TY - JOUR

T1 - Ancient DNA reveals genetic admixture in China during tiger evolution

AU - Sun, Xin

AU - Liu, Yue-Chen

AU - Tiunov, Mikhail P.

AU - Gimranov, Dmitry O.

AU - Zhuang, Yan

AU - Han, Yu

AU - Driscoll, Carlos A.

AU - Pang, Yuhong

AU - Li, Chunmei

AU - Pan, Yan

AU - Velasco, Marcela Sandoval

AU - Gopalakrishnan, Shyam

AU - Yang, Rui-Zheng

AU - Li, Bao-Guo

AU - Jin, Kun

AU - Xu, Xiao

AU - Uphyrkina, Olga

AU - Huang, Yanyi

AU - Wu, Xiao-Hong

AU - Gilbert, M. Thomas P.

AU - O’Brien, Stephen J.

AU - Yamaguchi, Nobuyuki

AU - Luo, Shu-Jin

N1 - All samples were recruited in compliance with the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) through permissions issued to the School of Life Sciences (PI: S.-J.L.), Peking University, by the State Forestry Administration of China. We thank all the collaborators, institutes and zoos that provided the specimens listed in Supplementary Table upon which this study is based. Special thanks are given to the following people who provided important help during various stages of the project: X. Zhou, L. Liao, J. Wu, C. Feng, S. Xiang, Y. Shen, C. Xie, L. Zhang, Y. Chen, F. Tang, E. Cappellini, M. Mackie, L. Miao, X. Hu, J. Huang, H. Yu, H. Meng, Q. Fu, E. Hoeger, M. Surovy, N. Duncan, S. Ketelsen, M.-D. Wandhammer, V. Rakotondrahaja, A. Abramov, I. Y. Pavlinov, E. I. Zholnerovskaya, N. V. Lopatina, X. Gu, H. Gu, D. Miquelle and D. Smith. We also pay tribute to the late U. Seal and P. Jackson for their dedication to tiger conservation and pioneer effort in assembling voucher specimens for genetic study. This work was supported by the National Key Research and Development Program of China (SQ2022YFF0802300), the National Natural Science Foundation of China (NSFC32070598) and the Peking-Tsinghua Center for Life Sciences. M.P.T. conducted the research within the state assignment of the Ministry of Science and Higher Education of the Russian Federation (theme No. 121031000153-7).

PY - 2023

Y1 - 2023

N2 - The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100–10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1–12×) and three Caspian tigers (4–8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000–10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.

AB - The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100–10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1–12×) and three Caspian tigers (4–8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000–10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.

UR - http://www.scopus.com/inward/record.url?partnerID=8YFLogxK&scp=85169163239

UR - https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=tsmetrics&SrcApp=tsm_test&DestApp=WOS_CPL&DestLinkType=FullRecord&KeyUT=001065143700003

U2 - 10.1038/s41559-023-02185-8

DO - 10.1038/s41559-023-02185-8

M3 - Article

VL - 7

SP - 1914

EP - 1929

JO - Nature Ecology & Evolution

JF - Nature Ecology & Evolution

SN - 2397-334X

IS - 11

ER -