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Genomic evidence reveals intraspecific divergence in the Hot-spring snake Thermophis baileyi, an endemic reptile of the Qinghai-Tibet Plateau
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  • Chaochao Yan,
  • Meng-Huan Song,
  • Dechun Jiang,
  • Jin-Long Ren,
  • Yunyun Lv,
  • Hussam Zaher,
  • Jiatang Li
Chaochao Yan
Chengdu Institute of Biology

Corresponding Author:[email protected]

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Meng-Huan Song
Chengdu Institute of Biology
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Dechun Jiang
Chengdu Institute of Biology
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Jin-Long Ren
Chengdu Institute of Biology
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Yunyun Lv
Chengdu Institute of Biology, Chinese Academy of Sciences,
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Hussam Zaher
Universidade de São Paulo
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Jiatang Li
Chengdu Institute of Biology, Chinese Academy of Sciences
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Abstract

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.