DOI: 10.5061/dryad.b5mkkwhrz
title: Adaptive genetic variation in black-and-white snub-nosed monkeys (<em>Rhinopithecus bieti</em>): low diversity and the role of balancing selection

description: 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.
description: # Data from: Adaptive genetic variation in black-and-white snub-nosed
 monkeys (*Rhinopithecus bieti*): low diversity and the role of balancing
 selection ### Data Description This repository contains the raw data that
 support the findings of our study. The following CSV files are included in
 this dataset: ## 1. `sample_metadata.csv` **Columns:** * `SampleID`:
 Unique identifier for each individual sampled. * `Sex`: Biological sex of
 the sample (Male/Female). * `AgeGroup`: The age group classification of
 the individual. * `Location`: Geographic location where the sample was
 collected. * `Herd`: Identifier of the individual's herd *
 `SamplingDate`: The date when the sample was collected. ## 2.
 `r_bieti_functional_mhcI_candidate_sequences.csv` **Columns:** *
 `Sequence_Name`: Name of the sequence. * `Sequence`: The nucleotide
 sequence of the candidate MHC-I gene. * `Sequence_Type`: Type of the
 sequence. * `Source_Genome_Assembly`: Genome assembly version the sequence
 is derived from. * `Reference_Accessions`: Reference sequence accessions
 from public databases. * `Notes`: Additional comments on the sequence. ##
 3. `allele_sequences_mhcI_exon2.csv` **Columns:** * `Allele_ID_Ex2`:
 Identifier for the allele sequence. * `Sequence`: The nucleotide sequence
 of the allele. * `Notes`: Additional comments on the allele. ## 4.
 `allele_sequences_mhcI_exon3.csv` **Columns:** * `Allele_ID_Ex3`:
 Identifier for the allele sequence. * `Sequence`: The nucleotide sequence
 of the allele. * `Notes`: Additional comments on the allele. ## 5.
 `mhcI_exon2_genotyping_results.csv` **Columns:** * `SampleID`: Unique
 identifier for each individual sampled. * `Alleles (7 total)`: Different
 alleles identified from each individual sampled. A total of 7 distinct
 alleles were identified in exon 2 across all samples. * `locus1a`,
 `locus1b`, `locus2a`, `locus2b`, `locus3a`, `locus3b`, `locus4a`,
 `locus4b`: Temporary genotyping labels for preliminary allele assignment
 during data processing. There are four distinct loci in exon 2, with
 locus4 being a monomorphic locus. "00" means missing values. ##
 6. `mhcI_exon3_genotyping_results.csv` **Columns:** * `SampleID`: Unique
 identifier for each individual sampled. * `Alleles (9 total)`: Different
 alleles identified from each individual sampled. A total of 9 distinct
 alleles were identified in exon 3 across all samples. * `locus1a`,
 `locus1b`, `locus2a`, `locus2b`, `locus3a`, `locus3b`, `locus4a`,
 `locus4b`, `locus5a`, `locus5b`: Temporary genotyping labels for
 preliminary allele assignment during data processing. There are five
 distinct loci in exon 3, with locus5 being a monomorphic locus.
 "00" means missing values. ## 7. `mhcI_haplotype.csv`
 **Columns:** * `SampleID`: Unique identifier for each individual sampled.
 * `POP`: Population identifier. * `E2a`, `E2b`, `E3a`, `E3b`: Haplotype
 groups for different MHC-I exons. E2 refers to exon 2, and E3 refers to
 exon 3. * `E2E3a (E2:01-07 | E3:01-09)`, `E2E3b (E2:01-07 | E3:01-09)`:
 Specific haplotype combinations across these exons. --- ### Notes ####
 **1. AgeGroup Classification Reference**: The classification of age groups
 in the `sample_metadata.csv` file is based on the following two
 publications: - Li, D., Ren, B., Grueter, C. C., et al. (2010). *Nocturnal
 sleeping habits of the Yunnan snub-nosed monkey in Xiangguqing, China*.
 *American Journal of Primatology*, 72(12), 1092–1099.
 [https://doi.org/10.1002/ajp.20871](https://doi.org/10.1002/ajp.20871) -
 Li, T., Ren, B., Li, D., et al. (2013). *Mothering Style and Infant
 Behavioral Development in Yunnan Snub-Nosed Monkeys (Rhinopithecus bieti)
 in China*. *International Journal of Primatology*, 34(4), 681–695.
 [https://doi.org/10.1007/s10764-013-9687-7](https://doi.org/10.1007/s10764-013-9687-7) #### **2. Locus Naming Consistency for MHC-I Genotyping Results** #### 2.1 For `mhcI_exon2_genotyping_results.csv` The "locus1-locus4" labels in this table are temporary preliminary identifiers and do not correspond to the formal MHC loci assigned by MHC-TYPER. The formal locus assignment (via MHC-TYPER v1.0) for exon 2 alleles is: * *loc1*: *Rhbi-E2***01/04* * *loc2*: *Rhbi-E2***02/03* * *loc3*: *Rhbi-E2***05/06* * *loc5*: *Rhbi-E2***07* #### 2.2 For `mhcI_exon3_genotyping_results.csv` The "locus1-locus5" labels in this table are temporary preliminary identifiers and do not correspond to the formal MHC loci assigned by MHC-TYPER. The formal locus assignment (via MHC-TYPER v1.0) for exon 3 alleles (linked to exon 2 alleles) is: * *loc1*: *Rhbi-E3***01/04* * *loc2*: *Rhbi-E3***02/03* * *loc3*: *Rhbi-E3***07/08* * *loc4*: *Rhbi-E3***05/06* * *loc5*: *Rhbi-E3***09*