Mitochondrial DNA (mtDNA) is a powerful tool for phylogenetic studies due to its maternal inheritance and presence in multiple copies within cells [27–28]. Unlike nuclear DNA, mtDNA has a higher nucleotide substitution rate, which allows for a finer resolution of genetic differences and evolutionary relationships [29]. This characteristic makes mtDNA an invaluable resource for investigating genetic relationships and evolutionary history, offering insights that are often not possible with nuclear DNA alone. The mitochondrial D-loop region, a non-coding part of mtDNA, plays a crucial role in studying genetic diversity and phylogenetic relationships due to its high mutation rate and rapid evolution [30–32]. The high mutation rate of mtDNA, particularly in the D-loop region, provides a comprehensive view of genetic diversity and population structure [33–34]. A total of eighteen Arunachali yak samples from Arunachal Pradesh were sequenced in this study. Their genetic diversity was evaluated by comparing their mtDNA sequences with each other and with sequences from other bovine species retrieved from the GenBank database. This comparison facilitated the construction of a comprehensive phylogenetic tree, highlighting the genetic relationships and diversity within and between yak populations and other bovines.
Phylogenetic relationship analyses conducted in this study revealed that the populations of yak and as well as other bovine animals were separable into three distinct branches. Compared to previous findings [34, 21], this experiment identified a new phylogenetic branch that includes all five bovine species along with the outgroup Capra hircus.
The phylogenetic analysis in this study revealed a significant genetic similarity between yaks (Bos grunniens) and Bos indicus, providing new insights into the evolutionary relationships within bovine species. This similarity suggests a relatively recent divergence from a common ancestor when compared to other bovine species included in this study, such as Bos frontalis and Bubalus bubalis. These findings are consistent with previous research [35, 36] that utilized complete mitochondrial DNA and Y chromosomal DNA markers, indicating that yaks and Bos indicus share a closer evolutionary trajectory, likely influenced by geographic proximity and similar environmental adaptations.
Similar to studies by [37] and [38], which employed Capra hircus as an outgroup with mitochondrial DNA and microsatellite markers, the phylogenetic tree observed in this study also showed Capra hircus consistently serving as the outgroup.
The analysis of the complete mitochondrial Cyt b gene and partial D-loop sequences from 143 Pakistani domestic yaks revealed that Bos grunniens (yak) is more closely related to bison than to Bos indicus (zebu cattle) [38]. The nucleotide sequence divergence between yaks and bison was lower compared to that between yaks and Bos indicus, with 7.8% for the Cyt b gene and 15.75% for the D-loop. Additionally, Bos grunniens and Bos mutus (wild yak) was clustered together, indicating a higher genetic similarity between these two species than between yaks and Bos indicus. Although Capra hircus (GU295658) was not directly compared in this analysis, it is known to be more distantly related to bovines, including yaks. The distinct genetic divergence of Capra hircus from the studied bovine species reinforces the robustness of the phylogenetic framework used. This separation highlights the evolutionary distance between caprids and bovines, underscoring the distinct evolutionary pathways of these groups.
The genetic closeness between yaks and Bos indicus raises intriguing questions about potential historical interbreeding events or parallel adaptation strategies to similar ecological niches, as suggested by previous findings [40–42] and in understanding these genetic connections can offer valuable insights into the domestication processes and migratory patterns of these species, contributing to a broader understanding of bovine evolution. Furthermore, the evolutionary tree demonstrated that the three highly differentiated genetic branches all had high support rates. This high support excluded the influence of nuclear genes, verifying the reliability of the phylogenetic branches.
The classification of yaks within the Bovidae family has long been debated. Historically, Linnaeus placed yaks in the genus Bos alongside domestic cattle (Bos taurus) and zebu (Bos indicus). Recent studies, however, have revealed a more complex relationship between yaks and cattle, highlighted by mitochondrial DNA (mtDNA) evidence of past hybridization and gene flow between these species. Such genetic introgression is notably prevalent in specific regions, such as the Qinghai-Tibet Plateau (QTP) and parts of Mongolia and Russia [42]. In the present study, a median-joining network of 108 sequences from various bovine species and one ruminant (Capra hircus) categorized the data into six haplogroups. Notably, Arunachali yaks predominantly clustered with Bos indicus and, to a lesser extent, with Bos frontalis within the same haplogroup (haplogroup 3). This clustering pattern aligned with earlier findings by [43, 34]. Specifically, ten haplotypes in yak populations, all belonging to the T3 haplogroup, were identified by [43], which is also common in European cattle. Similarly, the T3 haplogroup was reported to be predominant in Chinese taurine cattle by [34]. In addition, another study [44] found cattle-specific alleles within yak populations, further indicating significant genetic introgression. Additionally, the analysis of three microsatellite loci (ILSTS013, ILSTS050, SPS115) revealed distinct alleles between yaks and cattle, suggesting a more pronounced cattle introgression in the QTP region. This indicates a notable genetic overlap between the two species.
The present findings may be influenced by potential haplogroup bias due to the limited selection of species and sample sizes in the study. Future research with broader sampling and additional genetic markers may provide a more comprehensive understanding of the genetic relationship between yaks and cattle.
Genetic diversity is an integral part of all biological diversity, serving as the basis for biological evolution, species differentiation, and is crucial for population maintenance, reproduction, and adaptation to habitat changes. High Hd and π values indicated high genetic diversity in Bos gaurus, Bubalus bubalis, and Bos indicus. However, Arunachali yak exhibited zero haplotype and nucleotide diversity, indicating no genetic variation in the studied sample sequences. This was likely due to a recent bottleneck, strong selection pressure, or inbreeding, which potentially limited the adaptability and long-term viability of these populations. Low level of genetic diversity lead to inbreeding and decreased population fitness [45], and this result differed significantly from previous studies by [27, 46–47] where higher degrees of haplotype and nucleotide diversity were observed in some yak breeds.
Despite the wide distributional range, interpopulation comparisons (Kxy, Dxy, Gst, and Da) revealed varying levels of genetic differentiation among the studied populations. Arunachali yak and Bos indicus showed low divergence and shared common genetic variations. However, gene flow (Nm) and Fst values were very high for Arunachali yak compared to other bovine species and domestic goat, Capra hircus, suggesting that Arunachali yak was relatively isolated with minimal gene flow. This observation was also supported by AMOVA analysis, which indicated 30.05% of the variance among the studied populations.