Genome‐wide single nucleotide polymorphisms reveal recurrent waves of speciation in niche‐pockets, in Europe's most venomous snake

Abstract

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 (i) utilized genome-wide single nucleotide polymorphisms to infer genetic structure and build a time-calibrated speciestree, and (ii) applied species distribution modelling 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 (Pindos Mountain Range, the Cyclades islands, etc.), but in most cases speciation is incomplete. At the other end of the speciation continuum, we recognize two well-differentiated lineages, currently lacking any evidence of gene flow; one is distributed in the Northwestern Balkans and the other in the Southeastern Balkans, further expanding into Asia.Despite their split 5 million years ago, there is no evidence of ecological divergence, as speciation probably occurred in niche-pockets of analogous environments. These two lineages probably represent different species, while V. transcaucasiana does not merit species status. By comparing the genomic phylogenies to an updated mitochondrial one, we propose an evolutionary scenario that resolves all mitonuclear conflicts, according to which the history of the V. ammodytes species-complex was shaped by complex processes, including a major event of introgressive hybridization with asymmetric mitochondrial capture.

Venomics and Peptidomics of Palearctic vipers: Clade-wide analysis of seven taxa of the generaVipera,Montivipera,MacroviperaandDaboiaacross Türkiye

“…The Pelias group includes the common adder V. berus and meadow vipers of the V. ursinii-renardi complex. The other two groups in Vipera 1, comprising Vipera aspis , Vipera latastei and Vipera monticola, and Vipera 2, the nose-horned viper V. ammodytes-meridionalis complex, with its most recent changes 88 . Several of those species are of medical relevance in Europe, i.a.…”

Hidden in the sand: phylogenomics unravel an unexpected evolutionary history on the desert-adapted vipers of the genusCerastes

“…We used BEAST2 v.2.6.4 (Bouckaert et al, 2019) to reconstruct a Bayesian Inference (BI) time-calibrated tree. We calibrated the phylogeny dating the deepest node in the phylogeny (between Echis and Cerastes ), as suggested by Stange et al, (2018) and also implemented in previous studies focused on reptiles (Burriel-Carranza et al, 2023a, 2023b; Thanou et al 2023), with a normal distribution from a mean age of 28 million years ago (Mya) (Šmíd & Tolley, 2019) and encompassing a 95% HPD interval (25.65-31.55 Mya). We selected a GTR model with four gamma categories (base frequencies and proportion of invariant sites were estimated), and a relaxed clock LogNormal was used with a coalescent constant population tree prior.…”