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Adaptive genetic variation in black-and-white snub-nosed monkeys (Rhinopithecus bieti): low diversity and the role of balancing selection

Long, Fei1; Ying, Meijing1; Shi, Tianqi1; Garber, Paul A.23; Pan, Ruliang241; Lai, Jiandong5; Huang, Zhipang2; Li, Baoguo671; Zhang, Pei1

Published Jan 21, 2026 on Dryad. https://doi.org/10.5061/dryad.b5mkkwhrz

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Abstract

Genetic variation provides the raw material for natural selection, enabling species to maintain adaptive potential, respond to environmental changes, and resist pathogens. Reduced genetic diversity can severely compromise long-term viability, particularly in small, isolated populations prone to inbreeding, genetic drift, and restricted gene flow—a vicious cycle known as the "extinction vortex". Assessing genetic diversity in threatened species is therefore critical for effective conservation strategies. The black-and-white snub-nosed monkey (Rhinopithecus bieti), is an Endangered primate that has experienced significant population decline and habitat fragmentation, raising concerns about its genetic diversity. We utilized major histocompatibility complex (MHC) class I genes, whose encoded proteins recognize antigens central to immune responses, to assess the adaptive genetic diversity of a semi-provisioned subpopulation of this species. Species-specific multi-locus primers targeting exons 2 and 3 of MHC class I genes were designed using published R. bieti whole-genome sequences. Amplicon-based next-generation sequencing was employed to genotype these exons in the studied subpopulation inhabiting Baima Snow Mountain National Nature Reserve, Yunnan, China. A total of 16 MHC class I sequences (7 exon 2 sequences and 9 exon 3 sequences) were identified from 47 individuals and assigned to 5 loci. Exon 2 exhibited low heterozygosity (He = 0.349) and moderate polymorphism (PIC = 0.281), whereas exon 3 showed extremely low heterozygosity (He = 0.147) and low polymorphism (PIC = 0.131). In addition, positive selection signatures were detected in both exons, and phylogenetic analyses indicated trans-species evolutionary patterns in class I loci. These results underscore the role of balancing selection in maintaining adaptive genetic variation. However, low genetic diversity is likely to have diminished the studied subpopulation’s capacity to adapt to environmental change, thereby undermining its long-term viability. This study emphasizes the urgent need to assess adaptive genetic diversity across all R. bieti populations in order to develop targeted management strategies. The data generated in this studied subpopulation provides the baseline for comparison.