Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina

Understanding the genetic basis of adaptation in response to environmental variation is fundamental as adaptation plays a key role in the extension of ecological niches to marginal habitats and in ecological speciation. Based on the assumption that some genomic markers are correlated to environmental variables, we aimed to detect loci of ecological relevance in the alpine plant Arabis alpina L. sampled in two regions, the French (99 locations) and the Swiss (109 locations) Alps. We used an unusually large genome scan [825 amplified fragment length polymorphism loci (AFLPs)] and four environmental variables related to temperature, precipitation and topography. We detected linkage disequilibrium among only 3.5% of the considered AFLP loci. A population structure analysis identified no admixture in the study regions, and the French and Swiss Alps were differentiated and therefore could be considered as two independent regions. We applied generalized estimating equations (GEE) to detect ecologically relevant loci separately in the French and Swiss Alps. We identified 78 loci of ecological relevance (9%), which were mainly related to mean annual minimum temperature. Only four of these loci were common across the French and Swiss Alps. Finally, we discuss that the genomic characterization of these ecologically relevant loci, as identified in this study, opens up new perspectives for studying functional ecology in A. alpina, its relatives and other alpine plant species.     

Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach

It is generally accepted that most plant populations are locally adapted. Yet, understanding how environmental forces give rise to adaptive genetic variation is a challenge in conservation genetics and crucial to the preservation of species under rapidly changing climatic conditions. Environmental variation, phylogeographic history, and population demographic processes all contribute to spatially structured genetic variation, however few current models attempt to separate these confounding effects. To illustrate the benefits of using a spatially-explicit model for identifying potentially adaptive loci, we compared outlier locus detection methods with a recently-developed landscape genetic approach. We analyzed 157 loci from samples of the alpine herb Gentiana nivalis collected across the European Alps. Principle coordinates of neighbor matrices (PCNM), eigenvectors that quantify multi-scale spatial variation present in a data set, were incorporated into a landscape genetic approach relating AFLP frequencies with 23 environmental variables. Four major findings emerged. 1) Fifteen loci were significantly correlated with at least one predictor variable (R _adj ²  > 0.5). 2) Models including PCNM variables identified eight more potentially adaptive loci than models run without spatial variables. 3) When compared to outlier detection methods, the landscape genetic approach detected four of the same loci plus 11 additional loci. 4) Temperature, precipitation, and solar radiation were the three major environmental factors driving potentially adaptive genetic variation in G. nivalis. Techniques presented in this paper offer an efficient method for identifying potentially adaptive genetic variation and associated environmental forces of selection, providing an important step forward for the conservation of non-model species under global change.     

Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree species Alnus glutinosa

The adaptive potential of tree species to cope with climate change has important ecological and economic implications. Many temperate tree species experience a wide range of environmental conditions, suggesting high adaptability to new environmental conditions. We investigated adaptation to regional climate in the drought‐sensitive tree species Alnus glutinosa (Black alder), using a complementary approach that integrates genomic, phenotypic and landscape data. A total of 24 European populations were studied in a common garden and through landscape genomic approaches. Genotyping‐by‐sequencing was used to identify SNPs across the genome, resulting in 1990 SNPs. Although a relatively low percentage of putative adaptive SNPs was detected (2.86% outlier SNPs), we observed clear associations among outlier allele frequencies, temperature and plant traits. In line with the typical drought avoiding nature of A. glutinosa, leaf size varied according to a temperature gradient and significant associations with multiple outlier loci were observed, corroborating the ecological relevance of the observed outlier SNPs. Moreover, the lack of isolation by distance, the very low genetic differentiation among populations and the high intrapopulation genetic variation all support the notion that high gene exchange combined with strong environmental selection promotes adaptation to environmental cues.     

Geomorphological disturbance affects ecological driving forces and plant turnover along an altitudinal stress gradient on alpine slopes

The altitudinal gradient is considered as a stress gradient for plant species because the development and fitness of plant communities tend to decrease as a result of the extreme environmental conditions present at high elevations. Abiotic factors are predicted to be the primary filter for species assemblage in high alpine areas, influencing biotic interactions through both competition for resources and positive interactions among species. We hypothesised that the relative importance of the ecological driving forces that affect the biotic interactions within plant communities changes along an elevation gradient on alpine debris slopes. We used multiple gradient analyses of 180 vegetation plots along an altitudinal range from ~1,600 to 2,600 m and single 100 m-bands in the Adamello-Presanella Group (Central Alps) to investigate our hypothesis; we measured multiple environmental variables related to different ecological driving forces. Our results illustrate that resource limitations at higher elevations affect not only the shift from competition to facilitation among species. A geomorphological disturbance regime along alpine slopes favours the resilience of the high-altitude species within topographic/geomorphological traps. An understanding of the ecological driving forces and positive interactions as a function of altitude may clarify the mechanisms underlying plant responses to present and future environmental changes.     

Ecology,environment and evolutionary history influence genetic structure in five mammal species from the Italian Alps

The identification and evaluation of the ecological and environmental factors shaping patterns of natural genetic variation are fundamental goals of population and conservation genetics. Many studies focus on factors affecting single species, but it is also important to test whether some influential biotic and abiotic factors are common drivers of genetic diversity across species, or if species or species groups are each affected by different forces; a multi‐species analysis is necessary for this. Here we analysed the molecular variation from five mammal species (roe deer, red deer, chamois, mountain hare and European brown hare) at mtDNA and microsatellite loci from the eastern Italian Alps. We use phylogeographical and landscape‐level analyses to test the relative influence of large‐scale geographical history and contemporary environmental characteristics of the landscape on genetic diversity and differentiation. We found: (1) all study species except brown hare are strongly differentiated into two main groups, located west and east of a major river valley; (2) significant correlations between levels of within‐population diversity at both mtDNA and microsatellite loci, and several landscape features such as alpine grassland, water courses and anthropized areas. We conclude that heterogeneous landscape has some influence on within‐population diversity, but biogeographical history has probably had the stronger influence on current genetic patterns, despite an apparently large dispersal potential of certain species. However, our results for brown hare show that management actions such as stocking may alter these large‐scale patterns.     

Break zones in the distributions of alleles and species in alpine plants

Aim We test for the congruence between allele‐based range boundaries (break zones) in silicicolous alpine plants and species‐based break zones in the silicicolous flora of the European Alps. We also ask whether such break zones coincide with areas of large elevational variation. Location The European Alps. Methods On a regular grid laid across the entire Alps, we determined areas of allele‐ and species‐based break zones using respective clustering algorithms, identifying discontinuities in cluster distributions (breaks), and quantifying integrated break densities (break zones). Discontinuities were identified based on the intra‐specific genetic variation of 12 species and on the floristic distribution data from 239 species, respectively. Coincidence between the two types of break zones was tested using Spearman’s correlation. Break zone densities were also regressed on topographical complexity to test for the effect of elevational variation. Results We found that two main break zones in the distribution of alleles and species were significantly correlated. Furthermore, we show that these break zones are in topographically complex regions, characterized by massive elevational ranges owing to high mountains and deep glacial valleys. We detected a third break zone in the distribution of species in the eastern Alps, which is not correlated with topographic complexity, and which is also not evident from allelic distribution patterns. Species with the potential for long‐distance dispersal tended to show larger distribution ranges than short‐distance dispersers. Main conclusions We suggest that the history of Pleistocene glaciations is the main driver of the congruence between allele‐based and species‐based distribution patterns, because occurrences of both species and alleles were subject to the same processes (such as extinction, migration and drift) that shaped the distributions of species and genetic lineages. Large elevational ranges have had a profound effect as a dispersal barrier for alleles during post‐glacial immigration. Because plant species, unlike alleles, cannot spread via pollen but only via seed, and thus disperse less effectively, we conclude that species break zones are maintained over longer time spans and reflect more ancient patterns than allele break zones.     

Can the effect of species ecological traits on birds' altitudinal changes differ between geographic areas?

The altitudinal distribution of mountain birds has recently changed following different patterns in space and time, probably due to the variability of the ongoing environmental processes. Although several studies have highlighted the effect of climate warming in affecting birds altitudinal responses, in the Alps, land abandonment and the consequential forest regrowth may have played a fundamental role.We applied the response curve shape method to investigate changes in the altitudinal distribution of breeding birds over a ten-year period in two different alpine areas (Central and Western Italian Alps) and we performed a log-linear analysis to depict the differential responses of species grouped according to their breeding habitat preferences.The patterns of change remarkably differed according to species ecological traits and between mountain areas. We did not highlight clear altitudinal changes in the Central Alps for any ecological groups, while in the Western Alps, woodland birds showed an expansion pattern and grassland birds suffered a retraction pattern. Since the two alpine areas did not suffer a significant temperature increase, but experienced different woodland cover dynamics, we believe that forest regrowth played a key role in shaping the different bird altitudinal responses between the two sites.Our findings illustrate the effect of ecological traits in shaping altitudinal changes and the role of local environmental factors in affecting spatial variation. Particularly, we strongly suggest considering woodland cover expansion as a key driver of bird altitudinal changes in alpine areas.     

Glacial survival and local adaptation in an alpine leaf beetle

The challenge in defining conservation units so that they represent evolutionary entities has been to combine both genetic properties and ecological significance. Here we make use of the complexity of the European Alps, with their genetic landscape shaped by geographical barriers and postglacial colonization, to examine the correlation between ecological and genetic divergence. Montane species, because of the fragmentation of their present habitat, constitute extreme cases in which to test if genetically distinct subgroups based on neutral markers are also ecologically differentiated and show local adaptation. In the leaf beetle Oreina elongata, populations show variation in host plant use and a patchy distribution throughout the Alps and Apennines. We demonstrate that despite very strong genetic isolation (F(ST) = 0.381), variation in host plant use has led to differences in larval life-history traits between populations only as a secondary effect of host defence chemistry, and not through physiological adaptation to plant nutritional value. We also establish that populations that are more ecologically different in terms of larval performance are also more genetically divergent. In addition, morphological variation used to define subspecies appears to be mirrored in the population genetics of this species, resulting in almost perfect clustering based on microsatellite data. Finally, we argue from their strong genetic structure and congruent distribution that the subspecies of O. elongata were divided among the same glacial refugia within the Alps that have been proposed for alpine plants.     

A biogeographic delineation of the European Alpine System based on a cluster analysis of Carex curvula-dominated grasslands

Biogeographic delineations within the European temperate mountains remain poorly understood, as there has been little effort to assemble and analyze vegetation relevés covering Pyrenees, Alps, Carpathians and Balkans altogether. Our study tackles this issue by focusing on the widely distributed alpine acidic grasslands dominated by Carex curvula. Cluster analysis of more than 800 vegetation relevés revealed the European-scale spatial patterns of vascular plant diversity in these alpine grasslands. The geographical distribution of floristic clusters was partly congruent with the physiography of European mountains. Southern European ranges (Southern Balkans and Pyrenees) exhibit a high level of endemism and corresponding floristic clusters are well separated from the others. Marked floristic similarities between the Easternmost Alps, the Carpathians, and the Northern Balkans (Stara Planina) supported a major floristic boundary that runs through the Austrian Alps and that is likely the legacy of a shared Quaternary history. Within the Alps, floristic clustering was mainly driven by ecological drivers and not geography. This paper presents the first detailed study of spatial patterns of species distribution within the European Alpine System, based on a comprehensive analysis of within- and between-community species diversity. It shows that the quantitative analysis of large and consistent data sets may question the traditional delineations of biogeographic regions within European mountains.     

Detecting adaptive evolution based on association with ecological gradients: Orientation matters!

Population genetic signatures of local adaptation are frequently investigated by identifying loci with allele frequencies that exhibit high correlation with ecological variables. One difficulty with this approach is that ecological associations might be confounded by geographic variation at selectively neutral loci. Here, we consider populations that underwent spatial expansion from their original range, and for which geographical variation of adaptive allele frequency coincides with habitat gradients. Using range expansion simulations, we asked whether our ability to detect genomic regions involved in adaptation could be impacted by the orientation of the ecological gradients. For three ecological association methods tested, we found, counter-intuitively, fewer false-positive associations when ecological gradients aligned along the main axis of expansion than when they aligned along any other direction. This result has important consequences for the analysis of genomic data under non-equilibrium population genetic models. Alignment of gradients with expansion axes is likely to be common in scenarios in which expanding species track their ecological niche during climate change while adapting to changing environments at their rear edge.     

Alien plant species distribution in the European Alps: influence of species’ climatic requirements

The paper provides the first estimate of the role of abiotic and anthropogenic variables driving both alien plant species richness and composition covering the whole region of the European Alps. To establish and spread in a new area, alien plants must be able to tolerate the prevailing climatic conditions. We therefore tested the hypothesis that climatic requirements modified by bioclimatic origin and elevational distribution influence the distribution of alien plants in the Alps. Despite most alien plant species showing a relatively restricted distribution in the Alps, some regions, however, were already more strongly invaded. Most of these species were adapted to warmer conditions, probably constrained by climatic factors. Environmental heterogeneity was the most important predictor of alien plant species richness, followed by anthropogenic disturbance. Due to the political/artificial delineation of the administrative districts in the Alps (i.e., ignoring ecological conditions) we did not find a direct influence of climatic constraints on alien distribution. Anyway, northern Holarctic alien species showed a broader climatic tolerance and the capability to grow across a wide environmental range. Our results also reveal a strong influence of human pressure on warmer tropical species, despite their low adaptability to anthropogenic habitats. To this aim, managers would profit from early warnings to prevent future invasions. Considering bioclimatic origin, our study can aid in identifying potentially invasive species in a more regional setting.     

Relative importance of spatial processes and environmental factors in shaping alpine meadow communities

Aims Spatial processes and environmental control are the two distinct, yet not mutually exclusive forces of community structuring, but the relative importance of these factors is controversial due to the species-specific dispersal ability, sensitivity towards environmental variables, organism's abundance and the effect of spatial scale. In the present paper, we explored spatial versus environmental control in shaping community composition (i.e. β-diversity) and species turnover (i.e. change of β-diversity) at an alpine meadow along a slope aspect gradient on the Qinghai–Tibetan Plateau at different spatial scales of sampling (quadrats and plots), by taking account of seed dispersal mode and abundance.Methods We examined the relative importance of spatial processes and environmental factors using all species and four additional subsets of selected species. Moreover, we attempted to explore the effect of scale (quadrat refers to scale of ~0.3 m and plot of ~8 m) on their counter balance. The data were analyzed both by variation partitioning and multiple regressions on distance matrices. The spatial structure was modelled using Moran's eigenvector maps (MEM).Important findings Both spatial processes and environmental factors were important determinants of the community composition and species turnover. The community composition in the alpine meadow was controlled by spatially structured environment (17.6%), space independent of environment (18.0%) and a negligible effect of environment independent of space (4.4%) at the scale of quadrats. These three components contributed 21.8, 9.9 and 13.9%, respectively, at the scale of plots. The balance between the forces at different spatial scales drove community structures along the slope aspect gradient. The importance of environmental factors on β-diversity at alpine meadow increased with scale while that of spatial processes decreased or kept steady, depending on dispersal mode and abundance of species comprising the subset. But the 'pure' effect of spatial processes on species turnover increased with scale while that of environmental factors decreased. This discrepancy highlights that β-diversity and species turnover were determined jointly by spatial processes and environmental factors. We also found that the relative roles of these processes vary with spatial scale. These results underline the importance of considering species-specific dispersal ability and abundance of species comprising the communities and the appropriate spatial scale in understanding the mechanisms of community assembly.     

Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps

Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here, we examine genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool‐Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using F_ST‐based analyses. We tested only the most strongly differentiated SNPs for associations with a nonredundant set of environmental factors using partial Mantel tests to identify topo‐climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo‐climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.     

Genome-Wide Association Analysis of Adaptation Using Environmentally Predicted Traits

Current methods for studying the genetic basis of adaptation evaluate genetic associations with ecologically relevant traits or single environmental variables, under the implicit assumption that natural selection imposes correlations between phenotypes, environments and genotypes. In practice, observed trait and environmental data are manifestations of unknown selective forces and are only indirectly associated with adaptive genetic variation. In theory, improved estimation of these forces could enable more powerful detection of loci under selection. Here we present an approach in which we approximate adaptive variation by modeling phenotypes as a function of the environment and using the predicted trait in multivariate and univariate genome-wide association analysis (GWAS). Based on computer simulations and published flowering time data from the model plant Arabidopsis thaliana, we find that environmentally predicted traits lead to higher recovery of functional loci in multivariate GWAS and are more strongly correlated to allele frequencies at adaptive loci than individual environmental variables. Our results provide an example of the use of environmental data to obtain independent and meaningful information on adaptive genetic variation.     

Environmental and land use determinants of grassland patch diversity in the western and eastern Alps under agro-pastoral abandonment

Agro-pastoral decline in European mountain areas has recently caused changes to traditional landscapes with negative consequences on semi-natural grassland conservation and the associated biodiversity and ecosystem services. In the Italian Alps, grassland patches enclosed in a forest matrix are progressively disappearing. Two alpine valleys (Pesio and Pejo), having similar land-use history, were chosen as representative of management conditions of western and eastern Italian Alps, respectively. This study aims at interpreting the effect of abandonment on grassland patch plant diversity, considering land cover changes of the last 60 years, and assessing the role of ecological, topographic, management and landscape configuration on current grassland species richness. The total area of grassland patches has declined by 54 and 91 % at Pesio and at Pejo, respectively. Actual grassland patch species richness was mostly influenced by ecological factors, such as quantity of light, soil moisture and reaction, then by topographic features, especially slope, and finally by management intensity. Landscape factors exerted a slightly significant effect on plant diversity. In the two valleys, differences on management practices were detected. Even though in the western valley the conservation of several grazing activities contributed to slow down the process of patch reduction, many species-rich grasslands were generally under-grazed. Conversely, in the eastern valley, despite a denser road network, the stronger decline of grassland patch extension was linked to the hay making decline. At the same time, overuse of grassland patches near farms reduced plant species richness. As a conclusion, plant species richness was weakly related to the area of grassland patches and current and historical landscape configuration were of relatively lower importance than ecological, topographic and management factors, when evaluated at patch-level.     

Finding needles in a genomic haystack: targeted capture identifies clear signatures of selection in a nonmodel plant species

Teasing apart neutral and adaptive genomic processes and identifying loci that are targets of selection can be difficult, particularly for nonmodel species that lack a reference genome. However, identifying such loci and the factors driving selection have the potential to greatly assist conservation and restoration practices, especially for the management of species in the face of contemporary and future climate change. Here, we focus on assessing adaptive genomic variation within a nonmodel plant species, the narrow‐leaf hopbush (Dodonaea viscosa ssp. angustissima), commonly used for restoration in Australia. We used a hybrid‐capture target enrichment approach to selectively sequence 970 genes across 17 populations along a latitudinal gradient from 30°S to 36°S. We analysed 8462 single‐nucleotide polymorphisms (SNPs) for F_ST outliers as well as associations with environmental variables. Using three different methods, we found 55 SNPs with significant correlations to temperature and water availability, and 38 SNPs to elevation. Genes containing SNPs identified as under environmental selection were diverse, including aquaporin and abscisic acid genes, as well as genes with ontologies relating to responses to environmental stressors such as water deprivation and salt stress. Redundancy analysis demonstrated that only a small proportion of the total genetic variance was explained by environmental variables. We demonstrate that selection has led to clines in allele frequencies in a number of functional genes, including those linked to leaf shape and stomatal variation, which have been previously observed to vary along the sampled environmental cline. Using our approach, gene regions subject to environmental selection can be readily identified for nonmodel organisms.     

Water–energy,land‐cover and heterogeneity drivers of the distribution of plant species richness in a mountain region of the European Alps

Aim To evaluate the relative importance of water–energy, land‐cover, environmental heterogeneity and spatial variables on the regional distribution of Red‐Listed and common vascular plant species richness. Location Trento Province (c. 6200 km²) on the southern border of the European Alps (Italy), subdivided regularly into 228 3′ × 5′ quadrants. Methods Data from a floristic inventory were separated into two subsets, representing Red‐Listed and common (i.e. all except Red‐Listed) plant species richness. Both subsets were separately related to water–energy, land‐cover and environmental heterogeneity variables. We simultaneously applied ordinary least squares regression with variation partitioning and hierarchical partitioning, attempting to identify the most important factors controlling species richness. We combined the analysis of environmental variables with a trend surface analysis and a spatial autocorrelation analysis. Results At the regional scale, plant species richness of both Red‐Listed and common species was primarily related to energy availability and land cover, whereas environmental heterogeneity had a lesser effect. The greatest number of species of both subsets was found in quadrants with the largest energy availability and the greatest degree of urbanization. These findings suggest that the elevation range within our study region imposes an energy‐driven control on the distribution of species richness, which resembles that of the broader latitude gradient. Overall, the two species subsets had similar trends concerning the relative importance of water–energy, land cover and environmental heterogeneity, showing a few differences regarding the selection of some predictors of secondary importance. The incorporation of spatial variables did not improve the explanatory power of the environmental models and the high original spatial autocorrelation in the response variables was reduced drastically by including the selected environmental variables. Main conclusions Water–energy and land cover showed significant pure effects in explaining plant species richness, indicating that climate and land cover should both be included as explanatory variables in modelling species richness in human‐affected landscapes. However, the high degree of shared variation between the two groups made the relative effects difficult to separate. The relatively low range of variation in the environmental heterogeneity variables within our sampling domain might have caused the low importance of this complex factor.     

Environmental factors prevail over dispersal constraints in determining the distribution and assembly of Trichoptera species in mountain lakes

Aiming to elucidate whether large‐scale dispersal factors or environmental species sorting prevail in determining patterns of Trichoptera species composition in mountain lakes, we analyzed the distribution and assembly of the most common Trichoptera (Plectrocnemia laetabilis, Polycentropus flavomaculatus, Drusus rectus, Annitella pyrenaea, and Mystacides azurea) in the mountain lakes of the Pyrenees (Spain, France, Andorra) based on a survey of 82 lakes covering the geographical and environmental extremes of the lake district. Spatial autocorrelation in species composition was determined using Moran's eigenvector maps (MEM). Redundancy analysis (RDA) was applied to explore the influence of MEM variables and in‐lake, and catchment environmental variables on Trichoptera assemblages. Variance partitioning analysis (partial RDA) revealed the fraction of species composition variation that could be attributed uniquely to either environmental variability or MEM variables. Finally, the distribution of individual species was analyzed in relation to specific environmental factors using binomial generalized linear models (GLM). Trichoptera assemblages showed spatial structure. However, the most relevant environmental variables in the RDA (i.e., temperature and woody vegetation in‐lake catchments) were also related with spatial variables (i.e., altitude and longitude). Partial RDA revealed that the fraction of variation in species composition that was uniquely explained by environmental variability was larger than that uniquely explained by MEM variables. GLM results showed that the distribution of species with longitudinal bias is related to specific environmental factors with geographical trend. The environmental dependence found agrees with the particular traits of each species. We conclude that Trichoptera species distribution and composition in the lakes of the Pyrenees are governed predominantly by local environmental factors, rather than by dispersal constraints. For boreal lakes, with similar environmental conditions, a strong role of dispersal capacity has been suggested. Further investigation should address the role of spatial scaling, namely absolute geographical distances constraining dispersal and steepness of environmental gradients at short distances.     

Signals of range expansions and contractions of vascular plants in the high Alps: observations (1994–2004) at the GLORIA* master site Schrankogel,Tyrol, Austria

High mountain ecosystems are defined by low temperatures and are therefore considered to react sensitively to climate warming. Responding to observed changes in plant species richness on high peaks of the European Alps, an extensive setup of 1 m × 1 m permanent plots was established at the alpine‐nival ecotone (between 2900 and 3450 m) on Mount Schrankogel, a GLORIA master site in the central Tyrolean Alps, Austria, in 1994. Recording was repeated in a representative selection of 362 quadrats in 2004. Ten years after the first recording, we observed an average change in vascular plant species richness from 11.4 to 12.7 species per plot, an increase of 11.8% (or of at least 10.6% at a 95% confidence level). The increase in species richness involved 23 species (about 43% of all taxa found at the ecotone), comprising both alpine and nival species and was pronouncedly higher in plots with subnival/nival vegetation than in plots with alpine grassland vegetation. Only three species showed a decrease in plot occupancy: one was an annual species, one was rare, and one a common nival plant that decreased in one part of the area but increased in the uppermost part. Species cover changed in relation to altitudinal preferences of species, showing significant declines of all subnival to nival plants, whereas alpine pioneer species increased in cover. Recent climate warming in the Alps, which has been twice as high as the global average, is considered to be the primary driver of the observed differential changes in species cover. Our results indicate an ongoing range contraction of subnival to nival species at their rear (i.e. lower) edge and a concurrent expansion of alpine pioneer species at their leading edge. Although this was expected from predictive distribution models and different temperature‐related habitat preferences of alpine and nival species, we provide first evidence on – most likely – warming‐induced species declines in the high European Alps. The projected acceleration of climate warming raises concerns that this phenomenon could become the major threat to biodiversity in high mountains.