Ancient DNA reveals genetic admixture in China during tiger evolution
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Ancient DNA reveals genetic admixture in China during tiger evolution. / Sun, Xin; Liu, Yue Chen; Tiunov, Mikhail P.; Gimranov, Dmitry O.; Zhuang, Yan; Han, Yu; Driscoll, Carlos A.; Pang, Yuhong; Li, Chunmei; Pan, Yan; Velasco, Marcela Sandoval; Gopalakrishnan, Shyam; Yang, Rui Zheng; Li, Bao Guo; Jin, Kun; Xu, Xiao; Uphyrkina, Olga; Huang, Yanyi; Wu, Xiao Hong; Gilbert, M. Thomas P.; O’Brien, Stephen J.; Yamaguchi, Nobuyuki; Luo, Shu-Jin.
In: Nature Ecology and Evolution, Vol. 7, No. 11, 2023, p. 1914-1929.Research output: Contribution to journal › Journal article › Research › peer-review
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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 - Publisher Copyright: © 2023, The Author(s), under exclusive licence to Springer Nature Limited.
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.
U2 - 10.1038/s41559-023-02185-8
DO - 10.1038/s41559-023-02185-8
M3 - Journal article
C2 - 37652999
AN - SCOPUS:85169163239
VL - 7
SP - 1914
EP - 1929
JO - Nature Ecology & Evolution
JF - Nature Ecology & Evolution
SN - 2397-334X
IS - 11
ER -
ID: 365964264