Genomic evidence reveals intraspecific divergence in the Hot-spring
snake Thermophis baileyi, an endemic reptile of the Qinghai-Tibet
Understanding how and why species evolve often requires knowledge of
intraspecific divergence. In this study, we examine intraspecific
divergence in the endangered hot spring snake Thermophis baileyi, an
endemic species of the Qinghai-Tibet Plateau. Genomic analyses using a
hybrid assembly strategy resulted in a revised, high-quality genome.
Whole-genome re-sequencing of 31 sampled individuals from 15 sites
served to identify drivers of intraspecific divergence, and explore the
potential role gene selection plays in divergence. Our analyses resolved
three groups, with inter-group admixture occurring in regions of
contact. Divergence seems to have occurred during the Pleistocene
because of glacial climatic oscillations and geomorphological changes.
Highly diverged regions (HDRs) that distinguish the groups most likely
owe to gene sorting. Inter-group HDRs involve genes under positive
selection that putatively relate functionally to ecological divergence,
and especially reproduction. Our findings reveal the need to integrate
multiple aspects to distinguish evolutionary processes potentially
involved in speciation.