Summary1. Species distribution models are increasingly used to address questions in conservation biology, ecology and evolution. The most effective species distribution models require data on both species presence and the available environmental conditions (known as background or pseudo-absence data) in the area. However, there is still no consensus on how and where to sample these pseudoabsences and how many. 2. In this study, we conducted a comprehensive comparative analysis based on simple simulated species distributions to propose guidelines on how, where and how many pseudo-absences should be generated to build reliable species distribution models. Depending on the quantity and quality of the initial presence data (unbiased vs. climatically or spatially biased), we assessed the relative effect of the method for selecting pseudo-absences (random vs. environmentally or spatially stratified) and their number on the predictive accuracy of seven common modelling techniques (regression, classification and machine-learning techniques). 3. When using regression techniques, the method used to select pseudo-absences had the greatest impact on the model's predictive accuracy. Randomly selected pseudo-absences yielded the most reliable distribution models. Models fitted with a large number of pseudo-absences but equally weighted to the presences (i.e. the weighted sum of presence equals the weighted sum of pseudoabsence) produced the most accurate predicted distributions. For classification and machine-learning techniques, the number of pseudo-absences had the greatest impact on model accuracy, and averaging several runs with fewer pseudo-absences than for regression techniques yielded the most predictive models. 4. Overall, we recommend the use of a large number (e.g. 10 000) of pseudo-absences with equal weighting for presences and absences when using regression techniques (e.g. generalised linear model and generalised additive model); averaging several runs (e.g. 10) with fewer pseudo-absences (e.g. 100) with equal weighting for presences and absences with multiple adaptive regression splines and discriminant analyses; and using the same number of pseudo-absences as available presences (averaging several runs if few pseudo-absences) for classification techniques such as boosted regression trees, classification trees and random forest. In addition, we recommend the random selection of pseudo-absences when using regression techniques and the random selection of geographically and environmentally stratified pseudo-absences when using classification and machine-learning techniques.

Functional and phylogenetic diversity are increasingly quantified in various fields of ecology and conservation biology. The need to maintain diversity turnover among sites, so-called beta-diversity, has also been raised in theoretical and applied ecology. In this study, we propose the first comprehensive framework for the large-scale mapping of taxonomic, phylogenetic and functional diversity and of their respective turnover. Using high-resolution data on the spatial distribution and abundance of birds at a country scale, we disentangled areas of mismatches and congruencies between biodiversity components. We further revealed unequal representation of each component in protected areas: functional diversity was significantly under-represented whereas taxonomic diversity was significantly over-represented in protected areas. Our results challenge the use of any one diversity component as a surrogate for other components and stress the need to adopt an integrative approach to biodiversity conservation.

Climate changes have profound effects on the distribution of numerous plant and animal species 1-3 . However, whether and how different taxonomic groups are able to track climate changes at large spatial scales is still unclear. Here, we measure and compare the climatic debt accumulated by bird and butterfly communities at a European scale over two decades (1990)(1991)(1992)(1993)(1994)(1995)(1996)(1997)(1998)(1999)(2000)(2001)(2002)(2003)(2004)(2005)(2006)(2007)(2008). We quantified the yearly change in community composition in response to climate change for 9,490 bird and 2,130 butterfly communities distributed across Europe 4 . We show that changes in community composition are rapid but different between birds and butterflies and equivalent to a 37 and 114 km northward shift in bird and butterfly communities, respectively. We further found that, during the same period, the northward shift in temperature in Europe was even faster, so that the climatic debts of birds and butterflies correspond to a 212 and 135 km lag behind climate. Our results indicate both that birds and butterflies do not keep up with temperature increase and the accumulation of different climatic debts for these groups at national and continental scales.Species are not equally at risk when facing climate change. Several species-specific attributes have been identified as increasing species' vulnerability to climate change, including diets, migratory strategy, main habitat types and ecological specialization [5][6][7] . Moreover, although phenotypic plasticity may enable some species to respond rapidly and effectively to climate change 8,9 , others may suffer from the induced spatial mismatch and temporal mistiming with their resources 10,11 . For instance, species such as great tits and flycatchers have been shown to become desynchronized with their main food supply during the nesting season 12 .However, beyond individual species' fates, climate change should also affect species interactions and the structure of species assemblages within and across different taxonomic groups over large spatial scales [13][14][15] . For instance, ectotherms should be more directly affected by climate warming and taxonomic groups with short generation time should favour faster evolutionary responses to selective pressures induced by climate changes 13 . Yet, whether different taxonomic groups are tracking climate change at the same rate over large areas is still unclear, and methods to routinely assess the mismatch between temperature increases and biodiversity responses at different spatial scales are still missing 16 .Here, we used extensive monitoring data of birds and butterflies distributed across Europe to assess whether, regardless of their species-specific characteristics, organisms belonging to a given group are responding more quickly or more slowly than organisms belonging to another group over large areas. We characterized bird and butterfly communities in 9,490 and 2,130 sample sites respectively by their community temperature index (CTI) for ea...

Range shifts of many species are now documented as a response to global warming. But whether these observed changes are occurring fast enough remains uncertain and hardly quantifiable. Here, we developed a simple framework to measure change in community composition in response to climate warming. This framework is based on a community temperature index (CTI ) that directly reflects, for a given species assemblage, the balance between low-and high-temperature dwelling species. Using data from the French breeding bird survey, we first found a strong increase in CTI over the last two decades revealing that birds are rapidly tracking climate warming. This increase corresponds to a 91 km northward shift in bird community composition, which is much higher than previous estimates based on changes in species range edges. During the same period, temperature increase corresponds to a 273 km northward shift in temperature. Change in community composition was thus insufficient to keep up with temperature increase: birds are lagging approximately 182 km behind climate warming. Our method is applicable to any taxa with large-scale survey data, using either abundance or occurrence data. This approach can be further used to test whether different delays are found across groups or in different land-use contexts.

Jonathan Rolland and colleagues show that the gradient of increased mammalian diversity towards the tropics is driven by both faster speciation and reduced extinction.

Each species generally has a close relationship with one or more habitats and can therefore be classified as either specialist or generalist. We studied whether specialist and generalist species are spatially distributed independently of each other. Repeating the analysis for 100 of the most frequent terrestrial bird species recorded over the 10 000 sampled sites of the French Breeding Bird survey, we found that specialists were more abundant if the rest of the community was specialized, and that the inverse was also true. This pattern was far subtler than just a simple dichotomy: most species actually presented a maximum abundance at a value of community specialization similar to their own level of specialization. Bird communities appear very well defined along a specialist-generalist gradient. We believe this pattern becomes more apparent with habitat degradation. The consequences on both ecological services and community resilience may well be considerable.

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Aim Worldwide, functional homogenization is now considered to be one of the most prominent forms of biotic impoverishment induced by current global changes. Yet this process has hardly been quantified on a large scale through simple indices, and the connection between landscape disturbance and functional homogenization has hardly been established. Here we test whether changes in land use and landscape fragmentation are associated with functional homogenization of bird communities at a national scale. Location France.Methods We estimated functional homogenization of a community as the average specialization of the species present in that community. We studied the spatial variation of this community specialization index (CSI) using 1028 replicates from the French Breeding Bird Survey along spatial gradients of landscape fragmentation and recent landscape disturbance, measured independently, and accounting for spatial autocorrelation. ResultsThe CSI was very sensitive to both measures of environmental degradation: on average, 23% of the difference in the CSI values between two sample sites was attributed to the difference in fragmentation and the disturbance between sites. This negative correlation between CSI and sources of landscape degradation was consistent over various habitats and biogeographical zones. Main conclusionsWe demonstrate that the functional homogenization of bird communities is strongly positively correlated to landscape disturbance and fragmentation. We suggest that the CSI is particularly effective for measuring functional homogenization on both local and global scales for any sort of organism and with abundance or presence-absence data.