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Barbet-Massin M.,CNRS Science Conservation Center | Thuiller W.,CNRS Alpine Ecology Laboratory | Jiguet F.,CNRS Science Conservation Center
Ecography | Year: 2010

Climate suitability models are used to make projections of species' potential future distribution under climate change. When studying the species richness with such modeling methods, the extent of the study range is of particular importance, especially when the full range of occurrence is not considered for some species, often because of geographical or political limits. Here we examine biases induced by the use of range-restricted occurrence data on predicted changes in species richness and predicted extinction rates, at study area margins. We compared projections of future suitable climate space for 179 bird species breeding in Iberia and North Africa (27 of them breeding only in North Africa though potential colonizers in Europe), using occurrence data from the full Western Palaearctic (WP) species range and from the often-considered European-restricted range. Current and future suitable climatic spaces were modeled using an ensemble forecast technique applied to five general circulation models and three climate scenarios, with eight climatic variables and eight modeling techniques. The use of range-restricted compared to the full WP occurrence data of a species led to an underestimate of its suitable climatic space. The projected changes in species richness across the focus area (Iberia) varied considerably according to the occurrence data we used, with higher local extinction rates with European-restricted data (on average 38 vs 12% for WP data). Modeling results for species currently breeding only in North Africa revealed potential colonization of the Iberian Peninsula (from a climatic point of view), which highlights the necessity to consider species outside the focus area if interested in forecasted changes in species richness. Therefore, the modeling of current and future species richness can lead to misleading conclusions when data from a restricted range of occurrence is used. Consequently, climate suitability models should use occurrence data from the complete distribution range of species, or at least within biogeographical areas. © 2010 The Authors.

Barbet-Massin M.,CNRS Science Conservation Center | Thuiller W.,CNRS Alpine Ecology Laboratory | Jiguet F.,CNRS Science Conservation Center
Global Change Biology | Year: 2012

Many species have already shifted their distributions in response to recent climate change. Here, we aimed at predicting the future breeding distributions of European birds under climate, land-use, and dispersal scenarios. We predicted current and future distributions of 409 species within an ensemble forecast framework using seven species distribution models (SDMs), five climate scenarios and three emission and land-use scenarios. We then compared results from SDMs using climate-only variables, habitat-only variables or both climate and habitat variables. In order to account for a species' dispersal abilities, we used natal dispersal estimates and developed a probabilistic method that produced a dispersal scenario intermediate between the null and full dispersal scenarios generally considered in such studies. We then compared results from all scenarios in terms of future predicted range changes, range shifts, and variations in species richness. Modeling accuracy was better with climate-only variables than with habitat-only variables, and better with both climate and habitat variables. Habitat models predicted smaller range shifts and smaller variations in range size and species richness than climate models. Using both climate and habitat variables, it was predicted that the range of 71% of the species would decrease by 2050, with a 335 km median shift. Predicted variations in species richness showed large decreases in the southern regions of Europe, as well as increases, mainly in Scandinavia and northern Russia. The partial dispersal scenario was significantly different from the full dispersal scenario for 25% of the species, resulting in the local reduction of the future predicted species richness of up to 10%. We concluded that the breeding range of most European birds will decrease in spite of dispersal abilities close to a full dispersal hypothesis, and that given the contrasted predictions obtained when modeling climate change only and land-use change only, both scenarios must be taken into consideration. © 2011 Blackwell Publishing Ltd.

Thebault E.,Imperial College London | Thebault E.,Wageningen University | Fontaine C.,Imperial College London | Fontaine C.,CNRS Science Conservation Center
Science | Year: 2010

Research on the relationship between the architecture of ecological networks and community stability has mainly focused on one type of interaction at a time, making difficult any comparison between different network types. We used a theoretical approach to show that the network architecture favoring stability fundamentally differs between trophic and mutualistic networks. A highly connected and nested architecture promotes community stability in mutualistic networks, whereas the stability of trophic networks is enhanced in compartmented and weakly connected architectures. These theoretical predictions are supported by a meta-analysis on the architecture of a large series of real pollination (mutualistic) and herbivory (trophic) networks. We conclude that strong variations in the stability of architectural patterns constrain ecological networks toward different architectures, depending on the type of interaction.

Pavoine S.,University of Oxford | Pavoine S.,CNRS Science Conservation Center | Bonsall M.B.,University of Oxford | Bonsall M.B.,St Peters College
Biological Reviews | Year: 2011

One of the oldest challenges in ecology is to understand the processes that underpin the composition of communities. Historically, an obvious way in which to describe community compositions has been diversity in terms of the number and abundances of species. However, the failure to reject contradictory models has led to communities now being characterized by trait and phylogenetic diversities. Our objective here is to demonstrate how species, trait and phylogenetic diversity can be combined together from large to local spatial scales to reveal the historical, deterministic and stochastic processes that impact the compositions of local communities. Research in this area has recently been advanced by the development of mathematical measures that incorporate trait dissimilarities and phylogenetic relatedness between species. However, measures of trait diversity have been developed independently of phylogenetic measures and conversely most of the phylogenetic diversity measures have been developed independently of trait diversity measures. This has led to semantic confusions particularly when classical ecological and evolutionary approaches are integrated so closely together. Consequently, we propose a unified semantic framework and demonstrate the importance of the links among species, phylogenetic and trait diversity indices. Furthermore, species, trait and phylogenetic diversity indices differ in the ways they can be used across different spatial scales. The connections between large-scale, regional and local processes allow the consideration of historical factors in addition to local ecological deterministic or stochastic processes. Phylogenetic and trait diversity have been used in large-scale analyses to determine how historical and/or environmental factors affect both the formation of species assemblages and patterns in species richness across latitude or elevation gradients. Both phylogenetic and trait diversity have been used at different spatial scales to identify the relative impacts of ecological deterministic processes such as environmental filtering and limiting similarity from alternative processes such as random speciation and extinction, random dispersal and ecological drift. Measures of phylogenetic diversity combine phenotypic and genetic diversity and have the potential to reveal both the ecological and historical factors that impact local communities. Consequently, we demonstrate that, when used in a comparative way, species, trait and phylogenetic structures have the potential to reveal essential details that might act simultaneously in the assembly of species communities. We highlight potential directions for future research. These might include how variation in trait and phylogenetic diversity alters with spatial distances, the role of trait and phylogenetic diversity in global-scale gradients, the connections between traits and phylogeny, the importance of trait rarity and independent evolutionary history in community assembly, the loss of trait and phylogenetic diversity due to human impacts, and the mathematical developments of biodiversity indices including within-species variations. © 2010 The Authors. Biological Reviews © 2010 Cambridge Philosophical Society.

Barbet-Massin M.,CNRS Science Conservation Center | Jiguet F.,CNRS Science Conservation Center
PLoS ONE | Year: 2011

The Corsican Nuthatch (Sitta whiteheadi) is red-listed as vulnerable to extinction by the IUCN because of its endemism, reduced population size, and recent decline. A further cause is the fragmentation and loss of its spatially-restricted favourite habitat, the Corsican pine (Pinus nigra laricio) forest. In this study, we aimed at estimating the potential impact of climate change on the distribution of the Corsican Nuthatch using species distribution models. Because this species has a strong trophic association with the Corsican and Maritime pines (P. nigra laricio and P. pinaster), we first modelled the current and future potential distribution of both pine species in order to use them as habitat variables when modelling the nuthatch distribution. However, the Corsican pine has suffered large distribution losses in the past centuries due to the development of anthropogenic activities, and is now restricted to mountainous woodland. As a consequence, its realized niche is likely significantly smaller than its fundamental niche, so that a projection of the current distribution under future climatic conditions would produce misleading results. To obtain a predicted pine distribution at closest to the geographic projection of the fundamental niche, we used available information on the current pine distribution associated to information on the persistence of isolated natural pine coppices. While common thresholds (maximizing the sum of sensitivity and specificity) predicted a potential large loss of the Corsican Nuthatch distribution by 2100, the use of more appropriate thresholds aiming at getting closer to the fundamental distribution of the Corsican pine predicted that 98% of the current presence points should remain potentially suitable for the nuthatch and its range could be 10% larger in the future. The habitat of the endemic Corsican Nuthatch is therefore more likely threatened by an increasing frequency and intensity of wildfires or anthropogenic activities than by climate change. © 2011 Barbet-Massin, Jiguet.

Fontaine B.,CNRS Science Conservation Center | Perrard A.,French Natural History Museum | Bouchet P.,French Natural History Museum
Current Biology | Year: 2012

A large part of biodiversity is still unknown, and it is estimated that, at the current pace, it will take several centuries to describe all species living on Earth. In the context of the ongoing 'sixth extinction', accelerating the completion of the inventory of living biota is an issue that reaches far beyond the taxonomic community. However, the factors that influence the accretion of known species remain poorly understood. Here, we study how long it takes from the first collection of a specimen of a new species to its formal description and naming in the scientific literature [1,2] - a period we refer to as a species' 'shelf life'. Based on a random set of species described in 2007 across all kingdoms of life, we determine that the average shelf life between discovery and description is 21 years. The length of the shelf life is impacted by biological, social and geopolitical biases. © 2012 Elsevier Ltd.

Pavoine S.,CNRS Science Conservation Center | Pavoine S.,University of Oxford
Methods in Ecology and Evolution | Year: 2012

1. Quadratic entropy (QE) was developed as a fundamental function for measuring the diversity within a collection, such as a community, or population, from indices of abundance and distance among categories, such as species or alleles. Based on a literature review in the fields of genetics, ecology and statistics and new developments, I analyse the potential of this function for biodiversity studies. 2.Quadratic entropy was established as a generalisation of well-known diversity indices, and has been widely used in molecular ecology and genetics research. It is now integrated within more general frameworks for analysing functional and phylogenetic diversity in ecology. 3.Quadratic entropy can be maximised by removing categories, and several collections can share the maximum diversity, even with highly distinct compositions. Clarifying these statements, I identify all potential indices of the abundance of the categories that maximise QE. 4.By quantifying changes in diversity when mixing collections together, QE can measure differences among collections. Here, I provide a geometric interpretation of these differences that demonstrates their relevance as classical geometric distances. 5.A critical aspect of these distances is obtained if QE is strictly concave; that is, diversity always strictly increases by mixing distinct collections together. More generally, QE can be used to evaluate the effects of various factors on diversity in a framework designated ANOQE (analysis of QE). Generalising ANOVA (analysis of variance), ANOQE uses QE to measure distances between centroids. 6.Importantly, QE is estimated from sampled data and thus requires estimators. Based on these estimators, tests have been developed to compare levels of diversity. Tests of factor effects are evaluated by parametric, jackknife, bootstrap and permutational approaches. However, the procedures associated with these tests that have been suggested thus far only treat a few factors. 7.There is an urgent need for the development of such approaches in biology to deal with experimental factors, observed population and community structure, and different spatial and temporal scales. Together, QE and the ANOQE procedure are likely to have a critical impact on all scientific disciplines interested in any form of diversity. © 2012 The Author. Methods in Ecology and Evolution © 2012 British Ecological Society.

Elias M.,CNRS Systematics, Biodiversity and Evolution Institute | Fontaine C.,CNRS Science Conservation Center | Frank Van Veen F.J.,University of Exeter
Current Biology | Year: 2013

Uncovering the processes that shape the architecture of interaction networks is a major challenge in ecology. Studies have consistently revealed that more closely related taxa tend to show greater overlap in interaction partners, fuelling the idea that interactions are phylogenetically conserved [1-8]. However, local ecological processes such as exploitative or apparent competition (indirect interactions) might instead cause a decrease in overlap in interacting partners. Because of the taxonomic and geographic coarseness of existing studies [2-5, 7], the structuring effect of such processes has been overlooked. Here, we assess the relative importance of phylogeny and ecological processes in a local, highly resolved, four-level antagonistic network. Across all network levels we consistently find that phylogenetic relatedness among resource species is correlated with consumer overlap but that phylogenetic relatedness among consumer species is not or negatively correlated with resource overlap. This pervasive pattern indicates that the antagonistic network has been shaped by both phylogeny on resource range and by exploitative competition limiting resource overlap among closely related consumer species. Intriguingly, the strength of phylogenetic signal varies in a consistent way across the network levels. We discuss the generality of our findings and their implications in a changing world. © 2013 Elsevier Ltd.

Robert A.,CNRS Science Conservation Center
BMC Evolutionary Biology | Year: 2011

Background: While the ultimate causes of most species extinctions are environmental, environmental constraints have various secondary consequences on evolutionary and ecological processes. The roles of demographic, genetic mechanisms and their interactions in limiting the viabilities of species or populations have stirred much debate and remain difficult to evaluate in the absence of demography-genetics conceptual and technical framework. Here, I computed projected times to metapopulation extinction using (1) a model focusing on the effects of species properties, habitat quality, quantity and temporal variability on the time to demographic extinction; (2) a genetic model focusing on the dynamics of the drift and inbreeding loads under the same species and habitat constraints; (3) a demo-genetic model accounting for demographic-genetic processes and feedbacks. Results: Results indicate that a given population may have a high demographic, but low genetic viability or vice versa; and whether genetic or demographic aspects will be the most limiting to overall viability depends on the constraints faced by the species (e.g., reduction of habitat quantity or quality). As a consequence, depending on metapopulation or species characteristics, incorporating genetic considerations to demographically-based viability assessments may either moderately or severely reduce the persistence time. On the other hand, purely genetically-based estimates of species viability may either underestimate (by neglecting demo-genetic interactions) or overestimate (by neglecting the demographic resilience) true viability. Conclusion: Unbiased assessments of the viabilities of species may only be obtained by identifying and considering the most limiting processes (i.e., demography or genetics), or, preferentially, by integrating them. © 2011 Robert; licensee BioMed Central Ltd.

Teplitsky C.,CNRS Science Conservation Center | Millien V.,McGill University
Evolutionary Applications | Year: 2014

Climate change is expected to induce many ecological and evolutionary changes. Among these is the hypothesis that climate warming will cause a reduction in body size. This hypothesis stems from Bergmann's rule, a trend whereby species exhibit a smaller body size in warmer climates, and larger body size under colder conditions in endotherms. The mechanisms behind this rule are still debated, and it is not clear whether Bergmann's rule can be extended to predict the effects of climate change through time. We reviewed the primary literature for evidence (i) of a decrease in body size in response to climate warming, (ii) that changing body size is an adaptive response and (iii) that these responses are evolutionary or plastic. We found weak evidence for changes in body size through time as predicted by Bergmann's rule. Only three studies investigated the adaptive nature of these size decreases. Of these, none reported evidence of selection for smaller size or of a genetic basis for the size change, suggesting that size decreases could be due to nonadaptive plasticity in response to changing environmental conditions. More studies are needed before firm conclusions can be drawn about the underlying causes of these changes in body size in response to a warming climate. © 2013 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.

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