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Article

Whole-Genome Resequencing Reveals Population Genetic Structure and Selection Signatures in the Golden Wild Yak

by
Jianhua Yu
†,
Wei Cong
†,
Xiuming Li
,
Lu Wang
,
Kun Jin
* and
Yuguang Zhang
*
Key Laboratory of Biodiversity Conservation of State Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Diversity 2025, 17(10), 687; https://doi.org/10.3390/d17100687
Submission received: 31 August 2025 / Revised: 23 September 2025 / Accepted: 25 September 2025 / Published: 30 September 2025
(This article belongs to the Special Issue Bison and Beyond: Achievements and Problems in Wildlife Conservation)
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Abstract

The wild yak (Bos mutus) is a flagship species on the Qinghai–Tibet Plateau, possessing significant ecological functions and conservation value. Using single-nucleotide polymorphism markers from whole-genome resequencing, we systematically analyzed golden wild yak (n = 37), common wild yak (n = 106), and domestic yak (Bos grunniens) (n = 20) to characterize the population genetic structure and adaptive selection signals in the golden wild yak. Genetic diversity analyses revealed that the golden wild yak had the lowest nucleotide diversity (π = 0.00148) and the highest inbreeding coefficient (FHom = 0.043). Population structure analyses integrating principal component analysis, phylogenetic tree, and ancestral component clustering indicated that the golden wild yak formed a relatively independent evolutionary lineage. However, its genetic differentiation from sympatric common wild yak population was limited (fixation index = 0.031). Selective sweep analysis identified a set of candidate positively selected genes in the golden wild yak genome associated with key traits and physiological functions, including coat color (TYRP1), hypoxia adaptation (MYH11, POLQ), reproductive function (SLC9C1, SPAG16, CFAP97D1), and immune response (CASP8, PGGT1B, BIRC6). Overall, our study reveals a distinct genetic background and selection signatures in the golden wild yak and provides genomic insights to inform the conservation and management of the wild yak.

1. Introduction

The wild yak (Bos mutus) is a keystone herbivore on the Qinghai–Tibet Plateau (QTP) with distinct genetic features, important ecological functions, and deep cultural significance [1,2]. It is listed as a Class I nationally protected species in China and as Vulnerable on the IUCN Red List [3]. The wild yak is mainly distributed in high-altitude regions (3000–6000 m) of the QTP, including the Changtang in Xizang Autonomous Region, the Hoh Xil in Qinghai Province, and the Altun Mountains in Xinjiang Uygur Autonomous Region [4,5]. Having undergone millions of years of natural selection, the wild yak has developed remarkable physiological and metabolic adaptations to hypoxia, intense radiation, and cold, making it an ideal model for studying vertebrate high-altitude adaptation [6,7]. Notably, a rare golden wild yak morph has been reported from Ritu and Geji counties in Xizang Autonomous Region, China, whose conspicuous golden coat contrasts sharply with the common wild yak’s blackish-brown phenotype [8]. Field surveys found that golden wild yak and common wild yak living in sympatry sometimes form mixed herds, suggesting the potential for genetic exchange between them. Mitochondrial genome studies have revealed a certain degree of genetic divergence between golden wild yak and common wild yak [8,9]. However, due to the limited genetic markers and small sample sizes used in previous studies, the phylogenetic status of golden wild yak remains unresolved. Furthermore, the nuclear genomic characteristics of this specific population have rarely been investigated.
The innovation of high-throughput sequencing technology is driving conservation genetics into the genomic era [10]. With the advantages of high abundance and polymorphism, single-nucleotide polymorphism (SNP) markers are widely used in population genomics [11,12]. Genome-wide SNP analyses showed that global snow leopard (Panthera uncia) populations have low genetic diversity and two major lineages, with EPAS1 implicated in plateau adaptation in the southern lineage [13]. Similarly, phylogenetic analysis of takin (Budorcas taxicolor) demonstrated geographic divergence between Himalayan subspecies (B. t. taxicolor) and Qinling subspecies (B. t. bedfordi), with the lighter coat coloration in the Qinling lineage associated with PMEL gene variation [14]. Yaks have a conserved bovid karyotype (2n = 60; 29 pairs of autosomes plus XY sex chromosomes) and a genome size of approximately 2.6–2.8 Gb, and chromosome-level assemblies have been generated by studies integrating long-read sequencing [15,16,17]. Based on genome-wide SNP data, numerous studies have further elucidated the patterns of genetic diversity, breed evolutionary relationships, and domestication-related selective genes in domestic yak [18,19,20]. Nevertheless, our understanding of genetic heterogeneity among wild yak populations remains limited, particularly concerning their geographic differentiation, gene flow dynamics, and local adaptation mechanisms.
From a conservation standpoint, clarifying whether the golden wild yak constitutes a distinct genetic unit is essential for delineating management units on the QTP. In this study, we sampled wild yaks from two major habitats on the QTP, specifically the Altun Mountain National Nature Reserve in Xinjiang and the Changtang National Nature Reserve in Xizang. Based on the high-density SNP dataset generated by whole-genome resequencing (WGR), we conducted analyses of genetic diversity, evolutionary relationships, and selective sweeps. Specifically, we aimed to: (1) characterize the genetic diversity and inbreeding pressure of the golden wild yak and common wild yak populations from different geographic regions; (2) clarify the evolutionary relationship of the golden wild yak relative to common wild yak populations; and (3) investigate the genomic selection signatures underlying the distinctive phenotype and environmental adaptation of the golden wild yak. These efforts provide new insights into the genetic resources of the wild yak and contribute to informed conservation management.

2. Materials and Methods

2.1. Sample Collection

A total of 143 skin tissue samples of wild yaks were collected in the Altun Mountains National Nature Reserve in Xinjiang Uygur Autonomous Region and the Changtang National Nature Reserve in Xizang Autonomous Region, China (Figure 1A–C). Among them, golden wild yak samples were collected from Ritu County, Xizang (RTGW, n = 37), while common wild yak samples originated from Ritu County (RTCW, n = 38), Gaize County (GZCW, n = 33), and Nima County (NMCW, n = 19) in Xizang, as well as the Altun Mountains in Xinjiang (AEJCW, n = 16). All samples were obtained from wild yaks that died of natural causes in the field and subsequently stored under low temperature and dry conditions. All work related to sample collection was approved by the local Wildlife Conservation and Management Department. In addition, the WGR data of Subei domestic yak (SBD, n = 20) from Subei County, Gansu, were downloaded from the NCBI (https://www.ncbi.nlm.nih.gov, accessed on 1 August 2025) database [21].

2.2. DNA Extraction and Genome Resequencing

Genomic DNA was extracted from the skin samples using the TIANamp Genomic DNA Extraction Kit (TIANGEN, Beijing, China) according to the manufacturer’s instructions. Subsequently, DNA concentration and purity were measured with a microspectrophotometer, and integrity was assessed by agarose gel electrophoresis. For WGR library construction, qualified DNA samples were sheared by sonication, and fragments of 200–300 bp were selected using the Agencourt AMPure XP (Beckman Coulter, Indianapolis, IN, USA). The amount of purified DNA samples was then detected using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA). PCR amplification was carried out on the products obtained after end repair, A-tail addition, and sequencing adapter ligation of fragmented DNA. The PCR products were denatured into single strands, then subjected to cyclization to generate single-stranded circular products. Linear DNA molecules were subsequently removed to obtain final sequencing libraries. The fragment size and concentration of libraries were detected using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), and libraries that passed the quality test were sequenced on the DNBSEQ platform. Library preparation and sequencing were performed at BGI-Shenzhen, China.

2.3. Sequence Quality Control and SNP Calling

Raw sequencing reads were filtered with SOAPnuke (v2.2.6) under the following filtering criteria: (1) removal of reads containing adapter sequences; (2) exclusion of reads with N (unknown bases) > 0.1%; and (3) removal of reads with >50% low quality bases [22]. Clean reads were then aligned to the yak reference genome (GCA_005887515.3; assembly size ~2.8 Gb) using BWA (v0.7.17), and alignments were written in SAM format [23]. Subsequently, these SAM files were transformed into sorted BAM files using SAMtools (v1.9) [24]. PCR duplicates were marked using the MarkDuplicates command in GATK (v4.2.6.1) [25]. Mapping metrics, including genome alignment rate and coverage depth, were subsequently assessed on the BAM files. SNPs were called with GATK (v4.2.6.1), and each variant site was quality-filtered and assigned a quality flag [25]. Functional annotation of SNPs was performed using SnpEff (v4.3t) with the corresponding reference genome and annotation file [26].

2.4. Genetic Parameters Estimation

In order to investigate genetic variability among yak populations, a variety of genetic parameters were calculated in this study, including nucleotide diversity (π) characterizing genetic diversity, observed heterozygosity (Ho), expected heterozygosity (He) and inbreeding coefficients (FHom) characterizing the level of inbreeding using VCFtools (v0.1.16) [27]. Runs of Homozygosity (ROH) were detected using PLINK (v1.90) [28]. In addition, Linkage Disequilibrium (LD) decay analysis was performed with PopLDdecay (v3.30), and the results were visualized and analyzed using the software’s own scripts [29].

2.5. Population Structure Analysis

The SNP dataset of autosomal genomes was subjected to LD pruning using PLINK (v1.90) software to eliminate redundant data and improve the reliability of subsequent analysis results [28]. The fixation index (Fst) values between populations were calculated with a sliding window method in VCFtools (v0.1.16) [27]. The principal component analysis (PCA) was performed on all samples using PLINK (v1.90) to obtain eigenvectors [28]. After converting the VCF file to PHYLIP format using the script (vcf2phylip.py), a phylogenetic tree of all samples was constructed in MEGA (v11.0.13) using the neighbor-joining method with 1000 bootstrap replicates [30]. The exported Newick-format result file was then uploaded to the online tool iTOL (https://itol.embl.de, accessed on 1 August 2025) for visualization [31]. Ancestral component clustering analysis was performed with ADMIXTURE (v1.3.0), and the results were visualized with pong (v1.5) [32,33].

2.6. Selective Sweep Analysis

Autosomal genomic regions of the golden wild yak (RTGW) and all common wild yak populations (including RTCW, GZCW, NMCW, and AEJCW) were comparatively screened using three selection signals, π ratio, Fst and cross-population composite likelihood ratio (XP-CLR). Genomic regions corresponding to the top 1% for these three indices were considered regions under positive selection [11]. XP-CLR scores were computed with the xpclr program (v1.1.2) in sliding windows (window size: 50 kb; step size: 20 kb) [34]. Candidate genes involved in the positive selection signal were extracted and then subjected to KEGG and GO functional enrichment analyses on the KOBAS (http://bioinfo.org/kobas, accessed on 1 August 2025) online platform [35]. The threshold condition for significantly enriched terms was the p-value ≤ 0.05, and partial results were visualized via the SRplot (http://sangerbox.com, accessed on 1 August 2025) online platform [36].

3. Results

3.1. Resequencing Statistics and SNP Annotation

WGR of 143 wild yak samples yielded 4805.9 Gb of raw sequence data. After quality control, 4609.9 Gb of clean data were retained, corresponding to an average of 32.2 Gb per sample. The filtered reads had ≥99.0% bases with Phred Q ≥ 20 and a GC content of 43.6%. Mapping to the reference genome achieved a mean sequencing depth of 10× and 95.5% genome coverage at 1× sequencing depth. These indicators suggest that the sequencing data quality is reliable. A total of 36,627,147 high quality SNPs were identified in all samples. Genomic annotation revealed SNPs were predominantly located in intronic (47.7%) and intergenic regions (35.2%), whereas exonic regions accounted for only 1.0%. Within protein-coding sequences, the functional consequences were mainly silent mutations (52.9%) and missense mutations (46.1%), with nonsense mutations (1.0%) being rare (Figure 2A).

3.2. Population Genetic Diversity

The analysis of nucleotide diversity showed that the π values of all yak populations ranged from 0.00148 to 0.00162, with RTGW having the lowest π value of 0.00148, and AEJCW and NMCW having the highest π value of 0.00162 (Table 1). The FHom values among the yak populations ranged from 0.015 to 0.043, with RTGW having the highest value and SBD the lowest (Figure 2B). The statistics of homozygous fragments indicated that all populations were dominated by ROHs of 0.5–1.0 Mb, accounting for more than 89%, among which RTGW and RTCW had significantly more ROHs than other populations, while NMCW, AEJCW and SBD had fewer ROHs (Figure 2C). The LD degree in yak populations was quantified by the correlation coefficient (r2). Notably, SBD exhibited significantly greater persistence of LD than the other wild yak populations (Figure 2D). Among wild yak populations, RTCW exhibited the slowest LD decay whereas AEJCW showed the most rapid decay, although inter-population differences were modest (Figure 2D).

3.3. Population Structure Stratification

To investigate the genetic structure and relationships among yak populations, PCA, phylogenetic tree, and ancestry component clustering were performed for population stratification analysis. The phylogenetic tree constructed using the neighbor-joining method revealed that RTGW clustered into a relatively distinct group, although some RTCW individuals were interspersed within it (Figure 3A). RTCW, GZCW, and NMCW exhibited close phylogenetic relationships, with a few individuals showing admixture among these populations (Figure 3A). AEJCW and SBD were closely related and each formed an independent branch (Figure 3A). PCA results indicated that six yak populations were primarily clustered into three groups: RTGW, SBD, and all common wild yak populations (Figure 3B). The first principal component explained 20.9% of the total variation and effectively distinguished the three clusters. It should be noted that some RTCW individuals overlapped with RTGW. The PCA results were consistent with the phylogenetic tree.
Ancestry component clustering showed that at K = 2, RTGW and the other yak populations formed two major genetic components (Figure 3C). At K = 3, domestic yaks (SBD) were separated into an independent genetic component, while some individuals of common wild yaks exhibited mixed ancestry from both domestic yaks and golden wild yaks, suggesting potential gene flow between them (Figure 3C). When K ≥ 4, the CV error gradually increased and exceeded 0.35, indicating reduced reliability of the clustering results. As shown in Figure 3D, RTGW displayed a higher degree of genetic differentiation from the other yak populations, with Fst values ranging from 0.031 to 0.074 (Table S1). Among these, the differentiation index between RTGW and NMCW, AEJCW, and SBD exceeded 0.05. In contrast, Fst values among common wild yak populations were all below 0.05. Moreover, the Fst values between domestic yak (SBD) and all common wild yak populations were also below 0.05. Collectively, these results indicate that RTGW is genetically more distantly related to other yak populations.

3.4. Selective Signals and Gene Function Annotation

Three selection statistics (π ratio, Fst, and XP-CLR) were utilized to identify selection signals in the golden wild yak. The top 1% positively selected regions characterized by these three indices were extracted for gene annotation (Figure 4A). Based on the π ratio, Fst, and XP-CLR methods, 368, 258, and 842 known functional genes were annotated, respectively, among which 29 overlapping genes were identified as potential positively selected genes (PSGs) in the golden wild yak (Figure 4B). Functional annotation results indicated that these genes might be involved in important traits and functions such as coat color (TYRP1), hypoxia adaptation (MYH11, POLQ), reproductive function (SLC9C1, SPAG16, CFAP97D1), and immune response (CASP8, PGGT1B, BIRC6). The genomic regions containing these genes in the golden wild yak have undergone strong selection, showing lower π values and higher Fst differences compared to the common wild yak. For instance, the TYRP1 gene (Chr7: 89,630,431–89,646,409) related to coat color regulation has only two SNPs (AF > 0.05) in the golden wild yak (Chr7: 89,637,108, AF = 0.10; Chr7: 89,638,347, AF = 0.97), while there are 116 SNPs (AF > 0.05) in the common wild yak.
These important candidate PSGs were significantly enriched in 4 KEGG pathways and 110 GO terms (Tables S2 and S3). The enriched KEGG pathways were related to disease mechanisms and cellular physiological regulation, including apoptosis-multiple species, tight junction, glycosaminoglycan degradation, and tyrosine metabolism (Figure 4C). The enriched GO terms encompassed a broad range of biological processes and functions, covering fundamental cellular activities, developmental processes, signal transduction, and disease mechanisms (Figure 4D). Typical examples include anion transmembrane transport (GO: 0098656), cerebellar mossy fiber (GO: 0044300), Rab GTPase binding (GO: 0017137), and activation of the IκB kinase/NF-κB signaling cascade (GO: 0043123).

4. Discussion

As the bedrock of evolutionary potential, genetic diversity underpins species viability and environmental adaptability, making it highly significant for the protection of endangered species [37]. Our analysis revealed differences in genomic diversity and inbreeding patterns among some wild yak populations on the QTP. Notably, compared with other common wild yak populations, the golden wild yak exhibited reduced nucleotide diversity and an elevated inbreeding coefficient, suggesting a smaller effective population size and recent genetic drift, which is consistent with its status as a rare phenotypic variant of the wild yak [38,39]. Similarly, genomic sequencing of mountain gorillas (Gorilla beringei beringei) has shown that subpopulations with smaller population sizes possess lower genetic diversity and autosomal heterozygosity [40]. In contrast, AEJCW and NMCW displayed higher π values, indicating a broader genetic background, which aligns with the recent population expansion of wild yak in the Altun Mountains Nature Reserve [41].
Analyses of mitochondrial genomes have revealed lineage divergence between golden and common wild yaks [8,9]. Population structure analyses revealed that RTGW constitutes a relatively distinct lineage within wild yaks, but still maintains some gene flow with the sympatric RTCW. This result is consistent with the phenomenon we observed in the field investigation that golden wild yaks and common wild yaks coexist within overlapping distribution ranges. Our previous correlation analysis based on whole-genome DNA methylation maps also revealed pronounced epigenetic differentiation between golden wild yaks and common wild yaks (populations from Ritu, Xizang and the Altun Mountains, Xinjiang). Given the evolutionary and genetic distinctiveness of the golden wild yak, we propose that it should be regarded as an Evolutionarily Significant Unit (ESU) of high conservation value [42]. Special attention should be paid to preventing genetic deterioration caused by elevated inbreeding, as well as mitigating the risk of genetic swamping through hybridization with large sympatric and neighboring populations of common wild yak [43]. Integrating genetic structure with geographic distribution, we infer that RTGW may have originated from a small historical subpopulation of wild yak in the northwestern QTP that experienced geographic or ecological isolation. During the isolation period, genetic drift and founder effects gradually accumulated unique genetic variations [38,44,45].
Our study found that the TYRP1 gene in the golden wild yak is under strong positive selection, and functional analysis indicates that this gene is significantly enriched in tyrosine metabolism pathway. The TYRP1 gene exhibits melanocyte-specific expression, encodes tyrosinase-related protein 1 (TYRP1), and contributes to the process of melanin biosynthesis within melanosomes [46]. Experimental evidence has verified that TYRP1 interacts with the rate-limiting enzyme TYR to regulate its stability and transportation, thereby influencing melanin synthesis [47]. Mutations in the TYRP1 gene that result in brown/golden coat color phenotypes have been documented in several mammals [48,49]. For instance, the golden-yellow coat of Liangshan pigs (Sus scrofa) has been attributed to the three mutations in TYRP1 [50]. Genome-wide association analyses in rhesus macaques (Macaca mulatta) identified two TYRP1 missense variants influencing the light golden coat [51]. In our study, the TYRP1 gene of the golden wild yak exhibited strong conservation, with only one unique high-frequency (AF = 0.97) intronic mutation detected. Although nearly fixed in the population, the regulatory impact of this variant on TYRP1 expression remains unclear. It may exert effects on gene expression via mechanisms including the alteration of splicing regulation and the modulation of cis-acting elements (e.g., promoters/enhancers), among others [52,53]. In conclusion, the strong selection signal in the TYRP1 gene region and the conservation of its pathway function implicate TYRP1 as an important molecular basis of the golden coat in the golden wild yak.
Selective sweep analyses identified candidate PSGs in the golden wild yak associated with hypoxia (MYH11, POLQ), reproduction (SLC9C1, SPAG16, CFAP97D1), and immunity (CASP8, PGGT1B, BIRC6). The myosin heavy chain encoded by MYH11 is involved in maintaining vascular contraction and blood flow, and helps regulate oxygen delivery under hypoxic conditions [54]. Hypoxia can induce DNA damage through mechanisms such as elevated reactive oxygen species, whereas POLQ maintains genome stability by repairing DNA damage via base excision repair, mismatch repair, and replication stress responses [55]. SLC9C1 is specifically expressed in the testes and sperm and is essential for male fertility in mammals [56]. SPAG16 encodes two major transcriptional isoforms in mice that are indispensable for male fertility and sperm motility [57]. CFAP97D1 is also specifically expressed in the testes, and knockout experiments in mice have verified its critical role as a regulator of male fertility [58]. CASP8, encoding caspase-8, acts as a key regulator of apoptosis and inflammatory responses [59]. PGGT1B encodes an enzyme involved in lipid modification that supports normal immune cell function [60]. BIRC6, a ubiquitin-conjugating E2 enzyme, exhibits anti-apoptotic activity and negative regulation of autophagy, thereby contributing to cellular homeostasis [61]. The functional characteristics of these PSGs are highly consistent with the survival requirements of the golden wild yak in extreme high-altitude environments [62]. This suggests that the environmental adaptation of the golden wild yak may result from polygenic interactions, involving integrated regulation across multiple systems including energy metabolism, blood circulation, DNA repair, immune response, and reproductive function.

5. Conclusions

Based on genome-wide SNP markers, this study comprehensively analyzes the genetic diversity, population structure, and selection signatures of the golden and common wild yak populations. The golden wild yak is at risk of genetic deterioration, characterized by reduced genetic diversity and elevated levels of inbreeding. Although genetic exchange occurs with the sympatric common wild yak population, population structure analyses indicate that the golden wild yak forms a relatively independent evolutionary lineage and may qualify as a candidate ESU. Genome selective sweeps identified a series of potential PSGs in the golden wild yak, which are involved in coat color regulation, hypoxia tolerance, reproductive function, and immune response, collectively forming the molecular basis for its adaptation to extreme high-altitude environments. Thus, this study provides critical genomic evidence for evaluating wild yak genetic resources, defining priority populations for conservation, and exploring gene resources related to plateau adaptation.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/d17100687/s1, Table S1: Fst values among yak populations; Table S2: KEGG pathways significantly enriched among positively selected genes in the golden wild yak; Table S3: GO terms significantly enriched among positively selected genes in the golden wild yak.

Author Contributions

Conceptualization, Y.Z. and K.J.; Supervision, Y.Z. and K.J.; Investigation, W.C., L.W. and X.L.; Methodology, W.C. and J.Y.; Formal analysis, J.Y.; Validation, J.Y. and W.C.; Writing—original draft preparation, J.Y. and W.C.; Writing—review and editing, J.Y., W.C., L.W., X.L., K.J. and Y.Z.; Visualization, J.Y.; Funding acquisition, Y.Z. and K.J. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Forestry and Grassland Bureau of Xizang Autonomous Region, China, under the project titled “Genetic Investigation and Monitoring of Wild Yak Population” (grant number: GZFCG2022-11579-003).

Institutional Review Board Statement

Ethical review and approval were waived for this study because no live animals were handled or subjected to procedures, and all skin tissues were obtained exclusively from wild yaks that had died of natural causes in the field.

Data Availability Statement

All raw sequencing reads have been deposited in the Genome Sequence Archive (GSA) of the China National Center for Bioinformation (CNCB) under the BioProject accession number PRJCA042419.

Acknowledgments

We sincerely thank our colleagues Jin Li and Ben Huang for their assistance with sample collection and processing.

Conflicts of Interest

The authors declare no conflicts of interest.

Abbreviations

The following abbreviations are used in this manuscript:
FHomInbreeding coefficient
FstFixation index
HeExpected heterozygosity
HoObserved heterozygosity
LDLinkage disequilibrium
PCAPrincipal component analysis
PSGPositively selected gene
QTPQinghai–Tibet Plateau
ROHRuns of homozygosity
SNPSingle-nucleotide polymorphism
WGRWhole-genome resequencing
XP-CLRCross-population composite likelihood ratio
πNucleotide diversity

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Figure 1. Geographic distribution and representative photographs of yak populations sampled in this study. (A) County-level distribution of sampling sites. (B) Golden wild yak. (C) Common wild yak. (Note: RTGW, golden wild yak samples from Ritu County, Xizang; RTCW, common wild yak samples from Ritu County, Xizang; GZCW, common wild yak samples from Gaize County, Xizang; NMCW, common wild yak samples from Nima County, Xizang; AEJCW, common wild yak samples from the Altun Mountains, Xinjiang; SBD, domestic yak samples from Subei County, Gansu).
Figure 1. Geographic distribution and representative photographs of yak populations sampled in this study. (A) County-level distribution of sampling sites. (B) Golden wild yak. (C) Common wild yak. (Note: RTGW, golden wild yak samples from Ritu County, Xizang; RTCW, common wild yak samples from Ritu County, Xizang; GZCW, common wild yak samples from Gaize County, Xizang; NMCW, common wild yak samples from Nima County, Xizang; AEJCW, common wild yak samples from the Altun Mountains, Xinjiang; SBD, domestic yak samples from Subei County, Gansu).
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Figure 2. SNP annotation and genetic diversity metrics. (A) SNP annotation results. (B) Inbreeding coefficient (FHom). (C) Number and distribution of Runs of Homozygosity (ROH). (D) Linkage disequilibrium (LD) decay analysis. (Note: RTGW, golden wild yak samples from Ritu County, Xizang; RTCW, common wild yak samples from Ritu County, Xizang; GZCW, common wild yak samples from Gaize County, Xizang; NMCW, common wild yak samples from Nima County, Xizang; AEJCW, common wild yak samples from the Altun Mountains, Xinjiang; SBD, domestic yak samples from Subei County, Gansu.).
Figure 2. SNP annotation and genetic diversity metrics. (A) SNP annotation results. (B) Inbreeding coefficient (FHom). (C) Number and distribution of Runs of Homozygosity (ROH). (D) Linkage disequilibrium (LD) decay analysis. (Note: RTGW, golden wild yak samples from Ritu County, Xizang; RTCW, common wild yak samples from Ritu County, Xizang; GZCW, common wild yak samples from Gaize County, Xizang; NMCW, common wild yak samples from Nima County, Xizang; AEJCW, common wild yak samples from the Altun Mountains, Xinjiang; SBD, domestic yak samples from Subei County, Gansu.).
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Figure 3. Population structure of yak populations. (A) Phylogenetic tree constructed using the neighbor-joining method. (B) The first three principal components from PCA. (C) Ancestral component clustering analysis at K = 2–4. (D) Pairwise Fst among yak populations. (Note: RTGW, golden wild yak samples from Ritu County, Xizang; RTCW, common wild yak samples from Ritu County, Xizang; GZCW, common wild yak samples from Gaize County, Xizang; NMCW, common wild yak samples from Nima County, Xizang; AEJCW, common wild yak samples from the Altun Mountains, Xinjiang; SBD, domestic yak samples from Subei County, Gansu).
Figure 3. Population structure of yak populations. (A) Phylogenetic tree constructed using the neighbor-joining method. (B) The first three principal components from PCA. (C) Ancestral component clustering analysis at K = 2–4. (D) Pairwise Fst among yak populations. (Note: RTGW, golden wild yak samples from Ritu County, Xizang; RTCW, common wild yak samples from Ritu County, Xizang; GZCW, common wild yak samples from Gaize County, Xizang; NMCW, common wild yak samples from Nima County, Xizang; AEJCW, common wild yak samples from the Altun Mountains, Xinjiang; SBD, domestic yak samples from Subei County, Gansu).
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Figure 4. Selective sweep analysis on autosomes in the golden wild yak. (A) Selective sweep results based on three indices: π ratio, Fst, and XP-CLR. (B) Intersection of annotated genes identified by the three indices. (C) Significantly enriched KEGG pathways of PSGs. (D) Significantly enriched GO terms of PSGs.
Figure 4. Selective sweep analysis on autosomes in the golden wild yak. (A) Selective sweep results based on three indices: π ratio, Fst, and XP-CLR. (B) Intersection of annotated genes identified by the three indices. (C) Significantly enriched KEGG pathways of PSGs. (D) Significantly enriched GO terms of PSGs.
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Table 1. Genetic diversity indices of yak populations.
Table 1. Genetic diversity indices of yak populations.
PopulationSample SizeπHoHeFHom
RTGW370.001480.2130.2220.043
RTCW380.001560.2050.2140.042
GZCW330.001600.2010.2070.029
NMCW190.001620.2150.2230.035
AEJCW160.001620.2380.2440.027
SBD200.001570.2250.2290.015
(Note: Ho, Observed heterozygosity; He, Expected heterozygosity; RTGW, golden wild yak samples from Ritu County, Xizang; RTCW, common wild yak samples from Ritu County, Xizang; GZCW, common wild yak samples from Gaize County, Xizang; NMCW, common wild yak samples from Nima County, Xizang; AEJCW, common wild yak samples from the Altun Mountains, Xinjiang; SBD, domestic yak samples from Subei County, Gansu.).
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Yu, J.; Cong, W.; Li, X.; Wang, L.; Jin, K.; Zhang, Y. Whole-Genome Resequencing Reveals Population Genetic Structure and Selection Signatures in the Golden Wild Yak. Diversity 2025, 17, 687. https://doi.org/10.3390/d17100687

AMA Style

Yu J, Cong W, Li X, Wang L, Jin K, Zhang Y. Whole-Genome Resequencing Reveals Population Genetic Structure and Selection Signatures in the Golden Wild Yak. Diversity. 2025; 17(10):687. https://doi.org/10.3390/d17100687

Chicago/Turabian Style

Yu, Jianhua, Wei Cong, Xiuming Li, Lu Wang, Kun Jin, and Yuguang Zhang. 2025. "Whole-Genome Resequencing Reveals Population Genetic Structure and Selection Signatures in the Golden Wild Yak" Diversity 17, no. 10: 687. https://doi.org/10.3390/d17100687

APA Style

Yu, J., Cong, W., Li, X., Wang, L., Jin, K., & Zhang, Y. (2025). Whole-Genome Resequencing Reveals Population Genetic Structure and Selection Signatures in the Golden Wild Yak. Diversity, 17(10), 687. https://doi.org/10.3390/d17100687

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