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 specie...

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Published in:	Nature communications Vol. 15; no. 1; pp. 8531 - 14
Main Authors:	Zhang, Liye, Leonard, Neahga, Passaro, Rick, Luan, Mai Sy, Van Tuyen, Pham, Han, Le Thi Ngoc, Cam, Nguyen Huy, Vogelnest, Larry, Lynch, Michael, Fine, Amanda E., Nga, Nguyen Thi Thanh, Van Long, Nguyen, Rawson, Benjamin M., Behie, Alison, Van Nguyen, Truong, Le, Minh D., Nadler, Tilo, Walter, Lutz, Marques-Bonet, Tomas, Hofreiter, Michael, Li, Ming, Liu, Zhijin, Roos, Christian
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 02-10-2024 Nature Publishing Group Nature Portfolio
Subjects:	45 631/158/857 631/181/2474 631/208/182 631/601/1737 Adaptation Adaptation, Physiological - genetics Animals Breeding Calcium Calcium - metabolism Chromosome 19 Chromosomes, Human, Pair 19 - genetics Conspecifics Consumption Endangered populations Endangered Species Endemic species Evolutionary genetics Gene Flow Gene sequencing Genetic diversity Genetic load Genetic Variation Genome - genetics Genomes Genomics Genomics - methods Homozygosity Homozygote Humanities and Social Sciences Humans Hydroxyapatite Inbreeding Limestone Mammals multidisciplinary Phylogeny Population decline Population Density Population genetics Population number Primates Saline water Science Science (multidisciplinary) Sibling species Threatened species Vietnam Whole genome sequencing Vietnam
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Summary:	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. Fewer than 100 wild Cat Ba langurs survive in Vietnam. Here, the authors use whole genome sequencing to demonstrate potential adaptations to saltwater consumption as well as maintenance of adaptive potential despite low levels of genetic diversity and high levels of inbreeding.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	2041-1723 2041-1723
DOI:	10.1038/s41467-024-52811-7