Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur

Liye Zhang (), Neahga Leonard, Rick Passaro, Mai Sy Luan, Pham Tuyen, Le Thi Ngoc Han, Nguyen Huy Cam, Larry Vogelnest, Michael Lynch, Amanda E. Fine, Nguyen Thi Thanh Nga, Nguyen Long, Benjamin M. Rawson, Alison Behie, Truong Nguyen, Minh D. Le, Tilo Nadler, Lutz Walter, Tomas Marques-Bonet, Michael Hofreiter (), Ming Li (), Zhijin Liu () and Christian Roos ()
Additional contact information
Liye Zhang: Leibniz Institute for Primate Research
Neahga Leonard: Cat Ba National Park, Cat Ba Island
Rick Passaro: Cat Ba National Park, Cat Ba Island
Mai Sy Luan: Cat Ba National Park, Cat Ba Island
Pham Tuyen: Cat Ba National Park, Cat Ba Island
Le Thi Ngoc Han: Cat Ba National Park, Cat Ba Island
Nguyen Huy Cam: Cat Ba National Park, Cat Ba Island
Larry Vogelnest: Taronga Conservation Society Australia
Michael Lynch: Zoos Victoria
Amanda E. Fine: Health Program
Nguyen Thi Thanh Nga: Vietnam Country Program
Nguyen Long: Vietnam Country Program
Benjamin M. Rawson: World Wildlife Fund for Nature (WWF) International
Alison Behie: The Australian National University
Truong Nguyen: Leibniz Institute for Primate Research
Minh D. Le: Vietnam National University
Tilo Nadler: Ninh Binh Province
Lutz Walter: Leibniz Institute for Primate Research
Tomas Marques-Bonet: PRBB
Michael Hofreiter: University of Potsdam
Ming Li: Chinese Academy of Sciences
Zhijin Liu: Capital Normal University
Christian Roos: Leibniz Institute for Primate Research

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: Abstract Many mammal species have declining populations, but the consequences of small population size on the genomic makeup of species remain largely unknown. We investigated the evolutionary history, genetic load and adaptive potential of the Cat Ba langur (Trachypithecus poliocephalus), a primate species endemic to Vietnam’s famous Ha Long Bay and with less than 100 living individuals one of the most threatened primates in the world. Using high-coverage whole genome data of four wild individuals, we revealed the Cat Ba langur as sister species to its conspecifics of the northern limestone langur clade and found no evidence for extensive secondary gene flow after their initial separation. Compared to other primates and mammals, the Cat Ba langur showed low levels of genetic diversity, long runs of homozygosity, high levels of inbreeding and an excess of deleterious mutations in homozygous state. On the other hand, genetic diversity has been maintained in protein-coding genes and on the gene-rich human chromosome 19 ortholog, suggesting that the Cat Ba langur retained most of its adaptive potential. The Cat Ba langur also exhibits several unique non-synonymous variants that are related to calcium and sodium metabolism, which may have improved adaptation to high calcium intake and saltwater consumption.

Date: 2024
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DOI: 10.1038/s41467-024-52811-7

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