A spatially explicit trait-based approach uncovers changes in assembly processes under warming.

The re-assembly of plant communities during climate warming depends on several concurrent processes. Here, we present a novel framework that integrates spatially explicit sampling, plant trait information and a warming experiment to quantify shifts in these assembly processes. By accounting for spatial distance between individuals, our framework allows separation of potential signals of environmental filtering from those of different types of competition. When applied to an elevational transplant experiment in the French Alps, we found common signals of environmental filtering and competition in all communities. Signals of environmental filtering were generally stronger in alpine than in subalpine control communities, and warming reduced this filter. Competition signals depended on treatments and traits: Symmetrical competition was dominant in control and warmed alpine communities, while hierarchical competition was present in subalpine communities. Our study highlights how distance-dependent frameworks can contribute to a better understanding of transient re-assembly dynamics during environmental change.

A new westward migration route in an Asian passerine bird.

The evolution of migration routes in birds remains poorly understood as changes in migration strategies are rarely observed on contemporary timescales.1-3 The Richard's Pipit Anthus richardi, a migratory songbird breeding in Siberian grasslands and wintering in Southeast Asia, has only recently become a regular autumn and winter visitor to western Europe. Here, we examine whether this change in occurrence merely reflects an increase in the number of vagrants, that is, "lost" individuals that likely do not manage to return to their breeding grounds, or represents a new migratory strategy.4-6 We show that Richard's Pipits in southwestern Europe are true migrants: the same marked individuals return to southern France in subsequent winters and geo-localization tracking revealed that they originate from the western edge of the known breeding range. They make an astonishing 6,000 km journey from Central Asia across Eurasia, a very unusual longitudinal westward route among Siberian migratory birds.7,8 Climatic niche modeling using citizen-science bird data suggests that the winter niche suitability has increased in southwestern Europe, which may have led to increased winter survival and eventual successful return journey and reproduction of individuals that initially reached Europe as autumn vagrants. This illustrates that vagrancy may have an underestimated role in the emergence of new migratory routes and adaptation to global change in migratory birds.9,10 Whatever the underlying drivers and mechanisms, it constitutes one of the few documented contemporary changes in migration route, and the first longitudinal shift, in a long-distance migratory bird.

The dimensionality and structure of species trait spaces.

Trait-based ecology aims to understand the processes that generate the overarching diversity of organismal traits and their influence on ecosystem functioning. Achieving this goal requires simplifying this complexity in synthetic axes defining a trait space and to cluster species based on their traits while identifying those with unique combinations of traits. However, so far, we know little about the dimensionality, the robustness to trait omission and the structure of these trait spaces. Here, we propose a unified framework and a synthesis across 30 trait datasets representing a broad variety of taxa, ecosystems and spatial scales to show that a common trade-off between trait space quality and operationality appears between three and six dimensions. The robustness to trait omission is generally low but highly variable among datasets. We also highlight invariant scaling relationships, whatever organismal complexity, between the number of clusters, the number of species in the dominant cluster and the number of unique species with total species richness. When species richness increases, the number of unique species saturates, whereas species tend to disproportionately pack in the richest cluster. Based on these results, we propose some rules of thumb to build species trait spaces and estimate subsequent functional diversity indices.

Global distribution and conservation status of ecologically rare mammal and bird species.

Identifying species that are both geographically restricted and functionally distinct, i.e. supporting rare traits and functions, is of prime importance given their risk of extinction and their potential contribution to ecosystem functioning. We use global species distributions and functional traits for birds and mammals to identify the ecologically rare species, understand their characteristics, and identify hotspots. We find that ecologically rare species are disproportionately represented in IUCN threatened categories, insufficiently covered by protected areas, and for some of them sensitive to current and future threats. While they are more abundant overall in countries with a low human development index, some countries with high human development index are also hotspots of ecological rarity, suggesting transboundary responsibility for their conservation. Altogether, these results state that more conservation emphasis should be given to ecological rarity given future environmental conditions and the need to sustain multiple ecosystem processes in the long-term.

Landscape does matter: Disentangling founder effects from natural and human-aided post-introduction dispersal during an ongoing biological invasion.

Environmental features impacting the spread of invasive species after introduction can be assessed using population genetic structure as a quantitative estimation of effective dispersal at the landscape scale. However, in the case of an ongoing biological invasion, deciphering whether genetic structure represents landscape connectivity or founder effects is particularly challenging. We examined the modes of dispersal (natural and human-aided) and the factors (landscape or founders history) shaping genetic structure in range edge invasive populations of the Asian tiger mosquito, Aedes albopictus, in the region of Grenoble (Southeast France). Based on detailed occupancy-detection data and environmental variables (climatic, topographic and land-cover), we modelled A. albopictus potential suitable area and its expansion history since first introduction. The relative role of dispersal modes was estimated using biological dispersal capabilities and landscape genetics approaches using genome-wide SNP dataset. We demonstrate that both natural and human-aided dispersal have promoted the expansion of populations. Populations in diffuse urban areas, representing highly suitable habitat for A. albopictus, tend to disperse less, while roads facilitate long-distance dispersal. Yet, demographic bottlenecks during introduction played a major role in shaping the genetic variability of these range edge populations. The present study is one of the few investigating the role of founder effects and ongoing expansion processes in shaping spatial patterns of genetic variation in an invasive species at the landscape scale. The combination of several dispersal modes and large proportions of continuous suitable habitats for A. albopictus promoted range filling of almost its entire potential distribution in the region of Grenoble only few years after introduction.

Climate-associated genetic variation in Fagus sylvatica and potential responses to climate change in the French Alps.

Local adaptation patterns have been found in many plants and animals, highlighting the genetic heterogeneity of species along their range of distribution. In the next decades, global warming is predicted to induce a change in the selective pressures that drive this adaptive variation, forcing a reshuffling of the underlying adaptive allele distributions. For species with low dispersion capacity and long generation time such as trees, the rapidity of the change could impede the migration of beneficial alleles and lower their capacity to track the changing environment. Identifying the main selective pressures driving the adaptive genetic variation is thus necessary when investigating species capacity to respond to global warming. In this study, we investigate the adaptive landscape of Fagus sylvatica along a gradient of populations in the French Alps. Using a double-digest restriction-site-associated DNA (ddRAD) sequencing approach, we identified 7,000 SNPs from 570 individuals across 36 different sites. A redundancy analysis (RDA)-derived method allowed us to identify several SNPs that were strongly associated with climatic gradients; moreover, we defined the primary selective gradients along the natural populations of F. sylvatica in the Alps. Strong effects of elevation and humidity, which contrast north-western and south-eastern site, were found and were believed to be important drivers of genetic adaptation. Finally, simulations of future genetic landscapes that used these findings allowed identifying populations at risk for F. sylvatica in the Alps, which could be helpful for future management plans.

Predicting the success of an invader: Niche shift versus niche conservatism.

Invasive species can encounter environments different from their source populations, which may trigger rapid adaptive changes after introduction (niche shift hypothesis). To test this hypothesis, we investigated whether postintroduction evolution is correlated with contrasting environmental conditions between the European invasive and source ranges in the Asian tiger mosquito Aedes albopictus. The comparison of environmental niches occupied in European and source population ranges revealed more than 96% overlap between invasive and source niches, supporting niche conservatism. However, we found evidence for postintroduction genetic evolution by reanalyzing a published ddRADseq genomic dataset from 90 European invasive populations using genotype-environment association (GEA) methods and generalized dissimilarity modeling (GDM). Three loci, among which a putative heat-shock protein, exhibited significant allelic turnover along the gradient of winter precipitation that could be associated with ongoing range expansion. Wing morphometric traits weakly correlated with environmental gradients within Europe, but wing size differed between invasive and source populations located in different climatic areas. Niche similarities between source and invasive ranges might have facilitated the establishment of populations. Nonetheless, we found evidence for environmental-induced adaptive changes after introduction. The ability to rapidly evolve observed in invasive populations (genetic shift) together with a large proportion of unfilled potential suitable areas (80%) pave the way to further spread of Ae. albopictus in Europe.

Spatio-temporal ecological niche modelling of multigenerational insect migrations.

Modelling ecological niches of migratory animals requires incorporating a temporal dimension, in addition to space. Here, we introduce an approach to model multigenerational migratory insects using time-partitioned environmental variables (by months and years) and time- and behaviour-partitioned records (breeding records to model reproductive habitat). We apply this methodology to modelling the Palearctic-African migratory cycle of the Painted Lady butterfly (Vanessa cardui), based on data encompassing 36 years (646 breeding sites from 30 countries). Each breeding record is linked to a particular time (month and year), and the associated values of the bioclimatic variables are used for an ensemble modelling strategy, to finally obtain monthly projections. The results show obligated movements, mostly latitudinal, for the species' successive generations across the overall range, and only scattered locations show high probabilities of reproduction year-round. The southernmost reproductive areas estimated for the Palearctic-African migratory pool reach equatorial latitudes from December to February. We thus propose a potential distribution for the winter 'missing generations' that would expand the V. cardui migration cycle to encompass about 15 000 km in latitude, from northernmost Europe to equatorial Africa. In summer, Europe represents the major temporary resource for V. cardui, while January and February show the lowest overall suitability values, and they are potentially the most vulnerable period for the species to suffer yearly bottlenecks. In summary, we demonstrate the potential of the proposed niche modelling strategy to investigate migratory movements of insects.

Uncertainty in ensembles of global biodiversity scenarios.

While there is a clear demand for scenarios that provide alternative states in biodiversity with respect to future emissions, a thorough analysis and communication of the associated uncertainties is still missing. Here, we modelled the global distribution of ~11,500 amphibian, bird and mammal species and project their climatic suitability into the time horizon 2050 and 2070, while varying the input data used. By this, we explore the uncertainties originating from selecting species distribution models (SDMs), dispersal strategies, global circulation models (GCMs), and representative concentration pathways (RCPs). We demonstrate the overwhelming influence of SDMs and RCPs on future biodiversity projections, followed by dispersal strategies and GCMs. The relative importance of each component varies in space but also with the selected sensitivity metrics and with species' range size. Overall, this means using multiple SDMs, RCPs, dispersal assumptions and GCMs is a necessity in any biodiversity scenario assessment, to explicitly report associated uncertainties.

Differences in the fungal communities nursed by two genetic groups of the alpine cushion plant, Silene acaulis.

Foundation plants shape the composition of local biotic communities and abiotic environments, but the impact of a plant's intraspecific variations on these processes is poorly understood. We examined these links in the alpine cushion moss campion (Silene acaulis) on two neighboring mountain ranges in the French Alps. Genotyping of cushion plants revealed two genetic clusters matching known subspecies. The exscapa subspecies was found on both limestone and granite, while the longiscapa one was only found on limestone. Even on similar limestone bedrock, cushion soils from the two S. acaulis subspecies deeply differed in their impact on soil abiotic conditions. They further strikingly differed from each other and from the surrounding bare soils in fungal community composition. Plant genotype variations accounted for a large part of the fungal composition variability in cushion soils, even when considering geography or soil chemistry, and particularly for the dominant molecular operational taxonomic units (MOTUs). Both saprophytic and biotrophic fungal taxa were related to the MOTUs recurrently associated with a single plant genetic cluster. Moreover, the putative phytopathogens were abundant, and within the same genus (Cladosporium) or species (Pyrenopeziza brassicae), MOTUs showing specificity for each plant subspecies were found. Our study highlights the combined influences of bedrock and plant genotype on fungal recruitment into cushion soils and suggests the coexistence of two mechanisms, an indirect selection resulting from the colonization of an engineered soil by free-living saprobes and a direct selection resulting from direct plant-fungi interactions.

Simulating plant invasion dynamics in mountain ecosystems under global change scenarios.

Across the globe, invasive alien species cause severe environmental changes, altering species composition and ecosystem functions. So far, mountain areas have mostly been spared from large-scale invasions. However, climate change, land-use abandonment, the development of tourism and the increasing ornamental trade will weaken the barriers to invasions in these systems. Understanding how alien species will react and how native communities will influence their success is thus of prime importance in a management perspective. Here, we used a spatially and temporally explicit simulation model to forecast invasion risks in a protected mountain area in the French Alps under future conditions. We combined scenarios of climate change, land-use abandonment and tourism-linked increases in propagule pressure to test if the spread of alien species in the region will increase in the future. We modelled already naturalized alien species and new ornamental plants, accounting for interactions among global change components, and also competition with the native vegetation. Our results show that propagule pressure and climate change will interact to increase overall species richness of both naturalized aliens and new ornamentals, as well as their upper elevational limits and regional range-sizes. Under climate change, woody aliens are predicted to more than double in range-size and herbaceous species to occupy up to 20% of the park area. In contrast, land-use abandonment will open new invasion opportunities for woody aliens, but decrease invasion probability for naturalized and ornamental alien herbs as a consequence of colonization by native trees. This emphasizes the importance of interactions with the native vegetation either for facilitating or potentially for curbing invasions. Overall, our work highlights an additional and previously underestimated threat for the fragile mountain flora of the Alps already facing climate changes, land-use transformations and overexploitation by tourism.

Extreme climate events counteract the effects of climate and land-use changes in Alpine treelines.

1. Climate change and extreme events, such as drought, threaten ecosystems worldwide and in particular mountain ecosystems, where species often live at their environmental tolerance limits. In the European Alps, plant communities are also influenced by land-use abandonment leading to woody encroachment of subalpine and alpine grasslands. 2. In this study, we explored how the forest-grassland ecotone of Alpine treelines will respond to gradual climate warming, drought events and land-use change in terms of forest expansion rates, taxonomic diversity and functional composition. We used a previously validated dynamic vegetation model, FATE-HD, parameterised for plant communities in the Ecrins National Park in the French Alps. 3. Our results showed that intense drought counteracted the forest expansion at higher elevations driven by land-use abandonment and climate change, especially when combined with high drought frequency (occurring every 2 or less than 2 years). 4. Furthermore, intense and frequent drought accelerated the rates of taxonomic change and resulted in overall higher taxonomic spatial heterogeneity of the ecotone than would be expected under gradual climate and land-use changes only. 5. Synthesis and applications. The results from our model show that intense and frequent drought counteracts forest expansion driven by climate and land-use changes in the forest-grassland ecotone of Alpine treelines. We argue that land-use planning must consider the effects of extreme events, such as drought, as well as climate and land-use changes, since extreme events might interfere with trends predicted under gradual climate warming and agricultural abandonment.

The Geography of Ecological Niche Evolution in Mammals.

Convergent adaptive evolution of species' ecological niches-i.e., the appearance of similar niches in independent lineages-is the result of natural selection acting on niche-related species traits ("traits" hereafter) and contrasts with neutral evolution [1-4]. Although trait convergences are recognized as being of importance at the species scale, we still know little about the impact of species convergence on the overall trait and niche structure of entire biotas at large spatial scales [5]. Here, we map the convergent evolution of four traits (diet, body mass, activity cycle, and foraging strata) for mammal species and assemblages (defined at 200 × 200 km resolution) at a global scale. Using data on the geographic distributions, traits, and phylogenetic relationships of species and by comparing observed patterns of trait ß-diversity to evolutionary neutral expectations, we show that trait convergence is not restricted to particular lineages but scales up to entire assemblages (i.e., whole species communities). We find region-wide biota convergence in traits between regions with similar climates, particularly between Australia and other continents. Pairs of assemblages that show trait divergence often involves Arctic regions where rapid evolutionary changes occurred in response to extreme climatic constraints. By integrating both macroecological and macroevolutionary approaches into a single framework, our study quantifies the crucial role of evolutionary processes such as natural selection in the spatial distribution and structure of large-scale species assemblages.

From species distributions to meta-communities.

The extent that biotic interactions and dispersal influence species ranges and diversity patterns across scales remains an open question. Answering this question requires framing an analysis on the frontier between species distribution modelling (SDM), which ignores biotic interactions and dispersal limitation, and community ecology, which provides specific predictions on community and meta-community structure and resulting diversity patterns such as species richness and functional diversity. Using both empirical and simulated datasets, we tested whether predicted occurrences from fine-resolution SDMs provide good estimates of community structure and diversity patterns at resolutions ranging from a resolution typical of studies within reserves (250 m) to that typical of a regional biodiversity study (5 km). For both datasets, we show that the imprint of biotic interactions and dispersal limitation quickly vanishes when spatial resolution is reduced, which demonstrates the value of SDMs for tracking the imprint of community assembly processes across scales.

Are different facets of plant diversity well protected against climate and land cover changes? A test study in the French Alps.

Climate and land cover changes are important drivers of the plant species distributions and diversity patterns in mountainous regions. Although the need for a multifaceted view of diversity based on taxonomic, functional and phylogenetic dimensions is now commonly recognized, there are no complete risk assessments concerning their expected changes. In this paper, we used a range of species distribution models in an ensemble-forecasting framework together with regional climate and land cover projections by 2080 to analyze the potential threat for more than 2,500 plant species at high resolution (2.5 km × 2.5 km) in the French Alps. We also decomposed taxonomic, functional and phylogenetic diversity facets into α and ß components and analyzed their expected changes by 2080. Overall, plant species threats from climate and land cover changes in the French Alps were expected to vary depending on the species' preferred altitudinal vegetation zone, rarity, and conservation status. Indeed, rare species and species of conservation concern were the ones projected to experience less severe change, and also the ones being the most efficiently preserved by the current network of protected areas. Conversely, the three facets of plant diversity were also projected to experience drastic spatial re-shuffling by 2080. In general, the mean α-diversity of the three facets was projected to increase to the detriment of regional ß-diversity, although the latter was projected to remain high at the montane-alpine transition zones. Our results show that, due to a high-altitude distribution, the current protection network is efficient for rare species, and species predicted to migrate upward. Although our modeling framework may not capture all possible mechanisms of species range shifts, our work illustrates that a comprehensive risk assessment on an entire floristic region combined with functional and phylogenetic information can help delimitate future scenarios of biodiversity and better design its protection.