Genome-wide SNPs reveal recurrent waves of speciation in niche-pockets, in Europe’s most venomous snake

Within the Balkan Peninsula, topographic and climatic agents have promoted biodiversity and shaped the speciation history of many ectotherms. Here, we targeted an iconic European reptile, the nose-horned viper species-complex (Vipera ammodytes), and explored its spatial and temporal evolution. We (1) utilized genome-wide SNPs to infer genetic structure and build a time-calibrated species tree, and (2) applied species distribution modeling (SDM) with niche-divergence tests among major phylogenomic clades. Geographically structured genetic diversity was found. Cycles of recurrent isolation and expansion during glacial–interglacial periods led to allopatric speciation and to secondary contacts and formation of multiple hybrid zones throughout the Balkan Peninsula. Deep divergence is still detected among populations separated by old and imminent biogeographical barriers (e.g. Pindos Mountain Range, the Cyclades islands, etc.), but in most cases, speciation is incomplete. At the other end of..., Please find details in the \"Materials and Methods\" section and the Supplementary material from the main paper., The appropriate program to open each datafile is provided in the READme document and more details are available in the \"Materials and Methods\" section and the Supplementary material from the main paper. All datafiles, except \"TREEMIX_75.gz\", can be also opened in any text editor.