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Ferrier S, Guisan A.. Spatial modelling of

biodiversity at the community level. J Appl Ecol
43: 393-404

Article in Journal of Applied Ecology March 2006

DOI: 10.1111/j.1365-2664.2006.01149.x


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Journal of Applied REVIEW
2006 Article
UK A. Guisan
Applied Journal
Ecology of biodiversity
Ltd compilation 2006 British Ecological Society

Ecology 2006
43, 393404 Spatial modelling of biodiversity at the community level
*New South Wales Department of Environment and Conservation, PO Box 402, Armidale, New South Wales 2350,
Australia; and Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland

1. Statistical modelling is often used to relate sparse biological survey data to remotely
derived environmental predictors, thereby providing a basis for predictively mapping
biodiversity across an entire region of interest. The most popular strategy for such
modelling has been to model distributions of individual species one at a time. Spatial
modelling of biodiversity at the community level may, however, confer significant
benefits for applications involving very large numbers of species, particularly if many of
these species are recorded infrequently.
2. Community-level modelling combines data from multiple species and produces
information on spatial pattern in the distribution of biodiversity at a collective
community level instead of, or in addition to, the level of individual species. Spatial
outputs from community-level modelling include predictive mapping of community
types (groups of locations with similar species composition), species groups (groups of
species with similar distributions), axes or gradients of compositional variation, levels
of compositional dissimilarity between pairs of locations, and various macro-ecological
properties (e.g. species richness).
3. Three broad modelling strategies can be used to generate these outputs: (i) assemble
first, predict later, in which biological survey data are first classified, ordinated or
aggregated to produce community-level entities or attributes that are then modelled
in relation to environmental predictors; (ii) predict first, assemble later, in which
individual species are modelled one at a time as a function of environmental variables,
to produce a stack of species distribution maps that is then subjected to classification,
ordination or aggregation; and (iii) assemble and predict together, in which all species
are modelled simultaneously, within a single integrated modelling process. These
strategies each have particular strengths and weaknesses, depending on the intended
purpose of modelling and the type, quality and quantity of data involved.
4. Synthesis and applications. The potential benefits of modelling large multispecies
data sets using community-level, as opposed to species-level, approaches include faster
processing, increased power to detect shared patterns of environmental response across
rarely recorded species, and enhanced capacity to synthesize complex data into a form more
readily interpretable by scientists and decision-makers. Community-level modelling
therefore deserves to be considered more often, and more widely, as a potential alternative
or supplement to modelling individual species.
Key-words: biodiversity, community, composition, modelling, prediction, spatial,
Journal of Applied Ecology (2006) 43, 393404
doi: 10.1111/j.1365-2664.2006.01149.x


2006 The Authors. Predictive spatial modelling has been used increasingly
Correspondence: Simon Ferrier, New South Wales Department
Journal compilation of Environment and Conservation, PO Box 402, Armidale, over the past 20 years to relate sparse biological survey
2006 British New South Wales 2350, Australia (fax +61 267722424; e-mail or collection data to remotely mapped environmental
Ecological Society attributes, thereby allowing distributions of biological
394 entities to be extrapolated across an entire region of weaknesses of these approaches within the context of
S. Ferrier & interest (see reviews by Franklin 1995; Austin 1998; various applications. We finish by suggesting a number
A. Guisan Guisan & Zimmermann 2000; Scott et al. 2002; Guisan of future directions that we feel are worth pursuing to
& Thuiller 2005). Commonly used predictors include extend and refine current approaches to spatial model-
terrain indices, long-term average climate surfaces, ling of biodiversity at the community level.
edaphic variables, land-cover variables and spectral
bands or indices from remote sensing. By far the most
Data inputs and outputs
popular strategy has been to model distributions of
individual species one at a time. Species-level model- All of the strategies described in this review work with
ling is, however, but one of a rich array of possible a regular spatial grid superimposed over the study area
approaches to spatial modelling of biodiversity (Fran- of interest (typically consisting of many thousands, or
klin 1995; Ferrier & Watson 1997; Guisan & Zimmer- millions, of cells depending on the spatial extent and
mann 2000; Ferrier 2002). resolution of the study). We assume the existence of
In this review we focus on community-level model- two types of input data relating to this grid: (i) biolog-
ling strategies. We define such a strategy as one that both: ical survey or collection data, typically for scattered
(i) combines data from multiple species at some stage in locations across the grid, and (ii) remotely derived envi-
the analytical process and (ii) produces information on ronmental predictors, covering the entire grid. These
spatial pattern in the distribution of biodiversity at a data would normally be stored within, or linked
collective (or emergent) community level instead of, directly to, a geographical information system (GIS).
or in addition to, the level of individual species. The ori- Biological data are usually available for only a small
gins of community-level modelling go back as far, if not proportion of grid cells in the study area. The best types
further, than those of species-level modelling (for early of data for the modelling approaches discussed in this
applications of the basic concepts discussed here see review are presenceabsence or abundance data collected
Kessell 1976; Strahler et al. 1978 ; for an overview of by systematic field surveys of species composition,
the history of this general approach see Franklin 1995). preferably based on a well-designed environmentally
The appropriateness of modelling biodiversity at the stratified sampling scheme (Austin 1998). Each species
community level, as opposed to the species level, is within the biological group of interest (e.g. diurnal
likely to vary depending on the purpose of a given study birds and vascular plants) is recorded as either present
and the type, quality and quantity of data involved. (optionally with a rating of relative abundance) or
Community-level modelling may confer significant absent at each surveyed location. Here we assume that
benefits for applications involving very large numbers each sampling unit is wholly contained within a single
of species, particularly where a sizeable proportion of grid cell, and that each cell contains no more than one
these species is rarely recorded in the data set. Unlike sampling unit. Problems that can be caused by depar-
species-level modelling, for which species with too little tures from this assumption (e.g. sampling plots smaller
data are usually excluded from further analysis (for sta- than modelling units) are discussed elsewhere (Guisan
tistical reasons), many community-level modelling & Thuiller 2005).
strategies make use of all available data across all spe- Biological data derived from natural history collec-
cies, regardless of the number of records per species. tions may also be used with many of the modelling
Hence, the data for more common species may help to approaches discussed here. However these data are
support the modelling of less frequent species (Guisan more problematic, as they typically consist of presence-
et al. 1999). By producing information on spatial pat- only records, i.e. locations where a species was col-
tern in biodiversity in a collective sense (Austin 1999), lected, without any explicit information on other
community-level modelling also provides a means of visited locations from which the species was not col-
synthesizing complex data on large numbers of species lected (Zaniewski et al. 2002; Graham et al. 2004).
into a simpler form that may be more readily interpret- Presence-only data sets pose similar challenges for
able by both scientists and decision-makers. community-level modelling as they do for species-level
Several community-level modelling strategies have modelling. Recent work by us and various collabora-
emerged during the past 20 years, along with a variety tors suggests that pseudo-absences generated from
of analytical techniques and software tools for imple- presences of other species in the same biological group
menting these strategies. Our aim in this review is to provide the best available basis for building models
provide a comprehensive overview of the current state from presence-only data. Thus we will generally
of the art of such modelling. To our knowledge this assume throughout this review that those species not
type of review has never been attempted before. We start collected at a location, where one or more other species
2006 The Authors. by defining the basic data inputs used in community- in the same biological group have been collected, are
Journal compilation
level modelling, and the various types of spatial out- treated as being absent at that location.
2006 British
Ecological Society, put that can be produced. We then describe three Remotely derived environmental predictors are nor-
Journal of Applied broad modelling strategies, and review specific tech- mally stored as a stack of GIS grid layers. However, it
Ecology, 43, niques that have been, or could be, used to implement may help to envisage both the biological and environ-
393404 each strategy. Next we examine the strengths and mental inputs structured as two simple data frames or
modelling of

Fig. 1. Data inputs and types of spatial output for species-level and community-level modelling.

matrices, one for the biological data and the other for production of this complete cells-by-species matrix is
the environmental predictors (Fig. 1). The rows of both supplemented or replaced by production of a matrix in
matrices correspond to grid cells, with the environmen- which the columns correspond to some set of derived
tal matrix containing data for every cell in the study community-level entities or attributes.
area and the biological matrix containing data only for In addition to distributions of individual species, the
those cells that have been surveyed. The biological data five main types of entities and attributes that can be
matrix has a column for each species, while the envi- predictively mapped by community-level modelling
ronmental matrix has a column for each predictor. are: community types, species groups, axes of com-
As for species-level modelling, the main objective of positional variation, dissimilarities between pairs of
community-level modelling is to use observed relation- cells and macro-ecological properties (definitions are
ships between biological data and remotely derived provided in Table 1; Fig. 1be). The first four of these
2006 The Authors. environmental predictors to extrapolate patterns communicate something about the way in which com-
Journal compilation
across an entire study area. With species-level model- munity composition changes across a study area. This
2006 British
Ecological Society, ling this can be viewed as filling blank rows (grid cells) family of output types is the main focus of our review.
Journal of Applied in the biological data matrix with the predicted occur- However, for the sake of completeness, we also devote
Ecology, 43, rence or abundance of each species in each unsur- some attention to the fifth type of output, i.e. emergent
393404 veyed cell (Fig. 1a). With community-level modelling, macro-ecological properties, such as species richness,
396 Table 1. The six main types of spatial output that can be generated using community-level modelling
S. Ferrier &
A. Guisan Spatial output Description Structure of derived grid layer(s)

Individual Predicted distributions of multiple species, A separate layer for each species, indicating
species as for species-level modelling the predicted probability of occurrence or
abundance of that species in each cell
Community Each community type defined as a group of Either (i) a single layer with each cell assigned
types locations (grid cells) that closely resemble one exclusively to one community type (depicted as a
another in terms of predicted species composition. map with different colours indicating different
Grouping normally achieved through some form types) or (ii) a separate layer for each community
of numerical classification type, indicating the probability of that type
occurring in each cell (depicted as multiple
grey-scale or colour-ramp maps)
Species Each species group defined as a subset of species A separate layer for each species group,
groups with similar predicted distributions. Grouping indicating the predicted prevalence or
again achieved through numerical classification, abundance of that group in each cell
but in this case the objects classified are species (depicted as multiple grey-scale of
rather than locations colour-ramp maps)
Axes of A set of continuous axes (or gradients) representing A separate layer for each axis, indicating the
compositional dimensions of a reduced space that summarizes the predicted score for that axis in each cell
variation compositional pattern exhibited by multiple species. (depicted either as multiple grey-scale or
These axes most commonly derived through some colour-ramp maps, or as a single map by
form of ordination assigning each of the first three axes to a
different colour dimension, e.g. red, blue, green)
Levels of The predicted level of dissimilarity in community In theory a complete matrix of pair-wise
compositional composition between all possible pairs of grid dissimilarities, but in practice these values are
dissimilarity cells in a region usually predicted dynamically as required by the
between pairs application of interest (difficult to depict
of cells spatially without prior conversion to community
types or axes of compositional variation)
Macro- Most commonly modelled property is species richness, A separate layer for each macro-ecological
ecological either of a whole group (e.g. all vascular plants) or of property (depicted as a grey-scale or
properties a functional subgroup (e.g. annuals and trees). Many colour-ramp map)
other macro-ecological properties (e.g. mean range
size and endemism) can potentially be modelled

that do not retain or communicate explicit information axes of compositional variation can be achieved using
about composition (Gaston & Blackburn 1999). any of the very wide range of pattern analysis tech-
niques routinely applied in community ecology (see
Appendix S1 in the supplementary material). Deriva-
Modelling strategies
tion of macro-ecological properties, such as species
Three broad modelling strategies exist for producing one richness, from the biological data for each surveyed
or more of the community-level outputs described in the location is a relatively straightforward procedure. The
previous section (Fig. 2). All of these strategies employ modelling approach used in the second stage of this
the same types of biological and environmental input data. strategy depends on the nature of the community-level
entities generated in the first stage. For example, com-
munity types can be modelled one at a time, by relating
1 : ,
the observed presence or absence of each community to

available environmental predictors (e.g. using general-
This strategy, also known as classification-then- ized linear, or additive, modelling), or a single model can
modelling (Ferrier et al. 2002), involves two distinct be fitted to all communities simultaneously by treating
stages. In the first stage the biological survey data are community membership as a multinomial response
subjected to some form of classification, ordination or (e.g. using classification and regression trees). Further
aggregation, without any reference to the environ- detail on these, and related, modelling approaches is
mental data (Fig. 2). This stage therefore involves only provided in Appendix S1 (see the supplementary material).
2006 The Authors. those locations with biological data. In the second
Journal compilation
stage the community-level entities generated for these
2006 British 2 : ,
locations are modelled as a function of environmental
Ecological Society,
Journal of Applied predictors (example studies are listed in Table 2).
Ecology, 43, Classification or ordination of the biological survey In this strategy, also known as predict first, classify later
393404 data to generate community types, species groups or (Overton et al. 2002) and classification-then-modelling
modelling of

Fig. 2. Three broad strategies for spatial modelling of biodiversity at the community level.

Table 2. Examples of studies employing different approaches to spatial modelling of biodiversity at the community level. Studies
predicting community-level responses to climate change are underlined

Broad strategy Specific approach References

1. Assemble first, 1a. Modelling of pre-derived Davis & Goetz (1990), Franklin & Wilson (1991), Lees & Ritman (1991),
predict later community types Moore et al. (1991), Fitzgerald & Lees (1992), Brzeziecki et al. (1993),
Brown (1994), Brzeziecki et al. (1995), Lewis (1998), Zimmermann &
Kienast (1999), Keith & Bedward (1999), Hilbert & Ostendorf (2001),
Ferrier et al. (2002)
1b. Modelling of pre-derived McKenzie et al. (1989), Bojrquez-Tapia et al. (1995),
species groups Ferrier et al. (2002)
1c. Modelling of pre-derived Faith et al. (2003), Chang et al. (2004)
ordination axes
1d. Modelling of pre-derived Pausas (1994), Heikkinen & Neuvonen (1997), Fraser (1998),
species richness levels Saetersdal et al. (1998); Wohlgemuth (1998); Leathwick et al. (1998);
Grytnes et al. (1999); Guisan & Theurillat (2000), Lehmann et al.
(2002); Lobo et al. 2004
2. Predict first, 2a. Derivation of community Ferrier et al. (2002), Lenihan (1993), Leathwick et al. (1996), Ferrier &
assemble later types from modelled species Watson (1997), Austin (1998), Zimmermann & Kienast (1999);
distributions Guisan & Theurillat (2000), Leathwick (2001); Cawsey et al. (2002),
Overton et al. (2002), Peppler-Lisbach & Schrder (2004)
2b. Derivation of species Nix (1991), Lehmann et al. (2002), Ferrier et al. (2002), Scotts &
groups from modelled Drielsma (2003)
species distributions
2c. Derivation of ordination Peters & Thackway (1998), Peppler-Lisbach & Schrder (2004)
axes from modelled species
2d. Derivation of richness Guisan & Theurillat (2000); Gioia & Pigott 2000; Lehmann et al.
levels from modelled species (2002); Peppler-Lisbach & Schrder 2004; Gelfand et al. 2005
Olden (2003), Joy & Death (2004), Leathwick et al. (2005)
2006 The Authors. 3. Assemble and 3a. Multiresponse modelling
Journal compilation predict together of multiple species
3b. Constrained ordination Ferrier & Watson (1997), Gottfried et al. (1998), Ohmann &
2006 British
Gregory (2002), Dirnbock et al. (2003)
Ecological Society,
3c. Constrained classification DeAth (2002), Ferrier et al. (2002)
Journal of Applied
3d. Modelling of Ferrier (2002), Ferrier et al. (2002), Ferrier et al. (2004)
Ecology, 43,
compositional dissimilarity
398 (Ferrier et al. 2002), individual species are initially 2005). While the primary output is usually a set of pre-
S. Ferrier & modelled one at a time as a function of environmental dicted distributions (one for each species), these tech-
A. Guisan predictors, thereby generating a separate predicted dis- niques may also provide valuable information on the
tribution map for each species. The resulting stack of relative importance of environmental predictors, or
extrapolated species distributions is then subjected to weighted combinations of these (e.g. hidden layers in
some form of classification, ordination or aggregation multiresponse neural networks), in explaining overall
to derive the required community-level output (Fig. 2). patterns of species composition. There is therefore the
The analytical techniques employed in this second potential to map important predictors revealed by such
stage are very similar to those used in the first stage of analysis as a means of visualizing major compositional
strategy 1. However, rather than applying them to bio- gradients across a region, but we could not find any
logical data from the original surveyed locations, strat- example of this in the literature.
egy 2 instead applies the techniques to predictions of Mapping of compositional gradients has been more
species occurrence (or abundance) for all grid cells in a often achieved using some form of constrained ordina-
region. Each cell is therefore effectively treated as a vir- tion (e.g. canonical correspondence analysis), in which
tual survey plot (Cawsey et al. 2002), with predicted ordination axes summarizing compositional variation
data for each species in place of direct observations. in the biological data are constrained to be weighted
Hence this strategy attempts to reconstruct community combinations of the environmental predictors (see
composition or macro-ecological properties from pre- Appendix S3 in the supplementary material). While
dicted species distributions in a bottom-up manner, in constrained ordination has been applied very widely as
contrast with the top-down approach of modelling pre- an analytical tool in community ecology, only a small
derived community-level entities (strategy 1). proportion of these applications has used the approach
As species are initially modelled individually, virtu- to extrapolate beyond surveyed locations, and thereby
ally any property of communities and ecosystems map predicted patterns of community composition
could theoretically be reconstructed with this strategy. across a whole region. However, if environmental var-
However, while many recent studies have modelled iables are mapped as GIS layers it is straightforward to
large numbers of species (Bakkenes et al. 2002; map each ordination axis as a weighted combination
Segurado & Araujo 2004), surprisingly few of these of these variables (Ohmann & Gregory 2002). Such
have proceeded to apply any community-level analysis mapping provides a useful way of visualizing the main
to the resulting stack of species distributions. Of those ecofloristic or ecofaunistic gradients across a region
studies that have proceeded to this second stage most and can also provide a basis for mapping predicted
have concentrated on reconstructing either species distributions of individual species, or of pre-defined
richness or community types. Further detail on the community types derived by a separate classification
techniques commonly employed to perform these two of surveyed locations. Such predictions of species or
types of reconstruction is provided in Appendix S2 (see communities are usually based on some measure of the
the supplementary material). This general modelling distance, in ordination space, of each unsurveyed grid
strategy has also been used less frequently to derive and cell from the centroid of the surveyed locations for a
map species groups and ordination axes (for examples given species or community type (Guisan et al. 1999;
see Table 2). Ohmann & Gregory 2002; Dirnbock et al. 2003).
An interesting variant of multiresponse modelling
can also be used to derive constrained classifications
(sensu Gordon 1996) from ecological data. This is an

extension of the classification and regression tree
Unlike the first two strategies, which treat the deriva- approach often used to model pre-defined community
tion of community-level entities or attributes and the types, which recursively splits a set of surveyed loca-
modelling of biologicalenvironmental relationships tions into nested subsets of sites using decision rules
as two distinct steps, this final strategy performs these based on environmental predictors. However, in this
two tasks together (Fig. 2). The strategy therefore particular application the explanatory power of candi-
works with the data for all species simultaneously, date decision rules is assessed directly using the raw
within a single integrated modelling process (see exam- species data, rather than in terms of community types
ple studies in Table 2). derived from a prior numerical classification of these
A number of the techniques traditionally used in data. The species data are used to evaluate and select
species-level modelling have been extended to allow a environmental decision rules that minimize biological
single multiresponse model to be fitted to data for heterogeneity within resulting subsets of locations,
2006 The Authors. multiple species, rather than modelling each species while maximizing differences between these groups.
Journal compilation
separately. These extended techniques include multi- Heterogeneity is usually assessed in terms of composi-
2006 British
Ecological Society, response neural networks (Olden 2003), vector gener- tional dissimilarity between pairs of locations. This
Journal of Applied alized linear (or additive) models (Yee & Mackenzie approach to constrained classification was first imple-
Ecology, 43, 2002) and a multiresponse implementation of multi- mented by Ferrier (1992) and later described in detail
393404 variate adaptive regression splines (Leathwick et al. by Ferrier et al. (2002). Another manifestation of the
399 approach, referred to as multivariate regression trees techniques, rather than on differences between broad
Community-level (MRT), has been described independently by Death analytical strategies or types of spatial output. Thus
modelling of (2002). The general approach not only produces a com- readers of this literature may gain the impression that
biodiversity munity classification but also automatically provides there is only one logical strategy for modelling biodi-
the environmental rules for predictively mapping each versity at the community level, and that the only choice
of these community types (Ferrier et al. 2002). that needs to be made concerns the exact analytical
If viewed in a slightly different way, constrained algorithm to be employed. This narrowness of focus on
classification is effectively a means of modelling com- low-level differences between analytical techniques
positional dissimilarity between locations by partition- within a given strategy, rather than on high-level dif-
ing environmental space into discrete, biologically ferences between alternative strategies, is consistent
homogeneous, classes (i.e. community types). An alter- with a similar focus within the species-level modelling
native approach is to treat compositional dissimilarity literature. We feel there is a real need for more broadly
between locations as a continuous function of the sep- focused consideration of the strengths and weakness of
aration of these locations in environmental space. This major alternative strategies for modelling biodiversity,
idea underpins the recently developed technique of at both the species level and the community level. Deci-
generalized dissimilarity modelling (GDM; Ferrier sions relating to the selection of a broad modelling
2002; Ferrier et al. 2002), a non-linear extension of per- strategy for any given study will probably have a much
mutational matrix regression (Legendre et al. 1994). greater impact on the effectiveness of such modelling
GDM models the compositional dissimilarity observed than decisions relating to the exact analytical algo-
between pairs of surveyed locations as a continuous rithm employed.
non-linear function of the relative position of these No single approach to community-level modelling is
sites along multiple environmental gradients. likely to be optimal for all purposes and across all data
Models fitted with GDM can be used to predict sets. Different approaches may be better suited to dif-
compositional dissimilarity between any pair of grid ferent situations. The real challenge should therefore
cells within a region, knowing only the environmental be seen not as one of searching for a single best
characteristics of these cells. The output from this approach, but rather of selecting the most appropriate
modelling is therefore a complete matrix of predicted approach in any given situation. Such decisions need to
dissimilarities between all possible pairs of grid cells. be informed by a good understanding of the respective
This matrix is difficult to depict spatially in its raw strengths and weaknesses of available options. In Table 3
form. However, it provides all the raw materials neces- we present a first attempt at summarizing the relative
sary to perform either a numerical classification of grid strengths of the various community-level modelling
cells to derive mappable groups of cells with similar approaches described earlier in this review. This evalu-
predicted composition (i.e. community types) or an ation considers only those approaches that retain and
ordination of grid cells to derive mappable axes of com- convey information on community composition.
positional variation. The predicted dissimilarities Each approach is first rated in terms of its capacity to
also provide a basis for predicting distributions of indi- analyse rapidly very large numbers of species (strength
vidual species, or of pre-defined community types (derived 1 in Table 3). Processing time may be an important con-
by a separate classification of surveyed locations), straint when dealing with data sets containing many
using the distance-based approach described above in hundreds or thousands of species. Approaches within
relation to constrained ordination. strategy 2 (predict first, assemble later) require that a
separate model be fitted and extrapolated for every
individual species, and are therefore likely to be more
Applicability of approaches in different contexts
time-consuming to implement than approaches within
the other two strategies. Strategy 3 (assemble and pre-

dict together) offers the best potential to minimize
As we have shown, approaches to community-level processing time, by performing all analyses simultane-
modelling are numerous and highly varied. Differences ously within a single integrated process. A related
between approaches occur at three levels: (i) the broad weakness of strategy 2 is that species occurring infre-
analytical strategy employed (Fig. 2); (ii) the type of quently in a data set may not be modelled reliably, or
spatial output produced (Fig. 1 and Table 1); and (iii) may not be modelled at all, because of insufficient
the exact analytical technique (algorithm) used to pro- records (strength 2). These species therefore contribute
duce a given spatial output employing a given broad little to the subsequent derivation of community-level
strategy (e.g. using generalized linear modelling vs. entities or attributes from the stack of modelled spe-
2006 The Authors. neural networks to model pre-classified community cies distributions. This could be a significant problem
Journal compilation
types). The existing literature on community-level for data sets in which a sizeable proportion of species is
2006 British
Ecological Society, modelling devotes very little attention to discussing the represented by very few records, particularly for con-
Journal of Applied relative strengths and weaknesses of available options servation-related applications requiring an emphasis
Ecology, 43, across these three levels. Published examples have on the needs of rare species. The other two strategies (1,
393404 focused on detailed differences between analytical assemble first, predict later, and 3, assemble and predict
Ecology, 43,
Journal of Applied
Ecological Society,
2006 British
Journal compilation
2006 The Authors.

A. Guisan
S. Ferrier &
Table 3. Relative strengths of different approaches to spatial modelling of community composition (approaches that predict species richness, or other macro-ecological properties, are not included). *Limited
capacity, **moderately developed capacity, ***highly developed capacity


1. Rapidly 2. Adds
analyses value to 3. Addresses 4. Allows 5. Combines 6. Produces 7. Enforces
very large data for interactions individualistic taxa surveyed individual congruence 8. Extrapolates
numbers rare species between species at different sets species with known beyond known
Broad strategy Specific approach of species by pooling species responses of locations distributions communities communities

1. Assemble 1a. Modelling of pre-derived ** *** ** * * * *** *

first, predict community types
later 1b. Modelling of pre-derived ** *** ** * * * ** **
species groups
1c. Modelling of pre-derived ** *** ** * * * * **
ordination axes
2. Predict 2a. Derivation of community * * * *** *** *** * **
first, assemble types from modelled species
later distributions
2b. Derivation of species * * * *** *** *** * **
groups from modelled
species distributions
2c. Derivation of ordination * * * *** *** *** * **
axes from modelled
species distributions
3. Assemble 3a. Multiresponse modelling *** ** *** ** ** *** * **
and predict of multiple species
together 3b. Constrained ordination *** *** ** * * ** * **
3c. Constrained classification *** *** ** ** * ** ** *
3d. Modelling of *** *** ** ** ** ** * ***
compositional dissimilarity
401 together) use data from all species, no matter how infre- The subsequent modelling stage therefore forces each
Community-level quently recorded, in deriving community-level entities unsurveyed grid cell to be assigned to one of these
modelling of or attributes. By pooling data from all species these known communities. Whether this enforced congru-
biodiversity strategies may provide more power to detect shared ence is regarded as a strength, rather than a weakness,
patterns of environmental response across infrequently is likely to depend on the purpose of modelling and the
recorded species than can be detected by analysing the nature of the data involved. For example, this might be
data for each of these species independently. Combin- viewed as a strength for an application requiring that
ing data in this way also provides more scope to address mapped entities concord directly with pre-defined
interactions between the distributions of different community types, and for which sufficient survey work
species, such as those resulting from competition or has been conducted to detect all community types
predation (strength 3). within the region of interest. However, where field
Despite the drawbacks just discussed, strategy 2 has sampling of communities is incomplete, or sparse, then
some unique strengths. By modelling species one at a enforcement of a one-to-one congruence between
time this strategy provides maximum opportunity, or surveyed community types and modelled entities may
flexibility, for each species to respond to the environ- instead be seen as a weakness. This situation may be
ment in an individualistic manner (strength 4). In con- better served by approaches with an ability to extra-
trast, approaches within the other two strategies place polate beyond sampled communities, thereby predicting
various constraints on the flexibility of speciesenvi- the occurrence of other community types, or species
ronment relationships, for example by assuming that assemblages, in as yet unsampled environments
all species are responding to the same set of environ- (strength 8). Most approaches other than 1a (model-
mental gradients or that the functional form (shape) of ling of pre-derived community types) offer at least
these responses is the same across all species. Another some capacity for such extrapolation.
unique strength of strategy 2 is the potential ability to The main conclusion to be drawn from Table 3 is
combine species models derived from different biolo- that the appropriateness of a given approach for a given
gical survey or collection data sets (strength 5). Imagine, application will depend on the relative importance of
for a hypothetical region, that animal species have been various strengths and weaknesses in relation to both
surveyed at one set of sites while plant species have been the purpose of the application and the type, quality and
surveyed at a different set of sites. Once models have quantity of data involved. We illustrate this point using
been derived for individual species of plants and ani- the application of community-level modelling to pre-
mals, the combined stack of extrapolated distributions dict distributional shifts in biodiversity in response to
can then be readily subjected to community-level clas- climate change.
sification, ordination or aggregation regardless of the
fact that these distributions were originally modelled
using different survey data sets (Scotts & Drielsma

2003). This capability also has benefits for the analysis
of presence-only data from museum collections, in Palaeoecology provides clear evidence that community
which data for different taxa are often derived from dif- types of the past were different from those observed
ferent sources, collectors or expeditions. In contrast, today (Huntley 1991; Ackerly 2003). Hence some
strategy 1 and, to a lesser extent strategy 3, assume that community-level modelling approaches may face serious
all species have been surveyed (i.e. recorded as present problems in predicting probable responses to climate
or absent) at the same set of sites. Another strength of change if they assume that the composition of commu-
strategy 2 is that modelled distributions of individual nities will remain fixed over time, i.e. that the same
species are produced as a standard by-product, thereby community types will continue to exist and only the
complementing any community-level outputs derived distributions of these types will change. Palaeoecology
from these models (strength 6). However, it should be also provides evidence of an even more fundamental
noted that several approaches within strategy 3 also problem, i.e. the realized niches of some species appear
offer this capability. to change over time (Ackerly 2003), probably as a result
The final two strengths evaluated in Table 3 are less of changing interactions (e.g. competition and preda-
closely aligned with any particular broad strategy and tion) between species (but see also Peterson et al. 1999).
relate more to individual approaches within these strat- Any approach to predicting climate change responses
egies. The first of these strengths concerns the extent to that treats the currently realized niche of a species as if
which an approach constrains the community-level it were the fundamental niche is therefore also likely to
composition predicted for each unsurveyed grid cell encounter problems (Austin 1992).
2006 The Authors. to match the composition observed at one or more All three modelling strategies described in this
Journal compilation
surveyed locations (strength 7). Such congruence is review have been used to predict community-level
2006 British
Ecological Society, enforced most strictly by approach 1a (modelling of responses to climate change (Table 2). However, if
Journal of Applied pre-derived community types) within strategy 1. This future community types are likely to differ in com-
Ecology, 43, approach treats community types, generated by the ini- position from those observed today then strategy 1 will
393404 tial classification of surveyed locations, as fixed entities. generate unreliable predictions. This strategy may
402 provide useful evidence that current community types 1992) to guide, or constrain, the derivation of commu-
S. Ferrier & will not be able to persist at their present locations, but nities from individual species models (see Appendix S4
A. Guisan cannot reliably predict where similar communities (if and Fig. S1 in the supplementary material).
maintained as such), or new community types, will be
distributed in the future. Strategy 2 may be a better

option in this regard (Guisan & Theurillat 2000) because
it can account for individual responses of species, and may Despite the current popularity of species-level
even allow different migration rates to be incorporated modelling, spatial modelling of biodiversity at the
into the modelling of distributional shifts for different community level may confer significant benefits for
species. However, a potential problem with most exist- applications involving very large numbers of species,
ing implementations of this strategy is that current spe- particularly if many of these species are recorded infre-
cies interactions, and therefore the realized (as opposed quently. Potential benefits in such situations include
to fundamental) niches of species, are assumed to remain faster processing, increased power to detect shared pat-
constant into the future. This is unlikely and thus inclu- terns of environmental response across rarely recorded
sion of species (and other biotic) interactions into the species, and enhanced capacity to synthesize complex
species-modelling stage of this strategy is expected to data into a form more readily interpretable by scien-
improve the rigour with which shifts in community tists and decision-makers. Community-level modelling
composition are predicted. Leathwick et al. (1996) is therefore deserves to be considered more often, and
the only example found so far where interactions were more widely, as a potential alternative or supplement
explicitly included in species models used to derive to modelling individual species.
spatially explicit climate change projections at the com- We have defined three very different strategies for
munity level. Strategy 3 has, to date, been employed much modelling biodiversity at the community level: assem-
less frequently in predicting climate change responses. ble first, predict later; predict first, assemble later; and
However, the potential for this strategy to provide an assemble and predict together, and we have described a
effective balance between the respective strengths of number of available approaches within each strategy. Each
the other two strategies warrants further attention. of these strategies and approaches has different strengths
and weaknesses, and therefore no single approach is likely
to be optimal for all purposes and across all data sets.
Future directions
Prospective users of community-level modelling should
There is a clear need for more attention to be directed therefore exercise care in selecting a modelling approach
to comparative evaluation of the efficacy of different that is best suited to their particular needs.
community-level modelling approaches. Surprisingly little
empirical testing of alternative approaches has occurred
to date. A small number of studies has compared the Acknowledgements
performance of strategies 1 and 2 for modelling species We thank our many colleagues at the GLM/GAM
richness (Guisan & Theurillat 2000; Lehmann et al. 2002). spatial modelling of species distributions workshop
Ferrier & Watson (1997) and Ferrier et al. (2002) have in Riederalp, Switzerland (August 2004) for valuable
also evaluated the performance of various approaches discussion regarding various issues addressed in this
to modelling community composition, although this paper. Information on the workshop, including a full
work was confined to a single region and a single appli- list of participants, is available at
cation, the selection of conservation areas. There is workshop, accessed 23.02.06. We also thank John
considerable scope to extend this type of evaluation to Leathwick and an anonymous referee for their con-
cover a wider range of modelling approaches, environ- structive comments on an earlier version of the paper.
ments, data types and applications. Much could also be
gained by supplementing assessments using real data
sets with testing based on artificial (simulated) data. References
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