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Societal Impact Statement: Native medicinal plants contribute essential health benefits to populations globally, constituting a major natural resource that human societies rely on. Being an integral part of terrestrial biodiversity, medicinal plants are detrimentally affected by ongoing climate and land‐use change, yet comprehensive studies on the risk that extinction will pose to medicinal biodiversity are lacking. Responding to ongoing scientific calls for conserving medicinal biodiversity, this study provides an integrated assessment of the impacts of environmental change on ironwort (Sideritis), a group of closely related endemic plants of great cultural significance as local medicinal resources in the Balkan Mountains. Summary: Mountain habitats harbour unique biodiversity and provide vital resources for human well‐being, including natural medicinal resources, yet they are amongst the environments most impacted by global change. While there is ample evidence of recent rapid climate and land‐use change on mountain ecosystems, the impacts of these processes on the habitats of culturally important medicinal plants are still poorly understood. Here, we assess the potential loss of mountain habitats for medicinal plant resources over the past four decades using the culturally important ironwort, a group of endemic medicinal plants of the Balkan Mountains extensively used by local human populations and the pharmaceutical industry for treating cough and cold and gastrointestinal disorders.We used information collected from major European natural history museums to guide extensive field campaigns across 15 separate mountain ranges. We integrate field data with thousands of satellite images, station‐validated climate reanalysis data and habitat suitability modelling. We finally used machine learning to assess the relative roles of climate and vegetation rates of change in driving rates of habitat suitability change.We show that rising temperatures and 'mountain greening' erode the habitats of ironwort at alarming rates. About 50% of the total habitat area across all considered mountain ranges shows a significant decline in habitat suitability.These past trends will most likely continue in the future and could lead to widespread local extinction of the species and other medicinal plants that share similar ecological preferences, threatening their future contributions to societal well‐being. [ABSTRACT FROM AUTHOR]

Summary: Introgression is an important source of genetic variation that can determine species adaptation to environmental conditions. Yet, definitive evidence of the genomic and adaptive implications of introgression in nature remains scarce.The widespread hybrid zones of Darwin's primroses (Primula elatior, Primula veris, and Primula vulgaris) provide a unique natural laboratory for studying introgression in flowering plants and the varying permeability of species boundaries.Through analysis of 650 genomes, we provide evidence of an introgressed genomic region likely to confer adaptive advantage in conditions of soil toxicity. We also document unequivocal evidence of chloroplast introgression, an important precursor to species‐wide chloroplast capture. Finally, we provide the first evidence that the S‐locus supergene, which controls heterostyly in primroses, does not introgress in this clade.Our results contribute novel insights into the adaptive role of introgression and demonstrate the importance of extensive genomic and geographical sampling for illuminating the complex nature of species boundaries. [ABSTRACT FROM AUTHOR]

Summary: Biodiversity hotspots, such as the Caucasus mountains, provide unprecedented opportunities for understanding the evolutionary processes that shape species diversity and richness. Therefore, we investigated the evolution of Primula sect. Primula, a clade with a high degree of endemism in the Caucasus.We performed phylogenetic and network analyses of whole‐genome resequencing data from the entire nuclear genome, the entire chloroplast genome, and the entire heterostyly supergene. The different characteristics of the genomic partitions and the resulting phylogenetic incongruences enabled us to disentangle evolutionary histories resulting from tokogenetic vs cladogenetic processes. We provide the first phylogeny inferred from the heterostyly supergene that includes all species of Primula sect. Primula.Our results identified recurrent admixture at deep nodes between lineages in the Caucasus as the cause of non‐monophyly in Primula. Biogeographic analyses support the 'out‐of‐the‐Caucasus' hypothesis, emphasizing the importance of this hotspot as a cradle for biodiversity.Our findings provide novel insights into causal processes of phylogenetic discordance, demonstrating that genome‐wide analyses from partitions with contrasting genetic characteristics and broad geographic sampling are crucial for disentangling the diversification of species‐rich clades in biodiversity hotspots. [ABSTRACT FROM AUTHOR]

Aim: Late Quaternary glaciations left an enduring imprint on the distribution of species and their genetic structure. The responses of plants endemic to the Alps can be summarized in three major demographic hypotheses: (i) post‐glacial expansion hypothesis; (ii) post‐glacial contraction hypothesis; and (iii) long‐term stability hypothesis. Here we test these hypotheses and reconstruct the time and extent of demographic responses of an endemic plant to the Late Quaternary climate dynamics. Location: European Alps. Taxon: Berardia subacaulis Vill. (Asteraceae). Methods: We used species distribution models to estimate the paleodistribution of B. subacaulis (Asteraceae) throughout the last 28 Ky and generated genome‐wide sequences to estimate current patterns of spatial structure of genetic diversity. We tested five demographic models by integrating the results of the two independent approaches in an Approximate Bayesian Computation framework. Results: The species has weak genetic differentiation among populations, with two main genetic groups. Species distribution models showed a reduction in potentially suitable areas for B. subacaulis during the post‐glacial climate warming and demographic models identified a recent split (2.46 Kya) between the two genetic groups and they slightly supported the post glacial contraction hypothesis. Main conclusions: Taken together, our results support the post‐glacial contraction of an endemic plant, differing from the main pattern observed for endemics species in the European Alps during the Late Quaternary. The different pattern observed in B. subacaulis might be due to several factors, including the less severe effects of glaciations and the environmental heterogeneity of the South Western Alps, combined with some features of the species (i.e. poor dispersal ability, slow growth and microhabitat preferences). Future research in areas where the ice cover was less extensive will contribute to a more complete understanding of the role of climatic changes in shaping the endemics of the European Alps. [ABSTRACT FROM AUTHOR]

Summary: The complex nature of species boundaries has been a central topic in evolutionary biology ever since Darwin. Despite numerous separate studies on reproductive isolation and hybridization, their relationship remains underinvestigated. Are the strengths and asymmetries of reproductive barriers reflected in the extent and directionalities of interspecific genetic exchange?We combined field, experimental, and molecular data to quantify strengths and asymmetries of sympatric reproductive barriers and hybridization between florally heteromorphic primroses. We also assessed whether generalist pollinators discriminate between different floral cues and contribute to reproductive isolation, a long‐debated topic.Sympatric reproductive isolation is high but incomplete, and most phenotypic intermediates are genetic F1 hybrids, whereas backcrosses are rare, revealing low interspecific gene flow. Species integrity rests on multiple barriers, but ethological isolation is among the strongest, demonstrating that even generalist pollinators crucially contribute to the maintenance of species boundaries. Furthermore, reproductive barriers are weaker for Primula veris and short‐styled plants, results corroborated by molecular data. Thus, in florally heteromorphic systems, both species‐ and morph‐dependent asymmetries affect permeability of species boundaries.Our study illustrates how the interactions between complex floral syndromes and pollinators shape species boundaries in unique, previously undescribed ways. [ABSTRACT FROM AUTHOR]

Understanding the effects of past climatic fluctuations on the distribution and population-size dynamics of cold-adapted species is essential for predicting their responses to ongoing global climate change. In spite of the heterogeneity of cold-adapted species, two main contrasting hypotheses have been proposed to explain their responses to Late Quaternary glacial cycles, namely, the interglacial contraction versus the interglacial expansion hypotheses. Here, we use the cold-adapted plant Primula farinosa to test two demographic models under each of the two alternative hypotheses and a fifth, null model. We first approximate the time and extent of demographic contractions and expansions during the Late Quaternary by projecting species distribution models across the last 72 ka. We also generate genome-wide sequence data using a Reduced Representation Library approach to reconstruct the spatial structure, genetic diversity, and phylogenetic relationships of lineages within P. farinosa. Finally, by integrating the results of climatic and genomic analyses in an Approximate Bayesian Computation framework, we propose the most likely model for the extent and direction of population-size changes in P. farinosa through the Late Quaternary. Our results support the interglacial expansion of P. farinosa, differing from the prevailing paradigm that the observed distribution of cold-adapted species currently fragmented in high altitude and latitude regions reflects the consequences of postglacial contraction processes. [ABSTRACT FROM AUTHOR]