From ”Spatial conservation prioritization:

computational methods and quantitative tools”.

Moilanen, Wilson & Possingham, editors.
Oxford University Press, in press (5/2009).

Supplementary material for “Optimointiopin

seminaari” Helsinki University of Technology /
2008. Do not distribute further.

3 - A mathematical classification of conservation prioritisation problems

Atte Moilanen, Hugh P. Possingham and Stephen Polasky

3.1 Introduction

The conservation prioritisation problem concerns efficient and informed allocation of resources
available for conservation (Margules and Pressey 2000; Sarkar et al. 2006; Chapters 1 and 2).
This problem is of relevance to anyone working in conservation management or science, and it
has been approached using a variety of heuristic, qualitative and quantitative solution methods
(Chapter 1). In this chapter we define this problem as a classical optimisation problem and show
how approaches found in the conservation planning literature and the rest of the chapters of this
book fit into this standard framework. Closely related chapters include those describing
optimization techniques (4 and 5), metapopulations (8), PVA (9), sequential planning (10), and
climate change (13). Chapters about software tools (14)-(17) demonstrate methods to implement
and solve variants of the conservation prioritisation problem. We also discuss data requirements
and computational complexity of the problem variants and implications for solution methods.

The application of optimization techniques brings a powerful set of tools to bear on conservation
problems. Since resources available to conservation organizations are insufficient relative to the
threats facing biodiversity, application of optimization techniques to achieve the “biggest bang
for the buck” can be important. Applying an optimization approach to conservation planning
requires that the analyst and stakeholders formulate their conservation problem. Any
conservation prioritisation problem has several essential components (Possingham et al. 2001;
Wilson et al. 2007):

1
 1) Clearly define a conservation objective (e.g., maximize the number of species conserved;
or minimise the number of species lost);
2) Specify the set of actions that can be taken (e.g., choose sites as biological reserves, or
engage in efforts to control invasive species);
3) Specify how actions contribute to the conservation objective (e.g., how many species are
conserved if a planning unit is chosen as a reserve or invasive species are controlled);
4) Specify the costs of actions and the resource constraints faced by the conservation
planner (e.g., how many sites can be chosen as reserves, or what is the monetary cost of
selecting a site or controlling invasive species and what is the total conservation budget).

We limit the scope of this chapter by concentrating on static and deterministically time-
dependent conservation prioritization problems. In this class of problems sites are assumed to be
available for conservation and the distributions of conservation features are assumed to either be
static or to evolve through time in a deterministically known manner (dependent on conservation
action). There is a more general class of the conservation prioritisation problem that involve
cases where yearly budgets are limited and possibly varying, areas are being degraded or lost
stochastically, sites are not always available for investment, and the overall goal is to maximize
conservation value at the end of the planning frame. This stochastic and dynamic prioritisation
problem, treated in Chapter 10, is significantly more complex than the conservation problems
treated here.

We emphasize that this chapter is about defining the conservation prioritisation problem as
opposed to solving the problem – problem definition and solution are separate steps, and solution
techniques are treated in chapters 4 and 5. We start from a conceptual level by relating the
conservation prioritization problem to the components of the classical framework of optimization
and control theory.

3.2 Overview of the conservation prioritisation problem

Conservation prioritisation problems can be coherently formulated as classical optimization

problems (e.g., Bazaraa et al. 1993). In the language of optimization, a well-posed problem for
conservation planning has the following elements (Possingham et al 2001):
1) Objective Function: statement of the objective with an explicit measure of performance
(conservation value)
2) Control Variables and constraints: the set of actions that can be chosen (conservation
action).
3) State Variables: the set of variables that characterise the environment (e.g. distributions of
species in the landscape).
4) State Equations: the set of equations that describe how state variables evolve as a
function of the state and control variables (e.g. how do the distributions of species change
based on current conditions and the conservation actions implemented).

2
Figure. 3.1. A schematic of how the components of the general conservation prioritization
problem link together.

Figure 3.1 shows the flow of analysis in a classical optimization problem. Starting from the
lower right of Figure 3.1, the choice of conservation actions (control variables) along with
information about the landscape (environmental data) are brought together in the state equations.
The state equations determine the distributions of features (state variables) as a function of
environmental conditions and choice of control variables. The levels of the state variables are
then evaluated in terms of their conservation value (the objective). Optimization involves
choosing the control variables in an intelligent manner to find a solution that has the highest
possible value of the objective. Constraints limit what combinations of control variables are
allowed. For example, the cost of the conservation actions may be limited by a budget. In
adaptive management the observed system state and performance are regularly compared to that
expected, and the control variables are updated as required.

The conservation prioritisation problem can take many forms. Exactly which form it takes
depends on the assumptions and/or simplifications that we wish to make (Table 3.1). The twelve
options outlined in Table 3.1 can be combined in different ways to create 8192 distinct variations
of the conservation prioritisation problem. For example, a simple problem would be to find a
solution that includes at least one population per species, not accounting for spatial patterns,
connectivity or habitat requirements for persistence. A comparatively complicated problem
would be a spatially explicit multi-feature problem, where persistence of features is maximized
via the allocation of funds to alternative conservation actions through the landscape. Some
options, such as whether performance is evaluated by measuring retention (Pressey et al. 2004;
Moilanen and Cabeza 2007) or representation, imply conceptually significant changes that
require only computationally minor adaptations – the only difference is what sites are included in
the evaluation of the performance of a candidate solution. Other options, while being
conceptually trivial, may offer great computational challenges. This is the case when we allow

3
multiple conservation actions at a site instead of a single conservation action. The only change is
a greater choice of conservation actions per site which is conceptually straightforward, but this
choice has major computational and data requirement implications.

Table 3.1. Structural options of the conservation prioritisation problem. In each case we evaluate
the increase in conceptual and computational complexity using a qualitative scale from minor to
moderate, major, and great.

Structural options Change in Change in

conceptual computational
complexity complexity
A Objectives and constraints
Single vs multiple objectives Moderate Moderate
Single vs multiple features Minor Major
Minimum set versus maximum coverage Minor Minor
B Control variables
Single vs multiple conservation actions Minor Major
Discrete (e.g., protect or not) vs continuous control variables Minor Moderate
(allocation of varying resources)
Scenario evaluation vs independent choice of conservation Minor Major
action in sites
C State variables and equations
Spatially implicit (linear) vs spatially explicit (nonlinear) Major Major
Static vs time-varying occurrence of features Minor Moderate
Deterministic vs stochastic dynamics Moderate Great
Stationary vs changing distributions of features Major Major
D Performance measurement and evaluation
Representation in reserves vs retention in the landscape Moderate Minor
Scoring vs complementarity-based Moderate Minor
Representation vs persistence Major Great

Before going on to discuss the kinds of problem that emerge from the options outlined in Table
3.1, we define symbols used in this chapter (Table 3.2). We use the following notation for
vectors and matrices: symbols in bold and lower case are vectors, symbols in bold with capital
letters are matrices or sets. For example, x={xi} is the vector of selected sites, with xi = 1 if site i
is selected and 0 otherwise for i = 1, 2, …, Ns. R = {ri} = [rij] is a sites species representation
matrix, where i = 1,2, …, Ns and j=1,2, …Nf; ri is the vector of representations of features in site
i. If a vector or matrix is marked as an argument for a quantity, this means that the quantity may
depend on one or all elements of the vector (or matrix). For example, notation rij(a) means that
the representation level of feature j in site i will depend on the location and kind of
(conservation) action taken all across the landscape, a. This is different from rij(ai), which would
indicate that the representation level only depends on conservation action taken locally at site i,
ai. Time-dependence of a quantity is marked by subscript t, for example, Rt is the matrix of
representation values at time t.

4
Table 3.2. Notation used in this chapter.

Symbol Explanation
i index for site
j index for feature (e.g. species)
Ns number of sites (planning units), i=1, 2, …, Ns
Nf number of features, j=1, 2, …, Nf
rij occurrence level of feature j in site i
Tj target representation level for feature j
Rj representation level for feature j
pij probability of occurrence or incidence of feature j in site i
t index for time
T length of planning horizon (time units)
xi indicator variable telling whether site is included in the evaluation set i, x={xi}
ai conservation action taken in site i; a={ai}
k index for the conservation action
ci cost of site i
ci(ai) cost of taking action ai in site i
S set of selected sites, {i | xi=1}
hi vector of environmental variables in site i
B total conservation budget

3.3 Objectives and constraints

In this section we cover several common classes of conservation prioritisation problem as

defined by the common combinations of options chosen for the objectives and constraints (Table
3.1).

3.3.1 Minimum set coverage

The minimum set coverage problem, which aims at efficiency of resource use, is a central
component of the systematic conservation planning philosophy (Margules and Pressey 2000).
This formulation is conceptually simple. The objective is to find a solution that achieves all
conservation targets at minimum cost. For example, a simple variant of the minimal set coverage
problem involves choosing the minimal cost set of conservation sites that ensures that the
occurrence level of all features achieves a certain target (Cocks and Baird 1989). In formal
terms, the simplest variant of this problem is
NS
min ci xi
i 1

given that (3.1a)

Ns
xi rij Tj , for all features j,
i 1

5
where rij is the occurrence level of feature j in site i, ci is cost of site i, Ns is the total number of
sites and Tj is the target level for feature j. The control variable xi has value 1 for selected sites
and value 0 for sites not selected. Variants of this formulation include (1) find the minimum cost
solution that achieves a given probability of representation when species ranges are uncertain
(Haight et al. 2000; Arthur et al. 2002), (2) find the minimum cost solution that includes a given
proportion of the distribution of the species (ReVelle et al. 2002; Cabeza 2003; Cabeza et al.
2004; Sarkar et al. 2004), and (3) find the minimum cost solution that includes a given
proportion of each land cover type in the region (Pressey and Tully 1994; Pressey et al. 1997;
McDonnell et al. 2002; Leslie et al. 2003). With this formulation target-setting is critical; targets
must be set so that the persistence of features is not compromised – the issue of adequacy
(Chapter 2). Choosing to represent a conservation feature in just one site is particularly
dangerous if the site is small or there is an unforeseen catastrophe at that site. Similarly,
choosing a single site may allow selection of a sink where the species cannot persist locally in
isolation. In this case minimizing cost to achieve one representation of a species can deliver a
result that is close to maximizing the extinction probability of a species (Cabeza and Moilanen
2003). In section (3.5) we investigate a wide range of possibilities for how rij may depend on the
control variables and other quantities.

A slightly more general variant of this problem can be written as

min ci (a)
i

given that (3.1b)

rij (a) T j , for all species j.
i
Here the notation ci(a) and rij(a) emphasizes that the cost of conservation at a location and the
occurrence of a feature there depends not only on what happens at the site itself (ai) but on the
allocation of the conservation action through the landscape, which is indicated by making the
quantity depend on the vector of conservation actions undertaken, a={ai}, where ai is not
necessarily binary but could allow for multiple choices (see Section 3.4). This allows for the
chance that a species persists at a site depends on what happens in the neighbourhood of the site
due to spatial population dynamics. The cost of protection also might be lower if conservation
action is applied both to the site itself and neighbouring sites. In Section (3.6.3) a broader view
of action a is adopted to emphasize that relevant harmful action could occur in sites not included
for conservation action.

3.3.2 Maximal coverage

The maximal coverage variation of the conservation prioritisation problem can be used when
resources are insufficient for satisfying all targets (Camm et al. 1996; Csuti et al. 1997; Pressey
et al. 1997; Snyder et al. 1999). According to this formulation, the objective is to find the
solution that satisfies the largest number of conservation targets given a budget constraint. The
maximal coverage problem is related to the minimum set coverage problem in that minimum set
coverage can be achieved by solving the maximal coverage problem at different budget levels
and finding the minimum budget level that satisfies all targets. A simple version of the maximal
coverage problem can be written as

6
max I j( xi rij T j ),
j i

given that (3.1c)

xi ci B,
i
where B is the conservation budget (money, trained personnel, time, etc.), and I(z) is an indicator
function, with Ij(z)=1 when condition z is true, i.e. the target for feature j is met when
( xi rij T j ), and Ij()=0 otherwise. As with the minimal set coverage problem, variants of this
i
problem exist such as maximizing expected coverage when species ranges or other information
is uncertain (Polasky et al. 2000, Camm et al. 2002). Other more general variants of the maximal
coverage problem can be obtained by introducing a more complicated function for rij (equation
Section 3.5). One difficulty with the maximal coverage problem as specified above is that it will
tend to triage particular feature types, that is, if meeting a target for a feature type is difficult,
there is no reward for partially meeting the target.

3.3.3 Utility maximization

The utility maximization problem is a generalised form of the maximal coverage problem. In this
approach the objective is to maximize the conservation value that can be obtained with limited
resources. The difference between utility maximization and maximal coverage is that for the
former the conservation value is defined in a more general manner than simply the number of
targets achieved.

A simple form of utility maximization in conservation prioritisation is to assume that the

conservation value for each feature is an increasing function of the level of representation of that
feature and the total value is an additive sum across features (Hof and Raphael 1993; Bevers et
al. 1995; Wilson et al. 2006, Arponen et al. 2005, 2007; Davis et al. 2006; Moilanen 2007;
Moilanen and Cabeza 2007). Nominal target levels could be assigned for features to differentiate
how much below or above the target the level of representation is

max w j f j R j ( x) ,
j

given that (3.1d)

ci (x) B,
i
where wj is the weight given for feature j, Rj(x)= i xirij is the representation level of the feature in
selected sites, and fj is a function transforming representation to benefit (Figure 3.2). As with
minimum set coverage (3.3.1), representation levels and costs could be a function of the
allocation of conservation actions across the landscape, a, instead of just the structure of the
reserve network x.

7
Figure 3.2. Different benefit functions that translate representation to conservation value. Panel
(a) shows two concave functions, the power function (1) and the ramp function (2). (b) Sigmoid
functions are in general more demanding with respect to optimisation than concave functions
(van Teeffelen and Moilanen 2007). The extreme case of a sigmoid is the step function (5). Of
these functions, (1), (3) and (4) give value to how much above or below a nominal target the
representation level for the feature is. The ramp function only values under-representation, it
actually corresponds to an objective of maximizing the (weighted) fraction of targets covered.
The step function, which is used by target-based planning, does not give value to under- or over-
representation.

3.3.4 Single vs multiple objectives

In some conservation planning situations there are multiple objectives that are difficult to
combine in a common metric. For example, in land-use planning, objectives may include
conservation (defined in terms of species or habitats), ecosystem services (e.g. recharge of
groundwater, pollination services), and recreational or agricultural production values (defined in
monetary terms). Chapter 4 describes examples and ways to solve some conservation
prioritisation problems with multiple objectives.

In general, multiple objectives should be investigated as independent components of the planning

problem. We believe that the temptation to combine multiple objectives into a weighted sum
should be avoided because the different components have different currencies. The value of a
candidate solution for multiple objectives is a multiple-dimension construct and reporting all
dimensions clarifies why a solution is good or bad. With multiple objectives, one should aim for
Pareto-optimal solutions (Box 3.1).

------------------------ Box text begins ------------------------------

8
Box 3.1. The concept of Pareto-optimality. A solution (reserve network; allocation of
conservation action through the landscape) is Pareto-optimal with respect to two or more
objectives (conservation value, forestry value, recreational value, etc.) when no other solution is
at least as good across all objectives. Pareto-optimal solutions are optimal in the sense that the
weighted sum of objectives is maximized for a particular choice of weightings; in the case of two
objectives, qV1+(1-q)V2 is maximized, where V1 and V2 are the values for the two objectives.
Pareto-optimality is a useful concept because different objectives can be described in
substantially different units or currencies, and it may not be easy to agree on the weighting by
which the objectives are combined. Pareto-optimality limits the set of reasonable solutions that
should be investigated further. A solution that is not Pareto-optimal should never be chosen,
because there are other solutions that can improve on at least one criterion while not causing a
loss for another. ). A number of papers have considered optimal forestry management where
objectives include both conservation of species and timber harvests (Hof et al. 1994; Bevers et
al. 1995; Hof and Bevers 2002; Calkin et al. 2002; Lichtenstein and Montgomery 2003; Nalle et
al. 2004)

Figure 3.3. Assuming maximization of a two-component objective, Pareto-optimal solutions are

at the outer boundary of the evaluated solutions. Different solution candidates are indicated by
dots, each has hypothetically been evaluated with respect to the two criteria. The small panels
illustrate different spatial plans, associated with Pareto-optimal solutions. See Polasky et al.
(2008) for an application of the use of Pareto-optimality.

3.3.5 Illustrative example

Here we present a small example to illustrate some alternative conservation prioritisation

problems.

Table 3.3. Data for the hypothetical example, wj is weight of species j and the score is the sum of
the weights of species occurring in the respective sites.

9
 Species 1 2 3 4 5 6 7 8 9 10
wj 5 1 1 1 1 1 1 1 1 4
Site Species occupancy Score
------------------------------------------------------------
A 1 1 1 1 1 1 1 0 0 0 11
B 1 1 1 1 1 1 0 0 0 0 10
C 1 1 1 1 1 1 0 0 0 0 10
D 0 0 0 0 0 0 0 1 1 0 2
E 0 0 0 0 0 0 0 1 0 1 5
F 0 0 0 0 0 0 0 0 0 1 4
-------------------------------------------------------------

Assuming a representation target of one for all species, an optimal minimum set coverage
solution (problem 3.1a) would be sites {A, D, E}, although {A, D, F} would cover all species as
well with some redundancy. Both deliver an objective function value of three – while the optimal
value is unique there may be more than one optimal solution. A maximum coverage solution
(problem 3.1b) with a budget of two sites would suggest the selection of sites A and D, or A and
E, which cover all except one species. A maximum utility solution using a benefit function
vj=rj(x)0.5 (problem 3.1c) suggests choosing first site A (value=11), and the most valuable two-
site solution would be A and E (value=16). Interestingly, the most valuable three site solution is
{A, E, (B or C)}, value 20.1, which leaves species number 9 unrepresented and therefore triaged.
Site B (or equally C) is chosen over site D because the increased representation for the six
species in site B outweigh the addition of site D to protect a missing species. Spatial
considerations would change the relative value that would be given to different combinations of
sites. The key point is that different problem formulations deliver different optimal solutions,
which means that it is important to settle on a planning philosophy and carefully articulate the
conservation prioritisation problem.

3.3.6 Constraints

In simple applications of maximal coverage or utility maximization approaches, the constraint

facing conservation planners is a limit on the number of sites (area constraint) that can be
selected or a budget constraint that can include the different costs of selecting different sites.
The budget constraint formulation is more realistic. Often the variability of land costs far
exceeds the variability of conservation features across landscapes. Including cost consideration
can result in far greater conservation efficiency (Ando et al. 1998, Balmford et al. 2000, Naidoo
et al. 2006) and costs can be more important for determining conservation priorities than
biological benefits (Wilson et al. 2006, Murdoch et al. 2007, Bode et al. 2008). Formulating a
budget constraint for the case where the set of conservation actions goes beyond purchasing land,
such as fire management or invasive species control, requires estimates of costs of these actions
(Wilson et al 2007). Other constraints besides the budget can arise from social, political, legal or
regulatory constraints that limit what set of actions are permissible.

3.4 Control variables – single versus multiple conservation actions

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By far the most common conservation prioritization problem in the literature concerns the spatial
allocation of a single conservation action, such as choosing sites for reservation to achieve the
best conservation outcome. We indicate such a choice by control variable x={xi}, where xi =1 if
the site was “selected” and xi =0 if not.

The general conservation prioritization problem is not so simple. Sites could be allocated varying
levels of protection, restoration (Chapter 12) or management, which could be represented by
control variable a={ai}, where ai is a continuous or variable not restricted to 0 or 1. Sites could
also be allocated to distinct categories of land use (e.g., agriculture, forestry, developed, natural).
In this case, ai could be categorical to indicate various discrete choices (1 = agriculture, 2 =
forestry, 3 = developed, 4 = natural, …). In a simplified variant of the problem, scenario
evaluation (see also Chapter 1), actions ai would not be independent from each other but they
would be determined by a policy choice, and the objective would be to evaluate which policy is
most favourable. In scenario evaluation there are typically only a limited number of strategies to
compare making the “optimization” very simple. However, the best scenario may well be
inferior to other potential strategies not considered.

Mathematically, a basic variant of the multi-action conservation prioritization problem with a

budget constraint is
max fj xi rij (a) ,
j i

given that (3.2)

ci (ai ) B,
i
where ci(ai) indicates the cost of action ai in site i. The optimization problem would be to find the
set of actions, a={ai}, that maximizes the conservation value. Note that the set of sites x used in
the performance evaluation could be, but would not need to be, the same set of areas where some
action is done. This somewhat fine distinction is particularly relevant when considering
representation in reserves versus retention in the landscape (Section 3.6.3). Also, actions could
actually include any actions that prevent full loss of conservation value, they could represent
some limits to the way land can be exploited. Conservation considerations in optimal land-use
planning involving many land uses has been analyzed by Montgomery et al. (1999), Polasky et
al. (2005, 2008), and Holzkämper et al. (2006).

Multi-action planning is structurally much more complicated than single-action planning. This is
because with multiple actions there may be tradeoffs between features and non-independence
between actions. An action that is good for one feature might be less beneficial or even harmful
for another feature (Polasky et al. 2005; van Teeffelen and Moilanen 2007). The influence of an
action in one site may influence features in another site and the combined impact of multiple
actions may differ from their sole effect. Consequently, multi-action conservation planning can
be a complicated nonlinear optimization problem with a solution space increasing from 2N to KN,
where K is the number of options for each site and N is the number of sites. Having multiple
actions makes both the performance evaluation of a candidate solution and the search for
solutions more complicated and computationally more demanding and the number of local
optima in the search space is likely to increase.

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Multi-action conservation planning has broad relevance as habitat restoration is becoming more
common than reservation in many developed countries (Chapter 12), and the general land-use
zoning problem attracts greater attention.

3.5 State equations: modelling representation and occurrence

The representation of feature j in site i , rij, is an integral part of evaluating the performance of a
candidate solution. Representation is a term used for the occurrence level of a feature in a site or
in a reserve network. Representation can be presence/absence, probability of occurrence,
abundance, density, coverage, or any appropriate quantitative measure of the conservation
objective. It is generally taken so that high representation is desirable and low representation
represents a poor solution.

To start with, how well a feature, j, is represented in a reserve network can be defined as a
straightforward summation over its representation in individual reserved sites;
R j (x) xi rij . (3.3)
i
However, the representation level of a feature in a site, rij, can either be defined in a simple or
complicated manner.

In the simplest version, representation can be defined as the definite presence/absence of feature
j in site i (e.g., Pressey et al. 1997; Csuti et al. 1997)
0, if the feature is absent from the site
rij . (3.4a)
1, if the feature is present in the site

In more general versions, rij is not restricted to 0 or 1. Information on rij may be imperfect and
estimates of rij may have to be inferred, often using a statistical model, from environmental data
and the occurrence is taken as
rij r~ij , (3.4b)
~
where r or p is some observed, statistical or model-based (non-binary) best estimate of the
ij ij

abundance or likelihood of occurrence respectively (Chapter 6) (e.g., Williams and Araújo 2000;
Haight et al. 2000; Polasky et al. 2000; Camm et al. 2002). Typically r~ij would be the estimate
of representation under either the current landscape conditions or under one from a few
conservation scenarios.

Technically we need to understand how the distributions of features conserved depend on the
environmental conditions and the conservation actions taken – that is the state equations. The
state equations determine the representation of each feature in each site and/or a suite of sites and
their estimation can be the most complicated component of formulating the conservation
prioritisation problem.

It is implicit in Equations 3.4a-b that occurrence is independent of the pattern of conservation

action taken in the landscape, as rij is not a function of any control variable outside site i. If
occurrence explicitly depends on the spatial pattern of selected sites, e.g. because of

12
connectivity-related factors, representation is non-linear and a function of the entire reserve
system design
rij f (~
rij ,x) , (3.4c)
~
where r < r if conservation is not done in the neighbourhood of the site, which has the
ij ij

ecological interpretation that the estimated local occurrence levels may not be achieved if the
habitat quality in the neighbourhood of the focal site deteriorates (Moilanen and Wintle 2007;
Moilanen et al. 2008). More generally, one can specify that local representation depends on the
best estimate for the site and actions taken all across the landscape
rij f (~rij ,a) . (3.4d)

In finer detail, the representation of a feature at a site can be a function of all the actions and all
the environmental variables at site i, so one could specify that
rij f (h i ,a) , (3.4e)
where hi is a vector of environmental variables at site i. This emphasizes that the local
occurrence level is a function of local environmental conditions and spatial pattern of selected
sites (Westphal and Possingham 2003). Predictions based on habitat models would frequently
have this kind of a structure (Chapter 6). Note that this formulation requires that all
representation levels are recalculated when allocation of conservation action changes (inside an
optimization routine).

Even more generally,

rij f (H,a) , (3.4f)
meaning that the local occurrence level of a feature would depend on the environmental variables
and conservation actions taken across the entire landscape (Polasky et al. 2005, 2008).

So far the features (species) represented have been assumed to exist in isolation, but one could
also write
rij f (H,a, R ) , (3.4g)
which emphasizes that the local occurrence level is also influenced by the presence of other
features in the site and its neighbourhood. This equation is implicit in that the same quantity (rij)
occurs on both sides of the equation, meaning that it must be iterated from a starting condition
until matrix R converges. In a simplified variant of (3.4g), Cabeza (2003) and Moilanen (2005)
assumed species-specific models with an autologistic structure of form rij=f(H, x, rj).

Up to this point it has been assumed that the landscape is static, i.e. that a certain allocation of a
conservation action will immediately result in a specific distribution of features across the
landscape. However, in reality occurrence levels of features are changing constantly due to
natural reasons (succession from disturbance) and anthropogenic causes (implementation of
conservation actions, land-use changes, climate change). If one wishes to emphasize time-
varying occurrence of features, one introduces dependence on time t, which looks something like
rijt f (H 0 ,H 1 , ...,H t ; a 0 , a1 , ...,at ; R 0 , R1 , ...,R t , (3.4h)
where the subscript indicates the time step. In this case the local representation of species j in site
i at time t depends on the history of habitat quality, conservation action and occurrence levels of
each species across the landscape and through time. This level of generality would be very hard

13
to achieve with an empirically parameterized model for many features, and some simplifications
would be needed to reduce the complexity to a manageable form. At this point one is heading
towards the need for spatially explicit population models for each species.

Going even further, one would note that even if our models are true and our knowledge of the
landscape is perfect, species population dynamics are an inherently stochastic process.
Consequently, the value of rij cannot be predicted exactly, but rather, one would in reality obtain
a distribution for it, denoted by rijt for a single feature in a site at a given time, or by R t for
the occurrences of features across the landscape at time t. Prioritisation based on distributions
means that uncertainty of predictions is accounted for (Chapter 11). When fitting such stochastic
models to empirical data observation error is an important consideration.

While representation could be predicted using a wide variety of models, and the details of the
dependencies between habitat quality variables, conservation actions and occurrence levels could
be written in many ways, our point is that specification of the occurrence level of a species is a
significant and potentially very complex part of the conservation prioritization problem. In the
following section, we use the simpler notations for conciseness, but one should keep in mind that
more complicated variants of the spatial prioritization problem immediately appear when
switching to a more complicated model of occurrence.

3.6 Performance measurement and evaluation – from conservation actions to distributions

of biodiversity features to conservation value

The state variables of our problem are the occurrence levels of features in sites, rij. Performance
measures aggregate over the state and control variables to produce measures of conservation
success: benefit, cost and, combining cost and benefit, efficiency.

3.6.1 Scoring versus complementarity-based methods

Variants of the conservation prioritisation problem can be defined by how the solution is
evaluated. We concentrate on complementarity-based approaches (Kirkpatrick 1983; Margules et
al. 19988; Vane-Wright 1991) (Chapter 2) as opposed to scoring methods. Scoring methods
evaluate candidate sites/planning units individually and independently from each other, and if
several sites are available for conservation investment, they are picked starting from the top of a
ranked list based on the scores evaluated for each site (e.g., Margules and Usher 1981; Dony and
Denholm 1985; Usher 1986; Cocks and Baird 1989; Pressey and Nicholls 1989). In
complementarity-based prioritization a proposed set of conservation sites is evaluated jointly as a
set, accounting for the similarity of features (species) in the sites (that is, their complementarity).
With scoring there is the possibility that areas with the highest scores are similar ecologically
and therefore inefficient, whereas complementarity-based approaches identify sets that jointly
cover a wide variety of features of high conservation value.

Scoring and complementarity-based approaches also entail different approaches to performance

evaluation of candidate sets. In scoring approaches the value of a reserve network implicitly is a
sum over the scores for the highest ranked planning units. This does not account for the fact that
the value of a whole reserve system (or set of conservation actions), is more than the sum of the

14
parts (Chapter 2). In complementarity-based planning the conservation value of each feature is
first aggregated over planning units, after which another possibly nonlinear aggregation is done
across species. Thus, a complementarity-based performance measure is of the form

F (a) f rij (a) , (3.5a)

j i

and a scoring-based measure that does not account for the complementarity between sites is of
the form
F ( x) xi f (rij ) , (3.5b)
i j

where f is a function that translates representation at a site to a score for conservation value.
Despite their serious conceptual flaws – scoring methods remain popular because they are very
easy to understand and implement.

3.6.2 Connectivity

Spatial considerations are relevant to conservation prioritisation both because of the logistics of
establishing and maintaining conservation areas, but also for biological reasons, as locations
close to each other in the landscape are, in general, connected with respect to species population
dynamics (Possingham et al. 2000; Moilanen 2005; Williams et al. 2005; Possingham et al.
2005). Connectivity influences dispersal success between populations and according to the
fundamental tenet of metapopulation biology (Chapter 8) lack of connectivity is harmful for the
persistence of a species in a patch network (Hanski 1998; Debinski and Holt, 2000; Gaston et al.
2002). If sites are isolated, dispersing individuals can experience high mortality, and isolated
local populations that go extinct may be slow to become recolonised. While the influence of
connectivity is conceptually well understood, operationalising the concept in the context of
spatial conservation prioritization is not straightforward conceptually or computationally.
Additionally, it is unclear how much connectivity is actually needed, as having all sites highly
connected could be like putting all eggs in the same basket, making the metapopulation
susceptible to extreme weather events, disease, invading species and any such spatially
correlated disturbances – a certain level of connectivity is needed, but too much could indeed be
harmful.

However, completely ignoring connectivity and associated spatial issues is potentially well
justified only when selection units are so large that they can support features independently and
locally, and interactions between areas (e.g. edge effects and population dynamics) can plausibly
be ignored. When planning is done at a scale relevant for real land use decisions, one could be
working at a spatial resolution of hectares. At this scale neighbouring selection units are far from
independent, as small selection units are influenced via edge effects and they have interactions
via spatial (meta)population dynamics. Consequently, occurrence and population levels of
features may be influenced by the spatial pattern of selected areas, and according to an
uncertainty-analytic argument it is much safer to select aggregated reserve networks than
dispersed ones (Moilanen and Wintle 2006). Accounting for connectivity in a potentially
species-specific manner complicates the computational problem significantly as the state
equations and consequently the performance measures may become strongly nonlinear, and the
level of multimodality of the decision problem increases (Chapter 5).

15
Connectivity has been implemented in reserve selection in a variety of ways (see also Chapter 2;
Chapter 4), which influence different parts of the prioritization problem. In this section we
describe where connectivity considerations have been placed in the structure of conservation
prioritisation problems. The boundary length penalty is a commonly used technique that is
implemented at the stage of performance evaluation (Possingham et al., 2000; McDonnell et al.,
2002.; Nalle et al., 2002; Önal and Briers, 2002a,b; Fischer and Church, 2003; Cabeza et al.,
2004; Chapters 14, 15 and 16). The objective function takes the form: (performance measure
over features) minus (measure of fragmentation of reserve network). The latter part is a function
of the boundary length to area ratio of the reserve network, which means that the boundary
length penalty actually includes a measure calculated over conservation actions (control
variables). The minimum set coverage formulation extended with the boundary length penalty
looks like

min ci (x) bf ( L(x) / A(x))

i

given that (3.6)

rij (x) T j , for all species j ,
i
where L(x) is the length of the boundary of the reserve network, A(x) is the area of the reserve
network, and b is a penalty parameter influencing the level of aggregation that is required.
Unless the boundary length is actually evaluated in financial terms, this formulation is actually a
multicriteria formulation with two criteria, the cost needed to achieve targets and the
fragmentation level of the reserve network. These two criteria are joined into one objective
function using the penalty parameter b, which models the weight given to the two components of
the objective, representation and spatial aggregation. This technique is used for example in the
MARXAN software (Chapter 14).

Other ways of accounting for connectivity have a different effect. It is possible that the allocation
of conservation actions in the landscape influences directly the occurrence levels of features,
which is the with the implementation of a neighbourhood quality penalty (NQP) (Moilanen and
Wintle 2007; Moilanen et al. 2008; Chapter 15). The NQP essentially states that the occurrence
of the feature in the site depends not only on the local quality of the site and action taken there,
but also on the actions taken in a feature-specific neighbourhood of the site. In effect, the state
equations have become a more complicated version of the general form
rij f ~ rij ,x(n j (i )) or rij f ~
rij ,a(n j (i )) , (3.7)
where a(nj(i)) indicates the conservation action taken in a species-specific neighbourhood, set of
planning units within species-specific distance from focal site i, nj(i).

It is also possible that the connectivity effects extend through the entire landscape, as in
Moilanen (2005), which used both neighbourhood and long-distance kernel measures in the
model of local abundance, and Polasky et al. (2005, 2008), which used distance among habitat
patches in a landscape and dispersal ability to adjust measures of species abundance.
Considerations such as least cost paths (Rouget et al. 2006) or spatially structured diffusion
(Ovaskainen 2004) could conceivably be utilized in spatial conservation prioritization, but with
the price that computational demands increase very quickly with the number of planning units.

16
3.6.3. Representation in reserves versus retention in the landscape

A simple but significant distinction between spatial prioritisation problems is whether the
objective is to maximize the conservation value in reserved areas (or areas to which some
conservation action is applied to) or whether the objective is to maximize biodiversity value in
the entire landscape (Hansen et al. 1993; Daily et al. 2001; Pressey et al. 2004; Polasky et al.
2005, 2008; Pereira and Daily 2006). Maximising value in reserves makes sense when there is no
guarantee that the conservation values outside of reserved areas will be degraded, which might
be the case, for example, when planning at the fringe of an expanding urban area.

Retention means the value of biodiversity remaining in the entire landscape, not only in reserve
areas as in the case of a representation approach. The difference between planning for retention
or representation is implemented at the level of performance evaluation. If planning for
representation, only those sites that have been selected to the reserve network (xi=1) are used
when aggregating performance (conservation value) over state variables:

F (x, a) f xi rij (a) , (3.8a)

j i

which emphasizes that the site only contributes to the value of the reserve network if it is
selected, but that conservation action may influence occurrence levels also in the neighbourhood
of a site where action is taken.

If planning is based on retention, the conservation value is aggregated over the entire landscape
taking into account actions done at all sites,

F (a) f rij (a) . (3.8b)

j i

Notably, even if no action is taken at a site, the location might still retain some conservation
value.

A general form of performance evaluation accounting for retention is the following,

F (x, a, d) f xi rij (a, d) , (3.8c)

j i

where a new quantity, d, is introduced; d is the set of planning units where some form of
potentially harmful (deteriorating) action happens. This action could, for example, include
various land-use changes that are not done for conservation purposes. Thus, Equation 3.8c
includes three components, (i) the set of areas from which success of conservation action is
evaluated, x, (ii) the set of areas where beneficial conservation action is taken, a, and (iii) the set
of areas where some harmful activity is occurring, d. In general, sets a and d would not be
overlapping, beneficial and harmful activity would occur at different locations. Sets x and a
could, but would not have to, coincide. Set x could be either the entire landscape or just a part of
it. Using entire sets as arguments emphasizes that effects of actions need not be limited to the
focal locality itself. All prior formulations throughout this chapter could be rewritten in terms of
these three sets, the point is that area of evaluation does not need to coincide with beneficial
action, and that harmful action should be accounted for when working with retention.

17
Planning for retention is generally a sensible objective, and it is especially appropriate when (a)
some forms of land-use, such as forestry or recreational use, can support conservation value
outside conservation areas or (b) when habitat loss or degradation of some (commercially
valuable) habitat types is occurring (see also Chapter 10). If there is no ongoing habitat
degradation and acquisition of areas is not required, targeting restoration or management action
to improve the quality of the landscape is the only real consideration (Chapter 12).

3.6.4. Representation vs. persistence

In its simplest form, a performance measure for a feature is just a sum over its occurrence levels
across chosen planning units (that is, representation). Measures of occurrence include observed
or predicted presence-absence, abundance, density or probability of occurrence. Commonly, one
requires either a given number of occurrences to be present in the reserve network (Equation
3.1a), or a given fraction of the distribution of the features to be protected (proportional
coverage). These numbers or fractions can be calculated directly from observational or
statistically predicted data (Chapter 6).

Planning based on persistence diverges at the stage of performance evaluation, the distributions
of state variables are analysed in a potentially complicated highly nonlinear process that
transforms the time-varying distribution of the feature (in this case most commonly a species)
into an estimate of extinction risk. The performance function becomes of the general form of

F (x, a) f E j R t (x, R 0 , h 0 ...hT , a 0 ...aT ) , T , (3.9)

j

where Ej is the predicted extinction risk of feature j, T is the length of the planning period, and
subscript t is understood to receive values 1, 2, …, T, meaning that the evolution of the
distribution of the feature through time is evaluated. The distribution of the feature-specific
distributions of occurrence levels at time t, <Rt>, depend on the habitat quality h0…ht and
conservation action a0…at taken though the landscape and through time, and also the initial
distributions of features R0. Notably, also habitat quality at locations where the species does not
occur (the habitat matrix) would generally influence extinction risk via modified dispersal
success and migration mortality (Hanski 1998). Here it is worth noting that some authors refer to
the principle that delivers persistence in conservation planning as the principle of “adequacy”
(Possingham et al. 2006) (Chapter 2).

It is the ultimate objective of conservation prioritization is to minimize extinction rates (Bevers

et al. 1995, Vane-Wright 1996; Margules and Pressey 2000; Cabeza and Moilanen 2001; Gaston
et al. 2002; Polasky et al. 2005, 2008; Nicholson et al. 2006; Nicholson and Possingham 2006,
2007). Thus, one might ask why this is not the explicit and direct goal of all quantitative
conservation prioritization methods? While the process implied by Equation 3.9 can undoubtedly
be substantially simplified in many cases (Chapters 8 and 9), the bottom line is that evaluation of
extinction risk is much more complicated than estimation of occurrence. In practise, the
distribution of a feature needs to be evaluated as a dynamic (stochastic) entity and the time-
varying predicted distribution must be translated into an extinction risk using metapopulation
models (Chapter 8) or a spatial PVA model (Chapter 9). Translation from abundance or habitat

18
distribution to extinction rates requires computationally difficult calculations and feature-specific
data about how the spatial pattern of occurrence translates to extinction risk. In particular,
theoretical and empirical observations verify that for most species there would be a threshold
effect (Chapter 8) – if the amount and density of suitable habitat goes below such a threshold, the
metapopulation is likely to spiral to extinction. Unfortunately, identification of the threshold for
any empirical system is complex. Lack of data, uncertainty of model components and
parameters, and computational limitations are the reasons why direct minimization of extinction
rates is an uncommon goal in multi-species conservation prioritization. Consequently, extinction
rates are most commonly minimized indirectly, for example assuming that higher representation
levels imply lower extinction rates, and by requiring spatial attributes of the reserve sites (e.g.,
connectivity and risk-spreading) that promote species persistence.

3.7 Static versus time-varying versus stochastic occurrence distributions

One form of time-varying distributions can be analysed using the framework described in this
chapter – when the distributions of features are changing through time in a deterministic manner.
Essentially, the state variables will be the representation of feature j in site i at time t, rijt. rijt will
depend deterministically on actions taken in that site (and in the neighbourhood of the site if
connectivity is considered) prior to time t, rijt = f(ai0, ai1, …, ai(t-1)), where ait is action taken at site
i at time t. This means that the numbers of state and control variables are multiplied by the
number of time steps included in the analysis. When the performance of a set of actions is
evaluated, it becomes necessary to evaluate the distributions of features through time, which
implies that the performance measure is necessarily more complicated than when time is not
accounted for. Two possibilities are to look at the minimum or mean representation levels of
individual features through time.

In contrast, if the distribution of habitat suitable for a feature, or the distribution of a feature, or
both are modelled via a stochastic model (such as a metapopulation model or spatial PVA), then
the entire modelling framework becomes stochastic, which implies significant changes to the
approach to the prioritization problem. These kind of stochastic decision problems are discussed
in chapters about metapopulations (Chapter 8), PVAs (Chapter 9), and sequential/dynamic
planning (Chapter 10). Further, allowing for climate change (Chapter 13) would mean that
distributions are not in a stochastic steady state, but rather, they are moving, which requires
modelling the transient dynamics of stochastic models.

3.8 Discussion and conclusions

The conservation prioritisation problem can be described in a standardized and structured

manner as a classical optimization problem. Problem structures identical at a mathematical level
are utilized across a wide variety of different applications, which is beneficial because solution
methods developed in one application field can be used elsewhere, often with little change.
Conservation science usually does not formulate problems in a standard manner. One exception
is the class of linear problems from the field of operations research that can be solved using
integer programming (Underhill 1994; Camm et al. 1996; ReVelle et al. 2002; Williams et al.
2004; Chapter 4). Other methods could potentially be imported to conservation science from

19
other fields such as nonlinear optimization, economics or control theory (Wilson et al. 2006,
McBride et al. 2007).

One should also note that conservation prioritisation is in reality a very demanding and
specialised problem, which will limit the number of ready solutions that can be found from other
scientific fields. In the conservation resource allocation problem one is essentially asking: what
is the distribution of biodiversity features in the landscape, how do conservation actions
influence those distributions, and which course of action would be best given our conservation
objectives, constraints, and measure of performance evaluation? The general conservation
resource allocation problem can be characterized by a potentially large state space, with many
selection units, features and time steps. The problem also involves nonlinear and stochastic
responses of features to the environment, and there may be interactions between features and
sites and feedback mechanisms that complicate prediction and analysis. Contrasting
requirements of features and interactions among them make it likely there will be numerous local
optima, making finding the global optimum of the problem complicated (Chapter 5). The
conservation prioritization problem also relies on predictions of land-use change and predictions
of the distributions of biodiversity features across the landscape. Such predictions are plagued by
incomplete information and pervasive uncertainties about ecological processes and socio-
economic dynamics, which can necessitate an analysis of uncertainty on top of an already
complicated analysis framework (Chapter 11).

Solving an optimization problem is often a difficult and time consuming process, and even when
it is possible to find the best, or at least very good, solution(s), obtaining the required input
information and defining the problem can prove problematic. While data collection, problem
definition and problem solution are conceptually and methodologically separate steps,
understanding the interplay between them is necessary before most useful variants of the
conservation prioritisation problem can be defined. We hope that the standard framework
described in this chapter will help facilitate the development of conservation science by
structuring the conservation prioritisation problem within a standard framework. Doing so will
help promote clear problem formulation, suggest what information is needed, and aid in
suggesting solution methods that might be profitably imported from other fields of science. Such
efforts are steps towards an increasingly convincing operational analysis capability that can be
used to support conservation management objectives (Pressey 1999; Noss 2003; Chapter 18).

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