Sébastien Lavergne

Consequences of climate change on the tree of life in Europe

Many species are projected to become vulnerable to twenty-first-century climate changes, with consequent effects on the tree of life. If losses were not randomly distributed across the tree of life, climate change could lead to a disproportionate loss of evolutionary history. Here we estimate the consequences of climate change on the phylogenetic diversities of plant, bird and mammal assemblages across Europe. Using a consensus across ensembles of forecasts for 2020, 2050 and 2080 and high-resolution phylogenetic trees, we show that species vulnerability to climate change clusters weakly across phylogenies. Such phylogenetic signal in species vulnerabilities does not lead to higher loss of evolutionary history than expected with a model of random extinctions. This is because vulnerable species have neither fewer nor closer relatives than the remaining clades. Reductions in phylogenetic diversity will be greater in southern Europe, and gains are expected in regions of high latitude or altitude. However, losses will not be offset by gains and the tree of life faces a trend towards homogenization across the continent.

Rare species support vulnerable functions in high-diversity ecosystems

The most unusual, and thus irreplaceable, functions performed by species in three different species-rich ecosystems are fulfilled by only the rare species in these ecosystems.

Ecophylogenetics: advances and perspectives

Ecophylogenetics can be viewed as an emerging fusion of ecology, biogeography and macroevolution. This new and fast‐growing field is promoting the incorporation of evolution and historical contingencies into the ecological research agenda through the widespread use of phylogenetic data. Including phylogeny into ecological thinking represents an opportunity for biologists from different fields to collaborate and has provided promising avenues of research in both theoretical and empirical ecology, towards a better understanding of the assembly of communities, the functioning of ecosystems and their responses to environmental changes. The time is ripe to assess critically the extent to which the integration of phylogeny into these different fields of ecology has delivered on its promise. Here we review how phylogenetic information has been used to identify better the key components of species interactions with their biotic and abiotic environments, to determine the relationships between diversity and ecosystem functioning and ultimately to establish good management practices to protect overall biodiversity in the face of global change. We evaluate the relevance of information provided by phylogenies to ecologists, highlighting current potential weaknesses and needs for future developments. We suggest that despite the strong progress that has been made, a consistent unified framework is still missing to link local ecological dynamics to macroevolution. This is a necessary step in order to interpret observed phylogenetic patterns in a wider ecological context. Beyond the fundamental question of how evolutionary history contributes to shape communities, ecophylogenetics will help ecology to become a better integrative and predictive science.

Competitive interactions between forest trees are driven by species' trait hierarchy, not phylogenetic or functional similarity: implications for forest community assembly.

The relative importance of competition vs. environmental filtering in the assembly of communities is commonly inferred from their functional and phylogenetic structure, on the grounds that similar species compete most strongly for resources and are therefore less likely to coexist locally. This approach ignores the possibility that competitive effects can be determined by relative positions of species on a hierarchy of competitive ability. Using growth data, we estimated 275 interaction coefficients between tree species in the French mountains. We show that interaction strengths are mainly driven by trait hierarchy and not by functional or phylogenetic similarity. On the basis of this result, we thus propose that functional and phylogenetic convergence in local tree community might be due to competition-sorting species with different competitive abilities and not only environmental filtering as commonly assumed. We then show a functional and phylogenetic convergence of forest structure with increasing plot age, which supports this view.

A road map for integrating eco-evolutionary processes into biodiversity models

The demand for projections of the future distribution of biodiversity has triggered an upsurge in modelling at the crossroads between ecology and evolution. Despite the enthusiasm around these so-called biodiversity models, most approaches are still criticised for not integrating key processes known to shape species ranges and community structure. Developing an integrative modelling framework for biodiversity distribution promises to improve the reliability of predictions and to give a better understanding of the eco-evolutionary dynamics of species and communities under changing environments. In this article, we briefly review some eco-evolutionary processes and interplays among them, which are essential to provide reliable projections of species distributions and community structure. We identify gaps in theory, quantitative knowledge and data availability hampering the development of an integrated modelling framework. We argue that model development relying on a strong theoretical foundation is essential to inspire new models, manage complexity and maintain tractability. We support our argument with an example of a novel integrated model for species distribution modelling, derived from metapopulation theory, which accounts for abiotic constraints, dispersal, biotic interactions and evolution under changing environmental conditions. We hope such a perspective will motivate exciting and novel research, and challenge others to improve on our proposed approach.

Functional species pool framework to test for biotic effects on community assembly

Functional trait differences among species are increasingly used to infer the effects of biotic and abiotic processes on species coexistence. Commonly, the trait diversity observed within communities is compared to patterns simulated in randomly generated communities based on sampling within a region. The resulting patterns of trait convergence and divergence are assumed to reveal abiotic and biotic processes, respectively. However, biotic processes such as competition can produce both trait divergence and convergence, through either excluding similar species (niche differences, divergence) or excluding dissimilar species (weaker competitor exclusion, convergence). Hence, separating biotic and abiotic processes that can produce identical patterns of trait diversity, or even patterns that neutralize each other, is not feasible with previous methods. We propose an operational framework in which the functional trait dissimilarity within communities (FDcomm) is compared to the corresponding trait dissimilarity expected from the species pool (i.e., functional species pool diversity, FDpool). FDpool includes the set of potential species for a site delimited by the operating environmental and dispersal limitation filters. By applying these filters, the resulting pattern of trait diversity is consistent with biotic processes, i.e., trait divergence (FDcomm > FDpool) indicates niche differentiation, while trait convergence (FDcomm < FDpool) indicates weaker competitor exclusion. To illustrate this framework, with its potential application and constraints, we analyzed both simulated and field data. The functional species pool framework more consistently detected the simulated trait diversity patterns than previous approaches. In the field, using data from plant communities of typical Northern European habitats in Estonia, we found that both niche-based and weaker competitor exclusion influenced community assembly, depending on the traits and community considered. In both simulated and field data, we demonstrated that only by estimating the species pool of a site is it possible to differentiate the patterns of trait dissimilarity produced by operating biotic processes. The framework, which can be applied with both functional and phylogenetic diversity, enables a reinterpretation of community assembly processes. Solving the challenge of defining an appropriate reference species pool for a site can provide a better understanding of community assembly.

Limited evolutionary rescue of locally adapted populations facing climate change

Dispersal is a key determinant of a populations evolutionary potential. It facilitates the propagation of beneficial alleles throughout the distributional range of spatially outspread populations and increases the speed of adaptation. However, when habitat is heterogeneous and individuals are locally adapted, dispersal may, at the same time, reduce fitness through increasing maladaptation. Here, we use a spatially explicit, allelic simulation model to quantify how these equivocal effects of dispersal affect a populations evolutionary response to changing climate. Individuals carry a diploid set of chromosomes, with alleles coding for adaptation to non-climatic environmental conditions and climatic conditions, respectively. Our model results demonstrate that the interplay between gene flow and habitat heterogeneity may decrease effective dispersal and population size to such an extent that substantially reduces the likelihood of evolutionary rescue. Importantly, even when evolutionary rescue saves a population from extinction, its spatial range following climate change may be strongly narrowed, that is, the rescue is only partial. These findings emphasize that neglecting the impact of non-climatic, local adaptation might lead to a considerable overestimation of a populations evolvability under rapid environmental change.

From barcodes to genomes: extending the concept of DNA barcoding

DNA barcoding has had a major impact on biodiversity science. The elegant simplicity of establishing massive scale databases for a few barcode loci is continuing to change our understanding of species diversity patterns, and continues to enhance human abilities to distinguish among species. Capitalizing on the developments of next generation sequencing technologies and decreasing costs of genome sequencing, there is now the opportunity for the DNA barcoding concept to be extended to new kinds of genomic data. We illustrate the benefits and capacity to do this, and also note the constraints and barriers to overcome before it is truly scalable. We advocate a twin track approach: (i) continuation and acceleration of global efforts to build the DNA barcode reference library of life on earth using standard DNA barcodes and (ii) active development and application of extended DNA barcodes using genome skimming to augment the standard barcoding approach.

Assessing rapid evolution in a changing environment.

Climate change poses a serious threat to species persistence. Effective modelling of evolutionary responses to rapid climate change is therefore essential. In this review we examine recent advances in phylogenetic comparative methods, techniques normally used to study adaptation over long periods, which allow them to be applied to the study of adaptation over shorter time scales. This increased applicability is largely due to the emergence of more flexible models of character evolution and the parallel development of molecular technologies that can be used to assess adaptive variation at loci scattered across the genome. The merging of phylogenetic and population genetic approaches to the study of adaptation has significant potential to advance our understanding of rapid responses to environmental change.

Using phylogenies in conservation: new perspectives.

The 2011 meeting of the European Ecological Federation took place in Ávila, Spain, from 26th September to 29th September. The French Ecological Society (SFE) and the Foundation for Research on Biodiversity (FRB) sponsored a session entitled ‘Evolutionary history, ecosystem function and conservation biology: new perspectives’. We report on the main insights obtained from this symposium.