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Gloydius is a widespread pitviper group occurring from Eastern Europe to Korea and Siberia, with only one known species, G. himalayanus (Günther, 1864), found south of the Himalayas. We provide combined genetic and morphological data for G. himalayanus from specimens collected from Himachal Pradesh, India. Bayesian Inference and Maximum Likelihood phylogenetic analysis were performed on four concatenated mitochondrial genes, along with a multi-locus coalescent analysis of these and five additional nuclear genes. Our results indicate that G. himalayanus from the Chamba Valley, in western Himachal Pradesh, are highly distinct from the remaining studied populations. Haplotype networks of each nuclear locus showed that G. himalayanus contains high haplotype diversity with low haplotype sharing between the Chamba Valley population and populations from further west. Principal component analysis and canonical variate analysis conducted on morphological data of live and museum specimens also highlight the morphological distinctiveness of the Chamba population and we herein describe this population as a new species, Gloydius chambensis sp. nov. Recent descriptions of other new species of snakes from this valley underscores its isolation and suggests that further herpetological investigation of the highly dissected landscapes of the western Himalayas is needed to assess the true diversity of the region.
Highlights
• Genomes for all five Natrix species, two represented by two distinct subspecies each, were sequenced.
• Two genomes were de-novo assembled to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp.
• Evidence for interspecific hybridization, both between allopatric and widely sympatric species.
• Fossil-calibrated molecular clock using genomes indicates that species are ancient several million-year-old lineages.
• Our findings imply that speciation took place despite continued gene flow.
Abstract
Understanding speciation is one of the cornerstones of biological diversity research. Currently, speciation is often understood as a continuous process of divergence that continues until genetic or other incompatibilities minimize or prevent interbreeding. The Palearctic snake genus Natrix is an ideal group to study speciation, as it comprises taxa representing distinct stages of the speciation process, ranging from widely interbreeding parapatric taxa through parapatric species with very limited gene flow in narrow hybrid zones to widely sympatric species. To understand the evolution of reproductive isolation through time, we have sequenced the genomes of all five species within this genus and two additional subspecies. We used both long-read and short-read methods to sequence and de-novo-assemble two high-quality genomes (Natrix h. helvetica, Natrix n. natrix) to their 1.7 Gb length with a contig N50 of 4.6 Mbp and 1.5 Mbp, respectively, and used these as references to assemble the remaining short-read-based genomes. Our phylogenomic analyses yielded a well-supported dated phylogeny and evidence for a surprisingly complex history of interspecific gene flow, including between widely sympatric species. Furthermore, evidence for gene flow was also found for currently allopatric species pairs. Genetic exchange among these well-defined, distinct, and several million-year-old reptile species emphasizes that speciation and maintenance of species distinctness can occur despite continued genetic exchange.