Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur
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.
Authors
- Christian Roos (ORCID: https://orcid.org/0000-0003-0190-4266)
- Pham Van Tuyen (ORCID: https://orcid.org/0000-0002-2847-2793)
- Tilo Nadler (ORCID: https://orcid.org/0009-0002-2421-572X)
- Lutz Walter (ORCID: https://orcid.org/0000-0001-9408-3131)
- Benjamin M. Rawson (ORCID: https://orcid.org/0000-0003-4141-5985)
- M Luan
- N. Leonard (ORCID: https://orcid.org/0009-0009-4683-8734)
- Michael Hofreiter (ORCID: https://orcid.org/0000-0003-0441-4705)
- Michael F. Lynch (ORCID: https://orcid.org/0000-0002-1653-0642)
- Ming Li (ORCID: https://orcid.org/0000-0001-5689-6270)
- Zhijin Liu (ORCID: https://orcid.org/0000-0003-2923-1120)
- Nguyen Van Long (ORCID: https://orcid.org/0000-0002-5665-1019)
- Larry Vogelnest
- Amanda E. Fine
- Tomàs Marquès‐Bonet (ORCID: https://orcid.org/0000-0002-5597-3075)
- Alison M. Behie (ORCID: https://orcid.org/0000-0002-7436-3694)
- Minh Đức Lê (ORCID: https://orcid.org/0000-0002-2953-2815)
- Truong Van Nguyen (ORCID: https://orcid.org/0000-0003-2004-6658)
- Liye Zhang (ORCID: https://orcid.org/0000-0002-8829-0588)
- Nguyen Huy Cam
- Rick Passaro
- Le Thi Ngoc Han
- Nguyễn Thị Thanh Nga
Institutions
- Australian National University (AU)
- Institució Catalana de Recerca i Estudis Avançats (ES)
- Universitat Autònoma de Barcelona (ES)
- Wildlife Conservation Society (US)
- University of Potsdam (DE)
- Vietnam National University, Hanoi (VN)
- German Primate Center (DE)
- Taronga Conservation Society Australia (AU)
- World Wide Fund for Nature (CH)
- VNU Central Institute for Natural Resources and Environmental Studies (VN)
- Wildlife Conservation Society United Kingdom (GB)
- Zoos Victoria (AU)
- Max Planck Institute for Biophysical Chemistry (DE)
- Institut de Biologia Evolutiva (ES)
- Cat Tien National Park (VN)
- Centre for Genomic Regulation (ES)
- Institut Català de Paleontologia Miquel Crusafont (ES)
- Institute of Zoology (CN)
- Capital Normal University (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-10-02
- DOI
- https://doi.org/10.1038/s41467-024-52811-7
- Citations
- 4
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.94
Funders
- Ministry of Science and Technology
- Centres de Recerca de Catalunya
- European Commission
- Deutsche Forschungsgemeinschaft
- National Natural Science Foundation of China
- Chinese Academy of Sciences
- Generalitat de Catalunya
- National Institutes of Health
- Agencia Estatal de Investigación