Will climate change drive alien invasive plants into areas of high protection value? An improved model-based regional assessment to prioritise the management of invasions.

Species distribution models (SDMs) studies suggest that, without control measures, the distribution of many alien invasive plant species (AIS) will increase under climate and land-use changes. Due to limited resources and large areas colonised by invaders, management and monitoring resources must be prioritised. Choices depend on the conservation value of the invaded areas and can be guided by SDM predictions. Here, we use a hierarchical SDM framework, complemented by connectivity analysis of AIS distributions, to evaluate current and future conflicts between AIS and high conservation value areas. We illustrate the framework with three Australian wattle (Acacia) species and patterns of conservation value in Northern Portugal. Results show that protected areas will likely suffer higher pressure from all three Acacia species under future climatic conditions. Due to this higher predicted conflict in protected areas, management might be prioritised for Acacia dealbata and Acacia melanoxylon. Connectivity of AIS suitable areas inside protected areas is currently lower than across the full study area, but this would change under future environmental conditions. Coupled SDM and connectivity analysis can support resource prioritisation for anticipation and monitoring of AIS impacts. However, further tests of this framework over a wide range of regions and organisms are still required before wide application.

Niche dynamics in space and time.

Niche conservatism, the tendency of a species niche to remain unchanged over time, is often assumed when discussing, explaining or predicting biogeographical patterns. Unfortunately, there has been no basis for predicting niche dynamics over relevant timescales, from tens to a few hundreds of years. The recent application of species distribution models (SDMs) and phylogenetic methods to analysis of niche characteristics has provided insight to niche dynamics. Niche shifts and conservatism have both occurred within the last 100 years, with recent speciation events, and deep within clades of species. There is increasing evidence that coordinated application of these methods can help to identify species which likely fulfill one key assumption in the predictive application of SDMs: an unchanging niche. This will improve confidence in SDM-based predictions of the impacts of climate change and species invasions on species distributions and biodiversity.

Land use improves spatial predictions of mountain plant abundance but not presence-absence

Question Does a land-use variable improve spatial predictions of plant species presence-absence and abundance models at the regional scale in a mountain landscape? Location Western Swiss Alps. Methods Presence-absence generalized linear models (GLM) and abundance ordinal logistic regression models (LRM) were fitted to data on 78 mountain plant species, with topo-climatic and/or land-use variables available at a 25-m resolution. The additional contribution of land use when added to topo-climatic models was evaluated by: (1) assessing the changes in model fit and (2) predictive power, (3) partitioning the deviance respectively explained by the topo-climatic variables and the land-use variable through variation partitioning, and (5) comparing spatial projections. Results Land use significantly improved the fit of presence-absence models but not their predictive power. In contrast, land use significantly improved both the fit and predictive power of abundance models. Variation partitioning also showed that the individual contribution of land use to the deviance explained by presence-absence models was, on average, weak for both GLM and LRM (3.7% and 4.5%, respectively), but changes in spatial projections could nevertheless be important for some species. Conclusions In this mountain area and at our regional scale, land use is important for predicting abundance, but not presence-absence. The importance of adding land-use information depends on the species considered. Even without a marked effect on model fit and predictive performance, adding land use can affect spatial projections of both presence-absence and abundance models.

Forecasting changes in population genetic structure of alpine plants in response to global warming.

Species range shifts in response to climate and land use change are commonly forecasted with species distribution models based on species occurrence or abundance data. Although appealing, these models ignore the genetic structure of species, and the fact that different populations might respond in different ways because of adaptation to their environment. Here, we introduced ancestry distribution models, that is, statistical models of the spatial distribution of ancestry proportions, for forecasting intra-specific changes based on genetic admixture instead of species occurrence data. Using multi-locus genotypes and extensive geographic coverage of distribution data across the European Alps, we applied this approach to 20 alpine plant species considering a global increase in temperature from 0.25 to 4 °C. We forecasted the magnitudes of displacement of contact zones between plant populations potentially adapted to warmer environments and other populations. While a global trend of movement in a north-east direction was predicted, the magnitude of displacement was species-specific. For a temperature increase of 2 °C, contact zones were predicted to move by 92 km on average (minimum of 5 km, maximum of 212 km) and by 188 km for an increase of 4 °C (minimum of 11 km, maximum of 393 km). Intra-specific turnover-measuring the extent of change in global population genetic structure-was generally found to be moderate for 2 °C of temperature warming. For 4 °C of warming, however, the models indicated substantial intra-specific turnover for ten species. These results illustrate that, in spite of unavoidable simplifications, ancestry distribution models open new perspectives to forecast population genetic changes within species and complement more traditional distribution-based approaches.

Suitability, success and sinks: how do predictions of nesting distributions relate to fitness parameters in high arctic waders?

AimAlthough habitat suitability maps derived from species distribution models (SDMs) are often assumed to highlight locations that can sustain healthy populations over time, the relationship between suitability scores and fitness parameters has rarely been tested thoroughly. LocationZackenberg Valley, north-east Greenland. MethodsUsing 14years of data (1997-2010) representing three wader species (dunlin Calidris alpina, sanderling Calidris alba and ruddy turnstone Arenaria interpres), we tested the relationships between modelled suitability and fitness parameters at nesting locations. ResultsAmong the three species examined, only the ruddy turnstone exhibited significant relationships between suitability and nest success, but over time rather than space. During years with extensive snow cover in the landscape, the nesting sites of ruddy turnstone occurred in different habitats than were typically used across years. Moreover, in years with extensive snow cover, the ruddy turnstone initiated nests later and suffered from higher egg predation rates. Main conclusionOur results suggest that SDMs derived from species occurrences that include years of low reproductive success may over-estimate the potential suitable habitat in the landscape. Whenever possible, variation in reproductive success should be considered when building models to inform species' response to environmental change. species' response to environmental change.

A better understanding of ecological conditions for Leontopodium alpinum Cassini in the Swiss Alps

Although Leontopodium alpinum is considered to be threatened in many countries, only limited scientific information about its autecology is available. In this study, we aim to define the most important ecological factors which influence the distribution of L. alpinum in the Swiss Alps. These were assessed at the national scale using species distribution models based on topoclimatic predictors and at the community scale using exhaustive plant inventories. The latter were analysed using hierarchical clustering and principal component analysis, and the results were interpreted using ecological indicator values. L. alpinum was found almost exclusively on base-rich bedrocks (limestone and ultramaphic rocks). The species distribution models showed that the available moisture (dry regions, mostly in the Inner Alps), elevation (mostly above 2000 m.a.s.l.) and slope (mostly >30°) were the most important predictors. The relevés showed that L. alpinum is present in a wide range of plant communities, all subalpine-alpine open grasslands, with a low grass cover. As a light-demanding and short species, L. alpinum requires light at ground level; hence, it can only grow in open, nutrient-poor grasslands. These conditions are met in dry conditions (dry, summer-warm climate, rocky and draining soil, south-facing aspect and/or steep slope), at high elevations, on oligotrophic soils and/or on windy ridges. Base-rich soils appear to also be essential, although it is still unclear if this corresponds to physiological or ecological (lower competition) requirements.

Combining palaeodistribution modelling and phylogeographical approaches for identifying glacial refugia in Alpine Primula

Aim We investigated the late Quaternary history of two closely related and partly sympatric species of Primula from the south-western European Alps, P. latifolia Lapeyr. and P. marginata Curtis, by combining phylogeographical and palaeodistribution modelling approaches. In particular, we were interested in whether the two approaches were congruent and identified the same glacial refugia. Location South-western European Alps. Methods For the phylogeographical analysis we included 353 individuals from 28 populations of P. marginata and 172 individuals from 15 populations of P. latifolia and used amplified fragment length polymorphisms (AFLPs). For palaeodistribution modelling, species distribution models (SDMs) were based on extant species occurrences and then projected to climate models (CCSM, MIROC) of the Last Glacial Maximum (LGM), approximately 21 ka. Results The locations of the modelled LGM refugia were confirmed by various indices of genetic variation. The refugia of the two species were largely geographically isolated, overlapping only 6% to 11% of the species' total LGM distribution. This overlap decreased when the position of the glacial ice sheet and the differential elevational and edaphic distributions of the two species were considered. Main conclusions The combination of phylogeography and palaeodistribution modelling proved useful in locating putative glacial refugia of two alpine species of Primula. The phylogeographical data allowed us to identify those parts of the modelled LGM refugial area that were likely source areas for recolonization. The use of SDMs predicted LGM refugial areas substantially larger and geographically more divergent than could have been predicted by phylogeographical data alone

The role of phylogeny in the spatial distributions and assembly of mountain plant communities.

A major challenge in community ecology is a thorough understanding of the processes that govern the assembly and composition of communities in time and space. The growing threat of climate change to the vascular plant biodiversity of fragile ecosystems such as mountains has made it equally imperative to develop comprehensive methodologies to provide insights into how communities are assembled. In this perspective, the primary objective of this PhD thesis is to contribute to the theoretical and methodological development of community ecology, by proposing new solutions to better detect the ecological and evolutionary processes that govern community assembly. As phylogenetic trees provide by far, the most advanced tools to integrate the spatial, ecological and evolutionary dynamics of plant communities, they represent the cornerstone on which this work was based. In this thesis, I proposed new solutions to: (i) reveal trends in community assembly on phylogenies, depicted by the transition of signals at the nodes of the different species and lineages responsible for community assembly, (ii) contribute to evidence the importance of evolutionarily labile traits in the distribution of mountain plant species. More precisely, I demonstrated that phylogenetic and functional compositional turnover in plant communities was driven by climate and human land use gradients mostly influenced by evolutionarily labile traits, (iii) predict and spatially project the phylogenetic structure of communities using species distribution models, to identify the potential distribution of phylogenetic diversity, as well as areas of high evolutionary potential along elevation. The altitudinal setting of the Diablerets mountains (Switzerland) provided an appropriate model for this study. The elevation gradient served as a compression of large latitudinal variations similar to a collection of islands within a single area, and allowed investigations on a large number of plant communities. Overall, this thesis highlights that stochastic and deterministic environmental filtering processes mainly influence the phylogenetic structure of plant communities in mountainous areas. Negative density-dependent processes implied through patterns of phylogenetic overdispersion were only detected at the local scale, whereas environmental filtering implied through phylogenetic clustering was observed at both the regional and local scale. Finally, the integration of indices of phylogenetic community ecology with species distribution models revealed the prospects of providing novel and insightful explanations on the potential distribution of phylogenetic biodiversity in high mountain areas. These results generally demonstrate the usefulness of phylogenies in inferring assembly processes, and are worth considering in the theoretical and methodological development of tools to better understand phylogenetic community structure.

Understanding the ecological niche to elucidate spatial strategies of the southernmost Tupinambis lizards

Understanding factors that shape ranges of species is central in evolutionary biology. Species distribution models have become important tools to test biogeographical, ecological and evolutionary hypotheses. Moreover, from an ecological and evolutionary perspective, these models help to elucidate the spatial strategies of species at a regional scale. We modelled species distributions of two phylogenetically, geographically and ecologically close Tupinambis species (Teiidae) that occupy the southernmost area of the genus distribution in South America. We hypothesized that similarities between these species might have induced spatial strategies at the species level, such as niche differentiation and divergence of distribution patterns at a regional scale. Using logistic regression and MaxEnt we obtained species distribution models that revealed interspecific differences in habitat requirements, such as environmental temperature, precipitation and altitude. Moreover, the models obtained suggest that although the ecological niches of Tupinambis merianae and T. rufescens are different, these species might co-occur in a large contact zone. We propose that niche plasticity could be the mechanism enabling their co-occurrence. Therefore, the approach used here allowed us to understand the spatial strategies of two Tupinambis lizards at a regional scale.

Extinction debt of high-mountain plants under 21st-century climate change

Quantitative estimates of the range loss of mountain plants under climate change have so far mostly relied on static geographical projections of species' habitat shifts(1-3). Here, we use a hybrid model(4) that combines such projections with simulations of demography and seed dispersal to forecast the climate-driven spatio-temporal dynamics of 150 high-mountain plant species across the European Alps. This model predicts average range size reductions of 44-50% by the end of the twenty-first century, which is similar to projections from the most 'optimistic' static model (49%). However, the hybrid model also indicates that population dynamics will lag behind climatic trends and that an average of 40% of the range still occupied at the end of the twenty-first century will have become climatically unsuitable for the respective species, creating an extinction debt(5,6). Alarmingly, species endemic to the Alps seem to face the highest range losses. These results caution against optimistic conclusions from moderate range size reductions observed during the twenty-first century as they are likely to belie more severe longer-term effects of climate warming on mountain plants.

Functional homogenization of bumblebee communities in alpine landscapes under projected climate change

Background: Bumblebees represent an active pollinator group in mountain regions and assure the pollination of many different plant species from low to high elevations. Plant-pollinator interactions are mediated by functional traits. Shift in bumblebee functional structure under climate change may impact plant-pollinator interactions in mountains. Here, we estimated bumblebee upward shift in elevation, community turnover, and change in functional structure under climate change. Method: We sampled bumblebee species at 149 sites along the elevation gradient. We used stacked species distribution models (S-SDMs) forecasted under three climate change scenarios (A2, A1B, RCP3PD) to model the potential distribution of the Bombus species. Furthermore, we used species proboscis length measurements to assess the functional change in bumblebee assemblages along the elevation gradient. Results: We found species-specific response of bumblebee species to climate change. Species differed in their predicted rate of range contraction and expansion. Losers were mainly species currently restricted to high elevation. Under the most severe climate change scenarios (A2), we found a homogenization of proboscis length structure in bumblebee communities along the elevation gradient through the upward colonization of high elevation by species with longer proboscides. Conclusions: Here, we show that in addition to causing the shift in the distribution of bumblebee species, climate change may impact the functional structure of communities. The colonization of high elevation areas by bumblebee species with long proboscides may modify the structure of plant-pollination interaction networks by increasing the diversity of pollination services at high elevation.

Predicting present and future intra-specific genetic structure through niche hindcasting across 24 millennia.

Paleoclimatic reconstructions coupled with species distribution models and identification of extant spatial genetic structure have the potential to provide insights into the demographic events that shape the distribution of intra-specific genetic variation across time. Using the globeflower Trollius europaeus as a case-study, we combined (1) Amplified Fragment Length Polymorphisms, (2) suites of 1000-years stepwise hindcasted species distributions and (3) a model of diffusion through time over the last 24,000 years, to trace the spatial dynamics that most likely fits the species' current genetic structure. We show that the globeflower comprises four gene pools in Europe which, from the dry period preceding the Last Glacial Maximum, dispersed while tracking the conditions fitting its climatic niche. Among these four gene pools, two are predicted to experience drastic range retraction in the near future. Our interdisciplinary approach, applicable to virtually any taxon, is an advance in inferring how climate change impacts species' genetic structures.

Modelling ecological niches with support vector machines

1. The ecological niche is a fundamental biological concept. Modelling species' niches is central to numerous ecological applications, including predicting species invasions, identifying reservoirs for disease, nature reserve design and forecasting the effects of anthropogenic and natural climate change on species' ranges. 2. A computational analogue of Hutchinson's ecological niche concept (the multidimensional hyperspace of species' environmental requirements) is the support of the distribution of environments in which the species persist. Recently developed machine-learning algorithms can estimate the support of such high-dimensional distributions. We show how support vector machines can be used to map ecological niches using only observations of species presence to train distribution models for 106 species of woody plants and trees in a montane environment using up to nine environmental covariates. 3. We compared the accuracy of three methods that differ in their approaches to reducing model complexity. We tested models with independent observations of both species presence and species absence. We found that the simplest procedure, which uses all available variables and no pre-processing to reduce correlation, was best overall. Ecological niche models based on support vector machines are theoretically superior to models that rely on simulating pseudo-absence data and are comparable in empirical tests. 4. Synthesis and applications. Accurate species distribution models are crucial for effective environmental planning, management and conservation, and for unravelling the role of the environment in human health and welfare. Models based on distribution estimation rather than classification overcome theoretical and practical obstacles that pervade species distribution modelling. In particular, ecological niche models based on machine-learning algorithms for estimating the support of a statistical distribution provide a promising new approach to identifying species' potential distributions and to project changes in these distributions as a result of climate change, land use and landscape alteration.

A new spin on a compositionalist predictive modelling framework for conservation planning: a tropical case study in Ecuador

Knowledge about spatial biodiversity patterns is a basic criterion for reserve network design. Although herbarium collections hold large quantities of information, the data are often scattered and cannot supply complete spatial coverage. Alternatively, herbarium data can be used to fit species distribution models and their predictions can be used to provide complete spatial coverage and derive species richness maps. Here, we build on previous effort to propose an improved compositionalist framework for using species distribution models to better inform conservation management. We illustrate the approach with models fitted with six different methods and combined using an ensemble approach for 408 plant species in a tropical and megadiverse country (Ecuador). As a complementary view to the traditional richness hotspots methodology, consisting of a simple stacking of species distribution maps, the compositionalist modelling approach used here combines separate predictions for different pools of species to identify areas of alternative suitability for conservation. Our results show that the compositionalist approach better captures the established protected areas than the traditional richness hotspots strategies and allows the identification of areas in Ecuador that would optimally complement the current protection network. Further studies should aim at refining the approach with more groups and additional species information.

Potential Impacts of Climate Change on Ecosystem Services in Europe: the Case of Pest Control by Vertebrates. BioScience.

Global environmental changes threaten ecosystems and cause significant alterations to the supply of ecosystem services that are vital for human well-being. We provide an assessment of the potential impacts of climate change on European diversity of vertebrates and their associated pest control services. We modeled the distributions of the species that provide this service using ensembles of forecasts from bioclimatic envelope models and then used their results to generate maps of potential species richness among vertebrate providers of pest control services. We assessed how potential richness of pest control providers would change according to different climate and greenhouse emissions scenarios. We found that potential richness of pest control providers was likely to face substantial reductions, especially in southern European countries that had economies highly dependent on agricultural yields. In much of central and northern Europe, where countries had their economies less dependent on agriculture, climate change was likely to benefit pest control providers