Genomic analysis reveals deep population divergence in the water snake Trimerodytes percarinatus (Serpentes, Natricidae)

Author:

Lyu Bing12ORCID,Liu Qin2,Wu Yayong2ORCID,Nguyen Truong Q.34,Che Jing5ORCID,Nguyen Sang N.6,Myers Edward A.7,Burbrink Frank T.8ORCID,Guo Peng2ORCID,Wang Jichao1ORCID

Affiliation:

1. Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences Hainan Normal University Haikou China

2. Faculty of Agriculture, Forestry and Food Engineering Yibin University Yibin China

3. Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam

4. Vietnam Academy of Science and Technology Graduate University of Science and Technology Hanoi Vietnam

5. State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology Chinese Academy of Sciences Kunming China

6. Institute of Tropical Biology Vietnam Academy of Science and Technology Ho Chi Minh City Vietnam

7. Department of Herpetology California Academy of Sciences San Francisco California USA

8. Department of Herpetology American Museum of Natural History New York New York USA

Abstract

AbstractAlthough several phylogeographic studies of Asian snakes have been conducted, most have focused on pitvipers, with non‐venomous snakes, such as colubrids or natricids, remaining poorly studied. The Chinese keelback water snake (Trimerodytes percarinatus Boulenger) is a widespread, semiaquatic, non‐venomous species occurring in China and southeastern Asia. Based on mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data, we explored the population genetic structure, genetic diversity, and evolutionary history of this species. MtDNA‐based phylogenetic analysis showed that T. percarinatus was composed of five highly supported and geographically structured lineages. SNP‐based phylogenetic analysis, principal component analysis, and population structure analysis consistently revealed four distinct, geographically non‐overlapping lineages, which was different from the mtDNA‐based analysis in topology. Estimation of divergence dates and ancestral area of origin suggest that T. percarinatus originated ~12.68 million years ago (95% highest posterior density: 10.36–15.96 Mya) in a region covering southwestern China and Vietnam. Intraspecific divergence may have been triggered by the Qinghai‐Xizang Plateau uplift. Population demographics and ecological niche modeling indicated that the effective population size fluctuated during 0.5 Mya and 0.002 Mya. Based on the data collected here, we also comment on the intraspecific taxonomy of T. percarinatus and question the validity of the subspecies T. p. suriki.

Funder

National Foundation for Science and Technology Development

Publisher

Wiley

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