed employing 382 stand-level measurements derived

*

Correspondence: peter.newton@nrcan.gc.ca

116 Peter F. Newton

from 155 permanent and temporary sample plots situated throughout the central portion

of the Canadian Boreal Forest Region, the taper and end-product modules were

developed employing published results from taper and sawmill simulation studies, and

the biomass and fibre attribute modules were developed using data from density control

experiments.

The potential of the system in facilitating the transformative change towards the

production of higher value end-products and a broader array of ecosystem services was

exemplified by simultaneously contrasting the consequences of density management

regimes involving commercial thinning treatments in terms of overall productivity, end-

product yields, economic efficiency, and ecological impact. This integration of

quantitative relationships derived from applied ecology, plant population biology and

forest science into a common analytical platform, illustrates the synergy that can be

realized through a multi-disciplinary approach to forest modeling.

Allometry; Operational utility.

1. INTRODUCTION

Density management within even-aged forest stands consists of regulating species

composition, density-stress levels and structural characteristics, by manipulating initial

planting densities at the time of establishment (initial espacement; IE) and (or) reducing stand

densities during subsequent stages of stand development (e.g., precommercial thinning (PCT)

at the sapling stage, and (or) commercial thinning (CT) at the semi-mature stage).

Ecologically, these treatments redistribute the finite environmental resources on a given site

(e.g., solar radiation, moisture, nutrients, and physical growing space) to selected crop trees

by controlling the intensity and frequency of symmetrical and asymmetrical competitive

interactions. Regulating site occupancy through density management has been a cornerstone

of silvicultural practice since it was first introduced in forestry by Reventlow in 1879

(Pretzsch, 2009). Density management continues to be an important component of intensive

forest management as evident by current efforts: over 500,000 ha of productive forest land

receive IE, PCT or CT treatments every year in both Canada and Finland (CCFM (2009) and

Peltola (2009), respectively).

A broad array of benefits at the tree, stand and landscape scale can be obtained when

implementing proper density management treatment protocols or prescriptions. Productivity

related benefits include increased growth and resultant yields leading to enhanced end-

products (e.g., Kang et al., 2004), early stand operability (e.g., Erdle, 2000), reduced self-

thinning rates and thus lower mortality losses (e.g., Pelletier and Pitt, 2008), spatial and

structural uniformity resulting in lower extraction, processing and manufacturing costs (e.g.,

Tong et al., 2005), and increased carbon sequestration rates (e.g., Nilsen and Strand, 2008).

Other tangible benefits include the production of coarse woody debris (e.g., Sturtevant et al.,

1996) and provision of hiding requirements (e.g., Smith and Long, 1987) for wildlife habitat,

controlling successional pathways in order to prevent the establishment and development of

ericaceous shrub species (e.g., Lindh and Muir, 2004), and enhanced biological diversity

(e.g., Verschuyl et al., 2011). Conversely, however, density management can result in

negative outcomes if regimes have not been optimally designed for a given management

Development and Utility of an Ecological-based Decision-Support System … 117

objective. Thinning treatments which remove too many trees resulting in large inter-tree

distances can promote the development of large branches and resultant knots thus lowering

lumber grades during the manufacturing stage (e.g., Zhang et al., 2005), extend the period of

juvenile wood production resulting in lower specific gravity and associated reductions in end-

product quality and value (e.g., Tong et al., 2009), and (or) reduce merchantable volume

productivity due to prolonged periods of insufficient site occupancy (e.g., Fleming et al.,

2005). Therefore, in order to attain the maximum benefits of density management treatments,

minimize exposure to the serious negative reunifications of incorrect prescriptions, and

provide an objective and transparent framework for justifying treatment decisions, decision-

support tools are required.

The stand density management diagram (SDMD) is a proven density management

decision-support tool which has been utilized by resource managers throughout many of the

world‘s forest regions. For example, SDMDs have been developed and utilized in managing

Japanese red pine (Pinus densiflora Siebold and Zucc.) plantations in Japan and South Korea

(Ando (1962, 1968) and Kim et al. (1987), respectively), Monterey pine (Pinus radiata D.

Don.) plantations in New Zealand and Spain (Drew and Flewelling (1977) and Castedo-

Dorado et al. (2009), respectively), Douglas fir (Pseudotsuga menziesii (Mirb.) Franco.)

plantations in the Pacific Northwest (Drew and Flewelling (1979) and Long et al. (1988)) and

Spain (López-Sánchez and Rodríguez-Soallerio, 2009), lodgepole pine (Pinus contorta var.

latifolia Engelm.) stands in the western USA (Flewelling and Drew (1985), McCarter and

Long (1986), and Smith and Long (1987)), black spruce plantations in central Canada

(Newton and Weetman, 1994), loblolly pine (Pinus taeda L.) plantations in the southern USA

(Dean and Baldwin, 1993), Scots pine (Pinus sylvestris L.) and Austrian black pine (Pinus

nigra Arn.) plantations in eastern Europe (Stankova and Shibuya, 2007), and Merkus pine

(Pinus merkusii Jungh. et de Vriese) plantations in Indonesia (Heriansyah et al., 2009). These

ecological-based decision-support tools are built upon (1) quantitative functional relationships

derived from applied ecology, plant population biology and forest production theory which

include the reciprocal equations of the competition–density and yield–density effect (Kira,

1953; Shinozaki and Kira, 1956), self-thinning rule (Yoda et al., 1963), and site occupancy-

production relationships (Drew and Flewelling, 1979), and (2) empirical allometric

relationships which include size–density relationships for describing the effect of population

density-stress on tree dimensions such as quadratic mean diameter, mean volume, and mean

live crown ratio (e.g., Drew and Flewelling, 1977)). These relationships represent the

cumulative effect of density-dependent resource competition processes on productivity,

allometry and survivorship patterns at both the individual and population levels.

Historically, the analytical development of SDMDs has been characterized by a sequence

of continuous incremental advancements in which increasingly complex and innovative

model variants have been proposed. The first model forms, static SDMDs, where initially

developed in Japan by Ando (1962) and later introduced into North America by Drew and

Flewelling (1977, 1979). However, the lack of mortality submodels to describe stand

dynamics during the self-thinning stage limited their use in density management decision-

making. In response, dynamic SDMDs in which an embedded mortality submodel was

explicitly incorporated within the SDMD model structure, were proposed in the mid 1990s

(e.g., Newton and Weetman 1993, 1994). Later, acknowledging the paradigm shift in

management focus from volumetric yield maximization to end-product recovery and value

118 Peter F. Newton

maximization (e.g., Barbour and Kellogg, 1990; Emmett 2006), and realizing the limitations

of both the static and dynamic variants in terms of addressing these new objectives, the

structural SDMD was introduced (Newton et al., 2004, 2005). Specifically, the structural

model incorporated a parameter prediction equation system for recovering diameter

distributions within the dynamic SDMD model structure and hence enabled the estimation of

size-dependent end-product and value attributes.

The most recent iteration of the SDMD modeling framework is represented by the

integrated modular-based structural stand density management model (SSDMM) developed

for natural and managed jack pine (Pinus banksiana Lamb.) stand-types (Newton, 2009). The

rationale for developing this model was to provide resource managers with a comprehensive

density management decision-support tool that could address volumetric, end-product,

economic and ecological objectives, simultaneously. While this modeling platform has been

successfully applied to monospecific stand-types, the mixed stand analogue has yet to be

developed. Consequently, the first objective of this study was to develop a modular-based

SSDMM and associated algorithmic analogue for natural (naturally regenerated stands

without a history of density regulation) black spruce (Picea mariana (Mill) BSP.) and jack

pine mixed stands. The second objective was to demonstrate the utility of the resultant model

by contrasting operationally plausible density control regimes using a broad array of

productivity, economic and ecological performance metrics (e.g., volumetric yield outcomes,

log-product distributions, biomass production and carbon yields, recoverable products and

associated values, economic efficiency, duration of optimal site occupancy, structural

stability, ﬁbre attributes, and operability status). Refer to Newton (2010) for a general

overview of SDMDs in terms of their history, modeling approach, foundation studies, and

current modeling activities, and to Drew and Flewelling (1979), Newton and Weetman (1993)

and Newton et al. (2004) for specific details regarding the quantitative foundation of the

static, dynamic and structural model variants, respectively.

2. METHOD

The hierarchical designed SSDMM consisted of six sequentially-linked estimation

modules which were denoted according to the following nomenclature: Module A - Dynamic

SDMD; Module B - Diameter and Height Recovery; Module C - Taper Analysis and Log

Estimation; Module D - Biomass and Carbon Estimation; Module E - Product and Value

Estimation; and Module F - Fibre Attribute Estimation Module. Analytically, Module A

involved the development of a dynamic SDMD via the parameterization and integration of a

set of static and dynamic yield–density relationships. Module B consisted of the development

of a Weibull-based parameter prediction equation system and an associated composite height-

diameter prediction equation for recovering diameter and height distributions. Module C was

developed through the employment of species-specific dimensional compatible taper

equations derived from the literature which were used to predict log products (number of

pulplogs and sawlogs) and stem volumes. Module D utilized species-specific allometric-

based composite biomass equations derived from both the literature (jack pine) and density

control experimental data (black spruce) to predict oven-dried masses and associated carbon

equivalents for all four above-ground components, bark, stem, branch and foliage. Module E

Development and Utility of an Ecological-based Decision-Support System … 119

employed species and sawmill (stud and randomized length mill) specific end-product and

value equations derived from the literature to predict the volume and monetary worth of the

manufactured end-products (wood chips and dimensional lumber). Module F involved the

development of composite equations for estimating wood density and mean maximum branch

diameter. An algorithmic analogue of the resultant modular-based SSDMM was also

developed and its utility exemplified by simultaneously contrasting a set of complex density

management regimes in terms of productivity metrics, log-product distributions, biomass pro-

duction and carbon yields, quantity and quality of recoverable end-products, economic

efficiency, duration of optimal site occupancy, and structural stability.

In presenting the methods, it should be noted that in cases where the required

relationships were previously developed in a concurrent investigation (i.e., parameter

prediction equation system, asymptotic size–density relationship, and the composite height-

diameter function) or reported in the literature (e.g., taper, end-product and value functions),

only an abridged version of the pertinent methods and results are included. In other cases

where the required relationships could not be derived from the core calibration data set

(described below) nor from the literature, supplemental data sets were acquired and analyzed

from which the required functions were developed (e.g., data from Nelder plots were used to

develop mean live crown ratio and mean maximum branch diameter prediction functions, and

data from other types of density control experiments were used to parameterized the biomass

and wood density prediction functions). Although similarities exist in regards to the

monospecific model presented by Newton (2009) for jack pine stand-types, the mixed model

variant presented in this study expands, modifies and extends the modeling platform through

the introduction of species invariant relationships for bivariate mixtures, a response delay

function for accounting for post-thinning effects on stand dynamics, and new performance

metrics. In order to facilitate replication and application to other species, the principal

analytical methods, model structure, and the computational sequence utilized, are provided in

their entirety.

Stands belonging to the natural even-aged black spruce and jack pine mixed stand-type,

denoted PImPNb(N), were defined as those which had the following attributes (Table 1): (1)

comprised principally of black spruce and jack pine in which the (i) density percentage had to

constitute a minimum of 90% and 10% on a collective and individual species basis,

respectively, for stands at the establishment stage of development, or alternatively, (ii) basal

area percentage had to constitute a minimum of 90% and 10% on a collective and individual

species basis, respectively, for stands past the establishment stage of development; (2)

situated on mineral soils and regenerated naturally following a stand-replacing disturbance

(e.g., wildfire or forest harvesting); and (3) a silvicultural history absent of artificial

regeneration, PCT or CT treatments.

The calibration data for Modules A and B were derived from measurements obtained

from temporary and permanent sample plots (denoted TSPs and PSPs, respectively) located

throughout the central region of the Canadian Boreal Forest Region. In total, 382 tree-list

measurements derived from 155 sample plots were utilized. Geographically, these plots were

largely concentrated within Forest Sections B-4, B-7, B-8, B-9, B-10, B-11 and B-14 (Rowe,

120 Peter F. Newton

1972) which fall within the northeastern, northcentral and northwestern administrative

regions of the Province of Ontario. Historically, the plots were initially established by various

forest-based industrial corporations and government agencies during the 1930-1990 period

and were distributed across the landscape using a stratified pseudo-random sampling design

(n., strata were based on the age-class structure and site quality variation within a given

region or tenured landbase). The plots were circular, square or rectangular in shape with a

mean overall area of 0.082 ha (standard deviation (SD) = 0.021 ha; minimum/maximum =

0.040/0.120 ha) and density of 189 trees/plot (SD = 104 trees/plot; minimum/maximum =

42/926 trees/plot). For the purposes of this study, the plots were also differentiated based their

utility in describing temporal change (stand dynamics): static plots were those that were only

measured once whereas dynamic plots were those that were measured more than once and

hence capable of providing change estimates in terms of surviver growth, ingress, ingrowth

and mortality. Table 1 summarizes the plot measurements according to the source

organization, series and type (static or dynamic) along with the number and frequency of

measurements obtained.

For each plot, its geographic location, disturbance history and the measurement

techniques utilized, were known. Generally, the measurements on each plot included species-

specific tree-lists consisting of diameter measurements at breast-height (1.37 m or 1.3 m) -

outside bark (D; ±0.25 cm) for all biotic trees greater than 2.54 cm in D, and D and total

height (H; ±0.30 m) measurements on a subset of approximately 10 black spruce and jack

pine sample trees, usually selected from across a plot‘s diameter range.

Combining the individual tree values (D and H measurements or estimates derived from

species-speciﬁc allometric-based height-diameter functions) with regional volume equations

and the plot area information, the following stand-level variables were calculated: (1) mean

dominant height (Hd; m), deﬁned as the mean height of the trees within the largest height

quintile; (2) quadratic mean diameter (Dq; cm); (3) basal area (G; m2/ha); (4) total volume (Vt

(m3/ha), computed as the sum of individual tree total volumes (vT; m3/tree) as determined

from the D and H values inputted into regional-wide standardized volume equations (Honer et

al., 1983); (5) merchantable volume (Vm (m3/ha), computed as the sum of the individual tree

merchantable volumes (vM; m3/tree) for all trees greater than 9 cm in D as determined from

the D and H values, vT estimate and speciﬁed merchantability limits (i.e., 0.15 m stump-

height and a 7.62 cm top diameter (inside-bark); Honer et al., 1983); (6) total density (N

(stems/ha)); and (7) relative density index (Pr (%/100) as defined as the ratio of N to the

maximum N attainable in a stand with the same mean volume (Drew and Flewelling, 1979;

Newton and Weetman, 1993; Newton, 2006a). The mensurational characteristics of the

datasets are summarized in Table 2.

Table 1. Defining attributes of the natural black spruce and jack pine mixed

stand-type and plot data sources, types and their measurement frequency

Stand-type Principal Defining Attributes Plot Series and Number of Plots by Measurement Type Measurement Sequence and Number

Denotation

Seriesa Typeb # of Consecutive Total

# of Plots

Measurements #

Static Dynamic

PImPNb(N) Even-aged black spruce and jack pine mixed Kimberly Clark (PSPs) 20 1 102 382

stands situated on mineral soils which regenerated

American-Can (PSPs) 33 2 1

naturally following a stand-replacing disturbance

(e.g., wildfire or forest harvesting) with no prior Boreal-Growth

66 3 2

history of artificial regeneration or density (OMNR/TSPs)

management treatments (e.g., precommercial or PGP (TSPs) 36 4 9

commercial thinning). Black spruce and jack pine 5 17

collectively constituted >90% of the total density

6 19

at the time of establishment, or >90% of the basal

area of established stands, with each species 7 3

constituting a minimum of 10% of either measure. 8 2

Similar to the JP2 working group analog (Watt et

al., 2001).

a - Plot series denoted according to Ontario-centric nomenclature where the host organization responsible for initial plot establishment is

acknowledged: corporation or governmental agency where OMNR refers to the Ontario Ministry of Natural Resources. Note, TSPs and PSPs

denote temporary and permanent sample plots, respectively.

b - Dynamic plots were those for which a remeasurement was obtained whereas static plots were those for which only a single measurement was

obtained.

122 Peter F. Newton

As described in detail below, the development of the dynamic SDMD consisted of the

parameterization of the following relationships: self-thinning line and the derived relative

density index function; yield–density relationships and the associated isolines for quadratic

mean diameter, mean dominant height and mean live crown ratio; mean volume–density

relationships at the time of initial crown closure and those delineating the zone of maximum

production; and net density change function for predicting post-crown-closure size–density

trajectories. Subsequent integration of these relationships within the traditional modeling

framework resulted in the dynamic SDMD for mixed stands.

For stands incurring density-dependent mortality, the asymptotic logarithmic relationship

between mean volume per stem ( v ; dm3) and density per unit area (N; stems/ha), commonly

referred to as the self-thinning line (Yoda et al., 1963), was quantified using Eq. (1).

where 0 and 1 are intercept and slope (self-thinning) coefficients, respectively, and is

an error term. The parameter estimates for self-thinning mixed stands, as previously reported

by Newton (2006a), were used in this study (Table 3). The function for calculating relative

density index (Pr; Drew and Flewelling, 1979), defined as the ratio of a stand‘s observed

density ( N o ) to that of the maximum density (Nmax) attainable in a stand with the same mean

volume vo , was derived from the self-thinning rule (Eq. (2); Table 3).

1

vo 1

Pr N o 100 (2)

Thus solving Eq. (2) for log10 v yielded the isoline function for a given Pr value (Eq.

(3)).

100

log10 v log10 1 1 log10 N (3)

Pr

Table 2. Mensurational characteristics of the sample trees and stands

utilized to develop the modular-based SSDMM for mixed stands

(np; ns; nt) (units) Deviation

PImPNb(N) A (yr) 100 26 33 170

(382; 362; Hd (m)

18.78 2.80 7.86 23.78

1290)

Dq (cm) 14.78 3.49 5.80 25.00

G (m2/ha) 35.16 7.94 3.24 52.82

v (dm3) 145.54 81.22 9.22 463.32

Vt (m3/ha) 270.60 71.84 11.29 428.52

Vm (m3/ha) 198.79 72.19 0.00 369.78

N (stems/ha) 2387 1281 543 8342

Pr (%) 83.38 21.00 4.12 126.92

SI (m) 14.84 2.18 9.75 25.44

Dmin (cm) 3.24 1.62 1.30 9.90

â 1.91 1.19 0.09 6.203

b̂ 13.16 4.00 3.39 23.38

ĉ 2.57 0.80 1.00 4.44

D (cm) 17.18 6.09 2.50 35.30

H (m) 15.73 4.43 2.45 25.60

a - As defined in Table 1; np denotes the number of plot measurements utilized to established the relationships used in the dynamic SDMD; ns denotes

the number of plot measurements associated with the development of the diameter distribution parameter prediction equation system (Newton and

Amponsah, 2005); and nt denotes the number of individual diameter at breast-height (D) and height (H) measurement pairs used to develop the

composite H-D relationship (Newton and Amponsah, 2007).

b - A, Hd, Dq, G, v , Vt, Vm, N, Pr, SI and Dmin denote the following stand-level variables: mean stand-age, mean dominant height, quadratic mean

diameter, basal area, mean volume, total volume, merchantable volume, total density, relative density index, mean site index value, and minimum

diameter observed within the empirical diameter frequency distributions, respectively. â , b̂ and ĉ denote maximum likelihood estimates of the

location, scale and shape parameters, respectively, of the 3-parameter Weibull probability density function. Note, site index was calculated as the

mean of the species-specific values using the functions developed by Carmean et al. (2001, 2006).

124 Peter F. Newton

for Dq, Hd and Live Crown Ratio

The yield-density relationships and associated isolines for quadratic mean diameter and

mean dominant height where developed using the model specifications and parameterization

techniques described by Newton and Weetman (1993). Firstly, the relationship between Dq

and v and N was quantified using Eq. (4).

analysis, and is an error term. The resultant relationship was evaluated on the basis of its

statistical significance, proportion of variation explained, and compliance with the principal

regression assumptions underlying OLS. Residual graphical analysis and associated statistical

indices were used to identify and remove outliers and inﬂuential observations. Specifically,

studentized deleted residuals and Cook‘s distance were used to detect outliers and influential

observations, respectively, where the probability level for exclusion was set at 0.01 for both

measures (Neter et al., 1990). The regression results suggested that fitted function described

the relationship well in that it was significant (p ≤ 0.05), explained a large proportion of

variation as determined from the multiple coefficient of determination (R2), and did not

violate the constant error variance, correct model specification and normality assumptions as

inferred from residual analyses (i.e., graphical examination of raw and studentized residual

plots, and normal probability plots). Table 3 lists the resultant parameter estimates and

associated regression statistics for Eq. (4).

The Dq isoline function which defines the relationship between log10 v and

log10 N for a given Dq value (Eq. (5)) was derived by solving Eq. (4) for log10 v .

log10 Dq 0 2 log10 N

log10 v (5)

1

Table 3. Parameter estimates and associated statistics for the regression relationships developed in Module A (Dynamic SDMD)

Symbol Value

Asymptotic ̂ 6.145 (1) Non-parametric bias-adjusted bootstrap parameter estimates obtained via bisector ordinary least squares

0

log10 v log10 N (OLS) regression analysis (Isobe et al., 1990).

̂1 -1.181

(Eq. (1)) (2) Bias-corrected 95% percentile confidence intervals (Meyer et al., 1986): 5.908 ̂ 0 6.353 and -

1.242 ̂1 -1.111.

(3) Regression statistics: degrees of freedom for regression (nreg) and residual error (nres) = 1, 31, respectively;

and product-moment correlation coefficient (r) = -0.993.

Pr N o / vo / 106.145 .

0.805

(4) Derived relative density index (Pr (%/100)) equation (Eq. (2)):

(5) Source: Newton (2006b).

Quadratic mean diameter = (1) Parameter estimates obtained from OLS regression analysis.

̂0 0.5155

f(mean volume and density) (2) The intercept parameter estimate includes a correction factor for the bias introduced via the logarithmic

(Eq. (4)) ˆ1 0.3674 transformation (Baskerville, 1972; Sprugel, 1983).

(3) Regression statistics: nreg = 2; nres = 358; multiple coefficient of determination (R2) = 0.981; standard error of

̂ 2 -0.0377 the estimate (SEE; log10(cm)) = 0.0147; and F-ratio = 9430* where * denotes a significant (p 0.05)

relationship.

Mean volume = f(mean ̂ 0 -1.3715 (1) Parameter estimates obtained from OLS regression analysis.

dominant height and (2) The intercept parameter includes a correction factor as described above.

quadratic mean diameter) ̂1 0.8576 (3) Regression statistics: nreg = 2; nres = 356; R2 = 0.995; SEE (log10(dm3)) =

(Eq. (6)) 0.0183; and F-ratio = 38547*.

̂ 2 2.0495

Mean live crown ratio =

ˆ0

3.4027 (1) Parameter estimates obtained from OLS regression analysis.

f(mean volume and density) (2) The intercept parameter includes a correction factor as described above.

(Eq. (8)) ˆ1 -0.3684 (3) Regression statistics: nreg = 2; nres = 1960; R2 = 0.545; SEE (log10(%)) = 0.1139; and F-ratio = 1170*.

ˆ0 7.5197 (1) Parameter estimates obtained from OLS regression analysis.

at crown closure (Eq. (9)) (2) The intercept parameter includes a correction factor as described above.

ˆ

1

-2.0724 (3) Regression statistics: nreg = 1; nres = 18; R2 = 0.999; SEE (log10(dm3) = 0.0113; and F-ratio = 33402*.

Net density change model ̂ 0 -0.1010 (1) Parameter estimates obtained from nonlinear regression analysis.

(Eq. (10)) (2) Regression statistics: nreg = 3; nres = 215; SEE (log10(stems/ha)) = 18.28; and F-ratio = 1164004*.

̂1 0.2756

̂ 2 -0.3055

̂ 3 -0.3716

126 Peter F. Newton

The Hd isoline function which defines the relationship between log10 v and

log10 N for a given Hd value (Eq. (7)) was derived by expressing v as function of Hd and

Dq using Eq. (6), substituting Eq. (4) into Eq. (6), and then solving for log10 v .

0 2 0 1 log10 ( H d ) 2 2 log10 ( N )

log10 (v ) (7)

1 2 1

term. Employing the same outlier and influential observation detection procedures and

statistical evaluation protocol as that described for Eq. (4) to Eq. (6), indicated that the fitted

relationship was significant (p ≤ 0.05), explained a large proportion of the variation, and was in

general compliance with the constant error variance, correct model specification and normality

assumptions. Table 3 lists the resultant parameter estimates and associated regression

statistics for Eq. (6).

Live crown ratio (Lr) is defined as the length of the live crown divided by total stem

height and is expressed as a percentage. The Lr isoline within the context of the SDMD

describes the relationship between log10 v and log10 N for a given Lr value. In this

study, the isoline was derived by expressing Lr as a function of v and N using Eq. (8), and

then solving the resultant equation for log10 v , as describe below.

term. The calibration data set used to parameterize Eq. (8) consisted of 1960 Lr, v and N

measurements obtained from thirty 40 year-old Nelder plots which were established within

the northeast region of the Province of Ontario. Briefly, these plots were established in the

late 1960‘s using the 1a configuration design as defined by Nelder (1962). Specifically, each

plot consisted of 24 concentric arcs transected by 60 equally-spaced radii or spokes, the radii

were 47 m in length and randomly clustered into twelve 5 radii sectors consisting of jack

pine, black spruce or white spruce (Picea glauca Moench), and 24 trees were planted at

geometrically increasing intertree distances along each spoke initiating at a 0.5 m and

terminating at a 4.32 m intertree radial distance (nominal density equivalents for these

spacings were 42698 stems/ha and 429 trees/ha, respectively). Employing these Lr, v and N

observations in combination with the same regression procedures as that previously described

for Eq. (4), OLS parameter estimates were obtained. Regression results indicated that the

equation describe the relationship moderately well given that the relationship was signiﬁcant

(p ≤ 0.05), explained a moderate proportion of the variation, and was in general compliance

with the constant error variance, correct model specification and normality assumptions. The

Development and Utility of an Ecological-based Decision-Support System … 127

actual parameter estimates and associated regression statistics for Eq. (8) are listed in Table 3.

In terms of deriving the isolines for Lr values of 35, 40, 50, 60, 70 and 80%, Eq. (8) was

rearranged with respect to log10 v log10 v log10 Lr 0 2 log10 N 1

and log10 v calculated across the density range, for the specified Lr value.

In order to generate v N values at the time of initial crown closure, species-specific

allometric equations for the relationship between crown width (Cw; m) and D, and between H

and D, for open grown trees, were used in combination with total stem volume equations, and

spatial pattern and crown cover assumptions. Linear regression analysis was then used to

establish relationships between the v and N values, thereby quantifying the size-density

condition at the time of initial crown closure.

More specificially, Cw, H and vT values were estimated across the range of Dq values

observed within the core dataset (Table 2). For black spruce, Cw and H for a given D were

calculated employing the allometric Cw-D and H-D equations developed by Newton and

Weetman (1993) for open grown trees situated on mineral sites throughout central insular

Newfoundland (Cw = 0.870D0.513 and H = 0.974D0.769, respectively). Given the resultant H

estimate, vT for a given D was estimated employing the total volume equation developed by

Honer et al. (1983). Similarly, for jack pine, Cw for a given D was estimated employing the

allometric Cw-D equations developed by Bella (1967; Cw = 0.844+0.208D), Vezina (1963; Cw

= 0.536+0.245D) and Newton (this study; Cw = 1.166D0.535 ) for open grown trees situated on

mineral sites in Manitoba and Quebec. A regional-invariant value for Cw was calculated as the

arithmetic mean of the 3 separate Cw estimates. H for a given D was estimated employing the

H-D allometric equation developed by Newton (this study; H=1.856D0.395) for open grown

trees situated on mineral sites in Manitoba. Given the resultant H estimate, vT for a given D

was estimated employing Honer‘s (et al., 1983) total volume equation. Note, (1) Newton‘s

Cw-D and H-D allometric equations for jack pine as described above were developed from

851 tree measurements obtained in 1973 from the 2.4 m and 3.0 m spacing treatments within

the Moodie spacing trial (Bella and de Franceschi, 1974); (2) all parameter estimates were

obtained via OLS regression analysis on logarithmically transformed data; and (3) resultant

regression statistics and residual analyses indicated the resultant equations adequately

described the Cw-D and H-D relationships (i.e., coefficients of determination (r2) = 0.653 (Cw-

D) and 0.847 (H-D); standard errors of the estimate (SEE (loge(m)) = 0.182 (Cw-D) and 0.080

(H-D) and significant (p ≤ 0.05) F-ratios = 1588.57 (Cw-D) and 4723.5 (H-D)). Thus given a

mean Cw estimate for a fixed D, unadjusted density estimates (N’ (stems/ha)) corresponding

to complete crown closure (contiguous crown cover of 10000 m2 of projected crown area per

ha) were estimated, based on expected mean interplant distance – density relationship for

randomly dispersed spatial patterns (Table 1 in De vos (1973)): N’ = 10000(1.0937/Cw)2

where Cw was used as a surrogate for the mean interplant distance between 4 nearest

neighbours within a randomly dispersed population. Acknowledging that complete crown

closure will not be attainable under the assumption that crown bases are circular is shape (i.e.,

circular crowns can only occupy a maximum 78.54% of the available area (Smith, 1989)), the

unadjusted density estimates were reduced by 21.46% (N = 0.7854N’). Employing these

computations and using vT as a surrogate for v , this sequence of computations resulted in a

128 Peter F. Newton

data set consisting of multiple v N data pairs for the initial crown closure condition. These

data pairs were then used to parameterized Eq. (9).

where i , 0,1 are parameters estimated employing OLS regression analysis, and is an

error term. Employing the same detection procedures and evaluation protocol as that specified

for Eq. (4), regression results suggested that relationship was adequate in describing the size-

density condition at the time of initial crown closure (i.e., the relationship was significant (p ≤

0.05), explained a moderate proportion of the variation, and was in compliance with the constant

error variance, correct model specification and normality assumptions). Table 3 lists the

parameter estimates and associated regression statistics for Eq. (9).

Net production within stands of a given species, site quality and stage of stand

development will increase with increasing site occupancy until a maximum level is reached,

according to the forest production theories espoused by Langsaeter (1941), Mar:Möller

(1954) and Assmann (1970). The generality of these hypotheses can be used by forest

managers to define the site occupancy or stocking levels at which forest productivity is

maximized. Based on output from hybrid biomass/carbon production model for upland black

spruce stands (Newton, 2006b), suggest that this productivity asymptote is achieved when

relative density indices are between 0.32 and 0.45. However, similar results for monospecific

jack pine stands or for black spruce and jack pine mixed stands have yet to be reported.

Consequently this necessitated the employment of the 0.32-0.45 relative density range as an

approximation to the optimal density management window for the mixed stand condition.

Given that both species share similarities in terms of allometric and scaling relationships,

competition processes and density-dependent mortality patterns, this approximation was

tentatively accepted.

A modified version of Khil‘mi‘s (1957) survival model was used to describe the temporal

pattern of net density change (survivor density – mortality density + ingress density) within

mixed stands. Specifically, assuming that the temporal change in stand density is dependent

on absolute density, intensity of competition, stage of stand development and site quality,

Khil‘mi‘s model was modified accordingly: i.e., embedding surrogate measures of these

factors, current density, Pr, stand age (A) and site index (SI), respectively, directly within the

functional form (Eq. (10)).

1 2 3

EXP 0 Pr A S I

Nt

Nt 1 N m (t ) (10)

N

min(t )

Development and Utility of an Ecological-based Decision-Support System … 129

where Nt+1 is the density at time t+1 (t = 1,…, T-1; T = rotation age), Nt is the density at time

t, N min(t ) is the minimum asymptotic density at which density-dependent processes initiate as

log10 ( v )0 1

defined as the density at the time of crown closure ( Nmin(t ) 10 as derived from

Eq. (9)), i , i 0,...,3 are model parameters, and is an error term. Computationally, mean

annual net density change estimates were derived from the dynamic sample plots as follows.

Initial and final densities for each successive plot measurement that had attained crown

closure status were calculated from which the mean annual net density change estimate was

derived: ΔN = (N2-N1)/(A2-A1) where ΔN is in units of stems/ha/yr, and N2 and N1 are the

densities (stems/ha) at stand ages A2 and A1, respectively. These change estimates (Nt (i.e., N1)

and Nt+1 (Nt + ΔN)) along with the corresponding Pr, A and SI values were used in

combination with nonlinear regression analysis to parameterize Eq. (10). Using the same

evaluation protocol as that described for Eq. (4), the regression results suggested that the

relationship was significant (p ≤ 0.05) and was in compliance with the constant error variance,

correct model specification and normality assumptions. Table 3 lists the resultant parameter

estimates and associated regression statistics for Eq. (10).

Superimposing the parameterized form of the asymptotic size-density relationship,

isolines for Hd, Dq, Pr and Lr, size-density condition at the time of initial crown closure,

lower and upper Pr isolines delineating the optimal density management window, and site-

specific size-density trajectories, on a logarithmic v N bivariate graph, yielded the

graphical version of the dynamic SDMD for black spruce and jack pine mixtures (n.,

presented later in Figure 3). As described below, this dynamic SDMD represents the core

prediction system within the modular-based SSDMM, in that, its output is used as input in all

the remaining modules.

Prediction Equations (Module B)

At each annual step of stand development, the grouped-diameter frequency distribution

was recovered from the stand-level variables generated from the dynamic SDMD employing

a parameter prediction equation (PPE) system. Conceptually, this technique is similar to the

parameter prediction method that is used to develop stand-level diameter distribution yield

models, in that, parameters of a specified probability density function (PDF) characterizing

the diameter frequency distribution are predicted from a set of stand-level variables (sensu

Hyink and Moser, 1983). Briefly, the method used to developed the PPE system consisted of

first modeling the diameter distribution within each of the PSPs and TSPs using the 3-

parameter Weibull PDF (Eq. (11); Weibull, 1951) and obtaining the resultant maximum

likelihood estimates (MLEs) for the location, scale and shape parameter (number of plot

measurements utilized = 362; Table 2).

130 Peter F. Newton

c D a c 1 D a c

exp if a D

f ( D; a, b, c) b b b (11)

0 if D < a

where a is the location parameter and is less than or equal to the minimum D value (Dmin), b

is the scale parameter which reflects the range of the distribution, and c is the shape parameter

which reflects the degree of skewness within the D distribution. These parameter estimates

were then expressed as direct or indirect functions of a set of stand-level variables, as shown

in Eqs. (12-15), using multiple regression analysis and cumulative density function regression

(CDFR; Cao, 2004) analysis.

+ 4 v or log e v 5 Vt or log e Vt +6 N or log e N (13)

7 Pr or log e Pr

+4 v or log e v 5 Vt or log e Vt +6 N or log e N (14)

7 Pr or log e Pr

+ 4 v or log e v +5 Vt or log e Vt + 6 N or log e N (15)

7 Pr or log e Pr

specific error term. Table 4 lists the resultant parameter estimates and associated regression

statistics for the CDFR-based PPE system. The actual grouped-diameter frequency

distribution for a specified set of stand-level variables is estimated using the cumulative

distribution function (CDF) analogue of Eq. (11), as shown in Eq. (16).

D a c

F ( D; a, b, c) 1 exp

b

(16)

Table 4. Parameter estimates and associated statistics for the regression relationships used in Module B (Diameter and Height

Recovery): parameter prediction equation (PPE) system and the composite height-diameter function

Symbol Value

Weibull-based ˆ0 20.9051 (1) Parameter estimates obtained employing OLS regression analysis where the independent variables

PPE ̂1 0.1547 were selected employing an all-possible best-subset regression procedure using the Cp (Mallows, 1973)

system: Dmin criterion; values in parenthesis are associated with logarithmically transformed independent variables.

ˆ2 -0.4202 (2) Regression statistics: nreg = 5, nres = 356, R2 = 0.336, SEE = 1.329, F-ratio = 30* and CP statistic =

(Eq. (13)) ˆ3 0.3728 6.15.

ˆ4 0.0170 (3) Source: Newton and Amponsah (2005).

ˆ5 -

ˆ6 (-2.5931)

ˆ7 -12.1053

Weibull-based ˆ0 -10.2463 (1) Parameter estimates obtained employing CDFR (Cao, 2004) where values in parenthesis are

PPE systems: ˆ1 (1.4935) associated with logarithmically transformed independent variables.

b̂ (2) Regression statistics calculated from the observed and predicted values and hence are approximations:

ˆ2 0.9551 nreg = 7, nres = 354, R2 = 0.779, SEE = 1.896, and F-ratio = 178.4*.

(Eq. (14)) ˆ3 (-0.7256) (3) Source: Newton and Amponsah (2005).

ˆ4 0.0021

ˆ5 0.0269

ˆ6 (0.9719)

ˆ7 -8.2411

Weibull-based ˆ0 - (1) Parameter estimates obtained employing CDFR (Cao, 2004) where values in parenthesis are

PPE system: ĉ ̂1 (-1.0673) associated with logarithmically transformed independent variables.

(Eq. (15)) (2) Regression statistics calculated from the observed and predicted values and hence are approximations:

ˆ 2 0.2005

nreg = 7, nres = 354, R2 = 0.578, SEE = 0.525, and F-ratio = 81*.

ˆ3 0.0589 (3) Source: Newton and Amponsah (2005).

ˆ 4 -0.0060

ˆ5 0.0666

ˆ6 (0.3549)

ˆ7 -22.8471

Table 4. (Continued).

Symbol Value

Height – ̂0 11.0470 (1) Parameter estimates obtained from OLS regression analysis where the independent variables were

diameter model selected employing an all-possible best-subset regression procedure using the Cp (Mallows, 1973)

(Eq. (17)) ̂1 0.5677 criterion.

̂2 -0.2329 (2) The intercept parameter estimate includes a correction factor for the bias introduced via the

logarithmic transformation (Baskerville,1972; Sprugel, 1983).

̂3

(3) Regression statistics: nreg = 5, nres = 1272, R2 = 0.872, SEE (loge(m)) = 0.1163, F-ratio = 1737*, and

0.0111 CP statistic = 5.48.

(4) Source: Newton and Amponsah (2007).

̂4 -

̂5 1.0711

̂6 -

̂7 -0.3878

a - Cp denotes Mallows‘ (1973) Cp statistic; all other denotations are as defined in Table 3.

Development and Utility of an Ecological-based Decision-Support System … 133

The composite regression function previously developed for black spruce and jack pine

mixtures by Newton and Amponsah (2007), was used to describe the relationship between H

and D. Briefly, in this companion study, a calibration dataset consisting of 1290 H-D pairs

and associated stand-level variables derived from 88 sample plots, were used to parameterize

5 nonlinear H-D models. The most applicable form, based on a comprehensive set of

evaluation criteria (e.g., goodness-of-fit measures, lack-of-fit indices, and predictive ability),

was selected. Specifically, a multivariate allometric-based composite model with the

inclusion of stand-level predictor variables reflecting both density-stress and stage of

development (Pr and Hd, respectively) performed the best (Eq. (17)), and hence was utilized.

where l (i ) , l 0,...,7 are parameters, and ε is an error term. The resultant parameter

estimates and associated regression statistics are given in Table 4.

Due to data limitation which prevented the development of a taper equation for the

natural mixed stand-type, composite variable exponent taper equations developed previously

for monospecific black spruce (Sharma and Parton, 2009) and jack pine (Newton, 2009)

stands, were utilized (Eq. (18a) and (18b), respectively).

2

h h G

1 2 3 4 2

h H H D H h

d D 0 (18a)

1.3 H 1.3

h G

1 2 4 2

h H D H h

d D 0

1.3 (18b)

H 1.3

where d is the inside-bark diameter (cm) at height h (m), i , i = 0,...,4 are model

parameters, and ε is an equation-specific error term. These equations arose from a concurrent

study in which the objective was to develop dimensional compatable taper equations for a

suite of boreal species (e.g., Newton and Sharma, 2008; Sharma and Parton, 2009). Briefly,

the equations were parameterized using stem profile data obtained from percent-height

destructive stem analysis sampling procedures on 113 jack pine and 1189 black spruce trees.

The sample trees were selected using a size-based stratified random sampling protocol within

9 jack pine and 25 black spruce stands. The actual parameter estimates are given in Table 5.

134 Peter F. Newton

The lack of available biomass data for mixed stands negated the development of stand-

specific equations. Alternatively, however, composite biomass functions previously

developed for estimating bark (periderm) mass per tree (Mp; oven-dry g), stem mass per tree

(Ms; oven-dry g), branch mass per tree (Mb; oven-dry g) and foliage mass per tree (Mf; oven-

dry g) within monospecific black spruce (Newton, unpublished) and jack pine (Newton,

2009) stands, were employed. Briefly, the composite models were based on a multivariate

extension of the simple equation of allometry in which stand-level measures of relative

density stress (Pr) and stage of development (Hd) were explicitly incorporated (e.g., Jolliffe et

al., 1988; Newton, 2006b). The resultant equations predict the oven-dried mass of each

component per tree using D, H, Pr and Hd as predictor variables (Eq. (19)).

m(i ) 0(i ) D 2 H

1( i ) 2( i ) Pr 3( i ) H d 4( i ) Pr H d

Pr H d

5( i ) 6( i ) 7 ( i )

Pr Hd (i ) (19)

where m(i) is the mass of the ith biomass component, j (i ) , j 0,...,7 are parameters specific

to the ith component estimated via OLS regression analysis (all-possible best-subset

regression procedure employing Mallows (1973) Cp selection criterion) following a double-

logarithmic transformation, and ( i ) is the error term specific to the ith component. For black

spruce, the parameterization data set consisted of mp, ms, mb, mf, D, H, Pr and Hd data derived

from 161 destructively sampled black spruce trees located in 52 variable-sized (minimum of

100 trees/plot) area plots which were established within 18 monospecific even-aged stands

located throughout Forest Section B28b (Rowe, 1972)). The stands were selected according to

a stratified pseudo-random sampling approach in which an approximately equal number of

stands within each of 5 age classes (15, 30, 45, 60 and 75 year) were sampled. Similarly, for

jack pine, the parameterization procedure consisted of obtaining estimates via OLS regression

analysis using mp, ms, mb, mf, D, H, Pr and Hd data derived from 186 semi-mature jack pine

trees situated within 6 stands located in northern and northeastern Ontario. The sample trees

were selected for destructive sampling according to a size-based stratified random sampling

protocol. Table 6 lists the resultant component-specific parameter estimates and associated

regression statistics.

Table 5. Parameter estimates and associated statistics for the composite

variable-exponent taper equations used in Module C (Taper Analysis and Log Estimation)

̂0 ̂1 ̂2 ̂3 ̂4

Black Spruce Eq. (7) in Table 3 of Sharma and

0.9088 -0.0667 0.5410 -0.3636 0.0755

(Eq. (18a)) Parton (2009)

Jack Pine 0.1877 Eq. (18) in Table 5 of Newton (2009)

0.9292 -0.0534 0.4035 -

(Eq. (18b))

a – As reported in the source publication.

Table 6. Parameter estimates and associated statistics for the regression relationships

used in Module D (Biomass and Carbon Estimation): composite biomass equations by component (Eq. (19))

Comp. ̂ ' ̂1 ̂ 2 ̂ 3 ̂ 4 ̂ 5 ̂ 6 ̂ 7 nreg nres CP R2 SEE F-ratio

0

Black Bark 4.8 0.9524 - - - - - -0.1507 2 156 2.39 0.992 0.2261 4613*

Spruce Stem 14.2 0.9325 - - - 0.0006 - 0.2611 3 154 1.90 0.998 0.1265 11996*

Branch 4.1 1.2048 - -0.0127 - - - -0.5282 3 154 2.34 0.898 0.5409 454*

Foliage 16.6 0.9611 0.1522 - -0.0121 - - -0.6127 4 154 3.96 0.892 0.4964 318*

Jack Bark 17.1 0.5787 0.2083 0.0136 -0.0175 - - - 4 181 3.74 0.808 0.2425 191*

Pine Stem 66.0 1.0096 -0.1471 - - 0.6895 - - 3 182 4.12 0.930 0.1716 802*

Branch 330.3 - 1.1513 0.0570 -0.0503 - - -2.6615 4 181 3.95 0.863 0.3191 286*

Foliage 345.1 - 1.1635 0.0551 -0.0498 - - -2.8438 4 181 3.91 0.836 0.3448 231*

a - Component-specific parameter estimates obtained from OLS regression analysis where the independent variables were selected according to an all-

possible best-subset regression procedure employing Mallows‘ (1973) Cp criterion. Note, the intercept parameter estimates, denoted ̂0' , includes

a correction factor for the bias introduced via the logarithmic transformation (Baskerville, 1972; Sprugel, 1983), and Comp. denotes Component.

b - As defined in Table 3.

136 Peter F. Newton

in the literature, were utilized for mixed stands: Eq. (20a) for black spruce (Lui and Zhang,

2005; Zhang et al. 2006) and Eq. (20b) for jack pine (Newton, 2009).

1( i ) 2( i )

Y(i ) 0(i ) D H (i ) (20a)

Y(i ) 0(i ) D2 H

1( i ) 2( i ) Pr 3( i ) H d 4( i ) Pr H d

Pr H d

5( i ) 6( i ) 7( i )

Pr Hd (i ) (20b)

where Y(i) is either the (1) total lumber volume per tree (vl(s) (dm3)), total lumber value per tree

(pl(s) (CAN$(2002))), or total product value per tree (pt(s) (CAN$(2002))) recovered under a

stud sawmill processing protocol, or (2) total lumber volume per tree (vl(r) (dm3)), total lumber

value per tree (pl(r) (CAN$(2002))) or total product value per tree (pt(r) (CAN$(2002)))

recovered under a randomized length sawmill processing protocol, j (i ) , j 0,..., 7 and

(i ) are equation-specific parameters and error terms associated with the ith dependent

variable. These equations were parameterized employing simulation results derived using

virtual taper profiles from tree measurements obtain from sample plots distributed throughout

the central region of the Canadian Boreal Forest. Specifically, the Optitek sawing simulator

(Forintek Canada Corp. 1994) software, employing conventional stud sawmill and

randomized length sawmill processing protocols, was used to derive product volumes and

value estimates. The stud sawmill processing protocol consisted of bucking each virtual stem

of a given diameter, length, taper and wane into 2.44 m sections and then sawing each section

into dimensional lumber products according to an algorithm which maximized lumber value

recovery. The randomized length sawmill processing protocol consisted of optimally bucking

the virtual stem into sections of variable length (4.88 to 1.22 m by approximately 0.6 m

intervals) and then sawing each section into dimensional lumber products employing a sawing

algorithm which similarly maximized lumber value recovery. The resultant sawdust, chip and

lumber volumes in combination with market-based economic values for the calendar year

2002, were used to generate tree-level estimates of lumber value and total product value by

species and sawmill-type. Combining these estimates along with the stand-level variables,

simple (Eq. (20a)) and composite (Eq. (20b)) equations were developed by sawmill-type.

Table 7 lists the resultant component-specific parameter estimates, regression statistics and

predictive performance measures for each equation.

Table 7a. Parameter estimates and associated statistics for the regression relationships used in Module E

(Product and Value Estimation): sawmill-specific product recovery and value functions (Eq. (20a))

Variable ˆ0 ˆ1 ˆ 2 Calibration Data Set Validation Data Set Source

2 2

R RMSE MAE R RMSE MAE

Black vl(s) 0.0001 2.4594 1.6032 0.939 27.66 15.74 0.901 29.41 18.71 Model 4 in Table 4 as

Spruce pl(s) 0.0000 2.8846 1.6010 0.944 6.46 3.34 0.924 7.57 4.23 reported by Liu and

pt(s) 0.0004 2.5544 1.2134 0.975 4.59 2.58 0.949 4.65 2.84 Zhang (2005)

vl(r) 0.0014 2.4516 1.1957 0.914 13.43 8.44 0.897 15.87 10.11 Model 4 in Table 4 as

pl(r) 0.0002 2.7569 1.2085 0.919 7.04 4.11 0.887 9.03 7.01 reported by Zhang et

pt(r) 0.0007 2.4463 1.2020 0.960 5.69 3.24 0.950 4.89 3.21 al. (2006)

a - As derived from the source publications; note, RMSE and MAE denote root mean square error and mean absolute error, respectively, and are in

units of dm3/tree for variables vl(s) and vl(r) and CAN$(2002) for variables pl(s), pt(s), pl(r) and pt(r)

Table 7b. Parameter estimates and associated statistics for the regression relationships used in Module E (Product and Value

Estimation): composite sawmill-specific product recovery and value functions (Eq. (20b))

Var. ̂ ' ˆ1 ˆ 2 ˆ 3 ˆ 4 ˆ5 ˆ6 ˆ7 nreg nres CP R2 SEE F-ratio

0

Jack vl(s) 0.00054 1.2528 0.2017 - -0.0069 -0.5462 0.2597 - 5 946 5.00 0.947 0.1561 3367*

Pine pl(s) 0.00005 1.5637 - -0.0030 - - - -0.0461 3 948 2.30 0.959 0.1561 7291*

pt(s) 0.00002 1.5305 0.0435 -0.0088 - -0.2880 0.5576 - 5 946 5.01 0.975 0.1133 7438*

vl(r) 0.00004 1.5929 - -0.0156 - -0.0993 - 1.2756 4 947 5.34 0.952 0.1525 4703*

pl(r) 0.00001 1.6632 - -0.0127 - -0.1313 0.9862 - 4 947 3.04 0.969 0.1319 7335*

pt(r) 0.00001 1.6130 - -0.0125 - -0.1248 0.9748 - 4 947 3.45 0.973 0.1180 8595*

a - Component-specific parameter estimates obtained from OLS according to an all-possible best-subset regression procedure employing Mallows‘

(1973) Cp criterion. The intercept parameter estimate ( ̂ 0' ) includes a logarithmic-based correction factor (Baskerville, 1972; Sprugel, 1983).

b - As defined in Table 3; SEE in units of loge(dm3) for dependent variables vl(s) and vl(r) and loge(CAN$(2002)) for dependent variables pl(s), pt(s), pl(r)

and pt(r).

138 Peter F. Newton

The composite wood density and mean maximum branch diameter functions previously

developed for black spruce (Newton, unpublished) and jack pine (Newton, 2009) were

utilized. Briefly, species-specific cross-sectional area-weighted mean wood density per tree

( wD (g/cm3)) was estimated using Eq. (21), and species-specific mean maximum branch

diameter within the first 4.9 m sawlog per tree ( bD (cm)) was estimated using Eq. (22).

wD 0 D 2 H

1 2 Pr 3 H d 4 Pr H d

Pr 5 H d 6 Pr H d 7

(21)

d B 0 D2 H

1 2 Pr 3 H d 4 Pr H d

Pr5 H d6 Pr H d 7

(22)

where j , j 0,...,7 and j , j 0,...,7 are model parameters estimated via OLS

regression analysis following a double-logarithmic transformation using an all-possible best-

subset regression procedure based on Mallows‘ (1973) Cp selection criterion, and is an

equation-specific error term. Table 8 lists the resultant parameter estimates and associated

regression statistics.

3.1. The Modular-based SSDMM and Associated

Computational Framework for Mixed Stands

(Module B), dimensional-compatible variable exponent taper equations (Module C),

allometric-based component biomass functions (Module D), sawmill-speciﬁc product

recovery and value functions (Module E), and composite ﬁbre quality attribute functions

(Module F), within the dynamic SDMD modelling framework, resulted in the modular-based

SSDMM for black spruce and jack pine mixtures (Figure 1). Computationally, the yield–

density relationships within the dynamic SDMD are used to predict the temporal size–density

trajectory for a given site quality and density management regime (Dynamic SDMD Module).

Most if not all, decision-support models built on the SDMD modeling approach assume

that the size-density trajectory of a recently thinned stand immediately follows that of a stand

which was always managed at the lower post-thinned density. However, trees within recently

thinned stands require a period of time to morphologically adjust to their newly allocated

growing space and additional resources. Consequently, a response delay function was

developed to account for this effect.

Table 8. Parameter estimates and associated statistics for the regression relationships used in

Module F (Fibre Attribute Estimation): composite wood density and mean maximum branch diameter functions

Symbol Value

Black Spruce Jack Pine

Composite wood ̂ ' 0.5247 11.6252 (1) Parameter estimates obtained from OLS regression analysis where

0

density equations the independent variables were selected according to an all-possible

̂ 1 -0.0075 -

(Eq. (21)) best-subset regression procedure employing Mallows‘ (1973) Cp

ˆ 2 -0.0115 -0.2495 criterion.

- 0.0034 (2) The intercept parameter estimate includes a correction factor for

ˆ 3

the bias introduced via the logarithmic transformation (Baskerville,

ˆ 4 - 0.0066 1972; Sprugel, 1983).

ˆ 5 - 0.6445 (3) Regression statistics: nreg = 2, nres = 157, R2 = 0.219, SEE

(loge(g/cm3)) = 0.0860, CP statistic = 0.00, and F-ratio =22*, for

ˆ 6 - -0.9660

black spruce; and : nreg = 5, nres = 171, R2 = 0.364, SEE (loge(g/cm3))

ˆ 7 - - = 0.0470, CP statistic = 6.17, and F-ratio =18*, for jack pine.

Composite mean ˆ0' 3.6137 0.4901 (1) Parameter estimates obtained from OLS regression analysis where

maximum branch the independent variables were selected according to an all-possible

ˆ - 0.2976

diameter 1 best-subset regression procedure employing Mallows‘ (1973) Cp

equation - -0.0338 criterion.

(Eq. (22))

ˆ2 (2) The intercept parameter estimates includes a correction factor for

ˆ - - the bias introduced via the logarithmic transformation (Baskerville,

3

- 0.0024 1972; Sprugel, 1983).

ˆ4 (3) Regression statistics: nreg = 1, nres = 117, R2 = 0.053, SEE

ˆ5

-0.0427 - (loge(cm)) = 0.1147, CP statistic = 2.92, and F-ratio =7*, for black

spruce; and nreg = 4, nres = 510, R2 = 0.483, SEE (loge(cm)) = 0.1440,

ˆ6 - -

CP statistic = 3.38, and F-ratio =119*, for jack pine.

ˆ7

- -0.2021

Module A -Dynamic SDMD

mean-tree and stand-level volumetric

yield estimates

(Figure 2(a))

Recovery

recovery and composite height-diameter

function for height estimation

(Figure 2(b))

Module C - Taper Analysis and Module D - Biomass and Carbon Module E – Product and Value Estimation Module F - Fibre Attribute Estimation

Log Estimation Estimation

Species-specific sawmill-specific product Species-specific composite wood density and

Species-specific composite taper equations Species-specific composite biomass equations recovery and value equations mean maximum branch diameter equations

(Figure 2(c)) (Figure 2(d)) (Figure 2(e)) (Figure 2(f))

Biomass: Diameter-class and stand-level

stand-level estimates of the number of Diameter-class and stand-level estimates Diameter-class and stand-level estimates Wood Density: Diameter-class-weighted

biomass estimates for bark, stem, branch,

sawlogs and pulplogs, and residual of recoverable lumber volumes by of the value of recoverable lumber by stand-level estimates of specific gravity

and foliage components

merchantable stem tip volumes sawmill-type sawmill-type

Taper-based stem volumes: Carbon: Diameter-class and stand-level Residual Chip Volume: Residual Chip Value:

Diameter-class-weighted stand-level

Diameter-class and stand-level estimates biomass-based carbon estimates for bark, Diameter-class and stand-level estimates Diameter-class and stand-level estimates of

estimate of mean maximum branch diameter

of merchantable and total volumes stem, branch and foliage components of residual chip volumes by sawmill-type the value of residual chips by sawmill-type

within the first sawlog

estimates of the value of dimensional

lumber and residual chips by sawmill-type

Development and Utility of an Ecological-based Decision-Support System … 141

The function was based on the difference in live crown ratios between trees within the

pre-thinned and post-thinned stand condition as initially conceptualized by Newton (2003).

To illustrate this idea, it is instructive to consider the empirical results derived from an IE

black spruce experiment as they are reported in the literature (i.e., Table 1 in McClain et al.,

1994). The differential in mean live crown ratio between a high density-stressed stand

(surrogate for the thinned stand just before the time of thinning (Lr = 44%)) and a low

density-stressed stand (surrogate for the thinned stand immediately following thinning (Lr =

80%)), situated on the same site and of equal age, was 36% after 41 years. If the high density-

stressed stand was thinned at an age of 41, SDMD-based models would assume there was no

differential between the stands and erroneously describe the post-treatment size-density

trajectory as being identical to that of a stand which was always managed at the lower

density. Thus in this example, the temporal duration of the response delay is approximated by

the length of time required for trees within the thinned stand to achieve a mean live crown

ratio of 80%. More precisely, by extending this concept and accounting for the intrinsic

change in live crown ratio within the lower density stand in the years immediately following

thinning, the exact number of years required for the live crown ratios in both stands to

converge, can be determined. Specifically, the number of years that the live crown ratio of the

tree of mean dominant height took to rebuild its live crown ratio (based on a static live crown

base), to be equivalent to that predicted for a similar tree growing at the lower density, was

defined as the response delay period. Given that trees within recently thinned stand would not

be fully occupying their newly allocated space and hence not competing nor incurring

density-dependent mortality until their live crown ratios recovered, stand densities were

conditionized to remain constant during this period (i.e., the net density change function was

disabled during this adjustment period).

The temporal rate at which the size–density trajectory tracks through the SDMD is site-

dependent and hence described by the mean values derived from species-specific height-age

functions (Eq. (23a) for black spruce (Carmean et al., 2006) and Eq. (23b) for jack pine

(Carmean et al., 2001)).

0.6167( S I 1.3)0.3116

0.1136 AB

H d 1.3 16.95( S I 1.3) 1 K 50

(23a)

1

( S I 1.3) 0.6167( S I 1.3)0.3116

where K 1 0.1136

16.95( S I 1.3)

1.3723( S I 1.3)0.0802

0.6224

AB

H d 1.3 4.1459( S I 1.3) 1 K

50

1

(23b)

( S I 1.3) 1.3723( SI 1.3) 0.0802

where K 1 0.6224

4.1459( S I 1.3)

142 Peter F. Newton

(Dynamic SDMD) provides a set of stand-level variables which are required as input to

Modules B-F. Module B utilizes the PPE system and the composite height-diameter function

to recover the grouped-diameter frequency distribution and estimate corresponding tree

heights (Diameter and Height Recovery Module), and similar to Module A, provides

prerequisite input to the remaining modules. The taper equations are used to derive a pooled

mean estimate of the upper stem diameters for each tree from which the number of sawlogs

and pulplogs, residual tip volumes, and merchantable and total stem volumes are calculated

(Taper Analysis and Log Estimation Module). The composite biomass equations are used to

derive a pooled mean mass and carbon equivalent estimate for each above-ground component

(Biomass and Carbon Estimation Module). The product recovery and value functions are used

to derive pooled mean estimates of the sawmill-specific chip and lumber volumes and

associated market-based monetary values (Product and Value Estimation Module). The

composite ﬁbre attribute functions are used to derive mean pooled estimates of wood density

and mean maximum branch diameter (Fibre Attribute Estimation Module).

In order facilitate interpretation of the model structure and the associated computational

sequence, a comprehensive schematic illustration is provided in Figure 2, and a corresponding

descriptive synthesis is given as follows. Module A (Figure 2(a)) provides estimates of the

ˆ , Gˆ , Vˆ and

system‘s driving variables for each time step (year; Hˆ d (t ) , Nˆ ( t ) , vˆ( t ) , Dq (t ) (t ) t (t )

Pˆr (t ) ) using the dynamic SDMD and its embedded functions. Module B (Figure 2(b))

recovers the corresponding location, scale and shape parameter estimates for the 3-parameter

Weibull PDF using the PPE system (Eqs. (12)-(15)) in combination with the stand-level

variable estimates derived from Module A, from which density estimates are derived for each

recovered diameter class using Eq. (16) and a 10% truncation threshold rule (Clutter et al.,

1983). Height estimates for each recovered diameter class are then calculated employing the

stand-level and diameter-class-specific variable estimates ( Pˆr ( t ) and Hˆ d (t ) (from Module A)

ˆ , respectively) via the composite height-diameter function (Eq. (17)). Module C

and D(t , j )

(Figure 2(c)) computes tree and diameter-class estimates of merchantable and total stem

volumes, log-type distributions and residual merchantable tip volumes at each time step via

the taper equations (Eqs. (18a) and (18b)) using stand-level and diameter-class-specific

ˆ from Module A, and Dˆ , Hˆ ˆ

predictor variable estimates ( G(t ) (t , j ) ( t , j ) and N ( t , j ) from Module

B, respectively). Module D (Figure 2(d)) provides bark, stem, branch, foliage and total

biomass estimates at the tree, diameter-class and stand levels for each time step using the

composite biomass equations (Eq. (19)) in combination with the stand-level and diameter-

class-specific variable estimates ( Pˆr ( t ) and Hˆ d (t ) from Module A and D

ˆ , Hˆ

(t , j ) ( t , j ) and

class and stand levels are estimated using a carbon/biomass ratio estimator. Module E (Figure

2(e)) calculates tree, diameter-class and stand-level estimates of the volume of chip and

lumber end-products and their associated monetary values by sawmill-type at each time step

using the product and value equations (Eq. (20a) and (20b)) in combination with the stand-

Development and Utility of an Ecological-based Decision-Support System … 143

level and diameter-class-specific variable estimates ( Pˆr ( t ) and Hˆ d (t ) from Module A, and

and diameter-class estimates of specific gravity (wood density) and branch diameters at each

time step using the composite fibre attribute equations (Eqs. (21) and (22), respectively) in

combination with the stand-level and diameter-class variable estimates ( Pˆr ( t ) and Hˆ d (t ) from

ˆ

Module A, and D ˆ

( t , j ) and H ( t , j ) from Module B, respectively). Stand-level estimates of

mean wood density for the merchantable tree population, and mean maximum branch

diameter for the sawlog-sized tree population, are subsequently calculated using a diameter-

class density-based weighing factor.

The above sequence represent the essential computations required for deriving volumetric

yields, diameter distributions, tree heights, log assortments, components-speciﬁc biomass and

carbon outcomes, sawmill-speciﬁc products and associated values, and ﬁbre attributes, for a

given density management regime, site quality and rotation age.

(a) Module A - Dynamic SDMD

Output

Variables

Fixed Hˆ d (t ) f β S

, β SI ( PNb ) , S I , A(t )

User-specified Constants

I ( PIm )

Hˆ d ( t )

Input Variables A(t )

(t )

Nˆ f β S , N I , Nˆ (t 1) , Pˆr (t ) , A(t ) , S I , T2 N ( i ) , T3N ( i )

Nˆ ( t )

S

I

β S

ˆ ˆ

v(t ) f β v , H d (t ) , N (t )

ˆ ˆ

v

( t )

N I

β Dq

β

Dˆ q (t ) f β Dq , vˆ(t ) , Nˆ ( t ) Dˆ

T2 A ( i ) q ( t )

2N ( i )

T

v

β

Gˆ ( t ) f Dˆ q ( t ) , Nˆ ( t )

Gˆ

(t )

Pr

Vˆt ( t ) f vˆ( t ) , Nˆ ( t ) Vˆ

T3A ( i ) β Lr t(t)

T β

N ( i )

3 S I ( PIm )

Pˆ f β , vˆ , Nˆ

r(t) Pr (t)

(t) Pˆ

r(t)

β ˆ Lˆr ( t )

SI ( PNb ) L

r ( t )

f β Lr , vˆ ( t) , Nˆ

( t)

Input Variables and Constants Computations: recovering Weibull parameters via PPEs

aˆ 0.5Dˆ where Dˆ = f β

Input (t ) min min

ˆ ˆ ˆ ˆ ˆ ˆ ˆ

Dmin , H d ( t ) , N ( t ) , v( t ) , Dq ( t ) , G( t ) , Pr ( t ) , Vt ( t )

(2) Height estimation by diameter class

ˆ

Variables ˆ

b(t ) f βW (b ) , Hˆ d (t ) , Nˆ (t ) , vˆ(t ) , Dˆ q (t ) , G(t ) , Pˆr (t ) , Vˆt (t ) Input Constants and Variables

ˆ

H d (t )

Nˆ

Fixed

cˆ(t ) f βW ( c ) , Hˆ d (t ) , Nˆ (t ) , vˆ(t ) , Dˆ q (t ) , Gˆ (t ) , Pˆr (t ) , Vˆt (t )

Input

( t ) Constants Output Variables Variables Fixed

ˆ

ˆ

v(t ) β Dmin Computations: obtaining resultant diameter frequency distribution Nˆ (t , j ) D( t , j ) Constants

Dˆ ˆ ˆ β

q ( t ) βW (b ) ˆ cˆ( t )

aˆ(t ) D(t , j ) Pr (t ) H

Nˆ (t , j ) Nˆ (t ) 1 exp (t , j 1)

D

Gˆ β Hˆ

( t ) W (c)

bˆ(t ) d (t )

Vˆ Computation

t ( t )

Output Variable

cˆ( t )

Pˆ

r (t )

Nˆ

(t )

ˆ

1 exp D(t , j ) aˆ(t )

Hˆ

( t , j )

f β H , Dˆ ( t , j ) , Pˆr ( t ) , Hˆ d ( t ) Hˆ (t , j )

bˆ(t )

(c) Module C - Taper Analysis and Log Estimation

(1) Estimating upper stem diameter at 2.59 m height intervals from stump height

Computation: upper stem diameter

Input Variables and Constants dˆ

f βT( PIm ) , h(t , j ) , Dˆ (t , j ) , Hˆ (t , j ) , Gˆ ( t ) f βT( PNb ) , h( t , j ) , Dˆ ( t , j ) , Hˆ ( t , j ) , Gˆ ( t )

Fixed (t , j )

2

Input

Variables Constants Hˆ ( t , j ) 0.3 Hˆ ( t , j ) 0.3

ˆ

where h( t , j ) =0.3, 0.3+1

100

,0.3+2

100

,..., H ( t , j )

Dˆ (t , j )

d

s

dp

ˆ

Hˆ if d d then increment sawlog count per tree ( ˆ

n ) by 1

(t, j) s ls ( t , j )

(t , j ) dt

Nˆ if dˆ d and dˆ = d then increment pulplog count per tree (nˆ

lp (t , j ) ) by 1

( t , j ) dm

( t , j ) s ( t , j ) p

Nˆ (t ) if dˆ d p and dˆ = d t then calculate residual tip volume per tree (vˆr (t , j ) )

βT( PIm )

(t , j ) (t , j )

Gˆ (t ) β

T( PNb )

ˆ

if d (t , j ) = d m then calculate merchantable stem volume per tree (vˆm (t , j ) )

ˆ

if d ( t , j ) = 0 then calculate total stem volume per tree (vˆt (t , j ) )

(2) Calculating diameter-class and stand-level estimates of the number of

sawlogs and pulplogs, residual tip volumes, and merchantable and total stem

volumes

J Output Variables

Nˆ ls (t , j ) Nˆ (t , j ) nˆls (t , j ) Nˆ ls (t ) Nˆ ls (t , j ) ˆ

j 5 N ls (t )

ˆ

Nˆ

J

N

lp (t )

lp (t , j ) N ( t , j ) nˆlp ( t , j ) N lp ( t ) Nˆ lp (t , j )

ˆ ˆ

ˆ

j 5

Vr ( t )

J ˆ

Vr ( t , j ) N ( t , j ) vˆr ( t , j ) Vt ( t ) Vˆr ( t , j )

ˆ ˆ ˆ Vm (t )

j 5 vˆ

m ( t , j )

J

Vm ( t , j ) N ( t , j ) vˆm ( t , j ) Vm ( t ) Vˆm (t , j )

ˆ ˆ ˆ '

ˆ Vˆ '

j 5

ˆ ) m(t )

J

V m ( t ) V t ( t

Vˆ '

Vˆt ( t , j ) Nˆ ( t , j ) vˆt ( t , j ) Vˆ ' Vˆt (t , j ) t (t )

t(t)

j 1

(d) Module D - Biomass and Carbon Estimation

mˆ p

( t , j )( PIm )

f β M p ( PIm ) , Dˆ (t , j ) , Hˆ (t , j ) , Hˆ d (t ) , Pˆr (t )

Calculating component-specific biomass and

ˆ ˆ

mˆ s( t , j ) ( PIm ) f β M s ( PIm ) , D(t , j ) , H (t , j ) , H d (t ) , Pr (t )

ˆ ˆ

carbon equivalents per stand

mˆ b( t , j ) ( PIm ) f β M b ( PIm ) , Dˆ (t , j ) , Hˆ (t , j ) , Hˆ d (t ) , Pˆr (t ) ˆ J mˆ p( t , j )( PIm ) mˆ p( t , j )( PNb )

M p( t ) N (t , j )

ˆ

2

mˆ f

( t , j ) ( PIm )

f β M f ( PIm ) , Dˆ (t , j ) , Hˆ (t , j ) , Hˆ d (t ) , Pˆr (t )

j 1

mˆ s( t , j )( PIm ) mˆ s( t , j )( PNb )

mˆ Mˆ Nˆ

J

s( t )

mˆ p( t , j ) mˆ s( t , j ) mˆ b( t , j ) mˆ f( t , j )

t( t , j )( PIm ) ( PIm ) ( PIm ) ( PIm ) ( PIm )

(t , j )

2

j 1

ˆ ˆ

mˆ p( t , j )( PNb ) f β M p ( PNb ) , D(t , j ) , H (t , j ) , H d (t ) , Pr (t )

ˆ ˆ J mˆ b( t , j )( PIm ) mˆ b( t , j )( PNb )

Output Variables

Input Variables and Constants Mˆ Nˆ Mˆ

b( t )

Fixed

ˆ ˆ

mˆ s( t , j ) ( PNb ) f β M s ( PNb ) , D(t , j ) , H (t , j ) , H d (t ) , Pr (t )

ˆ ˆ

j 1

(t , j )

2

p( t )

Mˆ

Input

Constants mˆ

b( t , j ) ( PNb )

f β M b ( PNb ) , Dˆ (t , j ) , Hˆ (t , j ) , Hˆ d (t ) , Pˆr (t ) J

Mˆ f Nˆ (t , j )

mˆ f( t , j )( PIm ) mˆ f (t , j )( PNb )

s( t )

Mˆ b( t )

( t ) j 1 2

Variables β

β m p ( PIm )

ˆ

mˆ f( t , j ) ( PNb ) f β M f ( PNb ) , D(t , j ) , H (t , j ) , H d (t ) , Pr (t )

ˆ ˆ ˆ

Mˆ

ˆ J mˆ t(t , j )( PIm ) mˆ t(t , j )( PNb ) f( t )

mˆ t( t , j ) ( PNb ) mˆ p( t , j )( PNb ) mˆ s( t , j ) ( PNb ) mˆ b( t , j ) ( PNb ) mˆ f( t , j ) ( PNb )

m

Mˆ t( ) Nˆ (t , j )

s ( PIm )

(t , j )

D β t

Mˆ t( t )

2

Hˆ mb ( PIm )

j 1

( t , j ) β ˆ ˆ ˆ

C p( t )

Nˆ m f ( PIm ) cˆ ˆ c c

0.5 mˆ p( t , j )

J

ˆ

C p(t ) N (t , j )

p ( , ) p( , )

( PIm ) ( PNb )

t j t j

(t , j ) β m p( t , j )( PIm ) ˆ

Cs( t )

( PIm )

2

Hˆ d (t )

p ( PNb )

cˆ 0.5 mˆ s( t , j ) j 1

β ms ( PNb ) ˆ

s( t , j )( PIm ) ( PIm )

cˆs( t , j )( PIm ) cˆs( t , j )( PNb ) Cb( t )

Pˆr (t ) cˆ ˆ Cˆ Nˆ

J

0.5

s( t )

m

β mb ( PNb ) b( t , j )( PIm ) b( t , j )

( PIm ) (t , j )

2 Cˆ f

cˆ 0.5 mˆ

j 1

(t )

β m f ( PNb ) f( t , j )( PIm ) f( t , j )

Cˆt

cˆb( t , j )( PIm ) cˆb( t , j )( PNb )

( PIm )

J

cˆt Cˆ Nˆ

b( t )

ˆ

c cˆs( t , j ) cˆb( t , j ) cˆ f( t , j ) (t )

( t , j )( PIm ) (t , j )

p

( t , j )( PIm ) ( PIm ) ( PIm ) ( PIm )

j 1

2

cˆ p( t , j ) 0.5 mˆ p( t , j )

( PNb ) ( PNb )

J cˆ f( t , j )( PIm ) cˆ f( t , j )( PNb )

cˆs 0.5 mˆ s( t , j ) Cˆ f Nˆ (t , j )

( t , j )( PNb ) ( PNb )

( t ) j 1 2

cˆb( t , j )

0.5 mˆ b( t , j )

( PNb ) ( PNb )

J cˆt( t , j )( PIm ) cˆt( t , j )( PNb )

cˆ f 0.5 mˆ Cˆt( t ) Nˆ (t , j )

( t , j )( PNb )

f (t , j )

( PNb ) 2

j 1

cˆt ˆ

c cˆs( t , j ) cˆb( t , j ) cˆ f( t , j )

( t , j )( PNb ) p ( t , j )( PNb ) ( PNb ) ( PNb ) ( PNb )

(e) Module E - Product and Value Estimation

Computations: stand-level

chip volumes, lumber volumes

Computations: tree-level chip volumes, and product values by

lumber volumes and product values by sawmill type

Input Variables and Constants

sawmill type J

Fixed Vˆc ( s ) Nˆ (t , j ) vˆc ( s )

Constants

vˆ

f β vl ( s ) , Dˆ (t , j ) , Hˆ (t , j ) f β vl ( s ) , Dˆ (t , j ) , Hˆ (t , j ) , Hˆ d (t ) , Pˆr (t )

( t )

j 5

(t , j )

Output Variables

Vˆ

l ( s )(t , j )

( PIm ) ( PNb )

β vl ( s )

J

2 Vˆ

l ( s ) ( t )

Nˆ (t , j ) vˆl ( s ) c(s) (t )

( PIm )

vˆ ˆ ˆ

c ( s ) ( t , j ) vm (t , j ) vl ( s ) (t , j )

(t , j )

β pl ( s )

j 5 ˆ

Vl ( s ) ( t )

( PIm )

ˆ J

Pl ( s ) ( t ) N (t , j ) pˆ l ( s ) ( t , j )

Input β ˆ

f β pl ( s ) , Dˆ (t , j ) , Hˆ (t , j ) f β pl ( s ) , Dˆ (t , j ) , Hˆ (t , j ) , Hˆ d (t ) , Pˆr (t )

ˆ

Pl ( s ) ( t )

pt ( s )

Variables pˆ j 5

( PIm )

( PIm ) ( PNb )

Dˆ β v l ( s )(t , j ) 2 ˆ J

ˆ

Pt ( s )

Pt ( s ) ( t ) N (t , j ) pˆ t ( s ) ( t , j )

( PIm ) ˆ

( )

l r

(t , j )

(t )

f β Pt ( s ) , Dˆ (t , j ) , Hˆ (t , j ) f β Pt ( s ) , Dˆ (t , j ) , Hˆ ( t , j ) , Hˆ d ( t ) , Pˆr ( t ) j 5 ˆ

Hˆ (t , j ) β pl ( r ) ( PIm ) Pc ( s ) ( t )

pˆ t ( s ) (t , j )

( PIm ) ( PNb )

ˆ

J

Nˆ (t , j ) β 2 Pc ( s ) ( t ) Nˆ (t , j ) pˆ c ( s )

(t , j ) Vˆc ( r )

t ( r ) ( PIm ) pˆ c ( s ) pˆ t ( s ) pˆ l ( s )

p

j 5

(t )

ˆ

Pr (t ) β (t, j) (t, j) (t, j)

ˆ J

Vˆ

Vc ( r ) ( t ) N ( t , j ) vˆc ( r ) ( t , j )

vl ( s )( PNb )

ˆ

f β vl( r ) , Dˆ ( t , j ) , Hˆ ( t , j ) f β vl( r ) , Dˆ ( t , j ) , Hˆ ( t , j ) , Hˆ d ( t ) , Pˆr ( t ) l (r )(t )

Hˆ d (t ) β p j 5

Pˆ

l ( s ) ( PNb ) vˆl ( r ) ( t , j )

( PIm ) ( PNb )

2 J

l (r )(t )

vˆm (t , j )

β pt ( s ) ( PNb ) vˆ Vˆl ( r ) ( t ) Nˆ ( t , j ) vˆl ( r ) ( t , j ) ˆ

c( r ) vˆm ( t , j ) vˆl ( r ) j 5

P

t (r )(t )

β (t, j) (t, j)

ˆ

J

Pˆl ( r ) Nˆ ( t , j ) pˆ l ( r )

vl ( r )

( PNb )

f β pl ( r ) , Dˆ (t , j ) , Hˆ (t , j ) f β pl ( r ) , Dˆ (t , j ) , Hˆ (t , j ) , Hˆ d (t ) , Pˆr (t ) Pc ( r ) ( t )

β ( t ) j 5 (t , j )

pˆ l ( r )

( PIm ) ( PNb )

pl ( r )

( PNb )

(t, j)

2 J

Pˆt ( r ) Nˆ ( t , j ) pˆ t ( r )

β

pt ( r ) ( PNb ) f β pt ( r ) , Dˆ (t , j ) , Hˆ (t , j ) f β pt ( r ) , Dˆ (t , j ) , Hˆ (t , j ) , Hˆ d (t ) , Pˆr (t ) ( t ) j 5 (t , j )

ˆ

( PIm ) ( PNb )

p Pˆ

J

c ( r ) ( t )

t ( r ) (t , j )

2 Nˆ ( t , j ) pˆ c ( r )

(t , j )

pˆ pˆ t ( r ) pˆ l ( r ) j 5

c ( r ) ( t , j ) (t , j ) (t , j )

(f) Module F - Fibre Attribute Estimation

Estimating wood density and mean maximum branch diameter per tree

Input Variables and Constants

Input

Variables

Fixed

Computations

Constants

Dˆ (t , j )

β wD

wˆ D( t , j )

f β wD , Dˆ (t , j ) , Hˆ (t , j ) , Hˆ d (t ) , Pˆr (t ) f β wD( PNb ) , Dˆ (t , j ) , Hˆ (t , j ) , Hˆ d (t ) , Pˆr (t )

( PIm )

ˆ ( PIm )

H 2

( t , j ) β

Nˆ

(t , j )

bD( PIm )

β

ˆ

bD (t , j )

f βbD , Dˆ (t , j ) , Hˆ (t , j ) , Hˆ d (t ) , Pˆr (t )

( PIm )

f β bD( PNb ) , Dˆ (t , j ) , Hˆ (t , j ) , Hˆ d (t ) , Pˆr (t )

wD( PNb )

Hˆ d (t )

2

βb

ˆ D( PNb )

P r ( t )

Calculating mean wood density and

mean maximum branch diameter per

stand

J Output Variables

ˆ

j 5

ˆ ˆ

wD ( t , j ) N ( t , j )

ˆ

WD ( t ) J

if D( t , j ) 10 WD ( t )

ˆ

Nˆ ( t , j )

B

j 5 D (t )

ˆ

J

bD (t , j ) Nˆ (t , j )

Bˆ D (t )

j 8

if D(t , j ) 16

J

Nˆ ( t , j )

j 8

Figure 2. Schematic illustration of the computational framework utilized in the modular-based SSDMM: (a) Module A - Dynamic SDMD; (b) Module

B - Diameter and Height Recovery; (c) Module C - Taper Analysis and Log Estimation; (d) Module D - Biomass and Carbon Estimation; (e) Module E

- Product and Value Estimation; and (f) Module F - Fibre Attribute Estimation. Refer to Table 9 for variable definitions and additional computational

details.

Table 9. Variable definitions and associated computational details associated

with the SSDMM are schematically illustrated in Figure 2

Module A - Dynamic SDMD (Figure 2(a))

SI Site index (m): mean dominant height at a breast-height age of 50 yr (Eqs. (23a) and (23b); Carmean et al., 2006 and 2001,

respectively).

NI Initial density (stems/ha) at time of stand establishment.

T2 A( i ) Regime 2 thinning treatment(s): stand age (yr) at the time of the ith thinning event (i=1,…,I; I=4).

T2 N ( i ) Regime 2 thinning treatment(s): density reduction (stems/ha) during the ith thinning event (i=1,…,I; I=4).

T3A ( i ) Regime 3 thinning treatment(s): stand age (yr) at the time of the ith thinning event (i=1,…,I; I=4).

T3N ( i ) Regime 3 thinning treatment(s): density reduction (stems/ha) during the ith thinning event (i=1,…,I; I=4).

Hˆ d (t ) Predicted mean dominant height (m) at time t. Estimated for each stand age A(t ) , t 1,..., T using the site-specific height-

age functions where β SI ( PIm ) and β SI ( PNb ) denotes the associated parameter estimate vector for black spruce ((Eq. (23a); Carmean et

al., 2006) and jack pine (Eq. (23b); Carmean et al., 2001), respectively. Notes: (1) based on the range of stand ages within the

data sets (Table 2), the maximum stand age (T) was set at 170 yr; (2) site-specific conversion of total to breast-height ages

required an estimate of the number of years required for dominant height to reach 1.3 m, consequently, Eqs. (23a) and (23b)

were rearranged with respect to the breast-height age term and solved for a zero height value; the absolute equivalent of the

returned value for a given site index is an estimate of the number of years required for dominant height to reach 1.3 m for the

specified site quality; and (3) given (2), estimates of dominant height for each year to breast-height was determined via linear

interpolation.

Nˆ ( t ) Predicted density (stems/ha) at time t. Estimated using Eq. (10) where β S denotes the associated vector of parameter

estimates

( β S [ˆl where l 0,...,3] ; Table 3).

vˆt Predicted mean volume per tree (dm3) at time t. Estimated employing Eq. (6) where βv denotes the associated vector of

parameter estimates ( βv ˆl where l 0,1,2 ; Table 3).

Dˆ q ( t ) Predicted quadratic mean diameter (cm) at breast height at time t. Estimated employing Eq. (4) where β Dq denotes the

associated vector of parameter estimates ( βDq ˆl where l 0,1,2 ; Table 3).

Gˆ ( t ) Predicted basal area (m2/ha) at time t: Gˆ (t ) 0.00007854 Dˆ q2(t ) Nˆ (t )

Vˆt (t ) Predicted total volume (m3/ha) at time t: Vˆt ( t ) 1000 vˆ(t ) Nˆ (t )

Pˆr ( t ) Predicted relative density index (%/100) at time t. Estimated employing Eq. (2) where β Pr denotes the associated vector of

parameter estimates ( β Pr ˆ 0 ˆ1 ; Table 3).

Lˆr ( t ) Predicted mean live crown ratio (%) at time t. Estimated employing Eq. (8) where β Lr denotes the associated vector of

aˆ(t ) Predicted location parameter of the Weibull PDF (Eq. 11) at time t. Calculated using the minimum diameter estimate D̂min

according to Eqs. (12) and (13) where β Dmin denotes the vector of parameter estimates associated with Eq. (13)

( β Dmin ˆl where l 0,...,7 ; Table 4).

bˆ( t ) Predicted scale parameter of the Weibull PDF (Eq. (11)) at time t. Estimated using Eqs. (14) where βW (b) denotes the

associated vector of parameter estimates ( βW (b ) ˆl where l 0,...,7 ; Table 4).

cˆ(t ) Predicted shape parameter of the Weibull PDF (Eq. (11)) at time t. Estimated using Eqs. (15) where βW ( c ) denotes the

associated vector of parameter estimates ( βW ( c ) ˆl where l 0,...,7 ; Table 4).

Nˆ (t , j ) Predicted number of trees (stems/ha) within the jth two-centimetre-wide diameter class (j = 1, 2,…, J) at time t. Estimating

using Eq. (16) in combination with Eqs. (12), (13), (14) and (15).

Dˆ (t , j ) Predicted diameter class midpoint (cm) for the jth two-centimetre-wide diameter class at time t.

Hˆ ( t , j ) Predicted height (m) of the trees within the jth two-centimetre-wide diameter class at time t. Estimated employing Eq. (17)

where β H denotes the associated vector of parameter estimates ( β H ˆl where l 0,...,7 ; Table 4).

dˆ( t , j ) Predicted inside bark diameter (cm) at stem height h(t,j) at time t. Estimated employing Eqs. (18a) and (18b) where

βT( PIm ) ˆ l where l 0,..., 4 and βT( PNb ) ˆ l where l 0,1, 2, 4 denotes the associated vector of parameter estimates for black

spruce and jack pine, respectively (Table 5).

nˆls (t , j ) Predicted cumulative number of sawlogs per tree (sawlogs/tree) within the jth merchantable-sized diameter class ( Dˆ (t , j ) ≥

10) at time t. Estimated employing Eqs. (18a) and (18b) according to specified merchantability limits for sawlogs (2.59 m log

lengths with a minimum small-end inside-bark diameter of 14.0 cm (ds)).

nˆlp(t , j ) Predicted cumulative number of pulplogs per tree (pulplogs/tree) within the jth merchantable-sized diameter class at time t.

Estimated employing Eqs. (18a) and (18b) according to specified merchantability limits for pulplogs (2.59 m log lengths with a

minimum small-end inside-bark diameter of 10.0 cm (dp)).

vˆr (t , j ) Predicted residual log tip volume per tree (m3/tree) within the jth merchantable-sized diameter class at time t. Estimated

employing Eqs. (18a) and (18b) according to specified dimensional requirements for merchantable volume (dt which is the

specified minimum dˆ which defines the merchantable height of the tree) via numerical integration techniques: sectional

(t , j )

volume summation between the height at the top of the last recovered pulp or saw log and the height (h(j,t)) at which the dˆ( t , j )

value is equivalent to the specified merchantability limit for merchantable stems (minimum inside bark diameter of 10.0 cm

(dm)).

vˆm(t , j ) Predicted merchantable stem volume per tree per tree (m3/tree) within the jth merchantable-sized diameter class at time t.

Estimated employing Eqs. (18a) and (18b) according to specified dimensional requirements for merchantable volume via

numeric integration techniques: sectional volume summation between a stump height of 0.30 m and the height (h(j,t)) at which

the dˆ value is equivalent to the specified merchantability minimum inside bark diameter (dm; 10.0 cm).

(t , j )

vˆt (t , j ) Predicted total stem volume per tree per tree (m3/tree) within the jth diameter class at time t. Estimated employing Eqs.

(18a) and (18b): (1) numeric integration via summation of sectional volumes between a stump height of 0.30 m and the height

(h(j,t)) at which a zero dˆ value first occurs; (2) calculating the volume of the 0.30 m stump; and (3) summing the both

(t , j )

Nˆ ls ( t , j ) Predicted number of sawlogs within the jth merchantable-sized diameter class (sawlogs/jth diameter class) at time t.

Nˆ lp (t , j ) Predicted number of pulplogs within the jth merchantable-sized diameter class (pulplogs/jth diameter class) at time t.

Vˆr (t , j ) Predicted residual log tip volume within the jth merchantable-sized diameter class (m3/jth diameter class) at time t.

Vˆr ( t ) Predicted residual log tip volume per unit area (m3/ha) at time t.

Vˆm ( t , j ) Predicted merchantable stem volume within the jth merchantable-sized diameter class (m3/jth diameter class) at time t.

Vˆm' ( t ) Approximated merchantable volume per unit area (m3/ha) at time t (estimate derived from the taper equations).

Vˆt ( t , j ) Predicted total stem volume within the jth diameter class (m3/jth diameter class) at time t.

Vˆt '(t ) Approximated total stem volume per unit area (m3/ha) at time t (estimate derived from the taper equations).

mˆ k( t , j ) Predicted bark (periderm; k=p), stem (k=s), branch (k=b), foliage (k=f) and total (k=t) oven-dry mass per tree (g/tree) within

the jth diameter class at time t for the nth species (n = PIm or PNb) . Estimated employing Eq. (19) where

(n)

k p , s , b, f , t

βmk , k p, s, b, f denotes the parameter estimate vectors specific to the kth component and nth species

(n)

( β mk ˆl where l 0,...,7 ; Table 6). Total mass calculated as the arithmetic sum of the individual component masses.

(n)

cˆk( t , j ) Predicted bark (periderm; k=p), stem (k=s), branch (k=b), foliage (k=f) and total (k=t) carbon equivalents per tree (g/tree)

(n)

within the jth diameter class at time t for the nth species. Calculated as a fixed proportion of the component mass estimates.

k p, s, b, f , t

Mˆ Predicted bark (k=p), stem (k=s), branch (k=b), foliage (k=f) and total oven-dry mass (k=t) per unit area (g/ha) at time t.

k( t )

k p , s , b, f , t

Cˆ k( t ) Predicted bark (k=p), stem (k=s), branch (k=b), foliage (k=f) and total carbon (k=t) per unit area (g/ha) at time t.

k p , s , b, f , t

vˆl ( k ) Predicted lumber volume recovered by a stud (k=s) and randomized length (k=r) sawmill processing protocol per tree

(dm3/tree) within the jth merchantable-sized diameter class at time t for the nth species. Estimated employing Eqs. (20a) and

( t , j )( n )

k s, r

(20b) where βvl ( k ) ˆl ( k ) where l = 0,1,2 and βvl ( k ) ˆl ( k ) where l = 0,...,7 denotes the black spruce and jack pine

( PIm ) ( PNb )

parameter estimate vectors for lumber volume, respectively, specific to the kth processing protocol (Table 7).

vˆc ( k ) Predicted chip volume recovered by a stud (k=s) and randomized length (k=r) sawmill processing protocol per tree

(dm3/tree) within the jth merchantable-sized diameter class at time t for the nth species. Note, calculated as the arithmetic

( t , j )( n )

k s, r difference between the taper-based merchantable volume per tree estimate and lumber volume per tree estimate.

pˆ l ( k ) Predicted value of dimensional lumber recovered by a stud (k=s) and randomized length (k=r) sawmill processing protocol

per tree (CAN$(2002)/tree) within the jth merchantable-sized diameter class at time t for the nth species. Estimated employing

( t , j )( n )

k s, r

Eqs. (20a) and (20b) where β pl ( k ) ˆl ( k ) where l = 0,1,2 and β pl ( k ) ˆl ( k ) where l = 0,...,7 denotes the black spruce and

( PIm ) ( PNb )

jack pine parameter estimate vectors for lumber value, respectively, specific to the kth processing protocol (Table 7).

pˆ t ( k ) Predicted value of lumber and chip products recovered by a stud (k=s) and randomized length (k=r) sawmill processing

protocol per tree (CAN$(2002)/tree) within the jth merchantable-sized diameter class at time t for the nth species. Estimated

( t , j )( n )

k s, r

employing Eqs. (20a) and (20b) where β pt ( k ) ˆl ( k ) where l = 0,1,2 and β pt ( k ) ˆl ( k ) where l = 0,...,7 denotes the

( PIm ) ( PNb )

black spruce and jack pine parameter estimate vectors for total value, respectively, specific to the kth processing protocol (Table

7).

pˆ c ( k ) Predicted mean value of chips recovered by a stud (k=s) and randomized length (k=r) sawmill processing protocol per tree

(CAN$(2002)/tree) within the jth merchantable-sized diameter class at time t for the nth species. Note, calculated as the

( t , j )( n )

k s, r arithmetic difference between the total and lumber mean value estimates.

Vˆc ( k ) Predicted chip volume recovered by a stud mill (k=s) and randomized length (k=r) sawmill processing protocol per stand for

(t )

all merchantable-sized trees at time t (dm3/ha).

k s, r

Vˆl ( k ) Predicted lumber volume recovered by a stud mill (k=s) and randomized length (k=r) sawmill processing protocol per stand

(t )

for all merchantable-sized trees at time t (dm3/ha).

k s, r

Pˆl ( k ) Predicted value of dimensional lumber recovered by a stud mill (k=s) and randomized length (k=r) sawmill processing

(t )

protocol per stand for all merchantable-sized trees at time t (CAN$(2002)/ha).

k s, r

Pˆt ( k ) Predicted value of all products (lumber and chip) recovered by a stud mill (k=s) and randomized length (k=r) sawmill

(t )

processing protocol per stand for all merchantable-sized trees at time t (CAN$(2002)/ha).

k s, r

Pˆc ( k ) Predicted value of chips recovered by a stud mill (k=s) and randomized length (k=r) sawmill processing protocol per stand

(t )

for all merchantable-sized trees at time t (CAN$(2002)/ha).

k s, r

Module F - Fibre Attribute Estimation (Figure 2(f))

wˆ D( t , j ) Predicted stem cross-sectional area-weighted mean wood density per tree within the jth diameter class at time t (g/cm3) for

the nth species. Estimated employing Eq. (21) where βwD denotes the parameter estimate vector specific to the nth species

(n)

(n)

(n)

Predicted mean maximum branch diameter (cm) within the first 4.9 m sawlog per tree within the jth sawlog-sized diameter

bˆD (i , j )( n )

class Dˆ

16 at time t. Estimated employing Eq. (22) where β denotes the parameter estimate vector specific to the nth

(t , j ) bD( n )

(n)

Wˆ D ( t )

Predicted diameter-class-weighted mean wood density within the merchantable-sized tree population Dˆ (t , j ) 10 at time t

3

(g/cm ).

Bˆ D ( t )

Predicted diameter-class-weighted mean maximum branch diameter within the sawlog-sized tree population Dˆ (t , j ) 16 at

time t (cm).

Development and Utility of an Ecological-based Decision-Support System … 155

A standardized set of stand-level performance indices were derived from the model‘s

output in order to simplify the decision-making process in terms of comparing alterative

density management regimes. These indices reflect overall productivity, type of products

produced, economic efficiency, degree of optimal site occupancy, structural stability, and

fibre quality attributes, over the rotation. Indices representing merchantable volume

production (mean annual merchantable volume increment; RMAI (Eq. (24)), biomass

accumulation rate (mean annual biomass increment; RBMI (Eq. (25)), and carbon sequestration

potential (mean annual carbon increment; RCAI (Eq. (26)) were used to quantify overall

productivity for a given regime.

K

RMAI Vm Vm ( k ) A(T ) (24)

k 1

where Vm is the standing merchantable volume (m3/ha) at rotation (A(T)) and Vm( k ) is the

merchantable volume removed during the kth thinning entry (k = 1,…,K; K = 4),

K

RBMI M t M t ( k ) A(T ) (25)

k 1

where M t is the standing total aboveground biomass (t/ha) at rotation and M t ( k ) is the total

aboveground biomass (t/ha) removed during the kth thinning entry (k = 1,…,K; K = 4),

K

RCAI Ct Ct ( k ) A(T ) (26)

k 1

where C t is the standing total aboveground carbon (t/ha) at rotation and Ct ( k ) is the total

aboveground carbon (t/ha) removed during the kth thinning entry (k = 1,…,K; K = 4).

Relative indices reflecting the type and quality of logs produced (percentage of sawlogs

produced; RSL; (Eq. (27)) and the resultant end-products manufactured (percentage of lumber

volume recovered by sawmill type; RLV(m) (Eq. (28)) were used to differentiate each regime in

terms of its potential to produce commercial-grade end-products.

K

Nls Nls ( k )

RSL 100 k 1 (27)

K

K

Nls Nls ( k ) N lp N lp ( k )

k 1 k 1

156 Peter F. Newton

where N ls and N lp are the total number of sawlogs (logs/ha) and pulplogs (logs/ha) at

rotation, respectively, and Nls ( k ) and Nlp ( k ) are the total number of sawlogs (logs/ha) and

pulplogs (logs/ha) removed during the kth thinning entry (k = 1,…,K; K = 4), respectively,

K

Vl ( m) Vl ( k , m)

RLV ( m ) 100 k 1 (28)

K

K

Vl ( m ) Vl ( k ,m ) Vc ( m ) Vc ( k ,m )

k 1 k 1

where Vl ( m) and Vc ( m ) are the lumber and chip volumes (m3/ha) recovered employing the mth

sawmill processing protocol (m = 1 (stud mill) or 2 (random length mill)) from the

merchantable-sized trees at rotation, respectively, and Vl ( k ,m ) and Vc ( k ,m) are the lumber and

chip volumes (m3/ha) recovered employing the mth sawmill processing protocol from the

merchantable-sized trees removed during the kth thinning entry (k = 1,…,K; K = 4),

respectively.

Economic efficiency was measured by the land expectation value (i.e., the maximum an

investor could pay for bare land to achieve a specified rate of return (discount rate)) of the

manipulated regimes, relative to the control regime (E(m); Eq. (29)).

LTE ( m ) LCE ( m )

E( m ) 100 where (29)

L C

E ( m )

K

PtT(m ) (1 I r ) A(T ) CFE (1 I r ) A(T ) CFT T (k ) (1 I r ) A(T ) A( k )

k 1

K

K T

k 1

Pt (k ,m ) (1 I r ) 1 I r

A( k )

A( T ) A( k )

CV T (k ) (1 I r )

T A( T ) A( k )

CVT H

LT

k 1

E (m )

(1 Dr ) (T ) 1

A

T Ys 2002

Pt ( m ) Pt ( m ) (1 I r )

T Ys 2002

Pt ( k ,m ) Pt ( k ,m ) (1 I r )

where CFT T ( k ) cFT T ( k ) (1 I r ) ( k )

A

T

CV T ( k ) cV T ( k ) (1 I r )

T A( k )

Vˆm ( k )

CVT H cVT H (1 I r ) A( T ) Vˆm (T )

C

Pt C( m) (1 I r )

A( T )

CFE (1 I r )

A( T )

CVC H where P C

t ( m) Pt ( m) (1 I r )Ys 2002

C

L

Vˆm (T )

E ( m)

(1 Dr ) 1 CV H cV H (1 I r )

A( T ) C A( T )

Development and Utility of an Ecological-based Decision-Support System … 157

where LE ( m ) and LE ( m ) are the land expectation values at rotation attained employing the

T C

mth sawmill processing protocol within the density manipulated and control stands,

respectively, Pt ( m ) and Pt ( m ) are the inflation-adjusted (to the year of simulation; Ys) total

T C

product values ($/ha) recovered employing the mth sawmill processing protocol from the

merchantable-sized trees within the density manipulated and control stands at rotation,

respectively, Pt ( k , m ) is the inflation-adjusted total product value ($/ha) recovered employing

T

the mth sawmill processing protocol from the merchantable-sized trees removed during the

kth thinning entry (k = 1,…,K; K = 4), CFE is the fixed cost ($/ha) incurred at the time of stand

establishment (e.g., regeneration assessment or vegetation management expenses), cF T ( k )

T

and CF T ( k ) are the inflation unadjusted and adjusted fixed costs ($/ha) incurred during the

T

kth thinning entry, respectively (e.g., logistical costs such as those associated with

transporting thinning equipment), cVC H and CVC H are the inflation unadjusted and adjusted

variable costs (dollars per cubic metre of merchantable volume harvested ($/m3)),

respectively, associated with crown charges (stumpage and renewal fees), harvesting,

transportation, processing and manufacturing at the time harvest within the control stand,

cVT H and CVT H are the inflation unadjusted and adjusted variable costs ($/m3), respectively,

at the time of harvest within the treated stand, cV T ( k ) and CV T ( k ) are the inflation

T T

unadjusted and adjusted variable costs ($/m3), respectively, at the time of the kth thinning

entry within the treated stand, Ir and Dr are the inflation and discount rate, respectively, and

A( k ) and A(T) are the stand ages at the time of the kth thinning entry and at rotation,

respectively.

In order to evaluate the regimes to the degree to which each optimally occupied the site

during the rotation, the percentage of years in which the size-density trajectory was within the

optimal density management window, was calculated (SO; Eq. (30)).

Y

SO 100 O (30)

YN

where YO is the number of years in which the size-density trajectory was within the

conceptual optimal relative density management zone as delineated by lower and upper

relative density index thresholds of 0.32 and 0.45, respectively, and YN is the rotation length

in years. The weighted mean height/diameter ratio for trees within the dominant crown

classes (SS; Eq. (31)) was used to differentiate the regimes in terms of stand stability.

J H (t , j )

N ( t , j )

1 j 1 100 D(t , j )

SS J (31)

T

if D(t , j ) D80

T t i

N (t , j )

j 1

158 Peter F. Newton

where D80 is the 80th percentile of the recovered diameter frequency distribution as

calculated from the Weibull (1951) scale and shape parameters (Bailey and Dell, 1973):

D80 bˆ log e 0.20 . Similarly, the weighted mean wood density for trees within the

1/ cˆ

merchantable tree population ( WD ; Eq. (32)) and the weighted mean maximum branch

diameter ( BD ; Eq. (33)) within the sawlog-sized tree population were used as indices of

wood and log quality, respectively.

J

T D (t , j ) (t , j )

w N

1

WD

j 5

(32)

T t 1 J

N (t , j )

j 5

where wD (t , j ) is the stem cross-sectional area-weighted mean wood density at time t of trees

within the jth merchantable size diameter class D(t , j ) 10 .

J

T D (t , j ) (t , j )

b N

1

BD j J

8

(33)

T t i

N (t , j )

j 8

where bD ( t , j ) is the mean maximum branch diameter within the first 4.9 m sawlog at time t

within the jth sawlog-sized diameter-class D(t , j ) 16 . Note, in the case of the thinned

stands, WD and BD values are calculated for the period since the last treatment, exclusively.

management, software analogues are usually required. Consequently, given the computation

burden associated with calculating the volumetric yields, log products, biomass and carbon

outcomes, recoverable products and associated monetary values, ﬁbre attributes and stand-

level performance indices, a VisualBasic.Net program was developed. This program predicts

site-dependent annual and rotational estimates for these variables at both the diameter-class

and stand levels. The program is structured so that 3 density management regimes can be

evaluated for any given simulation: a control regime with no thinning treatments versus two

other regimes which can include 1 to 4 thinning treatments each. The user must specific the

site quality as defined by site index, initial densities, thinning treatments in terms of time of

entry and removable densities, length of rotation, fixed and variable cost estimates, and

Development and Utility of an Ecological-based Decision-Support System … 159

interest and discount rate information. Essentially, the program carries out all the required

computations as described in Figure 2, calculates the performance indices, and presents the

results in both graphical and tabular formats.

Although the computational requirements are mitigated with the development of the

software program, designing the optimal density regime for a given objective is still a major

challenge considering the number of decision variables involved. For example, a silviculturist

must decide which sites should be treated, the number, type, intensity (removable densities)

and timing of thinning treatments, when to conduct the final harvest (rotation length), and

what economic values are most appropriate (fixed and variable costs estimates, and interest

and discount rates). Furthermore, the candidate regimes must comply with the local statutory

framework which may introduce a broad array of additional conditions that must be met

before treatments can be implemented. Thus in order to exemplify the complexity of density

management decision-making and illustrate the potential utility of the SSDMM, the software

was used to determine and evaluate the consequences of implementing CT treatments within

density-stressed mixed stands situated on sites of moderate productivity.

In this example, CT is used as a stand improvement practice in order to realize a diverse

set of stand-level objectives. These included (1) avoidance of density-dependent mortality

within the merchantable-sized classes during the later stages of stand development so that

potentially valuable crop trees are retained on the site until final harvest, (2) provision of

interim fibre supplies via the mid-rotational partial harvests (thinning yields), (3) reduction in

vertical and horizontal structure heterogeneity by increasing spatial pattern uniformity and

decreasing size variation within the crop tree population thus reducing variable costs

associated with harvesting, transportation and manufacturing, and (4) enhancing carbon

sequestration potential by increasing biomass production and reducing the generation of

abiotic masses.

Preferable, CT density management regimes are those which increased mean tree size

without incurring declines in merchantable volume production, do not unacceptably increase

the risk of volume losses to wind, snow, insects, and disease, and minimize the occurrence of

density-dependent mortality within the merchantable-sized diameter classes. Although

legislative and operational constraints placed on CT treatments vary by stand type and

jurisdiction, the ones proposed for coniferous stands within the central portion of the

Canadian Boreal Forest Region are used in this example (McKinnon et al., 2006): (1) CT

treatments should be implemented when density-dependent mortality is occurring or

imminent within the merchantable-sized classes; (2) CT should occur within stands where the

mean live crown ratio exceeds 35% and the stand basal area exceeds 25 m2/ha; and (3) CT

treatments should reduce basal areas by no more than 30-35% per entry. Furthermore, if the

goal is to enable stands to achieve an optimal level of production before thinning commences,

stands should be allowed to attain the upper threshold relative density value of at least 0.45,

before treatment.

Thus within the context of implementing CT treatments within density-stressed mixed

stands, a control regime (untreated) consisting of a stand with an initial density of 5000

stems/ha (NI) which naturally established on a moderately good site quality (SI = 17)

following forest harvesting was contrasted with two stands with identical initial conditions,

but subject to the following CT treatments. The first of two CT treatments was equivalent in

both stands: removing 1500 stems/ha from stands which had achieved all of the above CT

criteria in addition to having attained merchantable status (i.e., having a minimum quadratic

160 Peter F. Newton

mean diameter of 10 cm). Similarly, once the treated stands had re-achieved the criteria for

CT treatments, they were subsequently thinned again. Specifically, at a stand age of 65 yr,

30% of the basal area in the first CT stand, and 35% of the basal area in the second CT stand,

was removed. The control and treated stands were denoted Regime 1, 2 and 3 where Regime

3 was the stand that received the heaviest second CT treatment. The rotation age was set at 85

yr for all 3 regimes. The economic and operability variables were specified as follows: (1) a

cost of $100/ha were applied to all 3 regimes to cover the expense of a regeneration

assessment survey; (2) the fixed costs associated with equipment transport and basic

administration for each CT treatment was set at $100/ha; (3) the variable costs associated with

stumpage, renewal, harvesting, transportation and manufacturing in units of dollars per cubic

metre of merchantable volume harvested at rotation, was set at $100/m3 for the control

regime, and $60/m3 for the regimes involving the CT treatments; note, this cost differential is

principally due to the reduction in harvesting and manufacturing costs due to increased spatial

pattern uniformity and decreased piece-size variation commonly attributed to thinning

treatments; (4) similar to (3), the variable costs associated with the first and second thinning

yields were set at $100/m3 and $70/m3, respectively; (5) interest and discount rates were set at

2 and 4%, respectively; (6) a quadratic mean diameter of 16 cm was set as an operability

target; and (7) the simulation year was set to 2011.

Figure 3 illustrates the resultant mean volume-density trajectories for each regime within

the context of the traditional SDMD graphic. The stands at the time of the first thinning (45

yr) were at the midway point between the 14 and 16 m dominant height isolines, slightly

above the 10 cm quadratic mean diameter isoline, midway between the 0.6 and 0.7 relative

density isolines, and just above the 40% mean live crown ratio isoline. The interpolated

values for these and other values were as follows: mean dominant height of 15.2 m, quadratic

mean diameter of 10.3 cm, relative density of 0.64, mean live crown ratio of 41%, mean

volume of 52 dm3, stand density of 3575 stems/ha, and basal area of 29.7 m2/ha. Thus the

stands had met the minimum conditions for CT.

The first thinning reduced density stress levels by approximately 30% (relative density

indices declining from 0.64 to 0.45) and placed the residual stands exactly on the upper

threshold of the optimal density management window (i.e., 0.45 relative density index). The

treatment removed approximately 31% of the basal area and resulted in a merchantable

volume recovery of 33 m3/ha. At the time of the second thinning (65 yr), both of the treated

stands were almost on the 19 m dominant height isoline, midway between the 14 and 16 cm

quadratic mean diameter isolines, just above the 0.7 relative density isoline, and

approximately intersecting the 35% mean live crown ratio isoline, which is the minimum

value allowed for implementing a CT treatment. At this stage, the interpolated values for

these and other values were as follows: mean dominant height of 18.9 m, quadratic mean

diameter of 15.1 cm, relative density of 0.71, mean live crown ratio of 36%, mean volume of

138 dm3, stand density of 1750 stems/ha, and basal area of 31.4 m2/ha. For Regimes 2 and 3,

the second CT treatment removed 30% and 35% of the basal area, respectively, which

resulted in a merchantable volume recovery of 52 m3/ha and 61 m3/ha, respectively. Table 10

provides a complete list of the rotational and thinning yield estimates by regime. The derived

stand-level performance indices are given in Table 11.

Development and Utility of an Ecological-based Decision-Support System … 161

Figure 3. Graphical illustration of the dynamic SDMD for black spruce and jack pine mixtures. Note

the following principal components of the SDMD: (1) isolines for mean dominant height (Hd; 6-24 m

by 2 m intervals), quadratic mean diameter (Dq; 4-24 cm by 2 cm intervals), mean live crown ratio (Lr;

35, 40, 50,…, 80%), relative density index (Pr; 0.1-1.0 by 0.1 intervals); (2) self-thinning rule at a Pr =

1.0 (solid diagonal line delineating the outer boundary of the size-density region); (3) lower and upper

Pr values delineating the optimal density management window (Dm; 0.32 ≤ Pr ≤ 0.45); (4) crown

closure line (solid diagonal line delineating the inner boundary of the size-density region); and (5)

expected 85 yr size-density trajectories with 1 yr intervals denoted for 3 user-specified density

management regimes for stands situated on sites of moderate productivity (SI = 17). Regime 1 consisted

of a regeneration density of 5000 stems/ha with no thinning. Regime 2 consisted of a regeneration

density of 5000 stems/ha with 2 commercial thinnings: one at 45 yr in which 1500 stems/ha were

removed and a subsequent one at 65 yr in which 700 stems/ha were removed. Similarly, Regime 3

consisted of a regeneration density of 5000 stems/ha with 2 commercial thinnings: one at 45 yr in

which 1500 stems/ha were removed and a subsequent one at 65 yr in which 805 stems/ha were

removed. Source: SSDMM algorithm.

Evaluating the regimes in terms of the realization of the multiple objectives under

consideration, it is evident that commercial thinning is a viable treatment when managing

mixed stands. Density-dependent mortality rates within the thinned stands were considerably

less than those within the unthinned stand during the time from the first treatment to the time

of the second treatment: total densities declined by 1049 stems/ha within the control stand

versus 325 stems/ha within the thinned stands. Similar trends were observed from the time of

the second thinning to rotation age: total densities declined by 712 stems/ha within the control

stand versus 60 stems/ha for Regime 2, and 17 stems/ha for Regime 3.

162 Peter F. Newton

for black spruce and jack pine mixtures subjected to mid-rotation

commercial thinning treatments. Values in parenthesis denote yields

derived from the two CT treatments (ordered by time of treatment)

Attributea Regimeb

(t = T) 1 2 3

A(t ) (yr) 85 85 85

Hˆ d (t ) (m)

Dˆ q ( t ) (cm) 17.3 19.0 19.2

Gˆ ( t ) (m /ha)2

43 28 27

ˆ

P (%/100) 1.02 0.47 0.47

r (t )

127 78 (16, 26) 75 (16, 30)

Vˆc ( s ) (m3/ha)

(t )

Vˆl ( s ) (m3/ha)

(t )

(t )

(t )

a - As defined in Table 9.

Development and Utility of an Ecological-based Decision-Support System … 163

b - Regime 1 - NI = 5000 (control); Regime 2 - NI = 5000 with T2 A (1) = 45/ T2 N (1) = 1500 + T2 A ( 2 ) =

65/ T2N ( 2 ) = 700; Regime 3 - NI = 5000 with T3A (1) = 45/ T3N (1) = 1500 + T3 A ( 2 ) = 65/ T3N ( 2) = 805.

Table 11. Stand-level performance indices for black spruce and jack pine mixtures

subjected to mid-rotation commercial thinning treatments

Indexa Regimeb

1 2 3

RMAI (m3/ha/yr) 3.7 3.5 3.5

RBMI (t/ha/yr) 3.2 3.5 3.6

RCAI (t/ha/yr) 1.6 1.8 1.8

RSL (%) 46 37 37

RLV(s) (%) 59 58 58

RLV(r) (%) 68 68 69

EP(s) (%) - 15 16

EP(r) (%) - 5 5

SO (%) 7 8 8

SS (m/m) 102 95 94

WD (g/cm3) 0.45 0.47 0.47

BD (cm) 2.75 2.79 2.79

a - As defined in the text.

b- As defined in Table 10.

In terms of site occupancy, the thinned stands had fully reoccupied their sites by rotation

age as measured by their relative densities (0.65 and 0.62 for Regimes 2 and 3, respectively;

Table 10). Crop trees within the thinned stands had fully adjusted to their newly given space

from the second thinning just prior to rotation age (i.e., stand ages of 80 and 83 yr for Regime

2 and 3, respectively). Based on a 16 cm quadratic mean diameter threshold, the thinned

stands achieved operability status 10 years earlier than the control regime (66 versus 76 yr).

Although merchantable volumetric yields were slightly less for the thinned stands, biomass

productivity and carbon sequestration potential were greater (Table 11). The percentage of

lumber volume recovered over the rotation was approximately equivalent among the regimes,

irrespective of sawmill-type. The economic-based metrics suggested that CT resulted in an

approximate 10% gain in efficiency relative to the control regime. This differential is partially

due to the time-sensitive nature of the net revenues recovered from the end-products obtained

from the CT treatments. The lower costs of harvesting, transportation and manufacturing also

contributed to this result. The duration of optimal site occupancy did not vary much among

the regimes and with the exception of the years immediately following the CT treatments

(response delay period), all the regimes had fully occupied their sites once they had attained

initial crown closure status. Stand stability and branch diameters increased slightly with

thinning whereas mean wood density decreased slightly. Although these results present CT in

a positive light in terms of capturing expected mortality, increasing biomass productivity and

carbon sequestration potential, improving economic efficiency and enhancing stand stability,

the results are dependent on the specified regime chosen and the economic assumptions

employed. Apart from the specific applicability of this example, the demonstration clearly

164 Peter F. Newton

illustrates the utility of the SSDMM in terms of managing for multiple objectives within the

black spruce and jack pine mixed stand-type.

A large number of relationships derived from applied ecology, plant population biology

and forest science, are used in the development of SDMDs (Drew and Flewelling, 1977; Jack

and Long, 1996; Newton, 1997). These include the reciprocal equations of the competition–

density and yield–density effect (Kira, 1953; Shinozaki and Kira, 1956), self-thinning rule

(Yoda et al., 1963), relative density indices (Ando 1962, Drew and Flewelling, 1979), and

forest production theories (Langsaeter, 1941; Drew and Flewelling, 1979). The integration of

these biologically-based constructs within the modular-based SSDMM provides an ecological

foundation for density management decision-making.

One of the principal relationships employed is the self-thinning rule which is used to

represent the asymptotic size-density relationship within stands undergoing density-dependent

mortality. Quantitatively, the power exponent of this relationship for black spruce and jack

pine mixtures was found to be -1.2 which is significantly (p ≤ 0.05) different from the

theoretical expected value of -1.5, as postulated under the rule‘s traditional geometric

deviation (Yoda et al., 1963). However, the self-thinning exponent is much closer to the value

of -1.3 which was proposed for a wide range of tree species based on a mechanistic

reformation (Enquist et al., 1998) employing the universal scaling law (West et al., 1997).

This derivation is applicable to plant species which have a fractal-like biological resource

distribution network (West et al., 1997). Assuming that (1) individuals compete for spatially

limited resources, (2) resource use per individual Q scales with their mass (m) according

3/ 4

to Q m , and (3) and growth continues until all available resources have been utilized,

the maximum number of plants which can be supported per unit area (Nmax) can be related to

the rate of resource supply per unit area (R) and the average rate of resource use per

individual Q , according to the relationship, R Nmax Q N max m3/4 . As a population

reaches full site occupancy and the rate of resource use and the rate of resource supply

approaches equivalency within a given environment, R becomes a constant. Hence,

Nmax m3/4 , or more generally, m 0 Nmax

4/3

where 0 is a constant of proportionality.

Therefore by extension, self-thinning black spruce and jack pine mixed stands may be at a

stationary equilibrium condition in which the rate of resource supply is equivalent to the rate

of resource.

Self-thinning deviations proposed by Yoda et al. (1963) and Enquist et al. (1999) assume

that asymmetric competition for finite resources is the principal determinate underlying

density-dependent mortality within plant populations. Although this assumption has been

widely supported by numerous studies, other factors may also be at play within density-

stressed coniferous tree populations. Physical competition for space in which neigbhouring

crowns collide during high wind events commonly results in spatially noncontiguous

canopies due to the loss of branches and associated leaf area (Rudnicki et al., 2001). Over

time, such wind-induced crown abrasions and resultant loss of foliar mass for trees within the

Development and Utility of an Ecological-based Decision-Support System … 165

lower size classes, may produce a mortality pattern analogous to that observed for a light-

based dominance-suppression competitive relationship (i.e., resource pre-emption

competition process in which the smaller individuals do not receive sufficient solar radiation

due to shading from the larger individuals which eventually results in declining growth rates

and subsequent mortality (e.g., Newton and Jolliffe, 2003)). Newton (2006a) derived a

mechanical-based reformation of the self-thinning rule for monospecific jack pine stands

based on this concept. Given the sway dynamics, crown collisions and the noncontiguous

nature of crown cover (crown shyness) commonly observed within self-thinning mixed

coniferous stands at the later stages of stand development, and the concordance between the

empirical self-thinning exponent for mixed stands ( ̂ 1 = -1.2) and that predicted by Newton‘s

(2006a) reformulation ( 1.3 1 1.0 ), suggest this mechanical reformation and its

assumptions (e.g., competition for physical space is partially responsible for the observed

self-thinning pattern) may be applicable to mixed stands as well.

Another important linkage between the SSDMM and ecological theory relates to the

relationship between net production and site occupancy, which is used to define the optimal

density management window. Conceptually, net production increases with increasing site

occupancy until an asymptote is reached for a given species, site quality and stage of stand

development (Langseter, 1941; Mar:Möller, 1954; Assmann, 1970). Additional increases in

site occupancy results in a decline in net production, principally due to density-dependent

mortality arising from the self-thinning process. Thus if the objective is to maximize biomass

productivity and by extension carbon sequestration potential, then stands should be allowed to

achieve full occupancy. Once attained, they should be maintained at the asymptotic

occupancy-productivity condition via density management treatments. For black spruce and

jack pine mixed stands, this condition is represented by the optimal density management

window as delineated by relative densities indices between 0.32 and 0.45. Hence,

conceptually, mixed stands managed below the 0.32 relative density threshold are not

optimally occupying the site and thus not achieving their full productivity potential.

Conversely, stands in which density-stress levels are above the 0.45 relative density threshold

are likely to incur substantial density-dependent mortality which may result in productivity

losses and negative carbon balances. Operationally, however, maintaining stands within this

optimal window is currently impractical given the necessity to implement numerous light and

costly thinning treatments. Nevertheless, the maturing bio-economy along with developing

carbon markets may make this management proposition more economically amiable in the

future.

Ecologically, density management treatments directly affect the competitive

interrelationships within forest tree populations. Treatments such as PCT and CT within

density-stressed stands immediately reduce the intensity and occurrence of symmetrical and

asymmetrical competitive interactions. The temporary reduction or elimination of these

competition pressures increases the availability of moisture, nutrients, solar radiation and

physical growing space, for the remaining crop trees. Thinning from below in which the

smallest trees are removed provides the residual crop trees with an immediate influx of

moisture and nutrients which are shared equally. This competition process is also known as a

resource depletion process in which all competitors passively acquire an equal share of the

available below ground resources on a per-unit size basis (Newton and Jolliffe, 2003).

Conversely, selection thinning in which the trees with the greatest potential to respond to

166 Peter F. Newton

treatment are left and all others are removed, commonly results in a residual population

comprised mostly of trees from the co-dominant crown classes. Essentially, selection thinning

results in an immediate increase in the availability of both below and above ground resources.

In contrast to the passive nature of the resource depletion process, competition for solar

radiation and physical space is an asymmetrical process in which larger-sized competitors

acquire a disproportionate share of the these resources at the expense of the smaller-sized

competitors on a per-unit size basis (Newton and Jolliffe, 2003). The self-thinning stage of

stand development in which the smallest individuals incur mortality is largely driven by a

resource pre-emption process. Thus understanding resource competition processes and their

effects is an essential prerequisite to sound density management decision-making.

In essence, the modular-based SSDMM presented in this study for mixed stands provides

forest managers with an ecological-based decision-support tool for manipulating competitive

relationships within forest tree populations in order to realize single or multiple stand-level

management objectives. In relation to the evolving bio-economy and carbon markets, the

SSDMM can also be used to derive optimal density management regimes for these objectives.

For example, in a general sense, stands should be managed so that they (1) do not excessively

self-thin themselves and thereby do not generate large amounts of abiotic plant material that

could contribute to a negative carbon budget, (2) allocate a greater proportion of their

resources to foliage production in order to increase CO2 sequestration rates, and (3) produce

large volumes of dimensional lumber products so that the sequestrated carbon is stored

infinitely.

forecasting and contrasting volumetric, product, economic and ecological rotational outcomes

of mixed stands to density manipulation. The SSDMM represents a consequential

contribution to the growing list of comprehensive models that have been developed for

addressing multiple resource management objectives (e.g., Di Lucca, 1999; Pretzsch et al.

2002; Hynynen et al., 2005; Kotze and Malan, 2007) and likewise will enable boreal resource

managers to address a broader range of management objectives. As management objectives

shifts towards the production of high-value end-products, bio-energy and carbon

sequestration outcomes, the modular-based SSDMM has the potential to be at the forefront in

facilitating this transformative change. The approach employed in which concepts from

ecology, plant population biology and forest science are combined and integrated within a

common analytical framework, exemplifies the synergy that can be realized through a multi-

disciplinary approach to model development.

ACKNOWLEDGEMENTS

The author expresses his appreciation to: (1) Dave Wood, Forest Ecosystem Science Co-

operative Inc, Thunder Bay, Ontario, Canada, for access to the temporary and permanent

sample plot measurements and records used for model calibration; (2) Dr. I. Amponsah,

Development and Utility of an Ecological-based Decision-Support System … 167

Sustainable Resource Development, Alberta, Canada, Dr. D. Reid, Research Scientist, Centre

for Northern Forest Ecosystem Research, Lakehead University, Thunder Bay, Ontario,

Canada, Dr. M. Sharma, Research Scientist, Ontario Forest Research Institute, Sault Ste.

Marie, Ontario, Canada, and John Parton, Provincial Growth and Yield Coordinator, Ontario

Ministry of Natural Resources (OMNR), Timmins, Ontario, Canada, for analytical advice; (3)

NaturaLogic Inc., North Bay, Ontario, Canada, for VB.Net software design assistance; and

(4) Forestry Research Partnership and the Canadian Wood Fibre Centre for fiscal support.

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Editor: WenJun Zhang, pp. 173-204 © 2012 Nova Science Publishers, Inc.

Chapter 8

HERPETOLOGY: PAST, PRESENT AND FUTURE

and Raimundo Real5

1

'Rui Nabeiro' Biodiversity Chair, CIBIO (Centro de Investigação em Biodiversidade e

Recursos Genéticos) – University of Évora, 7004-516 Évora, Portugal.

2

Department of Life Sciences, Imperial College London,

Silwood Park Campus, Ascot (Berkshire) SL5 7PY, United Kingdom.

3

CICGE (Centro de Investigação em Ciências Geo-Espaciais), Faculty of Sciences,

University of Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal.

4

CIBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos) – University

of Porto, Instituto de Ciências Agrárias de Vairão,

R. Padre Armando Quintas, 4485-661 Vairão, Portugal.

5

Biogeography, Diversity and Conservation Lab,

Department of Animal Biology,

Faculty of Sciences, University of Málaga,

29071 Málaga, Spain.

ABSTRACT

We present a review of the concepts and methods associated to ecological niche

modeling illustrated with the published works on amphibians and reptiles of the

Mediterranean Basin, one of the world's biodiversity hotspots for conservation priorities.

We start by introducing ecological niche models, analyzing the various concepts of niche

and the modeling methods associated to each of them. We list some conceptual and

practical steps that should be followed when modeling, and highlight the pitfalls that

should be avoided. We then outline the history of ecological modeling of Mediterranean

amphibians and reptiles, including a variety of aspects: identification of the ecological

niche; detection of common distribution areas (chorotypes) and other biogeographical

patterns; analysis and prediction of species richness patterns; analysis of the expansion of

native and invasive species; integration of molecular data with spatial modeling;

174 A. Márcia Barbosa, Neftalí Sillero, Fernando Martínez-Freiría et al.

status; and prediction of future conservation problems, including the effects of global

change. We conclude this review with a discussion of the research that still needs to be

developed in this area.

1.1. What Are Ecological Niche Models?

ecological niche of a species (for reviews see Guisan and Zimmermann, 2000, Austin, 2002,

Rushton et al., 2004, Guisan and Thuiller, 2005, Araújo and Guisan, 2006, Guisan et al.,

2006; Peterson, 2006, Austin, 2007, Jiménez-Valverde et al., 2008, Morin and Lechowicz,

2008). The primary objective of an ENM is to relate different types of eco-geographical

(environmental, topographical, human, or purely spatial) variables to the distribution of a

species, in order to identify the factors that limit and define its niche. The final result of an

ENM may be a spatial representation of the habitats that favor the presence of a species

(Guisan and Zimmermann, 2000). An ENM can be used to predict suitable habitats in poorly

sampled areas (Engler et al., 2004), or in the future under expected environmental changes

(e.g. Shugart, 1990, Sykes et al., 1996, Teixeira and Arntzen, 2002, Araújo et al., 2006). It

can also be related to trends in species abundance (Araújo and Williams, 2000, Real et al.,

2009) or to their probability of persistence in certain areas (Araújo and Williams, 2000).

ENMs have become popular due to the need for efficiency in the design and implementation

of conservation management (Bulluck et al., 2006).

Several definitions of ecological niche have been proposed over time. The first one is due

to Grinnell (1917), who understood the ecological niche as a subdivision of the habitat

containing the environmental conditions that allow the individuals of a species to survive and

reproduce. This concept is based on variables for which the species compete (climatic or

scenopoetic variables according to Soberón, 2007; see also Hirzel and Le Gay, 2008, Wiens

et al., 2009). On the other hand, Elton (1927) emphasized the functional role of a species in a

community, especially its position in the food chain, depending on variables that can be

consumed by the species (nutrients or bionomic variables in Soberón, 2007). Finally,

Hutchinson (1957) defined mathematically the fundamental and the realized niche (Figure 1).

The fundamental niche is an n-dimensional volume of environmental space within which a

species can maintain a viable population and persist over time without immigration. Each

dimension is an environmental variable that influences the niche. The realized niche is a part

of the fundamental niche where the species is not excluded by competition. The main

difference between Grinnell‘s and Elton's niche concepts relative to Hutchinson‘s one is that

the former two used the term niche to refer to places in the environment that can

Ecological Niche Models in Mediterranean Herpetology 175

accommodate the species, while for Hutchison, species, and not the environment, have

niches.

Jackson and Overpeck (2000) replaced the concept of realized niche by that of potential

niche, which is the part of the fundamental niche that is available for the species; some parts

are not available because not all possible combinations of variables under which the species

could survive currently exist in the environment. Similarly, Colwell and Rangel (2009) and

Soberón and Nakamura (2009) considered that there are three different niches: the

fundamental niche, the potential niche (i.e. the existing part of the fundamental niche), and

the realized niche. Finally, Pearson (2007) introduced the concept of occupied niche, to which

species distributions are limited by historical, geographical, and biotic factors (dispersal

ability, competition, predation, parasitism, symbiosis).

Figure 1. The easiest way to visualize the different ecological niches is the BAM (biotic, abiotic,

movement) diagram (see Soberón and Peterson, 2005, Soberón, 2007), which represents the theoretical

environmental space divided into the three main factors that limit the distribution of a species. The

suitable habitat corresponds to the area common to all three factors, which represents the occupied

niche (ON; sensu Pearson, 2006). The area shared by A and M represents Grinnell's niche (GN). The

area shared by A and B is Elton's niche (EN). The whole A area is Hutchinson's fundamental niche

(FN). A species can live in climatically favorable regions to which it has been able to disperse and from

which it is not excluded by biotic interactions. Regions that fail to meet all these conditions are not

suitable for the species' presence.

176 A. Márcia Barbosa, Neftalí Sillero, Fernando Martínez-Freiría et al.

To these concepts we must add two other important ones: the source-sink theory

(Pulliam, 1988, Pulliam, 2000) and dispersal limitation (Holt, 2003). According to the source-

sink theory, some populations may occupy unsuitable habitats (sinks) due to immigration

from healthier nearby populations (sources). Although individuals in the sinks may die due to

the adverse conditions, they are replaced by new immigrants. Here, the realized distribution

goes beyond the fundamental niche, as the species occupies habitats that are inadequate and

not contained in the niche (Pulliam 1988, Pulliam 2000). With dispersal limitation, a species

can be absent from suitable habitats for historical reasons or due to limitations in its ability to

disperse to those habitats (Holt, 2003).

(predictive). Mechanistic models are based on hypothetical cause-effect relationships between

the variables and the species' distribution, which makes them more ecologically meaningful.

They use variables that, according to existing theory or experimental results, have a direct

effect on the species' survival, such as temperature or humidity. In contrast, correlative ENMs

are based on statistical correlations between species occurrence and variables that do not

necessarily have a direct effect on the species, such as altitude or latitude, but that summarize

the effects of various direct factors, and are easier to measure (Guisan and Zimmermann,

2000). Correlative models tend to provide more accurate predictions than mechanistic ones,

and they can also have an explanatory component: more than simply predicting the species'

geographic distribution, they may reflect important aspects of its biology and natural history,

and suggest underlying ecological factors not included in the existing theory (e.g. Peterson

and Cohoon, 1999).

Stoms et al. (1992) proposed an alternate classification into deductive and inductive

models, based on the conceptual approach used to define the species-environment

relationship. Deductive models use expert opinion on the ecological requirements of a species

to infer where the appropriate areas are within the studied territory. Such models are

subjective and limited to the few species and habitats whose relationship is sufficiently

known (Araújo et al., 2005). Conversely, inductive models perform an environmental

characterization, through statistical analyses, of the species' distribution range, to infer its

ecological preferences. Then, following a more objective deductive process, these preferences

are extrapolated to the studied territory (Pereira and Itami, 1991, Aspinall and Matthews,

1994, Woodward and Cramer, 1996).

The existence of a correlation between a variable and the distribution of a species does

not imply a cause-effect relationship. The explanatory interpretation of ENMs should thus be

taken with caution, as the causal effect of one variable on the species can be masked by the

effects of other non-causal variables that are correlated with it (MacNally, 2000; see section

1.7). In fact, Kerney (2006) believes that only mechanistic models can predict the niche of a

species, as they are the only ones that rely on a theoretical foundation for such cause-effect

relationships. However, the theoretical basis necessary for building mechanistic ENMs (e.g.

MacNally, 2000) is seldom available. If there is not sufficient knowledge about the species to

identify the direct determinants of its distribution, correlative ENMs based on statistical

Ecological Niche Models in Mediterranean Herpetology 177

relationships can be very helpful, as long as the constraints and limitations inherent to the

statistical analyses are taken into account (MacNally, 2000).

The correlative methods of modeling species' niches can be classified into three main

groups: presence/absence methods, profile methods, and presence-only methods. The first

kind relates a binary dependent variable (i.e., with only two possible values, such as presence

and absence, one and zero) to a series of independent variables, so it induces the conditions

that make a species present rather than absent. This kind of methods includes generalized

linear models (GLM), such as discriminant analysis (Lachenbruch, 1975), logistic regression

(Hosmer and Lemeshow, 1989), and the favorability function (Real et al., 2006); and

generalized additive models (GAM; Hastie and Tibshirani, 1990), which are more complex

and usually fit the data better, but may be less general, i.e., less applicable to other data sets.

Profile methods compare the environmental conditions in the observed presence areas

with the conditions available in the whole study area, thus outlining presence against a

background. These methods include ecological niche factor analysis (ENFA; Perrin, 1984,

Hirzel et al., 2002), the genetic algorithm for rule-set production (GARP; Stockwell and

Noble, 1992), and maximum entropy (Maxent; Phillips et al., 2004). The definition of these

methods as "presence-only" is incorrect, as they compare presence areas with all the

environmental space analyzed (the so-called background), which includes both presence and

non-presence areas (e.g. Phillips et al., 2009). From this background, some authors select

pseudo-absences (e.g. Chefaoui and Lobo, 2008).

Presence-only data can be modeled, for example, with overlap analysis (Brito et al., 1999,

Arntzen and Teixeira, 2006), which overlays the species‘ presence area to the environmental

variables to derive the range of environmental conditions under which the species can live.

Mahalanobis distance (Etherington et al., 2009), the multidimensional envelope (MDE) used

in BIOCLIM (Busby, 1991), and the HABITAT (Walker and Cocks, 1991) and DOMAIN

models (Carpenter et al., 1993) are other examples of truly presence-only methods. Another

way to analyze only presence data is to use binary models such as logistic regression to

confront, rather than presence and absence of a species, the presence of one species or

subspecific variant against the presence of another one (Romero and Real, 1996, Brito and

Crespo, 2002, Arntzen and Alexandrino, 2004, Real et al., 2005, Arntzen and Espregueira

Themudo, 2008).

There are more complex methods, such as random forests, classification and regression

trees (CART), multivariate adaptive regression splines (MARS), and artificial neural

networks (ANN). Moisen and Frescino (2002) compared the effectiveness of various methods

in modeling the distribution of simulated and actual data on forest variables. The models built

with more sophisticated techniques showed better results with simulated data, but for real data

the difference were not significant and a simple linear model worked almost as well as

complex models. Complex methods may describe species‘ distributions more accurately, but

produce models more difficult to interpret from an ecological point of view. Moreover, they

seldom provide intelligible information on which and how environmental variables are related

to species‘ distributions, an information that can be valuable from a conservation standpoint.

178 A. Márcia Barbosa, Neftalí Sillero, Fernando Martínez-Freiría et al.

A compromise between complexity and intelligibility may be desirable in ENMs meant for

use in conservation and management.

Some absence records may actually correspond to presences that were not detected for

various reasons, including insufficient or no surveying effort. This affects not only

presence/absence modeling methods, but also profile methods, which will include these false

absences in the background but outside the presence area; and presence-only methods, which

will fail to include these undetected presences in the analysis. When the survey is not too

deficient or spatially biased (Reese et al., 2005), explicitly including absence data can

improve the ENM by providing information on locations that may be less suitable for the

species (Hirzel et al., 2001; see also section 1.5) due to historical (e.g. barriers to dispersal),

biotic (competition, predation) or human restrictions (Guisan and Zimmermann, 2000,

Anderson et al., 2002). Even when the data include false absences, these are often associated

to low local abundance of the species, so their inclusion can improve the relationship between

ENM predictions and actual species abundance (Real et al., 2009, Barbosa et al., 2009).

If the aim is to obtain the fundamental niche of the species, the use of absence data may

have an undesirable effect by excluding suitable environmental areas where the species is not

present due to historical limitations or biotic interactions. But if the goal is to approach the

realized niche and the data are of generally good quality, it is advisable to explicitly include

absences, even if they are not all correct. In any case, the quality of absence data is as

important for the models as the quality of the presence data.

The application of profile or presence-only methods may be more desirable in the case of

very limited or dispersed presence data, such as those taken from herbaria or museum

collections (Elith et al., 2006) or from samples identified through molecular analysis (Real et

al., 2005). Presence/absence models based on distribution atlases have been widely used with

success and have shown good relationships with independent data on species abundance (Real

et al., 2009) and good extrapolation ability, both to contiguous geographic areas (Barbosa et

al., 2009) and to finer resolution scales (Barbosa et al., 2010). To be able to model presences

and absences with more reliable data, it would be useful to publish information on areas that

have been surveyed but where the target species were not found.

Abundance data can also be modeled (e.g. Anadón et al. 2010). Abundance provides

more information than the simple presence or absence of species, but it also contains more

noise and is more costly to measure, so it is rarely available. Abundance data can be analyzed

with generalized linear models that assume a Poisson distribution, suitable for count data, or a

negative binomial distribution, when there is over-dispersion of these data (i.e., when the

variance is greater than the mean). When the data contain many more zeros than would be

expected according to any of these distributions, zero-inflated models are more appropriate

(Zuur et al., 2009).

Not all ENMs represent the same niche: the result varies depending on the method and

the type of variables used (Soberón and Nakamura, 2009; Figures 1 and 2). It is widely

accepted that mechanistic ENMs predict the fundamental niche (Pearson and Dawson, 2003,

Kearney and Porter, 2004, Kearney and Porter, 2009, Rodder et al., 2009) and correlative

ENMs are closer to the realized niche, since the recorded presences are determined by biotic

Ecological Niche Models in Mediterranean Herpetology 179

and abiotic factors (Pearson and Dawson, 2003, Araújo and Guisan, 2005, Guisan and

Thuiller, 2005, Soberón and Peterson, 2005, Kearney, 2006, Morin and Lechowicz, 2008,

Pearman et al., 2008, Colwell and Rangel, 2009, Lobo et al., 2010). Within correlative ENMs,

those calculated with presence/absence data yield the probability of finding the species in

each portion of the study area. Above a chosen probability threshold, these models can be

considered to represent the spatial distribution of the habitats that are both suitable and

occupied by the species (Guisan and Zimmermann, 2000; Pearson, 2007). Models based only

on presence data provide an indication of the suitability of the habitat, not necessarily

implying that the species will be found there.

Correlative methods forecast the distribution of the species through correlations among

environmental variables. The values of these variables are determined by the geographical

positions of the species‘ records. In other words, correlative ENMs are sensitive to the

topology of presences (their geographical positions and the relationships between them). If

we want to calculate a species‘ potential distribution without considering its geographical

records, we should use a mechanistic modeling method.

Figure 2 The idea of habitat suitability actually corresponds to a gradient (Soberón, 2010) with

extremely favorable habitats on one end, and completely unfavorable ones (where the species simply

cannot survive) on the other. The position of the species in this gradient depends on the intensity with

which climate, dispersal and biotic interactions act. In habitats with unfavorable climate, the species can

survive for some time if there is immigration and there are no competing species. In contrast, the

species may be absent from a climatically favorable area if it is excluded by other species or if

geographical barriers prevent its access. Intermediate situations represent small populations that subsist

despite unfavorable climatic conditions and biotic interactions. See abbreviations in Figure 1.

180 A. Márcia Barbosa, Neftalí Sillero, Fernando Martínez-Freiría et al.

However, not all authors acknowledge that ENMs predict the ecological niche. For

Kearney (2006), the niche is a mechanical rather than descriptive concept. In this way,

correlative ENMs model only habitats. In contrast, mechanistic ENMs model the niche and

are the only ones that establish a mechanical connection between the model and the species.

Kearney (2006) considers that the niche is determined by the factors that allow a species to

survive, which implies a mechanical relationship between the species and these factors, while

the habitat is simply the place where the species lives. Jiménez-Valverde et al. (2008) and

Lobo (2008) also argue that correlative ENMs predict habitats rather than niches: if the

absences of the species are recorded in areas where they are excluded by biotic factors, the

model calculates the realized distribution; if they are taken from areas where the species is

excluded only by abiotic factors, the model calculates the potential distribution. However,

these "distributions" do not correspond to the realized and fundamental niches, respectively.

Godsoe (2010) goes further by proving mathematically that it is impossible to calculate the

niche: the only thing that can be determined is whether the set of variables used to calculate

an ENM belongs to the niche or not.

Modeling, and Which Situations Should Be Avoided?

The first step in modeling the distribution of a species is to decide which is the motive for

the work (to know the potential distribution, the limiting factors…) and which are the most

appropriate modeling parameters (distribution data, environmental variables, study area,

modeling method, resolution scale). Once these are defined, we must gather chorological (i.e.

location) data of the species and create a database, for example from distribution atlases

(Sillero et al., 2009), museum collections (Brito et al., 2008) or systematic surveys (Hirzel

and Guisan, 2002, Martínez-Freiría et al., 2008, Sillero, 2009). Such surveys can be oriented

to establish only the presence of the species (Martínez-Freiría et al., 2008) or to record also

their absence (Anadón et al., 2006). The spatial distribution of absences determines the type

of ecological niche that will be predicted and, therefore, can significantly alter the outcome of

the models (Figure 1). It is also important that the database has no geographical errors (Sillero

et al., 2005). Even if the ENM is to be produced with a low (i.e., coarse) spatial resolution, it

is recommended that the records of the species are taken with a GPS. This will minimize

errors in the geographical coordinates and allow the data to be used for ENMs with different

spatial resolutions (Carretero et al., 2008, Kaliontzopoulou et al., 2009).

The chorological records should be independent of one another, i.e. should not be

spatially autocorrelated (Koenig, 1999, Dormann, 2007, Dormann et al., 2007). This

condition can only be fulfilled with systematic surveys. The autocorrelation of the surveying

effort must be uniform. Thus, the distribution of the records should correspond as much as

possible to the actual distribution of the species, or at least to the one observed in the field.

For example, the distribution of a species can be strongly aggregated or fragmented. This

variation in the degree of clustering observed in the sample of distribution records must have

a correspondence with reality. An appropriate sampling design with a consistent surveying

effort is the best way to minimize the problem of autocorrelation in the data.

Sample size also influences the results of ENMs (Hirzel and Guisan, 2002, McPherson et

al., 2004, Pearson et al., 2007, Wisz et al., 2008). The accuracy of the ENM first increases

Ecological Niche Models in Mediterranean Herpetology 181

substantially with sample size, and then stabilizes, reaching an asymptote (Stockwell and

Peterson, 2002). Teixeira and Arntzen (2006) study the variation in the number of records of

Chioglossa lusitanica throughout history and its effect on ENMs: from a certain number of

records, the ENM does not improve significantly. There is a minimum sample size below

which it is not possible to calculate an ENM, which depends on the modeling method used.

The types of modeling algorithms that can be used depend on the chorological data

available. Not all methods are equivalent or useful in all situations. To build a mechanistic

ENM, the knowledge on the biology and physiology of the species must be substantial

(Kearney and Porter, 2004, Kearney and Porter, 2009). For correlative ENMs, the

chorological data available will determine the type of modeling method that can be used. If

we have both presence and absence data, we can apply a variety of methods such as GLM or

GAM. If we have presence data within a wider background with environmental data, we can

apply profile methods such as Maxent (Phillips et al., 2004, Phillips et al., 2006), ENFA

(Hirzel et al., 2002) or GARP (Stockwell and Noble, 1992). When data are available only for

the presence area, we can apply presence-only methods such as Mahalanobis distance

(Etherington et al., 2009), BIOCLIM (Busby, 1991), HABITAT (Walker and Cocks, 1991) or

DOMAIN (Carpenter et al., 1993). In each case, we will get an approximation to a different

ecological niche (Soberón and Nakamura, 2009). Moreover, depending on the position of

absences in the BAM diagram (Figure 1), i.e., which factor they derive from, the ENM will

also be different (Lobo et al., 2010).

Lobo et al. (2010) classify absences into three different types: contingent absences, which

correspond to environmentally suitable areas that are not occupied for historical or biotic

reasons; environmental absences, when the environment is in fact unsuitable for species

presence; and methodological absences, caused by survey deficiency. Contingent absences

are outside the realized niche but inside the fundamental one; environmental absences are

outside both niches; and methodological absences are included in both niches (Lobo et al.,

2010). The latter can be very important in amphibian and reptile species, as it is difficult to

ensure that a species is really absent from a place where it has not been detected. This is why

profile and presence-only modeling methods are largely used in herpetology. For comparison,

in the Mediterranean Basin in the last three years, thirteen modeling works were published in

which profile methods were used (Ficetola et al, 2007, Brito et al., 2008, Carretero et al.,

2008, Kaliontzopoulou et al., 2008, Martínez-Freiría et al., 2008, Ficetola et al., 2009, Santos

et al., 2009, Martínez-Freiría et al., 2009, Ribeiro et al., 2009, Rödder and Lötters, 2009,

Sillero, 2009, Sillero et al., 2009, Sillero, 2010), against four works with presence/absence

models (Arntzen and Espregueira Themudo, 2008, Real et al., 2008, Bombi et al., 2009, Real

et al., 2010).

There are differences in the way each method works. For example, ENFA cannot work

with categorical variables: they must be converted to quantitative values. GLM, GAM, GARP

and Maxent models can be projected to other geographical areas or sets of variables; ENFA,

on the other hand, does not allow the projection of the ENM. All methods mentioned here are

affected by correlations between variables, except for ENFA, which previously transforms the

variables into a set of uncorrelated factors, similar to the axes of principal component analysis

(Hirzel et al., 2002). The ability of many methods to discriminate between presences and

absences can be assessed, for example, with the Area Under the ROC (receiver operating

characteristic) Curve (AUC), although Lobo et al. (2008) warn against equating higher

discrimination with higher accuracy when models differing in species prevalence are

182 A. Márcia Barbosa, Neftalí Sillero, Fernando Martínez-Freiría et al.

compared. It is thus not advisable to compare the AUC of models for the same species in

different areas, or for different species in the same area (VanDerWal et al., 2009). ENFA does

not make it possible to calculate the AUC for comparison with other modeling methods and

algorithms. In some cases (GLM, GAM, ENFA) the result is unique, as there is not a random

process associated (e.g. Arntzen, 2006, Espregueira Themudo and Arntzen, 2007, Soares and

Brito, 2007, Arntzen and Espregueira Themudo, 2008, Santos et al., 2006, Ribeiro et al.,

2009, Santos et al., 2009; Sillero et al., 2009). Maxent, on the other hand, produces a different

ENM each time, requiring the calculation of multiple replicas (e.g. Martínez-Freiría et al.,

2008, Martínez-Freiría et al., 2009, Sillero, 2009, Sillero, 2010) and a final averaged ENM

(ensemble model; Araújo and New, 2007). In conclusion, each modeling method has its own

peculiarities, which must be taken into account before undertaking any modeling project.

The next step is the selection of variables that can theoretically influence and limit the

species‘ distribution. This selection is a subjective process and depends on the ecological

relevance of these variables for the modeled species and on their availability, particularly in a

spatially geo-referenced format (see Sillero and Tarroso, 2010 for free environmental data

sources on the Internet). However, ENMs are not necessarily spatial. Actually, in some

methods the last step is the spatialization of the ENM, which is just a mathematical formula

that relates several variables. When the variables are available in a spatial format that can be

incorporated in a Geographic Information System (GIS), the ENM can be represented in

space (e.g. Brito and Crespo, 2002). To comply with statistical theory, the variables should

not be correlated (Keitt et al., 2002, Diniz-Filho et al., 2003, Betts et al., 2006, Segurado et

al., 2006; see section 1.7), which is rarely possible in the real world. At least, we should

remove one variable from each pair of variables that have a high correlation, for example

greater than 70-75% (e.g. Martínez-Freiría et al., 2008), and point to the same causal factor.

However, we cannot tell if we are eliminating the most causal variable (if it is one of the two)

or the variable that correlates with it.

The use of a large number of variables in relation to the number of localities can increase

the risk of over-parameterization of the model, i.e. of including variables whose relationship

with the species is due to chance, and that can only describe the species‘ distribution in the

study area. It is also important to note that the factors determining the ecological niche in the

ENM are expressed differently depending on the scale: historical and abiotic factors are more

relevant on coarse scales (i.e., large areas), while biotic factors act mainly on local scales

(Peterson, 2006).

Once the variables are selected, we should ensure that the study area is adequate. This is

an important step, though it is rarely taken into account, and should be decided at the

beginning of the process along with the modeling aims. Ideally, the study area should include

the entire ecological range of the species: if the area is too small, part of the ranges of some

variables may be left out of the analysis and lead to incorrect results. However, Thuiller et al.

(2004) found no difference between ENMs when they reduced the size of the study area, but

only when they projected ENMs outside their geographic boundaries (see also Barbosa et al.,

2009). In addition, environmental data are often not available for the entire distribution area

of a species. Albert and Thuiller (2008) recommend not using large areas if the distribution of

the species is small. Stockwell and Peterson (2002) propose to divide the area, since ENMs

may react differently to different sample sizes, showing that the species‘ response to

environmental variables is not uniform throughout the study area. Other authors consider that

the definition of the study area should respond to biogeographical criteria (e.g. Sillero et al.,

Ecological Niche Models in Mediterranean Herpetology 183

2009). Perhaps the best method is to check that the response curves of the variables are not

truncated (Guisan and Thuiller, 2005). If a curve is truncated, the study area should be

increased until a normal curve is reached (and then the correlations between variables should

be measured again). In any case, we should avoid to define study areas with political criteria

such as national divisions when they do not correspond to natural limits (e.g. Brito et al.,

1996, Teixeira et al., 2001, Teixeira and Arntzen, 2002, Arntzen, 2006, Arntzen and Teixeira,

2006 ), although data availability is often limited by political boundaries.

ENMs assume an equilibrium between the species and the environment, i.e., that the

species occupies all available favorable habitats and is absent from all unfavorable ones

(Araújo and Pearson, 2005, Wiens et al., 2009). However, it is very unlikely that this

condition is met. If a species is still expanding its distribution, chorological records do not

represent the breadth of its ecological niche, and the ENM may not identify all potentially

favorable areas. One solution is to increase the size of the study area; another is to divide the

data into groups that simulate the dispersion and calculate the respective ENMs over the same

area (Saddler, 2010): if the ENMs are similar, they can be considered robust. We can also

limit the chorological sample to proven breeding sites (Ficetola et al., 2008, Ficetola et al.,

2009), which correspond to populations and not to dispersing individuals (which are not in

equilibrium). In the case of introduced species, the best approach may be to model the

distribution in their original area and then project the ENM to the introduced area (Ficetola et

al., 2007, Pearman et al. 2008, Beaumont et al., 2009, Rodder and Lötters, 2009).

Once the modeling method and the study area are defined, the species‘ chorological data

are gathered, and the predictor (and uncorrelated) variables are selected, we can calculate the

ENM. Although each modeling method provides a different type of information, an ENM

should be composed primarily of three items: a map of the predictions (as long as it is a

spatial model), the importance with which each variable contributes to the model, and a

measure of its accuracy. The map depicts the favorable habitats for the species, and is usually

composed of continuous values, bounded between zero (completely unfavorable) and one

(completely favorable). In profile models, this result is often called habitat suitability map

(HSM; Hirzel et al., 2002). However, in some cases, it is of interest to convert the HSM into a

(potential) distribution map, with only values of "present" and "absent". To do this, we have

to choose a threshold within the continuous range of the HSM to distinguish unfavorable

habitats (below the threshold) from favorable ones (above the threshold). The choice of

threshold is up to the researcher and depends on the modeling aims (for reviews see Liu et al.,

2005, Jiménez-Valverde and Lobo, 2007).

combination, so that the influence of each of them on the distribution of the species cannot be

distinguished, as they overlap each other. Strictly speaking, this occurs when the correlation

between the variables is 1, in which case the inclusion of one of these variables provides all

the predictive power of all of them. However, the explanatory power remains undetermined,

because we run the risk of attributing causal power to one variable when the one that actually

affects the species could be one excluded from the ENM.

184 A. Márcia Barbosa, Neftalí Sillero, Fernando Martínez-Freiría et al.

When there is correlation between the variables but it is lower than 1, which is what

occurs in the real world, the exclusion of correlated variables produces 1) a decrease in the

predictive ability of the ENM which is greater when the correlation between the variables is

lower, and 2) a loss of explanatory power of the variable kept in the ENM that increases with

increasing correlation. Therefore, in correlative ENMs, the elimination of highly correlated

variables simplifies the ENM with little loss of predictive power. However, ENMs can be

seriously affected in their explanatory power if the hypothetically relevant variables are not

all included, even when they are, and precisely because they are, correlated.

For example, Cartron et al. (2000) point out that if some of the relationships between

variables are negative, the effect that is operating on the variables may be weakened by

another, stronger mechanism, due to the relationships between them. Thus, in a system with

three variables, if two of the correlations are positive and one is negative, the predicted

relationships may not all be seen in the relationships between each pair of variables, since

there are effects operating in different directions (Bárcena et al., 2004). If, for example, a

species is favored by high temperatures and rainfall, but these variables are negatively

correlated in the analyzed territory (i.e., precipitation is higher where the temperature is

lower), the effect of each variable is weakened by the effect of the other. Only the inclusion

of the two correlated variables in the same ENM will allow detecting the actual effect of each

variable.

ENMs obtained inductively from the recorded distribution of a species follow certain

rules that guarantee their consistency with that distribution, and therefore do not require

validation with respect to their starting data. However, it is possible to validate whether an

ENM remains accurate when applied to similar chorological data sets in other geographical

areas or moments in time, or when it is used to determine other population parameters of the

species. An ENM should thus be validated with data different from those used to build it,

according to, and specifically for, the purpose for which it was built. For example, an ENM

made to be transferred to the future, such as those that predict species‘ potential distributions

under climate change scenarios (e.g. Araújo and Pearson, 2005, Araújo et al., 2006, Araújo et

al. 2008, Sillero, 2010) cannot be validated in the present.

We can, however, determine if the ENM is spatially transferable within the analyzed

area. To do this, we can divide the territory into sub-areas of recalibration and pseudo-

validation. The general ENM, obtained with data from the complete study area, can be

recalibrated in the first sub-area to then check if it works equally well in the second sub-area.

The two sub-areas can be defined either randomly or by applying the formula proposed by

Fielding and Bell (1997):

[1+(p-1)1/2]-1,

where p is the number of predictors in the ENM. The degree of agreement between the results

of recalibration and pseudo-validation can be estimated by comparing their respective values

of Kappa (Cohen, 1960), sensitivity, specificity, correct classification rate, or AUC (Fielding

and Bell 1997, Manel et al., 2001). However, we must keep in mind that a discrepancy

Ecological Niche Models in Mediterranean Herpetology 185

between recalibration and pseudo-validation does not imply that the recalibrated ENM is

incorrect, and certainly not that the general ENM is incorrect. It simply indicates that the

factors that act predominantly in the area of recalibration differ from those that do in the area

of pseudo-validation. The ENM to be used should, in any case, be the one based on the entire

study area, as general models tend to work better than those based on subsets of data (e.g.

Barbosa et al., 2009).

1.9. Are We Really Modeling the Ecological Niche, or Can We Overcome the

Concept of Niche When Modeling?

Environmental processes are inherently complex and vary with spatial and temporal

scales. This complexity is often based on the definition of laws or assumptions about the way

these processes work, often expressed in the form of mathematical or logical relationships,

which are the core of ENMs. Mechanistic ENMs, as correlative ones, are based on the

previous acceptance of relationships between a species and the factors that supposedly

determine its distribution. A considerable degree of idealization is therefore necessary to

describe the distributions of species with mechanistic ENMs.

Among other things, a mechanistic ENM requires accepting a mechanism on which to

base it. This approach is based on Newtonian mechanics, called into question since the early

Twentieth Century by quantum mechanics, which is formulated on the basis of subatomic

phenomena. Biological phenomena are also subject to uncertainty, which is one of the pillars

of quantum mechanics. This uncertainty arises not only from the inability to identify all the

factors involved in the process, but also from the inability to determine the final outcome of

the process even when all relevant factors are controlled. The different degrees of coherence

between phenomena are mathematically translated to correlations. Correlative ENMs may

thus represent coherence between natural phenomena more adequately than mechanistic

Newtonian models. Furthermore, living organisms not only respond to environmental factors:

environmental factors are also strongly conditioned by the action of living organisms. The

classic formulation of logic and mathematics is not well equipped to handle this formulation

on physical systems, and even less on live systems and the relationships between them. A

more realistic interpretation of the complex ecological and biological systems can come from

the application of fuzzy logic.

Fuzzy logic is a form of multi-valued logic that allows for several values of truth, but also

takes into account that these values are inaccurate. Fuzzy logic and its applications have their

origin in the theory of fuzzy sets proposed by Zadeh (1965), who established that a fuzzy set

is characterized by a membership function that assigns to each object in the set a degree of

membership ranging (with continuous values) from zero to one. The need for fuzzy sets arises

in situations where it is difficult to determine if an element belongs to a set or not. Classical

sets are special cases of fuzzy sets in which only two degrees of membership (0 and 1) are

allowed. Fuzzy logic has been used to predict species‘ distributions (Robertson et al., 2004),

to detect favorable areas for species (Real et al., 2005, Real et al., 2008, Real et al., 2009), to

analyze gaps in the protection of biodiversity using distribution models (Estrada et al., 2007,

2008, Real et al., 2006b), and to assess the impact of climate change on species‘ distributions

(Levinsky et al., 2007, Real et al., 2010).

186 A. Márcia Barbosa, Neftalí Sillero, Fernando Martínez-Freiría et al.

The theory of complexity can also be used in the interpretation of ENMs. Historical and

ecological factors, together with the idiosyncratic response of each species to these factors,

determine the current configuration of species‘ distributions. These factors dynamically

delimit the biogeographic responses of biodiversity in time and space. In this type of complex

scenario, distributions are the geographical response of the species to the past and present

factors that act(ed) in a particular area. The interpretation of ENMs as the degree of

membership of each locality to the fuzzy set of suitable areas for a species allows obtaining a

measure of how much the species has been influenced towards each location by the various

factors.

MEDITERRANEAN HERPETOFAUNA

The Mediterranean Basin is one of the world‘s biodiversity hotspots for conservation

priorities (Mittermeier et al., 2004). It presents broad topographical and environmental

variation, and has undergone a rich and eventful biogeographic history. Amphibians and

reptiles display particularly high specific and genetic diversity, with numerous endemics to

the Mediterranean region. This has provided an optimal scenery for modeling studies.

Besides species' distributions and ecological niches, it is also possible to model spatial

patterns in many other biological or ecological variables, such as species richness,

morphological characters, or genetic diversity. In this second part of the chapter, we review

the published works on different types of ecological modeling of amphibians and reptiles in

the Mediterranean Basin.

One of the most important applications of ENMs is the identification of the species'

ecological niche. Various studies have specifically aimed at identifying the potential

distribution of species and the variables that determine it within the Mediterranean Basin, for

example in Portugal (Brito et al., 1996, Sá-Sousa, 2000, Teixeira et al., 2001, Teixeira and

Ferrand, 2002, Arntzen, 2006), in Spain (Real et al., 2005, Anadón et al., 2006, Roman et al.,

2006, Carretero et al., 2010) and, recently, in Morocco (Beukema et al., 2010). Among these

works, Brito et al.‘s (1996) is the first one on ecological niche modeling within the

Mediterranean Basin, and uses logistic regression to calculate the potential distribution of

Lacerta schreiberi in Portugal. Using similar methodologies, Sá-Sousa (2000) and Teixeira et

al. (2001) analyze, respectively, the biogeography of Podarcis hispanica and Chioglossa

lusitanica in Portugal. Sá-Sousa (2000) separates the two forms of P. hispanica (type 1 and

type 2), confirming that their distributions are parapatric and influenced by different factors.

Teixeira et al. (2001) calculate an ENM of C. lusitanica in Portugal and project it to Spain.

Like Sá-Sousa (2000), Real et al. (2005) use logistic regression to distinguish the niches of

two cryptic species with parapatric distributions: Discoglossus galganoi and D. jeanneae.

Anadón et al. (2006) and Roman et al. (2006) provide examples of modeling applications at

the local level; both studies use GLM, the former for Testudo graeca in the Spanish region of

Ecological Niche Models in Mediterranean Herpetology 187

Murcia, and the latter for Podarcis carbonelli in Doñana (Southern Spain), although without

developing the spatial component of the ENM. Carretero et al. (2010) use Maxent to model

the distribution of the endemic lizard Algyroides marchi at three scales in southern Iberia, and

identify suitable areas and environmental factors related to its presence. Beukema et al.

(2010) combine distributional and genetic data of Salamandra algira in Morocco for studying

its phylogeny and biogeography. They model the distributions of viviparous and oviparous

populations of these species using Maxent, and compare both niches using ENMtools

(Beukema et al., 2010).

Ecological modeling is also used to identify chorotypes, i.e., distinct distribution patterns,

often shared by several species and significantly different from other distribution patterns.

Chorotypes can be determined from the observed distributions of various taxa (e.g. Real et

al., 1992, 1997) or by previously modeling these distributions (e.g. Sillero et al, 2009). Real

et al. (1997) document a gradual longitudinal replacement of reptile species in the eastern part

of the Rif region (northern Morocco). They attribute this to the northward movement of the

Saharan boundaries, which have not yet reached biogeographical equilibrium. Thus, Saharan

reptiles enter the Rif from the east, through the lower basin of the River Moulouya. Seven

reptile chorotypes were identified in the western part of the Rif, and these comprise

Mediterranean species and others endemic to the Maghreb (the region that spans most of

North-western Africa, excluding the Sahara). These chorotypes are segregated from one

another according to altitude. Historical and ecological processes can account for the

distributions shared by these species, which have inhabited the Rif for longer than eastern

reptiles. Sillero et al. (2009) analyze the biogeography of Iberian herpetofauna and identify

seven chorotypes for amphibians and seven for reptiles from the classification of a

presence/absence matrix calculated from ENFA models and environmental variables obtained

from satellite images. These chorotypes separate the species of Atlantic and Mediterranean

affinity. Flores et al. (2004) and Real et al. (2008) use ecological modeling to characterize

environmentally chorotypes previously identified from observed distributions. Aragón et al.

(2010) compare the influence of climatic and non-climatic factors on the distribution of

Iberian species of endotherms and ectotherms. They use GAM and find that amphibians and

reptiles are more influenced by precipitation and temperature than birds and mammals

(Aragón et al., 2010). Rueda et al. (2010) generate analytically derived regionalizations for

multiple groups of European plants and animals and explore potential influences on the

regions for each taxonomic group. They use GLM for modeling the obtained coherent clusters

and identify a discernable biogeographic structure in the European biota, mainly influenced

by climate (Rueda et al., 2010).

ENMs can also be used to study and identify other biogeographical patterns, such as

spatial variations in species' morphology and genetics. The vast majority of species show

geographic differences in morphological traits in response to changing selective pressures of

188 A. Márcia Barbosa, Neftalí Sillero, Fernando Martínez-Freiría et al.

the environments in which they live (Stearns and Hoekstra, 2000, West-Eberhard, 2003), both

biotic (e.g. predation, competition) and abiotic (e.g. temperature, precipitation). The study of

geographic variation in phenotypic traits has been a recurring theme during the second half of

the Twentieth Century (see Thorpe, 1987) and, currently, has resurfaced under a new

approach owing to the use of GIS and ENMs. Within the Mediterranean area, two articles

address the geographical variation in the morphology of Iberian vipers using ENMs as a tool:

Brito et al. (2008) study the morphological variation of Vipera latastei throughout its

distribution range, and Martinez-Freiría et al. (2009) study the morphological variation and

convergence of V. aspis and V. latastei, both along their whole contact area in northeastern

Spain and, on a more local scale, at the contact zone of the upper Ebro River (northern Spain).

Both works employ the same methodology: a combination of geo-statistics and GIS to obtain

uni- and multivariate patterns of geographic variation in morphology. They then use ENMs to

analyze correlations between these patterns and environmental variables. Tomović et al.

(2010) study the morphological variation of V. ammodytes in its European distribution area,

using a similar approach to that of Brito et al. (2008) and Martínez-Freiría et al. (2009), and

identify three morphologically different groups and their climatic requirements using Maxent.

Luiselli (2006) uses logistic regression to examine which environmental factors have led two

species of whip snakes that are not phylogenetically close, Hierophis viridiflavus in Italy

(Europe) and Psammophis phillipsii in Nigeria (Africa), to converge morphologically and

ecologically. Ficetola et al. (2010b) identify the relationship between bioclimatic variables

and body size predicted a priori by several alternative hypotheses for the newt T. carnifex in

Italy. They explore the correlations among these features and use an information theoretic

approach (Akaike‘s information criterion) to select the best model (Ficetola et al., 2010b). In

a similar way, Romano et al. (2010) analyze the relationships between body size and climate

for two sister species of salamander (Salamandrina perspicillata and S. terdigitata) endemic

to Italy, using GLM and an information theoretic approach.

As with morphology, the study of genetic variability and structuring of species may lead

to the identification of geographical patterns (e.g. Alexandrino et al., 2004). However, the

importance of the geographical component in typical studies of phylogeography has been

recognized only recently (see Manel et al., 2003, Kidd and Ritchie, 2006). This new approach

is known as landscape genetics. Broadly speaking, these studies combine GIS and ENMs to

identify geographic patterns in the variation of genetic markers, to delimit genetically similar

groups, to identify routes of interconnectivity between populations, and to study their

relationships with eco-geographical variables (e.g. Spear et al., 2005, Cushman et al., 2006).

However, to our knowledge, no work has yet been published on Mediterranean herptile

species using the methodologies employed in this field.

Alexandrino et al. (2004) combine the study of both morphological and genetic

variations, comparing ENMs obtained for C. lusitanica (Teixeira et al., 2001) with maps of

genetic and phenetic variation. However, this comparison is made in a descriptive way,

without investigating in depth the environmental factors that can be related to both

geographic variations.

Ecological Niche Models in Mediterranean Herpetology 189

Species richness can also be estimated using ENMs, either through direct modeling

(Nogués-Bravo and Martínez-Rica, 2004, Araújo et al., 2008) or through the addition of

individual species‘ ENMs (Soares and Brito, 2007, Estrada et al., 2007, Estrada et al, 2008,

Sillero et al., 2009). In any case, the arithmetic difference between observed and estimated

species richness shows the areas where there may be a deficit in knowledge, that is, where

there are probably species yet to record (Sillero et al., 2009). Thus, ecological modeling is a

useful tool to manage and plan chorological atlas surveys (Loureiro and Sillero, 2010). ENMs

may also allow identifying environmental factors that influence species richness (Soares and

Brito, 2007, Araújo et al., 2008). However, it is necessary to model separately the

distributions of species with different biogeographic affinities (see Nogués-Bravo and

Martínez-Rica, 2004, Ribeiro et al., 2009).

ENMs can be used to identify areas not yet occupied by expanding species (e.g. Hyla

merdionalis in the Iberian Peninsula; Sillero, 2009, Sillero, 2010) or by invasive species (e.g.

Rana catesbeiana and Trachemys scripta in Italy; Ficetola et al., 2007, Ficetola et al., 2009;

Ficetola et al. 2010a).

Sillero (2009) and Sillero (2010) develop ENMs at local scale (Salamanca province,

Spain) and at continental scale (Europe and North Africa) in which they note that H.

meridionalis occupies almost all suitable habitats available. They conclude that this species

cannot expand its distribution much more and that it is valid to assume that is in equilibrium

with the environment.

Ficetola et al. (2007) and Ficetola et al. (2009) use Maxent to identify suitable areas for

the expansion of R. catesbeiana and the reproductive populations of T. scripta in Italy,

respectively. Also with Maxent, Ficetola et al. (2010a) model the historical and current

distributions of R. catesbeiana in Italy to infer how changes in the landscape are involved in

the expansion of this invasive species. Moreover, they use five scenarios of landscape

variation (derived from the ALARM project) to predict the future expansion of this species

(Ficetola et al., 2010a).

ENMs have also been used to model chorotypes of several invasive species in the Iberian

Peninsula, including the red-eared slider Trachemys scripta, determining the most influential

environmental and human factors (Real et al., 2008). Chorotype modeling can aid

conservation or management measures for the entire set of species considered; it can also help

determine the areas that are most prone to invasions (Real et al., 2008).

The "taxonomic inflation‖ (Isaac et al., 2004, Harris and Froufe, 2005) that has affected

both amphibians and reptiles in recent years has led to the subdivision of species into several

new species whose presence records cannot be distinguished a posteriori. Moreover, many of

these species are cryptic (not distinguishable by morphological characters), making the

190 A. Márcia Barbosa, Neftalí Sillero, Fernando Martínez-Freiría et al.

correct identification of these records difficult even after their definition as new species. The

clear-cut distinction of cryptic species often requires genetic or molecular analyses that can be

very expensive and time-consuming. In cases like these, ENMs may help to distinguish the

distributions of such species from the characteristics that define their areas of occurrence.

Starting from the genetic identification of a sample of individuals, we can build ENMs that

allow inferring to which species or subspecific variety other individuals will belong, based on

their location (e.g. lineages of C. lusitanica in Portugal: Arntzen and Alexandrino, 2004; D.

galganoi and D. jeanneae in Spain: Real et al., 2005). Spatial modeling of genetic data can

also serve to compare the niches of distinct populations of a species, as is done by Beukema

et al. (2010) with viviparous and oviparous forms of Salamandra algira in Morocco (see

section 2.1).

Contact zones, mainly those that occur between phylogenetically close species, are very

important in the study of evolutionary processes (Hewitt, 1988). They usually occur at the

limits of species‘ distributions, in areas of environmental transition (ecotones), where

environmental factors and biotic interactions play a major role in the local distribution and

population dynamics of the species in contact (e.g. Martínez-Freiría et al., 2008, Martínez-

Freiría et al., 2010). ENMs allow identifying environmental factors that affect these species,

the responses of each species to the variations in these factors, and the areas where species

can potentially coexist (areas of potential sympatry).

In the study of contact zones, Brito and Crespo (2002) use logistic regression to calculate

for the first time a single ENM for two species simultaneously, with the aim of identifying

environmental requirements and areas of sympatry between Vipera latastei and V. seoanei in

northern Portugal. Since the distributions of both species are parapatric, they calculate two

separate ENMs where the absence data for each species correspond to the presences of the

other species. Espregueira Themudo and Arntzen (2007) use the same methodology to

determine the factors the influence the local distribution of Triturus marmoratus and T.

pygmaeus in the area of Caldas da Rainha (Portugal). However, they only calculate one ENM

(for T. marmoratus). Arntzen and Alexandrino (2004) use logistic regression to analyze the

distribution of C. lusitanica in northern Portugal and obtain several models that identify the

environmental factors more closely related to the distribution of each of the two genetically

distinct groups. Although they do not represent the likely areas of contact, they do identify the

environmental variables to which the two forms have a similar response, and identify a zone

of contact and eco-morphological transition for the two groups (north of the Mondego River,

Portugal). Martínez-Freiría et al. (2008) analyze the distribution of the three Iberian species of

vipers at their contact zone in the upper Ebro River (northern Spain). They use presence data

and Maxent, with which they obtain the responses of these species to environmental factors

and the areas of potential occurrence and sympatry. By representing and comparing the

responses of these species to certain environmental factors common to them, they identify

those factors for which these species show a similar pattern, and that thus allow their

coexistence; and the factors for which the species show different responses, which thus lead

to habitat segregation.

Ecological Niche Models in Mediterranean Herpetology 191

ENMs can also be used to infer the conservation status of species, to identify factors of

threat, and to propose management measures. The earliest such work with Mediterranean

herpetofauna is the one carried out by Brito et al. (1999) on the identification of priority areas

for conservation, delimitation of areas of high extinction risk, assessment of the degree of

protection, and definition of a conservation strategy for L. schreiberi in Portugal. The authors

combine the results obtained with previous works (ENM, Brito et al., 1996, habitat selection,

Brito et al., 1998) with other variables such as the protected area network in Portugal,

detected density, and electrophoretic data of allozymes of this species. Similarly, Teixeira and

Ferrand (2002) identify important areas for the conservation of the genetic diversity of C.

lusitanica by combining 1) ENMs for the current conditions, made with logistic regression

(Teixeira et al., 1996, Teixeira et al., 2001), discriminant analysis, classification trees, and

overlay analysis; 2) ENMs for the years 2050 and 2080, made with logistic regression and

discriminant analysis (Teixeira and Arntzen, 2002); and 3) analysis of the geographic

variation in molecular data (Alexandrino et al., 2004). Santos et al. (2006) and Santos et al.

(2009) use ENFA to identify biotic and abiotic factors involved in the distributions of V.

latastei and C. austriaca, respectively, in the Iberian Peninsula, and evaluate the conservation

status of both species. Santos et al. (2006) realize that V. latastei, though it should be

widespread in the Mediterranean part of the Iberian Peninsula due to its high environmental

adaptability, is relegated to mountainous regions by human activities. Santos et al. (2009)

combine ENMs of C. austriaca at regional scale in Iberia with local analyses of the isolated

populations of southern Spain (performed through intensive sampling), to infer why this

species has small isolated populations in the southern Iberian Peninsula.

Analyses of species richness are very important to determine the areas that should be

protected to preserve the largest possible number of taxa (Soares and Brito, 2007). For

example, Rey Benayas et al. (2006) evaluate the potential impact of future infrastructures on

Spanish herpetofaunal diversity. Estrada et al. (2007) and Estrada et al. (2008) use ENMs in

Andalusia (southern Spain) to assess the degree of agreement between the protected area

network and the important areas for amphibians and reptiles, according to their species

richness, rarity, endemism, and vulnerability. From another point of view, but similar to the

previous one, Ribeiro et al. (2009) use ENMs to evaluate the impact of human activities on

reptile diversity in Catalonia (north-eastern Spain). The authors correlate the differences

between observed and potential species richness (ENMs calculated from 25 species) with

different types of land use; agricultural areas appear to be the least favorable to reptiles,

having the largest differences between observed and potential richness (Ribeiro et al, 2009).

The NIM can be used to infer the state of conservation of the species, to identify factors

of threat and to propose management measures. The earliest work in this area is conducted by

Brown et al. (1999) on the identification of priority conservation areas, delimitation of areas

at high risk of extinction, assessing the degree of protection and definition of a conservation

strategy for L. schreiberi in Portugal. The authors combined the results of previous work

(ENM, Brito et al., 1996, selection of habitats, Brito et al., 1998), along with other variables

such as the network of protected areas in Portugal, density and electrophoretic data detected

of allozymes of the species. Similarly, Teixeira & Ferrand (2002) identified important areas

for conservation of genetic diversity of C. lusitanica by combining 1) ENM for current

conditions, using logistic regression (Teixeira et al., 1996, Teixeira et al., 2001), discriminant

192 A. Márcia Barbosa, Neftalí Sillero, Fernando Martínez-Freiría et al.

analysis, classification trees and overlay analysis, 2) for the years 2050 ENM and 2080, using

logistic regression and discriminant analysis (Teixeira & Arntzen, 2002), and 3) analysis of

geographic variation in molecular data (Alexandrino et al., 2004). Santos et al. (2006) and

Santos et al. (2009) ENFA used to identify biotic and abiotic factors involved in the

distribution of V. latastei and C. Austrian in the Mediterranean Basin, respectively, and

evaluate the conservation status of both species. Santos et al. (2006) found as V. latastei, even

though it should be present in almost all Mediterranean Iberia due to its high environmental

adaptability, is relegated to the mountainous areas due to human activities. Santos et al.

(2009) combined C. ENM Austrian regional scale in Iberia, along with a more local scale

analysis of isolated populations of southern Spain (performed by intensive sampling), to infer

why this species isolated populations with low effective population in the southern half of

peninsular.

Analyses of species richness are of great importance in determining the areas to be

protected and try to preserve the largest possible number of taxa (Soares & Brito, 2007). For

example, Benaiah Rey et al. (2006) evaluated the potential impact of future infrastructure in

Spain Spanish herpetofaunística diversity. Estrada et al. (2007) and Estrada et al. (2008) used

ENM restricted to Andalusia to assess the degree of agreement between the network of

protected areas and important areas for amphibians and reptiles, according to its richness,

rarity, endemism and vulnerability. From another point of view, but like the previous one,

highlights a recent study by Ribeiro et al. (2009), who used ENM to evaluate the impact of

human activities on the diversity of reptiles in Catalonia. The authors correlated the

differences between observed richness and potential richness (ENM calculated from 25

species of reptiles Catalan) with different land uses: agricultural use areas were less favorable

to the reptiles, having the largest differences between wealth (Ribeiro et al, 2009).

The current availability of climatic data for various possible scenarios of future climate

change (e.g. WorldClim: www.worldclim.org/futdown.htm; World Climate Research

Programme: http://ccr.aos.wisc.edu/model/ipcc10min/index.html) has increased the studies

that predict the response of organisms to this process. Due to the strong dependence of

amphibians and reptiles on environmental conditions, these studies can be a valuable tool to

identify the vulnerability of these species to climate change and to develop effective

conservation measures.

In the Mediterranean Basin, the first published ENM predicting the future range of a

species is the one by Teixeira and Arntzen (2002), which focuses on C. lusitanica in Spain

and Portugal. The modeling methods are logistic regression and discriminant analysis, and the

climatic variables include contemporary conditions and the predictions of the International

Panel for Climate Change from the year 2001, which predicted increases in July temperature

of 2 and 3ºC for the years 2050 and 2080, respectively. Whilst climate change does not

consist simply of an increase in temperature, in 2002 there was not enough information on

how precipitation and other variables would be altered. Araújo et al. (2006) use ENMs,

through a combination of GLM, GAM, classification trees and artificial neural networks, to

determine the potential effects of climate change (WorldClim data for the years 2020 and

2050 at a resolution of 50x50 km) on the distributions of European amphibians and reptiles.

Ecological Niche Models in Mediterranean Herpetology 193

Similarly, Carvalho et al. (2010) model the distributions of 37 Iberian endemics or quasi-

endemics (15 amphibians and 22 reptiles) under current weather conditions, and project them

to the future climatic conditions predicted for the years 2020, 2050, and 2080. This study uses

a finer scale (10x10 km) and combines various modeling methods, such as Maxent, GLM,

GAM, classification trees, artificial neural networks, Generalized Boosting Models (GBM),

random forests, mixed discriminant analysis, and MARS. Real et al. (2010) and Márquez et

al. (2011) evaluate the predicted effect of different greenhouse gas emission scenarios on the

distributions of Alytes dickhilleni and Vipera latastei in continental Spain using two global

circulation models. Ficetola et al. (2010a) forecast the future expansion of invasive R.

catesbeiana in Italy under five landscape variation scenarios (see section 2.5).

Mediterranean Basin

there is no doubt of their usefulness for amphibian and reptile species. Ecological niche

modeling in the Mediterranean Basin has nearly 20 years of development. There are many

research lines open: species richness modeling (Sillero et al., 2009, Ribeiro et al., 2009),

conservation status assessment (Santos et al., 2006, Estrada et al., 2008; Santos et al., 2009),

responses to climate change (Carvalho et al., 2010; Sillero, 2010; Real et al. 2010), hybrid

and contact zones (Martínez-Freiría et al., 2008, Martínez-Freiría et al., 2010), expansion of

native species (Sillero, 2009, Sillero, 2010). However, for other areas there still are no

published studies regarding Mediterranean herpetofauna: landscape genetics, adequacy of

protected areas, new modeling methods, local-scale modeling (resolution <1x1 km),

expansion of invasive species, modeling of past climate scenarios. This shows there is still a

long way to go in ecological modeling of the Mediterranean herpetofauna.

In addition, ecological niche modeling of Mediterranean amphibians and reptiles is an

optimal setting for works addressing very diverse issues in ecology, biogeography and

conservation. This is due to: 1) the high diversity of species, subspecies and genetic lineages

of amphibians and reptiles, many of them endemic to the Mediterranean Basin, which is one

of the world‘s biodiversity hotspots (Mittermeier et al., 2004); 2) the broad environmental

gradients that exist in this region, which facilitate the use and characterization of the species‘

niches; 3) the particular biogeographic history of this Basin; and 4) the human occupation of

this area for thousands of years, which has changed quite a few patterns of distribution. In

particular, it may be especially important to develop studies that jointly address the

distribution of species with genetic tools, studies on morphological variation, and niche

modeling analysis. With these three tools we can address numerous aspects related to

speciation, niche differentiation, or the expansion of distribution areas, which go beyond the

purely herpetological interest.

194 A. Márcia Barbosa, Neftalí Sillero, Fernando Martínez-Freiría et al.

ACKNOWLEDGMENTS

A version of this review focused on the Iberian Peninsula was previously published in

Spanish in the Boletín de la Asociación Herpetológica Española (Bulletin of the Spanish

Herpetological Association). We thank its editors Xavier Santos and Alexander Richter-Boix

for permission to reproduce it here in English. A.M.B., N.S. and F.M.-F. are supported by

post-doctoral fellowships (SFRH/BPD/26666/2006, SFRH/BPD/40387/2007 and

SFRH/BPD/69857/2010) from Fundação para a Ciência e a Tecnologia (Portugal), co-

financed by the European Social Fund. The ‗Rui Nabeiro‘ Biodiversity Chair is financed by

Delta Cafés.

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In: Ecological Modeling ISBN: 978-1-61324-567-5

Editor: WenJun Zhang, pp. 205-222 © 2012 Nova Science Publishers, Inc.

Chapter 9

ECOSYSTEM MODELLING IN FRESHWATER AND

MARINE ENVIRONMENTS: CONSIDERATION OF

INDIRECT INTERACTIONS, AND THE IMPLICATIONS

FOR INTERPRETING PAST AND FUTURE OVERALL

ECOSYSTEM FUNCTIONING

1

School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK.

2

Department of Ecology, Kharkov State University,

4 Svobody (Dzerzhinskiy) Square, Kharkov, USSR (Ukraine).

School of Ocean Sciences, University of Wales, Bangor,

Marine Science Laboratories, Menai Bridge, Bangor, Gwynedd LL59 5AB UK.

ABSTRACT

Numerical techniques (e.g. correlation, multiple regression and factor analysis, path

analysis, methods of network analysis, and, in particular, simulation modelling) may be

very helpful in investigations of indirect relationships in aquatic ecosystems. Here we

give a brief overview of some examples of the relevant studies, and focus on 1) a case

study of a freshwater eutrophic lake, where statistical analysis of the datasets obtained

within a comprehensive monitoring programme, and sensitivity analysis by a

mathematical model ‗Rostherne‘, helped to reveal the previously overlooked

relationships between Si and P biogeochemical cycles coupled through the dynamics of

primary producers, and 2) give an overview of how the coupling of physical, chemical,

and biological processes in the marine ecosystem models offers a basis for investigations

of indirect interactions in continental shelf seas. Complex aquatic ecosystem models

provide a numerical simulation of biogeochemical fluxes underpinned by coupling

* Corresponding author. Present address: SBE, Institute for infrastructure and environment, Heriot-Watt University,

Edinburgh EH14 4AS, UK.

E-mail: e96kri69@netscape.net.

206 V. Krivtsov and C. F. Jago

physical forcing functions with definitions simulating biological and chemical processes,

and offer a potential for quantitative interpretation of sediment proxies in the stratigraphic

record. Combination of models and sediment proxies, calibrated by training sets, can

provide information on water column structure, surface heating, mixing, and water depth,

thus providing a basis for reconstruction of the past, and predicting the future

environmental dynamics.

continental shelf seas, SPM, indirect effects, ecosystem modeling, CTEA.

INTRODUCTION

Natural ecosystems are complex, and are characterised by a multitude of interconnected

relationships between ecosystem components (Krivtsov, 2008). The understanding of these

complex interactions is paramount for sustainable management of environmental resources.

However, ecological research mainly tends to concentrate on investigations of direct

relationships, whilst indirect interactions (and especially the less obvious, e.g. the delayed

ones) are often overlooked or understudied (NB In this paper all the relations not restricted to

the effects of a direct transaction of matter and energy between the adjacent ecosystem

components will be treated as indirect). Mathematical techniques (e.g. correlation, multiple

regression and factor analysis, simulation modelling, path analysis and methods of network

analysis, etc.) may be very helpful in investigations of indirect relationships in ecosystems.

The origin of algorithms capable of studying indirect interactions within ecological

context can be traced back to the 18th century (Krivtsov, 2004). Here we refer to some

examples of the relevant aquatic studies, and, in particular, give a brief account how

mathematical techniques have been helpful in investigating indirect effects in a freshwater

eutrophic lake (see Krivtsov et al., 1998, 1999a,b,c, 2001, and references therein) where

indirect relationships appeared to occur on (and across) various levels of organisation. We

also give an overview of how the coupling of physical, chemical, and biological processes in

the models of continental shelf seas gives a potential for a breakthrough in the investigations

of indirect effects. Finally, we argue, that due to the importance of aquatic ecosystems, the

existence of comprehensive models linking physical, chemical, and biological processes, and

the experience accumulated in studies of indirect effects in the aquatic environment, complex

aquatic models are likely to continue to play a leading role in the investigations of indirect

effects, in particular within the framework of the comparative theoretical ecosystem analysis

(sensu Krivtsov, 2002, 2004).

AQUATIC ENVIRONMENT

Despite the claims (Wardle, 2002) that aquatic scientists have only recently recognised

and started to study indirect effects, awareness of indirect interactions in aquatic environment

has rather a considerably long history (e.g. Mortimer, 1941, 1942; Hutchinson, 1957;

Reynolds, 1984). In particular, in an earlier review it was even suggested that most studies

Some Aspects of Phytoplankton and Ecosystem Modelling … 207

ecosystems, while many of the early demonstrations of density-mediated indirect effects were

done in community studies in marine habitats (see Abrams et al., 1996 and references

therein). Likewise, much of the knowledge related to indirect ecological interactions has been

contributed through the development and applications of the methods of simulation modelling

(e.g. Jorgensen, 1980; Jorgensen, 1994) and network analysis (e.g. Patten, 1985; Patten et al.,

1976, and references therein) in relation to aquatic environment. Consequently, simulation

models capable of demonstrating indirect interactions in aquatic biogeocenoses (e.g. the Lake

2 model of J. Solomonsen, - see Jorgensen, 1994) are widely used for teaching in the

educational establishments across the world. Studies of indirect effects in aquatic

environment involved e.g. application of various statistical techniques, methods of network

analysis, and simulation modelling using ‗what–if‘ scenarios and sensitivity analysis.

Modifications of the model CASM were used by Bartell et al. (Bartell et al., 1999) and

Naito et al. (Naito et al., 2002) to study direct and indirect effects in the aquatic ecosystems

of Canada (Quebec) and Japan (lake Suwa), respectively. Numerical sensitivity analysis was

applied in both cases (sensitivity of a state variable on changes in a parameter was measured

as the percent change from the reference situation). For the Canadian case study it was found

that variability in the production of macrophyte population determines an indirect risk

component of toxic Hg effects on phyto- and zooplankton, periphyton and fish. In the

Japanese case study it was found that the annual production of piscivorous fish was

considerably influenced by the optimal consumption temperature of certain benthic insects.

Another interesting finding was that the physiological parameters of the diatom Melosira

were the important sources of the cyanobacterium Microcystis production variability.

Although the authors did not make a detailed interpretation of the latter relationship, their

results suggest that the underlying mechanism might be a common inverse relationship

between spring diatom and summer cyanobacterial blooms (see references related to the

Rostherne Mere case study below).

Dippner (Dippner, 1998) addressed indirect interrelations between Si and P availability.

On the basis of a simple numerical model it was concluded that indirect effect of the silicate

reduction in coastal waters causes an increased flagellate bloom, due to a high availability of

riverborne nutrient loads. These conclusions are highly in line with the results related to lakes

Suwa (referred to earlier) and Rostherne Mere, described below.

The simultaneous application of ANOVA and ANCOVA analysis allowed the

investigator to elicit direct and indirect effects between the biota inhabiting a North American

intertidal rocky shore (Wootton, 2002). The results indicated that consumers may have a

major influence on the dynamics of ecological succession. In an earlier study published by the

same author, path analysis was helpful in predicting which direct and indirect effects were

important in a seabird exclosure experiment (Wootton, 1994b). Statistical techniques

(including linear regressions and a number of variation of ANOVA analysis) were also

helpful in another intertidal rocky shore study (Navarrete and Menge, 1996).

Hanratty and Liber (Hanratty and Liber, 1996) studied indirect effects of a pollutant

diflubenzuron on growth of larval bluegill sunfish in a littoral enclosure. At very high

concentrations the model predictions were good, but at intermediate concentrations the

accuracy was variable, with some indirect responses being exaggerated due to cascading

effects through the ecosystem trophic levels.

208 V. Krivtsov and C. F. Jago

Hulot and coauthors (Hulot et al.. 2000) compared the performance of linear food chain

models and an intermediate complexity model, applied to data of a mesocosm experiment

simulating lake nutrient enrichment. The intermediate complexity model (with separation of

trophic levels into functional groups according to size and diet) was the only one which

performed satisfactory, thus highlighting the importance of functional diversity and indirect

interactions.

Another modelling study (Loladze et al., 2000) investigated how the interactions between

phytoplankton and zooplankton change if the Lotka-Volterra model incorporates chemical

heterogeneity for both trophic levels. It was found that indirect competition between two

populations for P can shift the relationship from a usual (+, −) type to an unusual (−, −) type,

leading to a very complex overall dynamics.

Structural equation modelling (a technique combining path, factor, and regression

analyses) was used by Malaeb et al. (Malaeb et al., 2000) to estimate the contribution of

indirect effects of sediment contamination and natural variability on biodiversity and growth

potential in a selection of North American estuaries. They found that a positive indirect effect

of natural variability (mediated through biodiversity) on growth potential exceeded a direct

negative effect, resulting in the overall positive relationship.

A simulation model of the Mediterranean infralittoral rocky bottom was used by

McClanahan and Sala, 1997) to study possible effects of various management options.

Running a number of ‗what–if‘ scenarios they concluded that many of potential changes are

likely to be indirect effects caused by changes in trophic composition. For example, if

invertivorous fish were removed as part of a management scenario, sea urchins would reduce

algal abundance and primary production, leading to competitive exclusion of herbivorous

fish. Although similar interactions were known from tropical seas, these results were not

anticipated by previous field studies in the Mediterranean.

Carrer and Opitz (Carrer and Opitz, 1999) investigated indirect interactions in the Lagoon

of Venice using ‗Ecopath‘, a software implementing methods of network analysis. Among

other interesting relationships, they found that about half of the food of nectonic benthic

feeders and nectonic necton feeders passed through detritus at least once, whilst there was no

direct transfer of such food according to the diet matrix. The paper contains a number of

references to other studies where network analysis was used to analyse indirect relationships

among ecosystem components (see also Patten, 1992; Fath and Patten, 1998; Fath and Patten,

1999, and references therein), as well as a reference to the Ecopath web site, which, in turn,

gives a list of studies (mainly aquatic) where this software was applied. A couple of examples

from this list are reviewed below.

Ortiz and Wolff, 2002a and Ortiz and Wolff, 2002b used Ecopath with Ecosim software

to study benthic communities in Chile. They found that a simulated harvest of the clam

Mulinia generated a complex interplay involving direct and indirect effects, and drastically

changed the properties of the whole system.

Another study utilizing network analysis provided an analysis of the extended path and

flow structure for the well documented oyster reef model (Whipple, 1999). Few simple paths

and large number of compound paths were counted. The study provided structural evidence

for feedback control in ecosystems, and illustrated importance of non-living compartments (in

this case detritus) for the ecosystem‘s functioning. Even for the model with a low cycling

index (i.e. 11%) multiple cyclic passage paths provided a considerable (22%) flow

Some Aspects of Phytoplankton and Ecosystem Modelling … 209

contribution. Therefore, it was envisaged that for ecosystems with higher cycling indexes the

patterns observed should be even more pronounced.

Application of mathematical modelling techniques has been helpful in furthering the

understanding of a number of aspects of marine ecosystem dynamics in the Menai Strait

(Krivtsov et al., 2008a) and in the Irish Sea and Liverpool Bay (see Krivtsov et al., 2008b

and references therein). In particular, these studies helped to elucidate a complex role played

in the ecosystem by suspended particulate matter (SPM), which is arguably thought to be one

of the most important ecosystem constituents affecting the majority of ecological processes

(Krivtsov et al., 2011). At present, most ecosystem models are in dire need of improving the

representation of the SPM dynamics, and it has been argued (Krivtsov et al., 2008b) that

many of the discrepancies between measurements and simulations commonly observed in

aquatic modelling studies may, in fact, have been caused by inadequate representation of the

SPM subsystem.

Detailed attention to indirect effects was given in a number of studies conducted at

Rostherne Mere, one of the best studied lakes in UK (see Krivtsov et al., 1998, 1999a,

1999b, 1999c, 2000a, 2001b, 2001c, 2002b, 2003a, and references therein). Indirect effects

were shown to occur on (and across) various levels of organisation, including intracellular,

population and ecosystem levels. A comprehensive monitoring data set was analysed by

means of statistical techniques, which facilitated the construction of a dynamic simulation

model. Statistical analysis of the observed data sets and sensitivity analysis (using

mathematical model ‗Rostherne‘) were used to elicit the hidden relationships between Si and

P biogeochemical cycles coupled through the dynamics of primary producers (Krivtsov,

2001; Krivtsov et al., 2000b). These results were then confirmed by new statistical analysis,

and ultimately resulted in changes of the contemporary ecological theory. It was shown that

there is an inverse relationship between spring diatom and summer cyanobacterial blooms,

which could be utilised as a new method of eutrophication control.

If the spring phytoplankton is limited by Si, then artificial Si additions should alleviate Si

limitation and result in the increased P and N removal from the water column (Krivtsov et al.,

2000a). This would consequently lead to a decreased peak of blue–greens in summer. Further

investigations (Krivtsov et al., 2000b), however, revealed a complex interplay between direct

and indirect effects in the ecosystem, including those related to the influences of temperature,

light, inflow/outflow characteristics, and interactions among nutrients, algae, detritus,

zooplankton and fish. Dynamic ecosystem modelling suggested that in cases where factors

other than nutrients make a considerable contribution to the limitation of spring diatom

increase, any event or measure which diminishes the negative effect of these factors, should

also result in a decreased summer cyanobacterial maxima, due to enhanced nutrient removal

in spring by diatoms.

Some of the indirect relationships studied within the Rostherne Mere research were

classified in relation to the underlying mechanisms (i.e. in this case directly and indirectly

mediated), which facilitated extrapolation of the conclusions for other types of ecosystems

(see Krivtsov, 2002, 2004, and references therein). A number of ‗what–if‘ scenarios examined

210 V. Krivtsov and C. F. Jago

cyanobacterial bloom in relation to, e.g., hydrological and morphological parameters, thus

assessing differences between ecosystem types (e.g. deep versus shallow lakes, lakes with

high versus lakes with slow retention time). These analyses have led to the derivation of the

‗indirect regulation rule for consecutive stages of ecological succession‘, which generalised

the most notable interdependencies observed for other types of ecosystems (Krivtsov et al.,

2000c), and to a general classification of the ecosystem effects (Krivtsov, 2001). It is intended

that further work should involve application of structural equation modelling, and the

comparison with the indirect relationships revealed for a terrestrial ecosystem (Krivtsov et al.,

2004), thus providing further basis for the ongoing development of the comparative

theoretical ecosystem analysis (CTEA) framework.

MODELLING BIOGEOCHEMICAL

FLUXES IN CONTINENTAL SHELF SEAS

Representation of a biogeochemical cycle in an ecological model should involve all

relevant physical forcing functions, biological and abiotic processes, and chemical fractions

associated with biota, dissolved nutrient pool, bottom sediments, and suspended particulate

matter (SPM). Among those, SPM is often the least appreciated, and is, consequently,

underrepresented in ecological models. The discussion below reviews a number of important

aspects related to biogeochemical cycling, with a particular emphasis on SPM.

SPM

and its characteristics influence overall ecosystem functioning through a wide range of

biogeochemical processes (Tett et al., 1993; Krivtsov et al., 2011) . The dynamics of SPM

fluxes in shelf seas is governed both by horizontal circulation and, on a shorter time scale, by

vertical mixing. SPM in shelf seas usually consists of aggregated material (organic and

inorganic) forming flocs. Flocs aggregate and rupture on short time scales in response to the

varying turbulence regime (e.g. aggregation at slack water and rupture at peak flows) with the

result that their size and settling velocity also vary on short time scales. SPM is important

ecologically as it constrains primary productivity while in the water column and constrains

benthic productivity when it accumulates rapidly on the seabed as benthic fluff. The vertical

flux of SPM is also the primary pathway for transfer of organic carbon from plankton blooms

to the seabed.

The vertical flux of particles primarily depends on the entrainment rate from the sea bed,

settling velocity (which, in turn, is dependent upon the size and density of the particles which

are usually in the form of flocs), and vertical mixing. Therefore, the parameters which may be

of interest for relevant mathematical models are biological (e.g. benthic and pelagic

production), hydrodynamic (e.g. hydrochemcial and hydrophysical profiles, tidal regime), and

sedimentological (particle composition, aggregation rate, settling velocity). Consequently,

relevant ecosystem models (e.g. Sharples and Tett, 1994; Luytens et al., 1999; Sharples,

Some Aspects of Phytoplankton and Ecosystem Modelling … 211

1999; Smith and Tett, 2000) capable of describing biogeochemical fluxes in shelf seas have,

albeit to a variable extent, included tidal mixing, water column dynamics, algal production

and loss processes, and SPM benthic fluff settling/resuspension.

Tidal Mixing

In continental shelf seas, daily inputs of turbulent kinetic energy from tidal and wind

stirring, and convective mixing, are opposed by buoyancy inputs due to solar heating. The

balance between these depends on seasonal variability of the surface heat flux. In deeper

regions, seasonal stratification develops whereby a thermocline separates surface and bottom

mixed layers (SML and BML, mixed by wind and tide, respectively – see Figure 1).

Shallower regions remain mixed for most of the time. During summer stratification develops,

and a tidal mixing front (which is the surface expression of the thermocline) is positioned

between stratified and mixed regions, where the intensity of tidal turbulent mixing is

sufficient to overcome the tendency to stratify due to surface heating. By equating turbulent

mixing to the potential energy difference before and after mixing, it has been shown that the

critical determinant of water column structure is tidal stirring, predicted by h/u3, where u is a

depth-mean average tidal current and h is water depth (Simpson and Hunter, 1974). A

reasonable precision of front prediction can be achieved by a combined wind and tide stirring

model (for details see Simpson and Bowers, 1981). Further improvements can be obtained

through formulations of water column structure based on consideration of turbulent kinetic

energy (tke) (e.g. Sharples and Tett, 1994; Simpson et al., 1996; Luytens et al., 1996;

Sharples, 1999). In such models, a turbulence closure scheme (e.g. Mellor and Yamada,

1982) links vertical stratification, driven by surface heating, and turbulence generated by tidal

friction at the seabed and wind stress at the surface; in effect, water column stability is related

to the efficiency of vertical turbulent transport. Thus, changes in tke (q2/2 where q is the

turbulent velocity scale) are given by:

(1)

where Kq is the vertical eddy diffusivity of tke, Nz is the depth-dependent coefficient of eddy

viscosity, Kz is the vertical eddy diffusivity, u and v are the x and y components of current

velocity, g is the acceleration due to gravity, ρ is water density, BI is a constant of the

turbulence closure scheme, and l is the constant turbulent length scale. This formulation

contains the vertical diffusion of tke, shear production of turbulence, work done against

buoyancy, and the dissipation of tke (the terms on the right hand side of Eq. 1, respectively).

Distribution of heat input from solar radiation is mediated by attenuation due to SPM and

algal biomass in the water column. Such models have been very successful in simulating

vertical mixing processes in general, and genesis of the thermocline in particular.

212 V. Krivtsov and C. F. Jago

Figure 1. Conceptual diagram of water column structure and water quality in tidal shelf seas. *=factor

which limits algal growth. 2.7 is a critical transition value of h/u3

It should be noted, that although frontal zones tend to be quite narrow (ca. 5 km wide), a

front is not an abrupt transition. The frontal density structure implies a pressure gradient

perpendicular to the front which drives an along-front current. The geostrophic balance is not

perfect, due to friction, and a small cross-stream flow is generated down the pressure

gradient. Consideration of the cross-frontal dynamical balance, including friction (James,

1978; Garrett and Loder, 1981 ), suggests a weak cross-frontal circulation with a surface

convergence close to the region of maximum horizontal gradient (e.g. Pingree et al., 1974).

The Simpson–Hunter stratification parameter predicts a lateral migration of fronts during the

lunar cycle of 10–20 km. Even after removing tidal advection, Simpson and Bowers (1979)

concluded that fronts migrate laterally by a few kilometers in response to the lunar cycle.

Numerical models (Simpson and Bowers, 1981; Sharples and Simpson, 1996) suggest that the

position of the frontal zone lags the spring-neap cycle by a few days. A major consequence of

lateral migration is that water from the mixed region is incorporated into the stratified region

as the front advances into shallower water on neap tides (Simpson and Hunter, 1974;

Simpson and Bowers, 1979). Furthermore, infrared satellite imagery and direct observations

show that baroclinic instabilities along the front grow into large eddies (typically 25–40 km)

which make a large contribution to cross-frontal mixing (Pingree and Griffiths, 1978). In

addition, some water from the BML may be mixed across the thermocline by spring tide

currents. Finally, some diffusion of the thermocline might occur due to dissipation of internal

tides.

Advection/Resuspension

Observations of SPM in continental shelf seas can be reasonably reproduced (Jago and

Jones, 1998) by the following conceptual model:

Some Aspects of Phytoplankton and Ecosystem Modelling … 213

t

dS

dx 0

S ( t ) S0 U x dt k U x , (2)

where

U x is the rectilinear current velocity

k is a function describing a combined effect of the entraiment from the sea bed and the

vertical distribution through the water column

Values of background concentration, combined function k, and the gradient along the

dS

tidal stream are usually calculated by linear regressions between observations of S(t), and

dx

tidal current displacement and speed.

The formulation presented above proved to be reasonable, and is capable of reproducing

the so-called ‗twin peaks signal‘ in SPM concentration, which results from the

superimposition of the quarter-diurnal signal due to the resuspension of benthic fluff and

semi-diurnal signal caused by longitudinal concentrational gradients in SPM in long-term

suspension. Further improvements in the performance can be gained by introducing a

numerical model which includes horizontal advection of a particulate concentration gradient

and vertical diffusion, and the bottom boundary conditions including fluxes due to

resuspension and diffusion, with entraiment rate being a function of the bed shear stress (for

details see Jago and Jones, 1998, and references therein).

and growth rate. Growth rate mainly depends on nutrient availability (Droop, 1983) and light,

while peak biomass is constrained by nutrients (Tett et al., 1993). Tidal stirring controls the

availability of both nutrients and light.

In mid and high latitude shelves, where plankton dynamics are dominated by transients

such as the spring bloom, it is likely that growth rate is the most important regulator of the

observed changes in population density (Tett et al., 1993). The temporal evolution of

phytoplankton biomass is determined by growth and vertical turbulent transport, tempered by

grazing (Sharples and Tett, 1994; Sharples, 1999; Sharples et al., 2001):

(3)

where X is biomass and is the specific growth rate, Kz is vertical eddy diffusivity, and g is

the loss of algal biomass to grazers.

214 V. Krivtsov and C. F. Jago

It should be noted that in summer 30–80% of the total algal production in the euphotic

zone takes place in the thermocline (Fransz and Gieskes, 1984) and that the greatest

production occurs near tidal mixing fronts (Pingree et al., 1975, 1978; Savidge, 1976;

Holligan, 1981; Holligan et al., 1983; Loder and Platt, 1985. ; Tett et al., 1993; Tett and

Walne, 1995). This could be a passive response to the convergent flows which have been

observed at fronts but it is more likely to result from in situ growth of plankton. This is where

the combination of light and nutrients is optimal (Dufour and Stretta, 1973): nutrient renewal

during the summer, due to mixing by tide and wind, and surface stabilisation and reduction of

h1 during fairweather and neap tides. Thus a chlorophyll maximum is observed at the

thermocline and at fronts. The optimal conditions for rapid algal growth are at the front, as

lateral mixing across the front is greater than vertical mixing across the thermocline (Garrett

and Loder, 1981; Tett, 1981; Tett et al., 1986).

The growth rate of phytoplankton may be nutrient-limited:

(4)

where m is the maximum growth rate, kQ is the subsistence cell nutrient quota, and Q is the

cell nutrient quota (=the ratio of algal cell internal nutrient concentration to chlorophyll

biomass). Unlike in most freshwater ecosystems, in continental shelf seas nitrogen is usually

less available for growth, and is therefore more limiting, than is phosphorus (Tett and Droop,

1988), while silicon may be more limiting than nitrogen for diatoms (Brzezinski, 1985).

In addition to nutrient limitation, phytoplankton growth may be slowed down by low

light and/or temperature. There are numerous definitions how exactly these limitations may

be combined with the limitations imposed by nutrient availability, and the detailed

consideration of the matter would be beyond the scope of this paper. Low light due to high

SPM concentrations is a major control in mixed regions of shelf seas. The insight into one of

the more simple representations may be seen in the definitions of the freshwater ecosystem

model Rostherne presented elsewhere (see Krivtsov et al. 2000b).

There are a number of models which provide coupling of the relevant physical,

biological, and chemical processes manifesting in the continental shelf seas. For example,

SEDBIOL (Smith and Tett, 2000) is a 1-D depth-resolving model which couples water

column dynamics, algal production, and SPM/benthic fluff settling/resuspension . The model

provides seasonally varying turbulent diffusivities which drive nutrient cycles and

interactions with phytoplankton (grazed by zooplankton) and SPM, including settling flux

and deposition of benthic fluff. The model predicts annual net primary productivity and

carbon fluxes to the seabed. COHERENS (Luytens et al., 1999) is an advanced 3-D coupled

model which uses turbulence closure schemes to provide the dynamical framework for

plankton cycling and SPM settling and exchange with the benthic fluff layer. It simulates

plankton dynamics, settling flux and fluff deposition rate and resolves mesoscale and seasonal

scale processes. Such models provide conceptual insights and numerical solution of

Some Aspects of Phytoplankton and Ecosystem Modelling … 215

biogeochemical fluxes in stratified and mixed regions of tide-driven shelf seas. Importantly,

the coupled models provide numerical relationships between factors such as water

temperature and seabed anoxia (which are potentially recorded in the sediments by biological

and geochemical proxies) and governing variables such as water depth, mixing, and

turbulence.

Another relevant example in this respect is POLCOMS (the Proudman Oceanographic

Laboratory Coastal Ocean Modelling System, see www.pol.ac.uk/home/research/polcoms), a

three-dimensional modelling system whose main elements are a three-dimensional baroclinic

hydrodynamic model (Holt and James, 2001) linked to a surface wave model (Wolf et al.,

2002; Osuna et al., 2007), a sediment resuspension and transport model (Holt and James,

1999) and an ecosystem model (ERSEM, the European regional seas ecosystem model, see

e.g. Baretta et al., 1995; Blackford et al., 2004) with benthic and pelagic components. This

modelling system has been developed primarily to investigate physical–biogeochemical

interactions in shelf seas, see for example Proctor et al. (2003).

Coupled models are capable of reproducing a complex interplay between ecosystem

components, and simulating spatial and temporal variation of algal productivity and the

dynamics in tidal shelf seas. Simulations suggest that plankton are constrained in mixed

regions by the transparency of the water column (high nutrients but high turbidity), and that

productivity seems to be greater in areas where h1 (i.e. the 'mixed layer optical thickness',

where is an attenuation coefficient, h1 is the thickness of the layer through which algae are

transported by vertical turbulence) is small rather than where nutrients are greatest (Tett et al.,

1993). Plankton are also constrained in the BML of stratified regions (high nutrients but low

light). In the SML of stratified regions, productivity is initially high in spring (high nutrients

and good light) but rapidly diminishes during the summer as nutrients are consumed and not

replaced. Grazing by herbivorous zooplankton and settling of algal cells (associated with

SPM aggregates) to the seabed reduce the standing stock in the SML. Subsequent predation

of zooplankton reduces grazing pressure and increase of nutrients by wind-driven mixing

stimulates a secondary autumn algal bloom in the SML. As the spring bloom wanes,

enhanced chlorophyll concentrations (up to 100 mg m−3) and maximum phytoplankton

biomass are generally seen at the thermocline in seasonally stratified regions (e.g. Anderson,

1969; Cullen and Eppley, 1981; Holligan et al., 1983). Turbulent tidal mixing generates new

production by periodically supplying nitrate from the BML. However, turbulent tidal mixing

also entrains algae into the BML where they are lost from the productive regions of the water

column (Sharples et al., 2001).

The nutrient status of algal cells has been shown to affect their cohesiveness (Kiorboe et

al., 1990) and enhanced post-bloom plankton agglutination has been attributed to an increase

in stickiness due to nutrient depletion (Logan and Alldredge, 1989; Smetacek, 1985). Such

stickiness has been linked to SPM aggregation with respect to flagellates and dinoflagellates

(Passow and Wassman, 1994; Jones et al., 1998) as well as to diatoms. Strong biological

mediation of SPM aggregation during the late stages of a flagellate bloom, resulting in

increased particle size and settling flux of SPM to the seabed, has been measured (Jago, et al.,

2007). Links between algal activity and particulate settling flux suggest that the greatest flux

per unit area of particulate matter to the seabed should occur in regions of greatest algal

production per unit volume, i.e. in frontal zones.In the aftermath of blooms, the enhanced

settling flux gives rise to low density, organic-rich, benthic fluff on the bed (Jago et al.,

1993). The correct understanding of the exact nature, and the dynamics of this fluff is crucial,

216 V. Krivtsov and C. F. Jago

because of its links with a number of important biological and chemical processes, and its

overall effect on biogeochemical cycling, and may be greatly facilitated by further

investigations combining experimental approaches, with comprehensive monitoring and

modelling studies.

IMPLICATIONS FOR INTERPRETING PAST AND FORECASTING FUTURE

ENVIRONMENTAL DYNAMICS

Comprehensive aquatic models are characterized by coupling of physical forcing

functions, with definitions describing relevant chemical and biological processes, and can,

therefore, assist in revealing complex multivariate interplay among components and processes

involved, as well as assist analysis of indirect interactions and their role in overall ecosystem

functioning (Krivtsov, 2002, 2000). Therefore, comprehensive aquatic models have a

considerable potential to aid interpretation of the past, and prediction of the future

environmental dynamics.

For example, in the fossil records of Rostherne Mere, Livingston (Livingston, 1979) was

the first to notice an inverse relationship between diatom and cyanobacterial remains

deposited, respectively, during the spring and the summer of the same year. However, it is not

until much later that this relationship was explained after careful interpretation of a

comprehensive set of ‗What if ?‘ scenarios simulated using the model ‗Rostherne‘, and was

attributed to the indirect effect of coupling between Si and P biogeochemical cycles by the

dynamics of primary producers (Krivtsov, 2001).

Since models such as COHERENS provide a numerical simulation of biogeochemical

fluxes underpinned by sophisticated treatment of shelf dynamics, they offer the potential for

quantitative interpretation of sediment proxies in the stratigraphic record. Combination of

models and sediment proxies (e.g. stable isotope chemistry of foraminifera), calibrated by

training sets, can provide information on water column structure, surface heating, mixing, and

water depth, thus providing a basis for reconstruction of past shelf sea regimes (see, for

example, Jago and Jones, 2002).

It has previously been argued (Krivtsov, 2002) that the correct understanding of indirect

relationships in environmental systems is crucial for sustainable development of humankind.

Considering the importance of aquatic ecosystems and the experience accumulated in studies

of indirect effects in the aquatic environment, complex aquatic models are likely to continue

playing a leading role in these investigations, in particular within the framework of the

comparative theoretical ecosystem analysis.

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Chapter 10

LABOR AND NUTRIENT ECONOMICS OF SOCIAL

INSECT COLONIES

Artificial Life Laboratory of the Department of Zoology

Karl-Franzens University Graz, Universitätsplatz 2, 8010 Graz, Austria.

ABSTRACT

In the evolution of social insects, the colony and not the (often sterile) individual

worker should be considered the major unit of selection. Thus, social insect colonies are

considered to be 'super-organisms', which have – like all other organisms – to perform

behaviors which affect their outside environment and which alter their own future

internal status. The way these behaviors are coordinated is by means of communication,

which is either direct or indirect and which involves information exchange either by

transmitting signals or by exploiting cues. Therefore, social insect colonies perform

information processing in a rather similar way as multicellular organisms do, where

behaviors result from the exchange of information among their sub-modules (cells). In

many cases, self-organization allows a colony to evaluate massive amounts of

information in parallel and to decide about the colony's future behavioral responses.

Many feedback systems that govern self-organization of workers have been investigated

empirically and theoretically. Here, we discuss models which have been proposed to

explain division of labor and task selection in social insects. We demonstrate how the

collective regulation of labor in eusocial insect colonies is studied by means of top-down

modeling and by bottom-up models, often analyzed with multi-agent computer

simulations.

Keywords: social insects, division of labor, task selection, colony integration, multi-agent

modeling, honeybees.

*

Tel: +43 316 380 8759, Fax: +43 316 380 9875.

224 Thomas Schmickl and Karl Crailsheim

1. INTRODUCTION

For any living organism, choosing an appropriate behavior is a crucial issue to survive

and to reproduce. Usually, the actions that compose behaviors are attributed to certain

functionality, like 'foraging for food', 'reproduction', or 'self-defense'. In most cases, a

successful performance of such behaviors significantly alters the constitution and the mode of

operation of this organism. This happens for example by increasing the activity of specific

organs in multicellular organisms or of specific organelles in unicellular organisms.

In our field of study, which is social insects, similar behaviors are observed in insect

colonies. Such colonies are usually conceived as 'super-organisms' (Moritz & Fuchs 1998,

Hölldobler & Wilson 2008). This is reasoned by the fact that in social insects, whole colonies

– and not individual workers – can be seen as units of selection, as was reviewed by Tarpy et

al. (2004) for honeybees. In most cases, female workers are sterile and colonies perform

reproduction by division of whole colonies (e.g., swarming in honeybees) or by producing

queens and males for founding new colonies (e.g., most ants, termites, wasps, bumblebees).

We adapt this super-organism approach and discuss colony-level decision-making and self-

regulation as a result from division of labor and from communication/interaction among

workers: We focus here on those eusocial insects which exhibit division of labor (DOL) and

partially also task partitioning (TP). The phenomenon of DOL refers to the fact that the

working duties in the colony are not distributed at random. In many social insect species,

specific groups of workers perform specific sets of tasks within the colony's collective

physiology, thus they have many similarities to organs in metazoa and to organelles in

protozoa and microbes. These analogies were already pointed out by Wilson (1985) as well as

by Robinson (1992), who showed the importance of adaptability and of self-organizational

aspects in DOL.

The predictions of our mathematical models of honeybees, which are discussed in this

chapter, suggest that the processes, which allow a social insect colony to perform collective

decision making and collective homeostasis, are influenced by the colony-wide physiological

network, where specific pathways (flow of nutrients, flow of workforce, flow of information

...) exist. In turn, colony-level decision making affects these colony-level physiology

significantly, making the collective physiology an important component of significant

feedback loops. Colony-level physiology is regulated again by feedback loops that establish

colony-level homeostasis. However, these feedback loops involve in most cases specific

behaviors of individual workers, thus modeling these networks quickly leads to models that

cannot be solved in mathematical closed form. Thus numerical simulation becomes

important. Often the behavior of individual agents that constitute a colony as well as their

environmental conditions are found to be so complex that individual-based modeling is

needed to generate plausible models of these focal systems. However, loss of generality is

often the price that has to be paid, whenever individual-based models are used. We are well

aware of that in our scientific approach, as our models tend to describe the modeled system in

a very detailed manner. However, this level of detail is needed to allow our models to answer

our focal scientific questions. We try to model the physiology of the whole colony by

modeling the physiology of the individuals with as much precision as is feasible. Our concept

is to fuse many physiological building blocks (worker physiology) to one single higher-level

physiology (colony). In turn, behavioral decisions of individual agents are mostly results of

Modeling Population Dynamics, Division of Labor … 225

their physiological status and their local environment, which are summarized as 'proximate

mechanisms' (Mayr 1961, Tinbergen 1963). These individual behaviors ultimately constitute

the collective behavior of the colony. Our modeling approach allows us to investigate how

such colony-level decision making and self-regulation affects energy economics and brood

production of insect colonies. Thus, these studies ultimately allow us to discuss also 'ultimate

causation' of colony-level behaviors (Mayr 1961, Tinbergen 1963).

Also in our work, the main scientific questions are focusing on proximate mechanisms

and on ultimate causation of colony-level reactions (or group-level behavior), which are a

response of a colony to a specific environmental stimulation. These questions can be grouped

into two distinct sets of questions:

Q1: How does the composition of the colony (different specialists) change in

response to these stimuli? How does colony structure (e.g. age structure) change?

How does the flow of nutrients and energy through the colony change? The answers

to this set of questions build the 'substrate' for investigating the second set of

questions, as the colony status restricts the availability of nutrients, building material,

energy and workforce which is available for the colony.

Q2: How does individual worker decision making affect the colony's global

physiological status and vice versa? How is the physiology of individual workers

correlated with the global physiology of the collective? How is the ratio of gain to

costs of specific worker actions related to the colony-wide economics of energy and

nutrients? Which information is spread, stored and filtered in the colony by specific

actions performed by workers? This set of questions is investigating the proximate

mechanisms involved in DOL, but – as we model also the physiology of workers –

the studies aimed to answer these questions deliver also predictions of colony-level

fitness parameters, which are survival and fecundity of colonies. Thus, these studies

link back also to the ultimate causation of observed behaviors. In this article we will

describe how studies of DOL can be performed with a set of models of honeybee

population dynamics and nectar energetics.

The degree of specialization found in social insect workers differs among species: The

phenomenon of specialization refers to the fact that workers are more likely to perform one

task over the other compared to other workers in similar situations. In contrast to that,

plasticity refers to the fact that one worker engages in a variety of tasks or that it changes the

performed task over time. Specialization of workers will be advantageous if the specialist

worker performs its specialized task more efficient than an average worker is able to (Jeanne

1986a). This is most obvious in ants and termites, where there exist sometimes huge

morphological differences among worker castes (Wilson 1985). In addition to morphological

differences between workers, drones and queens, there are also significant physiological

differences observable between worker specialists in honeybees. Due to this physiological

specialization a worker bee can be more efficient in its specialized task. Seeley (1982)

mentions additionally the fact that age-related groups are better in locating specific age-

226 Thomas Schmickl and Karl Crailsheim

related tasks in their local environment than the hypothetical generalist worker could do: For

example young bees most prominently find brood cells to clean nearby, as they just have

emerged from such cells a few hours ago. But specialization could be also disadvantageous: It

makes a colony vulnerable to losses of one specific caste and it maximizes searching time of

specialists to find the next suitable working site.

In honeybees, the observed correlation between task specialization and worker age is

called 'age polyethism' (AP). DOL, TP, and AP are very prominent features in eusocial

insects, as we will describe in more detail in the upcoming sections.

Wilson (1984, 1985) reports the case of the ants Pheidole guilelmimuelleri and Pheidole

pubiventris where even huge morphological differences between small workers (minors) and

huge workers (majors) do not prevent one caste to engage in a task that is typical for the other

caste in times of experimental removal of one caste. Workers with sufficient plasticity might

find the next spots to work sooner than specialists. We assume that natural selection found a

near-optimal trade-off between these two features for every species, according to the species

ecological constraints. Computational models help us to understand these ultimate reasons,

why an according mode of operation in DOL emerged in specific species.

In addition to specialization and plasticity, some social insects show also the

phenomenon of task partitioning. In contrast to DOL, which refers to splitting the workers

into task-specific groups, TP refers to splitting a task among several workers. In most cases of

task partitioning found in social insects, it was observed that the foraging task was

partitioned: Searching, cutting, transporting and storing of food is often performed by

specialist workers. In leaf-cutter ants, TP was reported for almost all tasks that involve

handling of material (also waste removal, see Hart et al., 2002). Ratnieks and Anderson

(1999) reviewed this issue in detail and discussed several important aspects of TP: (1) It

allows workers to specialize in specific parts of a whole task, thus possibly increasing

efficiency. (2) By doing so, reliability of a single subtask increases, as specialized workers are

more reliable to accomplish the sub-tasks, but (3) the reliability of the whole task decreases,

because if one sub-task fails, the whole task cannot be performed. In addition (4) food-

transfer times have to be short enough so that benefits of sub-task specialization are not

wasted. Again here, computational models are able to support ultimate reasoning of TP.

The organs in non-eusocial metazoan organisms show significant changes in activity

during specific behaviors. Also the task-specific groups in eusocial insects change their group

sizes and the activity levels of their members in association with specific colony-level

behaviors. It was found that those mechanisms that allow a social insect colony to decide

collectively for nesting sites or for important foraging targets are in most cases regulated in a

decentralized and self-organized way (Camazine et al., 2001), often also referred to by the

term 'swarm intelligence'. In such systems, a network of feedbacks regulates DOL and TP,

which arises from the flow of substances (food, pheromones) within the colony, as well as

from worker-to-worker interactions and communication. However, this is not totally different

from non-eusocial metazoan organisms, where hormones and other cell-to-cell interactions

also contribute to selection and shaping of the organisms' behaviors.

When reflecting on an observed behavior, scientists should concentrate on two distinct

sets of questions (Mayr 1961): The first set of questions refers to the individual local

mechanisms that cause the behavior. For example ―H ow does it work?‖ and ―Whe n and how

is it triggered?‖. The second set of questions refers to ultimate reasoning of the behavior, like

―Whyhas natural selection favored this behavior?‖. Computational models support scientists

Modeling Population Dynamics, Division of Labor … 227

in elaborating on both sets of questions, as we will discuss in the following sections of this

article. In the following sections we describe two major approaches how DOL and TP are

investigated by means of computational modeling: On the one hand, there are top-down

models, which often consider the population structure of the modeled colony or predict the

population dynamics that arise from DOL. These models often aim for an ultimate reasoning

of DOL. On the other hand, there exist many individual-based models, which often aim on

investigating the proximate mechanisms. By describing our own model 'TaskSelSim' in

detail, we show how an individual-based model is used for addressing questions of ultimate

reasoning.

The system of feedbacks that allows DOL in an insect society can be well studied by top-

down-approaches, for example by stock&flow modeling. This quantity-based modeling

approach was used to investigate the interplay between age demography and DOL in social

insects only rarely. However, we think that this modeling technique is an excellent way to

describe social insect populations: Stock&flow models are graphical representations of

coupled differential-equations. Besides the benefit of being easily understandable for the

broad public due to their graphical nature, they implicitly ensure conservation of mass, as

they track quantities in 'stocks' and 'flows' separately from other informational variables. In

such a stock&flow model of DOL in eusocial insects, available workers are the quantities that

reside in a 'stock' and which flow to other 'stocks' which represent worker groups of specific

tasks. Thus, these 'flows' represent the recruitment results of the recruitment system of the

modeled species. Another flow of workers connects back from the task-related stock to the

stock of un-recruited workers. In addition, birth of new animals increases the available

workforce over time, a process which might be affected by successful performance of specific

tasks. In parallel, death decreases the workforce, whereby mortality rates might be task-

related as well. This scheme represents a sort of system-dynamics skeleton that demonstrates

how DOL and population dynamics are easily described from a top-down perspective. As

DOL should be explained by some ultimate reasoning (e.g. by a fitness enhancement of the

colony), such a point of view is advantageous, as it helps to investigate how DOL potentially

enhances colony growth or stabilizes a colony's population dynamics.

We develop here first a simple basic skeleton of a top-down model of DOL. Figure 1

shows a simple stock&flow model of DOL, which we use as a starting point for our

elaboration: Birth is a flow from a source into a stock, as it produces new workers. In parallel,

workers are subject to death, depicted as flows from stocks into sinks. Workers that engage

into a task are tracked in another stock which exchanges quantities of workers with the stock

of un-recruited workers via two flows, called 'recruitment' and 'abandonment'. Abandonment

is proportional to the amount of recruited workers (fixed decay rate). Recruitment is

proportional to the number of recruited workers (active worker-to-worker recruitment), to the

number of unrecruited workers and to the current workload (stimulus). Birth is steadily

producing new workload but creates also new workforce. In contrast to that, task performance

is reducing the workload and, in parallel, is enhancing birth rates. This simplified sketch of a

model clearly demonstrates how population dynamics inside of a social insect colony affects

228 Thomas Schmickl and Karl Crailsheim

DOL and how DOL in turn affects population dynamics by influencing birth rates and by

task-specific mortality rates.

+

births

+

abandonment

Recruited Unrecruited

workers workers

+ recruitment +

death

of task

+ deaths

normal

group + +

Work to

+ be done

work done new work +

Figure 1. A stock&flow diagram of DOL that is embedded in a simple model of population dynamics.

Boxes indicate quantities of workers or quantities of work. Solid arrows indicate flows (transitions) of

quantities. Dashed arrows indicate causal relationships. Cloud symbols indicate sinks and sources.

From this basic modeling sketch, not only the recruitment and abandonment mechanisms

could be elaborated. In addition, the depicted age-structure should be modeled in higher

resolution for depicting DOL in a specific species. In some social insect species, workers are

morphologically (and possibly also physiologically) in-discriminable. Thus the above

depicted model holds for these species. In other species – especially in ants and termites –

there often exist strong morphological differences, which predispose worker castes for

specific jobs. Figure 2 sketches the basic principles of a model that describes DOL in a

species (of ants) that has two distinct morphological castes. As described by Wilson (1984,

1985), the huge 'majors' engage in brood caring only seldom. However, when 'minors' were

experimentally removed, they start with brood care already one hour after the experimental

disturbance of the colony's age structure. From the colony level perspective, the stock&flow

diagram depicted in figure 2 describes the observed flows of workers, as well as the change in

population structure. For the sake of simplicity, we omitted most of the arrows that indicate

causal relationships and depicted just those that are most significant for DOL. Thickness of

the arrows indicates the strength of the causal relationship.

Modeling Population Dynamics, Division of Labor … 229

births births

abandonment abandonment

majors majors minors minors

deaths

task normal normal task

majors minors

<births>

Jobs to be

done inside

of the nest

work done new work

Figure 2. A stock&flow diagram of DOL in a species having morphological castes. The model of DOL

is embedded in a simple model of population dynamics. Boxes indicate quantities of workers or

quantities of work. Solid arrows indicate flows (transitions) of quantities. Dashed arrows indicate causal

relationships. Cloud symbols indicate sinks and sources. Only relationships significant for DOL are

drawn.

specialisation occurs multiple times throughout the lifetime of a worker. These changes of

preferred tasks often correlate with distinct changes in physiological and sometimes also

morphological (e.g., gland development) modifications. Although 'minor' workers can engage

in the job of 'majors', they do not become 'majors'. In contrast to that, in bumblebees,

morphological and physiological changes stretch over a time span of one season: Spring-born

bumblebees are smaller and behave differently than late summer-born bumblebees. In

honeybees, a worker bee engages into several different tasks as it gets older (Seeley 1982;

Wilson, 1985). Figure 3 shows a simplified stock&flow sketch that depicts such a colony

which exhibits AP. In such models, tracking the age structure of the colony is an important

aspect and recruitment rates to specific tasks vary between the age classes. If an age class has

a low population size, less recruitment occurs to the task usually performed by workers of that

age, thus less work will be performed. In turn, the workload accumulates, enhancing the

recruitment rates also for the other age classes, which have a lower but non-zero recruitment

probability for this task. This way, more workforce is recruited from age classes that are less

predisposed for the specific task, in turn decreasing the effects of the experimentally induced

disturbance of DOL. Such phenomena are described in empiric studies of honeybees (e.g.,

Robinson et al., 1992). As figure 3 clearly shows, the feedback between DOL and colony

demography is an important feature to predict dynamics of DOL in social insects that exhibit

AP, especially when predictions are made throughout a longer time period.

230 Thomas Schmickl and Karl Crailsheim

foraging foraging

getting

births hatching older deaths

in-nest job

Figure 3. A stock&flow diagram of DOL in a species that shows AP concerning two tasks (foraging,

nursing). The model of DOL is embedded in a simple model of population dynamics. Boxes indicate

quantities of workers or quantities of work. Solid arrows indicate flows (transitions) of quantities.

Dashed arrows indicate causal relationships. Cloud symbols indicate sinks and sources. Only

relationships significant for DOL are drawn. Mortality of brood and age classes are omitted, to keep the

sketch simple.

Wakano et al. (1998) modeled a social insect colony with age structure, in which one

vector holds all populations of age classes. They modeled two tasks (in-nest and foraging).

The degree of specialization to foraging or in-nest work for every age-class n is defined by

setting one parameter xn. Their model incorporates task specific mortality rates. Brood

production is limited by performance of both tasks: with no brood care or with no foraging at

all, no brood is produced. Using this model, and by simulating several parameterizations, the

authors reached balancing between the two modeled tasks. They showed life time expectancy

as an ultimate reasoning of the fact that the risky foraging task is always performed by the

older workers in social insects with age polyethism. The model was used to test three regimes

of AP: Hard: age fixed the job; Soft: every age has a certain probability to perform the job;

Not: no age polyethism at all. The authors found that each kind of AP is predicted to be

advantageous under specific environmental and ecological conditions. In case those

environmental fluctuations affect the performance of both, inside and outside jobs, soft AP

was found to be most adaptive. If fluctuations affect only outside tasks (foraging) then hard

AP was found to be most adaptive. The model of Wakano et al. (1998) is not addressing a

specific species, it is a general modeling approach of AP in social insects.

The first issue to be solved in studying DOL in eusocial insects is to know which workers

are available for specific work. In connection with AP, this means to know how many

workers of each age class are available. In case of morphological different workers, it is

important to know how many workers of each morphe exist. As honeybees show an adaptive

regime of AP quite prominently (e.g., Seeley 1982), the age demography of honeybees was

Modeling Population Dynamics, Division of Labor … 231

studied intensively with classical top-down models and only rarely with bottom-up models. In

our work, we followed both modeling approaches. Empiric studies showed that a honeybee

colony can change its own colony structure in reaction to environmental conditions (e.g.

seasonal changes), for example by changing the egg laying behavior of the queen, the nursing

intensity of larvae or by cannibalizing brood (Schmickl & Crailsheim 2001). Thus, studying

these dynamics is an important aspect in the investigation of DOL.

AP is most prominent and most complex in honeybees, thus many demographic models

have been made in this field. Some of them also incorporate aspects of AP, in a way that

either age structure affects AP or vice versa. Omholt (1986, 1988, 1992) suggested several

closely related honeybee models that predict the egg laying of the queen, the workers deriving

from these eggs and how these workers in turn affect the egg laying. These models predict

plausible population dynamics, they predict foraging intensity (honey yields) and they show

that worker longevity could be a response of the nursing load a bee has encountered.

DeGrandi-Hoffman et al. (1989) published a model called BEEPOP, which models the

queen's laying of female (workers) and male (drones) eggs, and the resulting populations

(with age structure). The model assumed that bees up to a specific age work inside of the

colony and that older bees work outside. Thus, BEEPOP implements 'hard AP', according to

the definitions of Wakano et al. (1998). The model is parameterized by weather profiles and it

predicts population dynamics as well as the foraging workforce throughout the year.

Makela et al. (1993) described an object-oriented model called 'AHBsim', which models

the population dynamics and AP of africanized honeybee colonies. What makes this work

outstanding is the fact, that parameters were coded in a sort of 'artificial genome'. Also colony

level reproduction (swarming) and 'drone production' were part of this model. Thus, Makela

et al. (1993) programmed maybe the first 'Artificial Life'-like model of social insects, in

which evolution could be studied on the colony level. In AHBsim, there is also a hierarchical

order, in which worker bees are associated to specific tasks.

In Schmickl & Crailsheim (2007), we presented a model called 'HoPoMo' (honeybee

population model), which models the population dynamics of a honeybee colony from a given

egg laying pattern of the queen. This model, consisting of more than 60 equations,

incorporates a system of 'soft AP', in which adult workers are recruited on a daily basis for the

tasks of 'nursing', 'nectar handling', 'pollen foraging' and 'nectar foraging'. This is done based

on a hierarchical system of task priorities and according to the current status of supply and

demand on the current day. The model incorporates weather data, a seasonal environmental

resource profile and age demography. After elaborating on the basic model, the reproductive

act of a colony (swarming) was simulated, demonstrating that the population model is able to

predict even significant disturbances of colony structure in a qualitatively and quantitatively

plausible way. In addition, the model is able to predict the effects of changes in the colony's

age demography on the emerging DOL and resource dynamics inside of the colony. In turn,

these variables affect the future intra-colonial population dynamics, thus establishing a time

delayed feedback loop between population dynamics and DOL. Figure 4 depicts the most

important feedback loops that are modeled in HoPoMo.

In our HoPoMo model, DOL is based on a hierarchical system of task priorities, which

considers also the current status of supply and demand on the current day: The model assigns

the available pool of worker bees (workforce) to tasks according to the current colony

demand (nutrient flow, brood nursing demands …). As there is modeled a complex system of

interwoven feedback loops, the modeled colony achieves homeostatic regulation of DOL and

232 Thomas Schmickl and Karl Crailsheim

nutrient stores (see figure 4). After elaborating on the basic model, which was validated

against many sets of empiric measurements on honeybees and after exhaustive sensitivity

analysis of the model, the reproductive act of a colony (swarming) was simulated (see Figure

5, Schmickl & Crailsheim 2007). In future, the model will be used to interpret data from

empiric colony-level experiments on honeybees and to develop mesoscopic honeybee models,

as we have described them in the discussion section.

Figure 4. Major feedback loops regulating DOL and population dynamics in HoPoMo. Reprinted from

Schmickl & Crailsheim (2007). Boxes represent stocks that hold quantities (workers, resources). Grey

arrows represent flows. Black arrows represent causal relationships. Circular shapes represent sources

and sinks of quantities. ELR: daily egg laying rate of the queen. SUPcombs: Egg laying suppression

due to little space available on the combs.

Flows of nutrients have a regulating effect on dynamic regulation of DOL not only in

bees but also in other species: Karsai & Balazsi (2002) showed that the inflow of water into a

wasp colony (Polybia and Metapolybia wasps) dynamically regulates the pulp foraging and

thus regulates the nest building behavior. This was shown by a differential equation model,

yielding results that correspond well to empirical results (Jeanne 1986b, Karsai & Wenzel

1998, 2000). A corresponding individual-based model was published recently by (Karsai &

Runciman 2008).

Models that combine mechanisms of DOL in social insects with colony demography are

not frequently produced. Especially since computers became faster and faster in the last

decades, there is a trend of investigating DOL with microscopic, individual-based, bottom-up

approaches. Most of these studies focus on investigating proximate mechanisms of DOL and

TP, as is described in the upcoming section.

Modeling Population Dynamics, Division of Labor … 233

Figure 5. Application of the model HoPoMo. Using this model we simulated the population dynamics

and the change in colony weights (bees, nutrient stores and comb) during colony reproduction. Top

row: Predicted Intra-colonial population dynamics and weight development of a colony that does not

swarm. Lower two rows: Same predictions for a colony that duplicates by swarming. Middle row:

Colony that stays in the hive. Bottom row: Colony that is formed by the swarm that left the hive for a

new home. All: Day 0 corresponds to the 1 st of January in a year.

selection of hundreds or thousands of workers in parallel. Thus, much research has been done

on the proximate mechanisms that allow the workers to decide upon engaging in specific

tasks. Several classes of models have been proposed to describe which proximate

mechanisms make a single worker to engage in a specific task and how this is regulated on

the colony level. In the majority of models on DOL, a basic assumption is that the

engagement of an animal to a specific task is triggered by a neuronal or hormonal mechanism

that can be represented by a threshold. A stimulus that is intense enough to meet this

234 Thomas Schmickl and Karl Crailsheim

threshold triggers a behavior (Lorenz 1978). Beshers and Fewell (2001) give an overview

which classes of models have been proposed to explain the observed models of DOL by

different proximate mechanisms working on the individual worker level. These models are

not necessarily incompatible to each other, as mechanisms might differ with species or with

the kind of regulated tasks.

Bonabeau et al. (1996) showed that a model consisting of two distinct castes ('minors' and

'majors'), having different thresholds to perform the task of brood care, suffices to simulate

the colony-level plasticity in Pheidole ants reported by Wilson (1984, 1985). In this

individual-based model, the probability of each individual to engage in the brood caring task

is modeled by the following equation

st2

Pi ,t , (1)

st2 i2

where Pi denotes the probability of an individual of caste i to engage in the nursing task. The

variable t refers to the current time step in the simulation, s refers to the current stimulus

strength (workload to be performed) and Θi refers to a fixed threshold of caste i that has to be

met by the stimulus to trigger the task. In their simulations they set Θ1=8.0 and Θ2= 1.0.

Equation 1 has been used several times in literature to model behavioral response thresholds.

It became a quasi-standard, although a simple step-like function ( 'if s>Θ then act()')

would suffice in most cases. According to the parameter values used in Bonabeau et al.

(1996), the probabilities to engage in the brood-care task will scale with stimulus intensity as

depicted in figure 6. In their model, individuals abandoned a task with a fixed rate, assuming

a fixed time period for task performance. The dynamics of the stimulus were modeled as

follows: The stimulus increased by a linear term and was decreased proportionally to the

fraction of active workers of both castes in the number of all available workers. Thus, the

authors assumed equal efficiency of both castes in performing the task.

0,9

0,8

Probability of task engagement

0,7

0,6

0,5

0,4

0,3

0,2 minors

majors

0,1

0

0,1 1 10 100

Stimulus intensity

Figure 6. Probabilities of task performance of 'majors' and 'minors' in the model of Bonabeau et al.

(1996). It needs a higher stimulus intensity to trigger the nursing task in a 'major' than in a 'minor'.

Modeling Population Dynamics, Division of Labor … 235

Using this model of fixed thresholds, Bonabeau et al. (1996) could predict the dynamics

of experimental removal of 'minors' in Pheidole ants by assigning different values of Θi for

'minors' and 'majors' in a way that was comparable to empiric observations (Wilson 1984,

1985). This model was extended to a system with two tasks, where each caste is specialized to

one of the two tasks. The authors called the fixed-threshold model ―...t he arguably simplest

model that connects flexibility at the worker level with the resiliency observed at the colony

level...‖ (Bonabeau et al. 1998). Although the model is simple, they report in their extensive

paper that they have been able to simulate several aspects of dynamic DOL: Not only the

plasticity observed in Pheidole ants, but also spatial specialization of workers, and AP could

be modeled. The authors introduced also genetic (threshold) variability. For modeling AP,

they did not vary the individual's threshold over time, but the exposure or sensitivity to a

certain stimulus was depending on a worker's age. The fact that different ages of workers

occupy usually different spatial locations in the colony and are thus exposed to different sets

of stimuli, was also considered by the 'foraging-for-work' hypothesis (Tofts 1993, Tofts &

Franks 1992, Franks & Tofts 1994): This hypothesis is based on the assumption that spatial

displacement of workers, as they grow older, moves them from the central brood nest to the

periphery of the colony, as new workers constantly hatch in the brood nest. In consequence,

the encountered bouquet of local stimuli changes with this displacement. Thus workers

engage sequentially in tasks that correlate with their age, without requiring any intrinsic

specialization mechanism that explicitly reflects a worker's age.

The above mentioned models assumed fixed thresholds that stay constant for every

individual through time. Lorenz (1978) discussed the importance of such behavioral

thresholds and also described their adaptation: Both, the exposure to stimuli as well as the

successful performance of a stimulus-triggered behavior modulate such thresholds. The

phenomena of 'sensitization' and 'facilitation' refer to the fact that once a stimulus has

triggered a behavior, the animal is more likely to repeat this behavior again, even at a lower

stimulus level. This is equivalent to lowering behavioral thresholds. After some time without

such a stimulus, these effects disappear, what is equivalent to increasing these thresholds.

These mechanisms were incorporated into the previously described threshold-reinforcement

models, which assume that the behavioral threshold Θi,j,t of individual i to engage in task j at

time t is decreased each time a worker engages in a task. Thus the worker gets more

specialized to that task j. The same threshold is increased in each time step when the task is

not performed. Variants of this model were analyzed and published by Deneubourg et al.

(1987), by Plowright & Plowright (1988), and by Theraulaz et al. (1991, 1998): In these

models, the probability to engage in a task i for individual j is described by

si2, j ,t

Pi , j ,t (2)

si2, j ,t i2, j ,t

This is a variant of equation 1 in which si,j,t is the associated stimulus to perform task j, as it is

sensed by worker i at time t.

Like in the fixed-threshold models, performance of a task leads to a local decrease of the

associated stimulus strength, but stimuli accumulate again as new workload emerges

constantly. Using this mechanism, simulations showed (Theraulaz et al. 1998) that the

236 Thomas Schmickl and Karl Crailsheim

modeled colony members quickly split up into two groups: one specialized on the first task

and one specialized on the second task. It was also shown that removal of one worker group

leads to an increase in stimulus strength of the associated task and this fact ultimately allows

specialists of another task group to re-specialize. Theraulaz et al. (1998) modeled this

mechanism in a time-continuous way, considering the fractions of time spent by agent i with

and without engaging in task j. In contrast to that, Gautrais et al. (2002) modeled this process

in an individual-based model. They showed that such effects occur more prominently in

bigger simulated colonies compared to small colonies. Equation 3 gives the details for the

threshold adaptation mechanism:

i , j ,t 1 (3)

i , j ,t j else

The self-reinforcement model incorporates a strong positive feedback, which drives the

system into a state in which individuals are quickly caught by one of several basins of

attraction. If there are enough other individuals around performing the other task, they will

stay in this basin (of specialization) for a long time. Merkle and Middendorf (2004) identified

several shortcomings of the Gautrais et al. (2002) model: The observed non-specialization in

small colonies was shown to be an effect of initial conditions, because in the initial phase of

the simulation runs, workload (demand) was growing much slower in small colonies than in

bigger colonies. As only frequent task-performance leads to specialization of a worker, these

colonies developed mainly generalists. The authors also identified the maximum height of

thresholds as a crucial parameter: The bigger this maximum value is, the more often an

individual has to perform a task within a short window of time to become a perfect specialist.

In addition to changes of parameterization and simulation procedures, Merkle &

Middendorf (2004) introduced also extensions to the original model: They modeled a limited

life-span of workers and introduced new (grown) workers into the system. In addition, they

varied maximum thresholds with age (comparable to suggestions in Bonabeau et al., 1998),

thus extended the model to depict also AP. Their model extensions contained also a

'competition-for-work' aspect, where those individuals with the lowest thresholds for a given

task were