Predicting the fate of biodiversity using species' distribution models: enhancing model comparability and repeatability.
ABSTRACT Species distribution modeling (SDM) is an increasingly important tool to predict the geographic distribution of species. Even though many problems associated with this method have been highlighted and solutions have been proposed, little has been done to increase comparability among studies. We reviewed recent publications applying SDMs and found that seventy nine percent failed to report methods that ensure comparability among studies, such as disclosing the maximum probability range produced by the models and reporting on the number of species occurrences used. We modeled six species of Falco from northern Europe and demonstrate that model results are altered by (1) spatial bias in species' occurrence data, (2) differences in the geographic extent of the environmental data, and (3) the effects of transformation of model output to presence/absence data when applying thresholds. Depending on the modeling decisions, forecasts of the future geographic distribution of Falco ranged from range contraction in 80% of the species to no net loss in any species, with the best model predicting no net loss of habitat in Northern Europe. The fact that predictions of range changes in response to climate change in published studies may be influenced by decisions in the modeling process seriously hampers the possibility of making sound management recommendations. Thus, each of the decisions made in generating SDMs should be reported and evaluated to ensure conclusions and policies are based on the biology and ecology of the species being modeled.
- SourceAvailable from: Boris Leroy[Show abstract] [Hide abstract]
ABSTRACT: Aim To assess the exposure of 10 spider species to two drivers of global change (climate and land use), the suitability of the current network of protected areas with respect to this exposure, and the implications for a national conservation programme. Location The western Palearctic and France. Methods We predicted the current and future potential distributions of 10 spider species using species distribution models (SDMs). We explicitly quantified uncertainties in the models and estimated the future environmental suitability with discounted uncertainty. We analysed the predicted future suitability for protected versus unprotected occurrence cells. Results In this first forecast of the future of multiple spider species in the face of environmental changes, we showed that environmental changes could be confidently predicted to have serious impacts on all the studied species, with significant range contractions and expansions within a relatively short timescale (up to 2050). We predicted that for seven of the 10 species, the current network of protected areas will conserve at least one occurrence cell in suitable conditions in the future. However, we showed that there is considerable room for improvement. Main conclusions This study illustrated how SDMs could be applied to a conservation programme for an understudied taxon such as spiders, in spite of significant uncertainties in their predictions. In addition, the uncertainties raised here compel us to emphasize the pressing need to improve our knowledge on understudied taxa such as spiders. We advocate the necessity of increasing monitoring schemes, experiments and forecasts of environmental change effects on a larger and more diversified range of species than is currently the case in the literature. Keywords Arthropods, ensemble forecast, global changes, species distribution models, threatened species, uncertainty.Diversity and Distributions 06/2014; · 5.47 Impact Factor
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ABSTRACT: Aspalathus linearis (Burm. f.) R. Dahlgren (rooibos) is endemic to the Fynbos Biome of South Africa, which is an internationally recognized biodiversity hot spot. Rooibos is both an invaluable wild resource and commercially cultivated crop in suitable areas. Climate change predictions for the region indicate a significant warming scenario coupled with a decline in winter rainfall. First estimates of possible consequences for biodiversity point to species extinctions of 23% in the long term in the Fynbos Biome. Bioclimatic modelling using the maximum entropy method was used to develop an estimate of the realized niche of wild rooibos and the current geographic distribution of areas suitable for commercially production. The distribution modelling provided a good match to the known distribution and production area of A. linearis. An ensemble of global climate models that assume the A2 emissions scenario of high energy requirements was applied to develop possible scenarios of range/suitability shift under future climate conditions. When these were extrapolated to a future climate (2041-2070) both wild and cultivated tea exhibited substantial range contraction with some range shifts southeastwards and upslope. Most of the areas where range expansion was indicated are located in existing conservation areas or include conservation worthy vegetation. These findings will be critical in directing conservation efforts as well as developing strategies for farmers to cope with and adapt to climate change.Ecology and Evolution 04/2014; 4(8):1209-21. · 1.66 Impact Factor
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ABSTRACT: The outcome of plant introductions is often considered in binary terms (invasive or non-invasive). However, most species experience a time lag before naturalization occurs, and many species become naturalized at some sites but not at others. It is therefore important to understand the site-specific mechanisms underlying naturalization. Proteaceae is an interesting case as some species are widespread invaders, while others, despite a long history of cultivation, show no signs of naturalization. At least 26 non-native Proteaceae species have been introduced to, and are cultivated in, South Africa. We mapped populations and examined differences between naturalized and non-naturalized populations (e.g. propagule pressure, land use and bioclimatic suitability). Of the 15 species surveyed, 6 were naturalized at one or more sites. Of these, Hakea salicifolia is most widely cultivated, but is only naturalizing in some areas (32 naturalized populations out of 62 populations that were surveyed). We found propagule pressure to be the most important determinant of naturalization for H. salicifolia. However, in suboptimal climatic conditions, naturalization only occurred if micro-site conditions were suitable, i.e. there was some disturbance and water available. For the other naturalized species there were few sites to compare, but we came to similar conclusions – Banksia integrifolia only naturalized at the site where it was planted the longest; Banksia serrata only naturalized at a site influenced by fire regimes; while Banksia formosa naturalized at sites with high propagule pressure, absence of fires and where there is no active clearing of the plants. Naturalization of Proteaceae in South Africa appears to be strongly mediated by site-specific anthropogenic activities (e.g. many planted individuals and water availability). More broadly, we argue that invasion biology needs to focus more closely on the mechanisms by which species and pathways interact to determine the likelihood and consequence of an invasion.Acta Oecologica 08/2014; 59:62–71. · 1.84 Impact Factor
Predicting the Fate of Biodiversity Using Species’
Distribution Models: Enhancing Model Comparability
Genoveva Rodrı ´guez-Castan ˜eda1*., Anouschka R. Hof2,3., Roland Jansson2, Larisa E. Harding2
1Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America, 2Landscape Ecology Group, Department of Ecology and
Environmental Science, Umea ˚ University, Umea ˚, Sweden, 3Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences (SLU),
Umea ˚, Sweden
Species distribution modeling (SDM) is an increasingly important tool to predict the geographic distribution of species. Even
though many problems associated with this method have been highlighted and solutions have been proposed, little has
been done to increase comparability among studies. We reviewed recent publications applying SDMs and found that
seventy nine percent failed to report methods that ensure comparability among studies, such as disclosing the maximum
probability range produced by the models and reporting on the number of species occurrences used. We modeled six
species of Falco from northern Europe and demonstrate that model results are altered by (1) spatial bias in species’
occurrence data, (2) differences in the geographic extent of the environmental data, and (3) the effects of transformation of
model output to presence/absence data when applying thresholds. Depending on the modeling decisions, forecasts of the
future geographic distribution of Falco ranged from range contraction in 80% of the species to no net loss in any species,
with the best model predicting no net loss of habitat in Northern Europe. The fact that predictions of range changes in
response to climate change in published studies may be influenced by decisions in the modeling process seriously hampers
the possibility of making sound management recommendations. Thus, each of the decisions made in generating SDMs
should be reported and evaluated to ensure conclusions and policies are based on the biology and ecology of the species
Citation: Rodrı ´guez-Castan ˜eda G, Hof AR, Jansson R, Harding LE (2012) Predicting the Fate of Biodiversity Using Species’ Distribution Models: Enhancing Model
Comparability and Repeatability. PLoS ONE 7(9): e44402. doi:10.1371/journal.pone.0044402
Editor: Frederick R. Adler, University of Utah, United States of America
Received March 20, 2012; Accepted August 2, 2012; Published September 11, 2012
Copyright: ? 2012 Rodrı ´guez-Castan ˜eda et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which
permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported by a young researcher award from Umea ˚ University (to RJ) and a grant from the Nordic Council of Ministers. The funders had
no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: email@example.com
. These authors contributed equally to this work.
Europe has the world’s most extensive network of conservation
areas, which cover approximately 17% of the European Union’s
surface . However, climate change is expected to decrease the
effectiveness of such areas to protect their biodiversity . Indeed,
climate change is already having effects in parts of Europe; the
Arctic has, for instance, lost more than 26106km2of permanently
frozen area in the last 1450 years , and this region hosts a large
series of species specialized to circumpolar habitats . In
response to such effects, frameworks have been designed to assess
the threats and benefits of climate change to species that focus on
changes in their distributional ranges . For example, multiple
mammal and bird species in Mexico were modeled to predict these
species’ future responses to climate change . Another study
characterized climate influences on the current distribution of
endemic bird species of North America , and a recent study
conducted a complete assessment of how many threatened species
might be retained within the network of national versus the
network of Natura 2000 conservation areas in Europe . Many
more such studies have been undertaken and are currently
underway to help conserve biodiversity in the face of climate
change. Predictions of how species’ distributions responds to
changes in climate frequently use one of a suite of methods
variously called species’ distribution modeling (SDMs), habitat
modeling, or ecological niche modeling (ENM). These methods all
have a similar purpose: to provide a geographical distribution of
the environmental requirements of the species . They all stem
from Grinell’s idea that a species’ niche is closely related to the
area in which the species is distributed .
In the past 20 years SDMs have increasingly been used as a tool
to plan and design species’ conservation efforts. SDMs appear in
the literature in increasing numbers each year (data obtained from
ISI Web of Knowledge, Figure S1) and they are applied in new
contexts, such as epidemiology , agronomy , and the study
of invasive species . Furthermore, hindcasting (i.e., projecting
species’ geographic distribution backward in time) SDMs in
combination with molecular phlyogeography is used to infer the
role of climatic refugia for species. Likewise, when combined with
molecular studies, SDMs can help elucidate the phylogeography
 and description of the evolutionary paths  of species. The
increasing number of publications using SDMs, and the diversi-
fication of fields in which this method is applied, appeal to a real
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need to create consensus and set standards on how model
construction and results are reported to enhance interpretation
and comparability among studies. SDMs can also be used to
understand macroecological patterns. For example, forecasting
predictions across multiple species provides a better understanding
of the conservation value of geographic regions with regard to
their future potential importance in protecting biodiversity .
Hence, SDMs are increasingly being used to aid decisions and the
formulation of policies in such broad-reaching disciplines as
conservation, pest control and the management of introduced
species, as well as in human health issues [2,15,16]. On the other
hand, hindcasting the distribution of large numbers of species
provides information on which areas have acted as refugia in the
Other critical and exciting applications of SDMs include
comparing geographic range dynamics between species and
investigating how ensembles of species may respond to climate
change. For example, SDMs can be an important tool in
predicting future geographic distributions of multiple, co-distrib-
uted species to project the fate of biodiversity in specific areas and
to identify geographic locations with high conservation value.
These results in turn can aid policy makers in managing
There is an increasing tendency to group individual SDMs to
portray patterns across multiple species or whole taxonomic
groups . The rising need to generate predictions for groups of
species makes it essential that models generated for different
species can be both replicated and compared. More importantly,
the process of generating SDMs should be standardized and
clearly reported in publications so that attempts to compare
models constructed for different taxa are not confounded by
methodological or statistical artifacts, but reflect real ecological
and evolutionary tolerances of species to their climatic niches
Species’ distributions are largely determined by environmental
variables, such as climate, trophic interactions and dispersal
limitation, and the relative importance of these factors are likely to
vary depending on the scale at which species’ distributions are
modeled [7,21]. Another important issue to address in SDMs is
sample size; since all niche models require occurrence data, there
must be careful quality control based on basic knowledge of the
geographic range and biology of the organisms. Previous authors
have demonstrated how using different sets of occurrence data
render different results . Further, the extent of the geographic
region used to train the model is also of primary importance, since
the algorithms rely on background conditions to contrast with
conditions at species’ occurrences and absences, and different
results are obtained when using larger or tailored geographical
extents . Moreover, the AUC values that are currently
regarded as a standard method for assessing the model perfor-
mance are subject to large errors. Hence, AUC values are not a
reliable method to assess model performance . In addition, to
demonstrate the lack of standardization in SDMs, a recent review
of hindcasting studies found that four studies modeling climatic
refugia in the Amazon basin each resulted in different predictions
. As each of these studies made different decisions when
projecting species’ distribution to past climatic conditions, little
consensus could be reached on which regions of the Amazon were
predicted to be refugial areas, not just for one taxa, but for
biodiversity in general. Since the idiosyncrasies and consequences
of hindcasting and forecasting species’ geographic distributions are
similar, a lack of consensus over which areas should have high
priority for conserving future biodiversity is also plausible. The use
of hindcasting species’ geographic distributions to validate
evolutionary paths of speciation have been successfully applied
in studies investigating a small set of refugia, based on
phylogeographical studies such as speciation in the thrush-like
mourner . However, it is still uncertain whether the climatic
refugia inferred are relevant also for other taxa or other
hindcasting studies conducted in the same region.
Here, we first review recent publications applying SDMs and
assess whether they provide the relevant information needed to
ensure comparability among the predictions of the studies. This
assessment is based on whether the publication provides informa-
tion on how occurrence locations were handled and reported, the
geographical extent of the region studied (both for training and
projecting the model), the type of thresholds used to transform the
continuous prediction to a binary one and how the accuracy and
precision of the prediction was validated.
Second, we modeled the breeding distribution of six species of
Falco in northern Europe and examined how model results were
influenced by (1) spatial bias in species’ occurrence data, (2)
differences in the geographic extent of the region studied, and (3)
the effects of transformation (or thresholding) of a continuous
model output to presence/absence data applying thresholds. We
chose to model the breeding range of species within the Falco genus
because large birds of prey are predicted to negatively respond to
climate change since key natural history traits such as egg laying
and clutch size have been correlated with North Atlantic climatic
Materials and Methods
As SDMs are often referred to by other names, we performed a
literature search that considered both SDMs and ENMs. The term
SDMs was most commonly used in the literature; for example, a
search in the ISI web of knowledge on ‘‘species’ distribution
modeling for 2010–2011 and refined by the query ‘‘MaxEnt or
GARP or Artificial Neural Networks’’, popular machine learning
methods to model species distributions, returned 271 hits. Refining
this query by ‘‘ecological niche modeling’’ resulted into 91 hits.
When we searched for ‘‘ecological niche modeling’’ limited to the
years 2010–2011 and refined by the query ‘‘MaxEnt or GARP or
Artificial Neural Networks’’ first, there were only 97 hits. Refining
this query by ‘‘species distribution modeling’’ resulted into 91 hits
again. Therefore, 94% of the papers overlapped while searching
for ecological niche modeling or species distribution modeling, and
the latter returned a larger number of papers. Since the use of
‘‘species’ distribution modeling’’ returned a larger number of
papers, we focused our subsequent literature search on publica-
tions that had ‘‘species’ distribution modeling’’ either in the title,
keyword or abstract. We first counted how many recent
publications employed SDMs by conducting a search in the
Web of Science (http://apps.webofknowledge.com/) for the
period of 1992–2011, using ‘‘species’ distribution model*’’ as a
search term and extracted data to study trends in the use of this
method during the past 20 years in order to evaluate how SDMs
are applied and reported. We then selected the 317 studies that
published on SDMs during the past two years (i.e., 2010–2011).
We further restricted our analysis to studies that applied machine
learning models such as MaxEnt or GARP, resulting in 170
publications. From these, we randomly sampled about half of the
publications (77 publications), which we deemed a sample size
sufficient for the purpose of our study. We recorded whether
SDMs assessed one or multiple species and examined whether one
could replicate SDM constructions based on the 9 criteria outlined
below. We examined the selected publications to see if each
Predicting the Fate of Biodiversity Using SDMs
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reported (1) the number of species’ occurrences, (2) actions taken
to resolve possible biases in occurrence data, such as lack of or too
many occurrences in specific areas, (3) model evaluation by
splitting data into testing and training data, (4) the explicit
geographic extent of the region studied (i.e., we deemed it
insufficient to present only a map of the study area; we required a
statement on how the region from which climatic variables were
drawn in order to predict species’ distributions was delimited ,
(5) the modeling algorithm(s) used, (6) the maximum probability of
the resulting model, (7) the application of (a) threshold(s) to the
continuous probability surface to create binary presence/absence
data, (8) the type of precision test(s) employed, and (9) steps taken
to test the accuracy of the predictions. (For definitions of terms
applied here, see Table S1). We then calculated the proportion of
studies that met each of the criteria. Moreover, we tallied the
proportion of studies that reported and addressed the sources of
error in their SDMs based upon the steps displayed in Figure 1.
Next, we tested how the predicted (future) breeding season
ranges of six bird species in the genus Falco in northern Europe
were influenced by decisions taken in modeling their geographic
distributions. We focused on alternative decisions regarding (1) the
input of species’ occurrence data, (2) the selection of the
geographical extent of the environmental data, and (3) the effects
of transformation of model output when applying thresholds
(Figure 1). We then investigated how these decisions affected (1)
the area under the curve (AUC) of ROC plots , (2) the
maximum probability of the predicted suitable area, and (3) the
accuracy of the predictions when compared to published ranges
(Figure 1). Although there are numerous additional issues involved
in building SDMs, we chose to focus on these major decisions and
their consequences with regard to the reliability of predictions,
since these steps most likely affect how results from a published
SDM can be reviewed and its applicability assessed [19,20]. We
used MaxEnt  to illustrate and discuss the comparability of
SDMs, but the issues discussed here are also applicable to other
modeling algorithms. We chose MaxEnt because it has excelled
compared to other algorithms in predicting species’ distributions
that reflect the true physiological or mechanistic constraints of
species to climatic conditions . Furthermore, it performs better
than other models such as BIOCLIM and GARP in situations
where true absence data are unavailable [31,32], and MaxEnt
curently ranks among the most popular methods to construct
We included nineteen bioclimatic variables derived from recent
(195022000) monthly temperature and rainfall records described
and available at WorldClim (http://worldclim.org/futdown.htm,
). Although the use of multiple auto-correlated bioclimatic
variables is debated among species’ distribution modelers [22,31],
we included all 19 climatic variables, taking advantage of the
regularization application in MaxEnt . Regularization deals
with the selection of environmental variables (regulating some to
zero) and has performed well or even outperformed other
modeling procedures that pre-select variables . Furthermore,
MaxEnt minimizes autocorrelation between variables, as it gives
more weight to variables exhibiting high correlation with the
occurrence data . We used the default convergence threshold
(1026) and number of iterations (500). Hinge features were
applied, as recommended by a comprehensive evaluation of
MaxEnt . The future climate projection was taken from the
general circulation modelCGCM2 for 2080 downscaled to 30 arc-
seconds, under emission scenario A2 (http://www.worldclim.org/
Species’ occurrence data.
(June – August) occurrence data from 2000–2010 for six Falco
species that occur in northern Europe from national and global
artportalen.se, http://www.hatikka.fi, and http://data.gbif.org).
By means of randomized partition, 30% of the occurrence data
were set aside as testing data to validate the model. The remaining
localities were used to train the model. To test how biased or
under-sampled occurrence data affected MaxEnt models, we first
modeled species’ distributions with all available data points (i.e.,
biased set because some locations have clumped occurrences
whereas other locations have few occurrences [Figure 2]). We then
We collected breeding season
Figure 1. Schematic framework for generating, validating and processing SDMs for studying effects of climate on biodiversity.
Predicting the Fate of Biodiversity Using SDMs
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modeled species’ distributions after minimizing potential bias in
the occurrence data. To correct for clustered occurrence records
that affect SDM predictions , we used a raster grid with a
resolution of 10 arc-minutes and randomly selected one record per
cell in order to reduce the bias potentially introduced by
differences in human monitoring effort (i.e., unbiased set). Since
Falco occurrence records were unavailable in north-western
Russia, we projected predictions from Finland, Sweden and
Norway to the parts of north-western Russia within our target
region. The species modeled and numbers of occurrences
included in both datasets were: F. columbarius (Nbiased=1691,
Nunbiased=1249), F. peregrinus (Nbiased=618, Nunbiased=371), F.
rusticolus (Nbiased=94, Nunbiased=84), F. subbuteo (Nbiased=4644,
Nunbiased=1902), F. tinnunculus (Nbiased=5913, Nunbiased=2689),
and F. vespertinus (Nbiased=195, Nunbiased=169).
Geographic extent of the region modeled.
effect of altering the geographic extent of the region modeled (i.e.,
the area in which the model is trained) on predicted species’
distributions, we first generated SDMs using a wide geographical
extent including the entire region of Fennoscandia and north-
western Russia (map shown in Figure 3B). Due to the paucity of
Falco records in north-western Russia, using a full geographic
extent of the region modeled may characterize the realized
distribution of species in the genus poorly. Including large areas
increases the chance that the model samples pseudo-absences in
areas that have suitable conditions for the species but are falsely
To study the
classified as unsuitable because the species has not been properly
sampled in that region . Indeed, choosing the correct extent is
not a trivial task since the values where occurrence data are
lacking are taken as pseudo-absences that are meant to provide a
comparative data set to establish the conditions where a species
may occur. If large extents with great environmental variation are
selected, predictive models will be dominated by parameters that
serve to coarsely discriminate regional conditions and weaken the
ability to tease out fine-scale conditions determining presence or
absence of species . On the other hand, using a restricted
region for selection of pseudo-absences can be a serious error
when fitting models to project potential effects of climate change
, since future environmental conditions may not be repre-
sented. Since occurrence data for our model species was lacking
for north-western Russia, we used Fennoscandia, which accurately
mirrored the distribution of the occurrence data of the species
(map shown in Figure 3A).
First, we evaluated the effects of
decisions made during model construction by investigating
how locality data and geographical extent can affect the
probability range of the predicted suitability of conditions,
specifically the maximum probability generated by the models.
The probability range is represented as a continuous surface of
similarity values from low (0) to high (,1) similarity, with high
similarity values best representing environmental conditions
similar to the conditions at the species’ known localities .
Figure 2. Example on how occurrence data can alter predictions of SDMs. A. Biased occurrence, versus B. Unbiased occurrence data affect
the present and future SDM projections for Falco subbuteo, summarized in panel C.
Predicting the Fate of Biodiversity Using SDMs
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the probability range of projected conditions to a binary presence/
absence surface by setting thresholds. A threshold is set by defining
the probability value above which environmental conditions are
deemed suitable for the presence of a particular species, and below
Once predictions were generated, we converted
which environmental conditions are considered unsuitable. In
many applications, such as estimations of species’ range dynamics
with changing climate, setting thresholds is a critical step in how
model outcomes are interpreted. The selection of a threshold value
is especially complicated without true absence data providing
Figure 3. Example on how geographic extents impact conclusions made in SDMs of Falco subbuteo. A. Unrestricted extent versus, B.
Restricted extent, and C. Results drawn from SDMs.
Predicting the Fate of Biodiversity Using SDMs
PLOS ONE | www.plosone.org5September 2012 | Volume 7 | Issue 9 | e44402
information on conditions under which the species is unlikely to
occur. Here, we do not discuss the best approach in choosing a
threshold, but present a few strategies for setting a threshold to
assess how different thresholds can affect ecological conclusions. A
range of approaches can be used to determine which threshold is
most suitable [22,38,39]; one common approach is to set threshold
values based on receiver operating characteristic (ROC) plots .
Model predictions in the ROC plots of Falco suggested that low
threshold values may be appropriate, and we used one generous
(0.1) and one more conservative (0.4) threshold value and
compared the results.
SDM is a good way to evaluate the effects of decisions made
during model construction, since model predictions with high
maximum probability (close to 1) reflect a good correlation
between the variables included in the model and the species’
occurrence data used as input.
AUC values and overlap with published geographic
distributions of species.
Until recently, the area under the
curve (AUC) of a ROC plot  was commonly used as the single
measure to validate the predictions generated by SDMs. However,
concerns have risen with regard to the usefulness of the metric
[24,40]. Still, since the vast majority of studies continue to rely
solely on AUC values to validate the quality of models (see below),
we decided to state the values of both the training and testing data
and discuss how different decisions with regard to the input of the
models affected the AUC values. For a thorough discussion on the
usefulness of AUC values, we refer to papers dealing with this
matter [25,40] A practical approach to validate models is to use a
hierarchical fuzzy pattern-matching approach to compare predic-
tions generated by SDMs with published range maps . This
approach is not optimal since it assumes that published range
maps are accurately depicting the distribution of a species, which
might not be true. Furthermore, SDMs predict the potential niche
and not the realized niche of a species. Below we discuss the
limitations of this method more in depth, but due to the lack of an
un-criticized approach to validate models available, we compared
the predictions of the ranges generated by SDMs for current
climatic conditions with published geographic ranges of European
birds . We expressed the similarity between predicted and
published range maps using the percentage of the predicted
current range that lay within the published range and the
percentage of the published range that was covered by the
predicted current range. In order to test the relationship between
AUC values and overlap between published ranges and the SDMs
we generated, we correlated AUC and percent overlap using
Spearman’s rho (PASW statistics v. 18).
The maximum probability given by a
The use of SDMs has increased non-linearly over the last
decade (Figure S1). A sampling of recent publications (2010–2011;
Table S2) revealed that SDMs are now commonly used as a tool in
applied ecology (i.e., 80% of the reviewed SDM studies), such as to
inform decisions and direct policies in biodiversity conservation,
management of introduced species and pest control (Figure S2A).
Twenty-one percent of the investigated studies provided the
information necessary to replicate their models along with
information on how the models were evaluated (Figure S2B),
whereas in the remaining 79% of the studies, one or more of our
criteria for replication and evaluation were not met. The most
neglected criteria were, reports on possible biases in species’
occurrence data (39%),and the maximum probability range
produced by the models, with only 21% of the studies reporting
on it(Figure S2B). In contrast, some criteria are more frequently
reported; 83% of studies stated how many occurrence records
were included in models, and 94% reported the use of a
measurement to assess model performance in terms of precision,
with 78% relying solely on AUC values (Figure S2B).
Table 1 illustrates the effects of making different decisions in
SDM construction on predicting future geographic distributions
for species in the genus Falco. Combined, the different decisions
resulted in predictions ranging from reduced future range sizes in
five out of six species to no reduction in range size for any of the six
species. Graphical examples of the impact of occurrence records,
geographic extents and thresholds on the predicted breeding range
of the Eurasian hobby (Falco subbuteo) are given in Figures 2–4.
Using biased locality data, in which occurrences were clumped, led
to altered conclusions regarding the number of species predicted to
experience a future range contraction or expansion. In general,
applying biased occurrence data to SDMs resulted in poorer
predictions, i.e., decreased similarity between predicted current
ranges and published ranges and lower AUC values in the training
data (Table 1, Figure 2). Moreover, using biased data produced
more generous estimates of mean area gained in the future than
applying unbiased occurrence data. In addition, current and
future predictions for Falco species showed large differences in
predicted suitable breeding ranges in northern Europe when we
altered the geographic extent of the region modeled (Table 1,
Figure 3). Predicted suitable areas generally increased and became
more similar to published ranges when a restricted extent (Figure 3)
and lower thresholds (Figure 4) were applied. Restricting the
geographic extent generally increased the maximum probability
range but lowered the mean of the AUC values (Table 1). Thus
unbiased occurrence records, restricted geographic extents, and
low thresholds produced predictions that resembled most closely
the published species’ ranges. However, these SDMs did not have
the highest AUC values (Table 1). Indeed, AUC values of both
training and test data were significantly negatively correlated with
similarity between predicted current and published ranges (Spear-
man’s rho; train data: r=20.82, n=48, p,0.001; test data:
r=20.78, n=48, p,0.001). As such, AUC values were high for
SDMs with predictions that poorly reflected published ranges.
Decisions Altering Model Outcomes
We have demonstrated how decisions made while generating
SDMs can often significantly alter modeling outcomes. For
example, applying unbiased occurrence data to a restricted extent
of the region modeled in our Falco models improved the similarity
between predicted current and published ranges (Table 1).
Changing these criteria also influenced the maximum probability
of area suitability in the generated predictions, and thresholding
with different values across the probability surfaces modified
predicted range sizes. These decisions had far reaching conse-
quences in terms of conclusions that could be drawn from the
modeling effort. Compared to what we deemed the best modeling
strategy according to model evaluation, the conclusion regarding
future range expansion or contraction changed in five of six species
(Table 1). Although we do not know if the decisions made during
the modeling process affect predictions for Falco more or less than
they would any other genus, absence of such influence can only be
guaranteed by reporting the decisions made. Yet despite the
evident impacts made with each choice in designing SDMs, less
than half of the published studies we sampled reported their
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methods in a way that facilitated repeatability and comparability
to other SDMs. Failure to report on such variables as bias in
locality data, geographic extent of climatic layers, values of
resulting maximum probability surfaces or thresholds imposed on
those surfaces significantly hinders any generalizations that could
be made when comparing models across taxa .
The model with highest support for the accuracy and precision
tests suggests no Falco species will lose habitat (Table 1). Decisions
in modeling that improved the accuracy and precision of our
predictions were: 1. using unbiased data, 2. using a restricted
extent of the region modeled, and 3. using a generous threshold.
An even distribution of occurrences across the model is important
to ensure that the model will not rank conditions of a site as more
suitable because it is better known or has higher number of data
records . A different source of error, which should be
addressed before modeling, is the imprecision of GIS coordinates
in the occurrence data; this error is accentuated when the number
of occurrences available is small. Previous studies have shown that
boosted regression trees and MaxEnt are less influenced by these
types of error, ; however a recent study demonstrated that for
other species, GARP was less influenced, supporting the use of a
variety of modeling techniques as opposed to a single one .
Another important factor was to calibrate the models for regions
with good data availability (i.e., using a restricted extent of the
region modeled, which in our study meant excluding north-
western Russia from input in the models and then projecting to it)
instead of using large extents of suitable conditions for which poor
occurrence data exists [8,23]. However, if the geographic extent of
the region modelled is too small, the breadth of the environmental
conditions used to generate predictions may not capture the full
environmental niche of the species. This might also significantly
influence predictions . We therefore recommend considering
the boundaries of the geographic extent used in models carefully,
and it is likely optimal to use a geographic extent that captures as
much as possible from the environmental niche of the species as
long as there is no geographical bias in the occurrence data.
Choosing a threshold is not a trivial step in species’ distribution
modeling and there is not a ‘‘magic’’ value for thresholding
models, since the continuous probability range may not extend to
0.999. Secondly, the best threshold to use depends on the quality
of the model. Choosing thresholds that maximize the resemblance
of predicted current ranges with published ranges and contrast
with known physiological boundaries of the species may be a more
biologically meaningful method for choosing thresholds [39,44].
However, factors that are generally not included in models, such as
dispersal barriers, competitors and anthropogenic factors, might
constrain species’ distributions . Thresholding to maximize the
resemblance of predicted current ranges with published ranges
might bias the results when projecting to the future, because the
full breath of the environmental niche of the species might not be
captured. Ideally, non-climatic variables that may constrain
species ranges should , and could, to a limited extent ,
be included in models. When this is not feasible, it may be argued
that applying a threshold may substitute or account for constraints
to species’ ranges set by non-climatic variables, to a certain extent.
We found a negative correlation between AUC values and the
accuracy of the predicted current geographic ranges; which
implies that models with lower AUC values produced current
geographic ranges that were more in agreement with published
ranges. A possible cause of this counterintuitive finding might be
that the approach to validate SDMS by comparing generated
predictions with published ranges is invalid, as is further discussed
below. It however might also suggest that AUC values are not
useful for the evaluation of SDMs, or that there might be
fundamental problems within the model (e.g. pseudo-absences
might not closely represent true absences). A thorough investiga-
tion might clarify this. Nevertheless, previous findings show that
AUC values may indeed mislead readers to think that models are
Table 1. Mean effects of decisions made in SDM construction on six Falco species.
Extent of region
probability rangeTrain AUC Test AUC Similarity
BiasedFull 0.1mean0.8470.9130.90542% 107%Four losers
BiasedFull0.4 mean0.847 0.913 0.90537%100% Three losers
se0.042 0.0280.025 11%19%
BiasedRestricted 0.1mean 0.9640.834 0.81266%115% One loser
se 0.0220.038 0.03410%18%
BiasedRestricted0.4 mean 0.9640.8340.81254% 173% Two losers
se0.022 0.0380.034 9%37%
UnbiasedFull 0.1 mean0.904 0.9340.91744%112% Two losers
Unbiased Full 0.4mean 0.9040.934 0.917 37% 86%Five losers
se0.0380.0170.016 11% 25%
Unbiased Restricted 0.1mean0.9590.828 0.772 76% 118%No losers
se 0.0210.038 0.0338% 5%
UnbiasedRestricted0.4mean0.959 0.8280.772 58%142%No losers
se 0.021 0.0380.033 9% 17%
The bold option highlights the best criteria applied to the study. Similarity is expressed in the average between the percentage of the predicted current range that lay
within the published range, and the percentage of the published range that was covered by the predicted current range. The ‘percentage gained area’ and ‘trend’ are
based upon the difference between current and future prediction.
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accurate in predicting the distribution of species [24,47]. Despite
these findings, our literature review showed that a solid majority
(75%) of studies employed only AUC values to assess model
accuracy. Using ROC curves and AUC values could greatly be
improved by adding pseudoabsences or target group absences,
which are locations experts have surveyed for specific species and
reported their absence . However, these data are not available
for large numbers of species and expert knowledge is usually
difficult to implement when studying multiple taxa. Perhaps in
addition to reporting AUC values, models may be further
validated by comparing predicted current ranges with published
ranges  as we have done, assuming reliability of the latter.
Comparing the overlap of current predictions with published
ranges is one of the multiple suboptimal methods available to
compare the performance of models. One of the major problems
with this approach is that it assumes that the published range is
accurate, which may often not be the case. Single species often
have multiple published ranges that may disagree with one
another and provide no information on what presentation is more
accurate. Published ranges are also not available for many species.
Furthermore, the ecological niche of a species may be conservative
with low environmental tolerance, but this does not preclude the
possibility of adaptation to new conditions . The current
distribution of a species may also be constrained or enabled by,
e.g., anthropogenic factors, natural barriers or by biotic interac-
tions with other species . Ideally, predictions of a species’
geographic distribution should be compared with known limits in
fitness and tolerances to the environmental conditions that restrain
its niche  and the biotic conditions, like mutualisms and
predation, which enable/prevent local extinctions of populations
at range limits. However, such information is available for few
species. Besides, whilst published ranges are assumed to show
realized ranges of species, SDMs depict potential ranges; this
fundamental difference might be highly problematic for accurate
validation of predictions. Thus, the approach of comparing the
overlap between the model output and a published range is what
we deem a feasible, indicative (if yet somewhat limited) method for
model evaluation. Other authors concur that the comprehensive
knowledge of experts who published species’ distribution maps is
an acceptable form of confirming species’ distribution models,
especially since a better alternative is unavailable at present .
Predicting the risk for future range contractions/expansions of
species as a result of climate change is one of the most common
aims of SDMs. If results from SDMs are not shown to be immune
to influences from decisions made during model generation, they
should not be used as a sole basis for management recommen-
dations to protect species. Our results also have implications for
prioritization of areas for conservation. Current efforts intend to
Figure 4. Example on how threshold choice for distribution probabilities impact predictions of SDMs of Falco subbuteo. A. Threshold
greater than 0.4, B. Threshold greater than 0.1, C. the estimates of lost, gained and stable (refugial) areas of Falco subbuteo.
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PLOS ONE | www.plosone.org8September 2012 | Volume 7 | Issue 9 | e44402
identify areas of future conservation interest by identifying regions
where the most species are predicted to occur using the geographic
overlap from multiple SDMs. However, we demonstrated how the
overlap of species’ SDMs can range from a maximum to a
minimum level depending on the decisions taken to generate the
models. These results affect decisions and the design of migration
corridors and future viability of nature reserves. Thus, in order to
improve predictions that aid management and planning of nature
reserves, one must carefully determine each step of the SDM
model and ensure that the prediction of the geographic
distribution of a species is based on its biological constraints.
Similarly, if SDMs are used to predict areas vulnerable to invasion
of species, care must be taken to ensure that the SDM reflects the
key environmental and biological variables that may enable or
restrict the distribution of the invasive species.
In conclusion, since the approaches to generating and
evaluating SDMs affect model predictions, which can have far
reaching impacts for policy decisions such as in species’
conservation, we argue that modelers should consistently report
the criteria they used (e.g., geographic extent of climate layers,
thresholding values) and the limitations of the resulting models
(e.g., maximum probability values). Our study does not aim to
provide a ‘recipe’ for constructing SDMs. Rather, we have
demonstrated that decisions made while generating and trans-
forming predictions of species’ distributions affect the quality and
accuracy of the resultant models and their applications. Therefore,
selection of input data and model parameters should be
deliberated carefully so as to optimize model performance and
ecological applicability. Reporting of these parameters will also
allow for greater comparability and applicability among SDMs.
For SDMs to fulfill their role as an important tool in ecology,
authors of scientific papers, as well as journal editors and reviewers
need to raise the standards regarding the information on modeling
procedure and evaluation that needs to be disclosed when
reporting results of SDM efforts.
the Web of Knowledge from 1992–2010.
Number of studies using SDMs as listed in
SDM. A. Layout of the published ecological applications in which
SDMs are used. B. Proportion of SDM publications reporting on
species’ occurrences, bias in the input data, geographical extent,
maximum probability distribution, thresholds used to transform
continuous probability surfaces to binary surfaces, tests of SDM
precision, and tests of SDM accuracy.
The analyses of a subsample of papers using
Definitions of terms we used in species’
Individual studies analyzed.
The authors thank Christer Nilsson, Dolly Jørgensen and two anonymous
reviewers for valuable comments on the manuscript.
Conceived and designed the experiments: GRC ARH. Performed the
experiments: GRC ARH. Analyzed the data: GRC ARH. Contributed
reagents/materials/analysis tools: RJ. Wrote the paper: GRC ARH RJ
LEH. Literature search: LEH.
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