[Show abstract][Hide abstract] ABSTRACT: Whether the success of alien species can be explained by their functional or phylogenetic characteristics remains unresolved because of data limitations, scale issues and weak quantifications of success. Using permanent grasslands across France (50 000 vegetation plots, 2000 species, 130 aliens) and building on the Rabinowitz's classification to quantify spread, we showed that phylogenetic and functional similarities to natives were the most important correlates of invasion success compared to intrinsic functional characteristics and introduction history. Results contrasted between spatial scales and components of invasion success. Widespread and common aliens were similar to co-occurring natives at coarse scales (indicating environmental filtering), but dissimilar at finer scales (indicating local competition). In contrast, regionally widespread but locally rare aliens showed patterns of competitive exclusion already at coarse scale. Quantifying trait differences between aliens and natives and distinguishing the components of invasion success improved our ability to understand and potentially predict alien spread at multiple scales.
[Show abstract][Hide abstract] ABSTRACT: Phylogenetically related species share a common evolutionary history and may therefore have similar traits. In terms of interaction networks, where traits are a major determinant, related species should therefore interact with other species which are also related. However, this prediction is challenged by current evidence that there is a weak, albeit significant, phylogenetic signal in species' taxonomic niche, i.e., the identity of interacting species. We studied mutualistic and antagonistic plant-insect interaction networks in species-rich alpine meadows and show that there is instead a very strong phylogenetic signal in species' functional niches-i.e., the mean functional traits of their interactors. This pattern emerges because related species tend to interact with species bearing certain traits that allow biotic interactions (pollination, herbivory) but not necessarily with species from all the same evolutionary lineages. Those traits define a set of potential interactors and show clear patterns of phylogenetic clustering on several portions of plants and insect phylogenies. Thus, this emerging pattern of low phylogenetic signal in taxonomic niches but high phylogenetic signal in functional niches may be driven by the interplay between functional trait convergence across plants' and insects' phylogenies and random sampling of the potential interactors.
[Show abstract][Hide abstract] ABSTRACT: In accordance with their mission and as part of their long-term observation work, Ecrins National Park (NP) is making important contributions to the study and monitoring of phenomena related to climate change. Its work takes information collected at different meteorological stations and supplements it with analyses of vegetation changes through aerial and satellite images, measuring and monitoring of glaciers, and interdisciplinary programmes focused on high-altitude lakes, mountain pastures and indicator species. Through its mission and long-term observations, Ecrins NP (http://www.ecrinsparcnational. fr/) contributes to the environmental surveillance of many ecosystems. Working within many different networks and in partnership with various research teams, the park participates in the development of a better understanding of the important changes taking place.
[Show abstract][Hide abstract] ABSTRACT: Different assembly processes drive the spatial structure of meta-communities (β- diversity). Recently, functional and phylogenetic diversities have been suggested as indicators of these assembly processes. Assuming that diversity is a good proxy for niche overlap, high β-diversity along environmental gradients should be the result of environmental filtering while low β- diversity should stem from competitive interactions. So far studies trying to disentangle the relative importance of these assembly processes provided mixed results. One reason for this may be that these studies often rely on a single measure of diversity and thus implicitly make a choice on how they account for species relative abundances and how species similarities are captured by functional traits or phylogeny.
Here, we tested the effect of gradually scaling the importance of dominance (the weight given to dominant vs. rare species) and species similarity (the weight given to small vs. large similarities) on resulting β-diversity patterns of an alpine plant meta-community. To this end, we combined recent extensions of the Hill numbers framework with Pagel’s phylogenetic tree transformation approach. We included functional (based on the Leaf-Height-Seed spectrum) and phylogenetic facets of β-diversity in our analysis and explicitly accounted for effects of environmental and spatial covariates.
We found that functional β-diversity was high when the same weight was given to dominant vs. rare species and to large vs. small species’ similarities. In contrast, phylogenetic β-diversity was low when greater weight was given to dominant species and small species' similarities. Those results suggested that different environments along the gradients filtered different species according to their functional traits, while, the same competitive lineages dominated communities across the gradients.
Our results highlight that functional vs. phylogenetic facets, presence-absence vs. abundance structure and different weights of species’ dissimilarity provide complementary and important information on the drivers of meta-community structure. By utilizing the full extent of information provided by the flexible frameworks of Hill numbers and Pagel's tree transformation, we propose a new approach to disentangle the patterns resulting from different assembly processes.
[Show abstract][Hide abstract] ABSTRACT: Understanding the factors that shape adaptive genetic variation across species niches has become of paramount importance in evolutionary ecology, especially to understand how adaptation to changing climate affects the geographic range of species. The distribution of adaptive alleles in the ecological niche is determined by the emergence of novel mutations, their fitness consequences and gene flow that connects populations across species niches. Striking demographical differences and source-sink dynamics of populations between the centre and the margin of the niche can play a major role in the emergence and spread of adaptive alleles. Although some theoretical predictions have long been proposed, the origin and distribution of adaptive alleles within species niches remain untested.In this paper, we propose and discuss a novel empirical approach that combines landscape genetics with species niche modelling, to test whether alleles that confer local adaptation are more likely to occur in either marginal or central populations of species niches. We illustrate this new approach by using a published data set of 21 alpine plant species genotyped with a total of 2483 amplified fragment length polymorphisms (AFLP), distributed over more than 1733 sampling sites across the Alps. Based on the assumption that alleles that were statistically associated with environmental variables were adaptive, we found that adaptive alleles in the margin of a species niche were also present in the niche centre, which suggests that adaptation originates in the niche centre.These findings corroborate models of species range evolution, in which the centre of the niche contributes to the emergence of novel adaptive alleles, which diffuse towards niche margins and facilitate niche and range expansion through subsequent local adaptation. Although these results need to be confirmed via fitness measurements in natural populations and functionally characterised genetic sequences, this study provides a first step towards understanding how adaptive genetic variation emerges and shapes species niches and geographic ranges along environmental gradients.
Full-text · Article · Aug 2015 · Perspectives in Plant Ecology Evolution and Systematics
[Show abstract][Hide abstract] ABSTRACT: 1. The prevalence of phylogenetic niche conservatism (PNC) in nature is still a conflicting issue. Disagreement arises from confusion over its precise definition and the variety of approaches to measure its prevalence. Recent work highlighted that common measures of PNC strongly depend on the assumptions of the underlying model of niche evolution. However, this warning has not been well recognized in the applied literature and questionable approaches are still frequently applied.
2. The aim of this paper is to draw attention to the assumptions underlying commonly applied simple measures of PNC. We used a series of simulations to illustrate how misleading results can be if assumptions of niche evolution are violated, that the violation of assumptions is a common phenomenon and that testing assumptions requires in-depth pre-test.
3. We conclude that the seemingly simple measures of PNC, such as phylogenetic signal and evolutionary rate, are not so easy to apply if one accounts for the necessity to test model assumptions. In addition, these measures can be difficult to interpret. The common assumption that strong phylogenetic signal indicates PNC will be often invalid. In addition, the interpretation of some measures, e.g. the conclusion that evolutionary rate is slow enough to indicate PNC, requires a comparison with another clade, another trait or well-developed null model assumptions and thus additional data.
4. We suggest that studies investigating PNC should always compare alternative evolutionary models, and that model comparisons should in particular include flexible niche evolution models such as multiple-optima OU models, although these are computational intensive. These models are directly inherited from the concept of macro-evolutionary adaptive landscape, and can indicate PNC either by relative few peak shifts or by narrow peaks in the adaptive landscape. A test of PNC thus requires comparing these parameters of the macroevolutionary landscape between clades or time periods.
5. The general prevalence of PNC in nature should be evaluated only based on studies keeping up to the high standards of communicating the used definition of PNC, testing the assumptions made in the modelling approaches and including newly developed models in a model comparison approach.
Full-text · Article · May 2015 · Functional Ecology
[Show abstract][Hide abstract] ABSTRACT: Protected areas (PAs) are pivotal tools for biodiversity conservation on the Earth. Europe has had an extensive protection system since Natura 2000 areas were created in parallel with traditional parks and reserves. However, the extent to which this system covers not only taxonomic diversity but also other biodiversity facets, such as evolutionary history and functional diversity, has never been evaluated. Using high-resolution distribution data of all European tetrapods together with dated molecular phylogenies and detailed trait information, we first tested whether the existing European protection system effectively covers all species and in particular, those with the highest evolutionary or functional distinctiveness. We then tested the ability of PAs to protect the entire tetrapod phylogenetic and functional trees of life by mapping species' target achievements along the internal branches of these two trees. We found that the current system is adequately representative in terms of the evolutionary history of amphibians while it fails for the rest. However, the most functionally distinct species were better represented than they would be under random conservation efforts. These results imply better protection of the tetrapod functional tree of life, which could help to ensure long-term functioning of the ecosystem, potentially at the expense of conserving evolutionary history.
Full-text · Article · Feb 2015 · Philosophical Transactions of The Royal Society B Biological Sciences
[Show abstract][Hide abstract] ABSTRACT: Despite considerable efforts devoted to investigate the community assembly processes driving plant invasions, few general conclusions have been drawn so far. Three main processes, generally acting as successive filters, are thought to be of prime importance. The invader has to disperse (1st filter) into a suitable environment (2nd filter) and succeed in establishing in recipient communities through competitive interactions (3rd filter) using two strategies: competition avoidance by the use of different resources (resource opportunity), or competitive exclusion of native species. Surprisingly, despite the general consensus on the importance of investigating these three processes and their interplay, they are usually studied independently. Here we aim to analyse these three filters together, by including them all: abiotic environment, dispersal and biotic interactions, into models of invasive species distributions. We first propose a suite of indices (based on species functional dissimilarities) supposed to reflect the two competitive strategies (resource opportunity and competition exclu-sion). Then, we use a set of generalised linear models to explain the distribution of seven herbaceous invaders in natural communities (using a large vegetation database for the French Alps containing 5,000 community-plots). Finally, we measure the relative importance of compet-itive interaction indices, identify the type of coexistence mechanism involved and how this varies along envi-ronmental gradients. Adding competition indices signif-icantly improved model's performance, but neither resource opportunity nor competitive exclusion were common strategies among the seven species. Overall, we show that combining environmental, dispersal and biotic information to model invasions has excellent potential for improving our understanding of invader success.
Full-text · Article · Oct 2014 · Biological Invasions
[Show abstract][Hide abstract] ABSTRACT: 1.The α, β, γ diversity decomposition methodology is commonly used to investigate changes in diversity over space or time but rarely conjointly. However, with the ever-increasing availability of large-scale biodiversity monitoring data, there is a need for a sound methodology capable of simultaneously accounting for spatial and temporal changes in diversity.2.Using the properties of Chao's index, we adapted Rao's framework of diversity decomposition between orthogonal dimensions to a multiplicative α, β, γ decomposition of functional or phylogenetic diversity over space and time, thereby combining their respective properties. We also developed guidelines for interpreting both temporal and spatial β-diversities and their interaction.3.We characterised the range of β-diversity estimates and their relationship to the nested decomposition of diversity. Using simulations, we empirically demonstrated that temporal and spatial β-diversities are independent from each other and from α and γ-diversities when the study design is balanced, but not otherwise. Furthermore, we showed that the interaction term between the temporal and the spatial β-diversities lacked such properties.4.We illustrated our methodology with a case study of the spatio-temporal dynamics of functional diversity in bird assemblages in four regions of France. Based on these data, our method makes it possible to discriminate between regions experiencing different diversity changes in time. Our methodology may therefore be valuable for comparing diversity changes over space and time using large-scale datasets of repeated surveys.This article is protected by copyright. All rights reserved.
Full-text · Article · Oct 2014 · Methods in Ecology and Evolution
[Show abstract][Hide abstract] ABSTRACT: Since the ever-increasing availability of phylogenetic informative data, the last decade has seen an upsurge of ecological studies incorporating information on evolutionary relationships among species. However, detailed species-level phylogenies are still lacking for many large groups and regions, which are necessary for comprehensive large-scale eco-phylogenetic analyses. Here, we provide a dataset of 100 dated phylogenetic trees for all European tetrapods based on a mixture of supermatrix and supertree approaches. Phylogenetic inference was performed separately for each of the main Tetrapoda groups of Europe except mammals (i.e. amphibians, birds, squamates and turtles) by means of maximum likelihood (ML) analyses of supermatrix applying a tree constraint at the family (amphibians and squamates) or order (birds and turtles) levels based on consensus knowledge. For each group, we inferred 100 ML trees to be able to provide a phylogenetic dataset that accounts for phylogenetic uncertainty, and assessed node support with bootstrap analyses. Each tree was dated using penalized-likelihood and fossil calibration. The trees obtained were well-supported by existing knowledge and previous phylogenetic studies. For mammals, we modified the most complete supertree dataset available on the literature to include a recent update of the Carnivora clade. As a final step, we merged the phylogenetic trees of all groups to obtain a set of 100 phylogenetic trees for all European Tetrapoda species for which data was available (91%). We provide this phylogenetic dataset (100 chronograms) for the purpose of comparative analyses, macro-ecological or community ecology studies aiming to incorporate phylogenetic information while accounting for phylogenetic uncertainty.
[Show abstract][Hide abstract] ABSTRACT: AimTo reconstruct the historical assembly of the eudicot flora of Mediterranean sierras by examining compositional (CBD), phylogenetic (PBD) and functional (FBD) beta diversity between elevational belts among disjunct mountain ranges (sierras), and relating these measures of turnover to environmental and geographical distances.LocationBaetic ranges, Andalusia, southern Spain.Methods
We compiled eudicot species and subspecies (‘entities’) checklists for three elevational belts within each of eight sierras of Andalusia (‘sites’) and tested for non-random patterns of PBD and FBD of all entities and of endemic entities separately among sites between and within sierras. Multiple regression on distance matrices was used to determine the respective contribution of climate, lithology and geographical distance to CBD, PBD and FBD. Finally, we decomposed PBD into the turnover and nestedness components of beta diversity, and quantified the phylogenetic diversity (PD) within sites.ResultsThe observed PBD and FBD among elevational belts within sierras for all entities were generally higher than expected based on their respective null distributions, whereas CBD among elevational belts within sierras was similar or even lower than between sierras. In contrast, the observed PBD and FBD for endemics were non-significant in most of the comparisons. Temperature-related variables best explained patterns of CBD, PBD and FBD for all entities, whereas lithology and geographical distance were the main drivers of endemic CBD. The observed PBD among elevational belts within sierras was mainly attributable to differences in PD rather than ‘true’ turnover.Main conclusionsThere is strong structuring of plant lineages along elevational gradients in the Baetic range, probably due to habitat filtering acting on life forms and character syndromes that show strong phylogenetic signal. The differentiation of the endemic flora that contributed to the emergence of this western Mediterranean biodiversity hotspot was probably driven by geographical isolation and/or by repeated specialization to contrasting lithologies.
Full-text · Article · Aug 2014 · Journal of Biogeography
[Show abstract][Hide abstract] ABSTRACT: We investigate patterns of phylogenetic diversity in relation to species diversity for European birds, mammals and amphibians, to evaluate their congruence and highlight areas of particular evolutionary history. We estimate the extent to which the European network of protected areas (PAs) network retains interesting evolutionary history areas for the three groups separately and simultaneously.
Phylogenetic (QEPD) and species diversity (SD) were estimated using the Rao's quadratic entropy at 10' resolution. We determined the regional relationship between QEPD and SD for each taxa with a spatial regression model and used the tails of the residuals (QERES) distribution to identify areas of higher and lower QEPD than predicted. Spatial congruence of biodiversity between groups was assessed with Pearson's correlation. A simple classification scheme allowed building a convergence map where a convergent pixel equalled to a QERES value of the same sign for the 3 groups. This convergence map was overlaid to the current PAs network to estimate the level of protection in convergent pixels and compared it to a null expectation built on 1000 randomization of PAs over the landscape.
QERES patterns across vertebrates show a strong spatial mismatch highlighting different evolutionary histories. Convergent areas represent only 2.7% of the Western Palearctic, with only 8.4% of these areas being covered by the current PAs network while a random distribution would retain 10.4% of them. QERES are unequally represented within PAs: areas with higher QEPD than predicted are better covered than expected, while low QEPD areas are undersampled.
Patterns of diversity strongly diverge between groups of vertebrates in Europe. Although Europe has the world's most extensive PAs network, evolutionary history of terrestrial vertebrates is unequally protected. The challenge is now to reconcile effective conservation planning with a contemporary view of biodiversity integrating multiple facets.
Full-text · Article · Jun 2014 · Diversity and Distributions
[Show abstract][Hide abstract] ABSTRACT: Aim Phylogenetic diversity patterns are increasingly being used to better understand the role of ecological and evolutionary processes in community assembly. Here, we quantify how these patterns are influenced by scale choices in terms of spatial and environmental extent and organismic scales. LocationEuropean Alps.
Methods We applied 42 sampling strategies differing in their combination of focal scales. For each resulting sub-dataset, we estimated the phylogenetic diversity of the species pools, phylogenetic α-diversities of local communities, and statistics commonly used together with null models in order to infer non-random diversity patterns (i.e. phylogenetic clustering versus over-dispersion). Finally, we studied the effects of scale choices on these measures using regression analyses.
Results Scale choices were decisive for revealing signals in diversity patterns. Notably, changes in focal scales sometimes reversed a pattern of over-dispersion into clustering. Organismic scale had a stronger effect than spatial and environmental extent. However, we did not find general rules for the direction of change from over-dispersion to clustering with changing scales. Importantly, these scale issues had only a weak influence when focusing on regional diversity patterns that change along abiotic gradients.
Main conclusions Our results call for caution when combining phylogenetic data with distributional data to study how and why communities differ from random expectations of phylogenetic relatedness. These analyses seem to be robust when the focus is on relating community diversity patterns to variation in habitat conditions, such as abiotic gradients. However, if the focus is on identifying relevant assembly rules for local communities, the uncertainty arising from a certain scale choice can be immense. In the latter case, it becomes necessary to test whether emerging patterns are robust to alternative scale choices.
Full-text · Article · Jun 2014 · Global Ecology and Biogeography
[Show abstract][Hide abstract] ABSTRACT: Patterns of adaptation in response to environmental variation are central to our understanding of biodiversity, but predictions of how and when broad-scale environmental conditions such as climate affect organismal form and function remain incomplete. Succulent plants have evolved in response to arid conditions repeatedly, with various plant organs such as leaves, stems, and roots physically modified to increase water storage. Here we investigate the role played by climate conditions in shaping the evolution of succulent forms in a plant clade endemic to Madagascar and the surrounding islands, part of the hyper-diverse genus Euphorbia (Euphorbiaceae). We used multivariate ordination of 19 climate variables to identify links between particular climate variables and three major forms of succulence - succulent leaves, cactiform stem succulence, and tubers. We then tested the relationship between climatic conditions and succulence, using comparative methods that account for shared evolutionary history. We confirm that plant water storage is associated with the two components of aridity, temperature and precipitation. Cactiform stem succulence, however, is not prevalent in the driest environments, countering the widely held view of cactiforms as desert icons. Instead, leaf succulence and tubers are significantly associated with the lowest levels of precipitation. Our findings provide a clear link between broad-scale climatic conditions and adaptation in land plants, and new insights into the climatic conditions favoring different forms of succulence. This evidence for adaptation to climate raises concern over the evolutionary future of succulent plants as they, along with other organisms, face anthropogenic climate change.
Full-text · Article · May 2014 · Systematic Biology
[Show abstract][Hide abstract] ABSTRACT: Evolutionary adaptation is a key driver of species’ range dynamics. Understanding the factors that affect rates of adaptation at range margins is thus crucial for interpreting and predicting changes in species’ ranges. The spatial structure of environmental conditions is one of the determinants of whether and how quickly adaptations occur. However, while landscape structures at range edges are typically complex, most theoretical work has so far focused on relatively simple environmental geometries.Using an individual-based allelic model, we explore the effects of different landscape structures on the rate of adaptation to novel environments and investigate how these structures interact with the genetic architecture of the trait governing adaptation and the dispersal capacity of the considered species. Generally, we find that rapid adaptation is favored by a good match between the coarseness of the trait's genetic architecture (many loci of small effects versus few loci of large effects) and the coarseness of the landscape (abruptness of transitions in environmental conditions). For example, in rugged landscapes, adaptation is quicker for genetic architectures with few loci of large effects, while for shallow gradients the opposite is true. Moreover, dispersal capacities affect the rate of adaptation by modulating the ‘apparent coarseness’ of the landscape: a gradient perceived as smooth by species with limited dispersal capacities appears rather steep for highly dispersive ones. We also find that the distribution of evolving phenotypes strongly depends on the interplay of landscape structure and dispersal capacities, ranging from two distinct phenotypes for most rugged landscapes, over the co-occurrence of an additional third phenotype for highly dispersive species, to the whole range of phenotypes on smooth gradients.By identifying basic factors that drive the fixation probability of newly arising beneficial mutations, we hope to further broaden the understanding of evolutionary adaptation at range margins and, hence, species’ range dynamics.