Pleistocene climate oscillations influenced the biogeographical history of most species. In the European Alps, mountain plants were restricted to refugial areas during cold phases of glacial cycles and recolonized newly available habitats during warm periods. The current ranges of alpine plants represent a transient stage of a continuous and dynamic recolonization process that started after the last glaciations. Differences in recolonization rate and range filling are observed between different mountain plant species, but the reasons remain insufficiently explored. Here, we investigated hybridization between two related willow species pairs that came into secondary contact to assess contemporary dynamics of selection and the potential effects of hybrid zones on range expansion. RAD sequencing data was used to infer the biogeographical history of each species pair, to characterize individuals across the whole distribution area including the secondary contact zones, and to quantify patterns of genomic clines. Genetic results were supported by morphometric measurements, ecological data, and species distribution modeling. Results suggest that peripheral glacial refugia played a major role in the history of the species. For both species' pairs, the secondary contact zones showed homoploid hybridization between parents, which is also supported by the morphometric analyses. Habitat preferences showed large overlaps of parental species and a broad range of niches for the hybrids. One hybrid zone is geographically broader than expected and characterized by introgression, while the other one is narrow and shows asymmetric patterns. Current projections of species distributions identified suitable habitats beyond the secondary contact zone, suggesting an incomplete range filling.

Polyploids recurrently emerge in angiosperms, but most polyploids are likely to go extinct before establishment due to minority cytotype exclusion, which may be specifically a constraint for dioecious plants to evolve polyploid populations. Investigations into the frequency and distribution of polyploids in natural populations is thus necessary for understanding polyploid evolution in plants. This study determined the ploidy levels of 28 populations and 351 individuals of Salix polyclona, and identified the type of polyploidy (auto- vs. allo-) using whole genome re-sequencing data. We further investigated the phylogeny, population genetic diversity and species range shifts to explore the origin and spatiotemporal evolution of the polyploid complex. Our analyses revealed a high frequency (52%) of autopolyploids in it with a clear geographic distribution confined to the western part of its range where complex mountain systems create higher levels of environmental heterogeneity. Comparisons of diploid male and female genomes suggested a female heterogametic sex-determining factor on chromosome 15, which likely also acts in the dioecious polyploids. Fossil-calibrated phylogeny showed a more recent diversification of the polyploids (ca. 2.3 Ma) than the diploid (ca. 6.2 Ma), and population demographic histories largely corroborated the geological and climatic history of the region. Our results suggest that climatic oscillations and uplift of eastern Qinghai-Tibetan Plateau and the connecting mountains may have facilitated the preservation and establishment of polyploid populations. This study provides an example of the evolution of a diploid-polyploid complex in a willow species and illustrates a role of polyploidization in mountain biodiversity.