Genomic analyses reveal three phylogenetic species and their evolutionary histories in the big-headed turtle

Shiping Gong; Chatmongkon Suwannapoom; Minh Le; Truong Quang Nguyen; Yan Ge; Yufeng Wei; Yangchun Gao

doi:10.1016/j.isci.2023.107343

Genomic analyses reveal three phylogenetic species and their evolutionary histories in the big-headed turtle

iScience. 2023 Jul 10;26(8):107343. doi: 10.1016/j.isci.2023.107343. eCollection 2023 Aug 18.

Authors

Shiping Gong^{1

2}, Chatmongkon Suwannapoom³, Minh Le^{4

5}, Truong Quang Nguyen⁶, Yan Ge², Yufeng Wei², Yangchun Gao²

Affiliations

¹ College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
² Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, 105 Xingang Road West, Guangzhou 510260, China.
³ School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand.
⁴ Faculty of Environmental Sciences, University of Science & Central Institute for Natural Resources and Environmental Studies (CRES), Vietnam National University, Hanoi, Vietnam.
⁵ Department of Herpetology, American Museum of Natural History, New York, NY, USA.
⁶ Institute of Ecology and Biological Resources, Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi 10072, Vietnam.

Abstract

The critically endangered big-headed turtle (Platysternon megacephalum) is currently classified into three subspecies. However, the classification is still controversial and their evolutionary histories are still unclear. Here, multiple genetic analyses consistently revealed three phylogenetic groups with substantial genetic divergences and distinct demographic histories, suggesting three phylogenetic species (P. megacephalum, P. peguense, and Baise clade). Phylogeographical analyses revealed that the Red River plains and Guangxi basins are largely coincident with the boundaries between the three phylogenetic species, highlighting the key role of lowland areas in driving speciation in the big-headed turtle. The Baise clade is characterized by high-linkage disequilibrium but the lowest effective population size, indicating that the cryptic phylogenetic species is more vulnerable to human activities and environmental disturbance, and urgently needs more protection. Our findings provide fundamental insights into the taxonomy and scientific conservation of the family Platysternidae.

Keywords: Biological classification; Evolutionary biology; Phylogenetics; Zoology.