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Background <p>Genetic diversity plays a crucial role in influencing evolution and adaptation. The order <i>Primates</i> is distinguished by advanced social structures, ecological adaptability, and extensive geographic distribution. These factors suggest that genetic variation within primate species is formed by both natural selection and historical population changes. Rhesus macaques (<i>Macaca mulatta</i>) occupy a broad range across India. Their extensive genomic variation reveals significant intra-specific differences among populations.</p> Methods and Results <p>We sequenced and analyzed approximately 565 bases of the mitochondrial DNA (mtDNA) control region from 236 fecal samples of wild Indian rhesus macaques, collected from 25 locations across 12 Indian states. We identified 66 haplotypes with overall haplotype and nucleotide diversity of 0.833 ± 0.023 and 0.0174 ± 0.0031, respectively. Among states, West Bengal_Sundarban showed the highest haplotype diversity (1.000 ± 0.126), while Delhi showed the lowest (0.182 ± 0.144). Phylogenetic analysis revealed two divergent clades. Clade 1 comprised North Indian cluster, including those from the Himalayan foothills, and Clade 2 comprised East Indian cluster. Genetic difference (Fst) of 80.05% observed between the two clades, indicating the presence of two deeply divergent mitochondrial lineages, suggesting the possible presence of two subspecies of rhesus macaques in India. However, this inference should be further validated using additional nuclear markers to confirm the taxonomic status. PCA plot and Median-joining (MJ) network analysis further revealed two haplogroups: Haplogroup I was primarily associated with North Indian cluster, while Haplogroup II from East Indian cluster. Interestingly, some individuals from the South Indian cluster, Telangana appeared in both Clade suggesting possible southward dispersal. Telangana, Manipur, Assam, West Bengal_Sundarban, and Odisha populations showed signatures of geographical and historical isolation. Demographic analyses indicated historical population contraction. The pronounced genetic structure and mtDNA divergence, when compared with rhesus macaques from other countries, further support the existence of two subspecies that can be confirmed with nuclear markers for robust taxonomic inference.</p> Conclusions <p>Our study contributes to understanding genetic connectivity, population structure and migration patterns, which will aid in the long-term monitoring of Indian rhesus macaques.</p>

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Assessment of genetic diversity and population structure of wild populations of Indian Rhesus macaque (Macaca mulatta) using mitochondrial DNA control region sequences

  • 期刊论文

  • 发表日期：

    2026年3月31日

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  • E. Agnita Sharon,
  • Ranjana Bhaskar,
  • Kumarapuram Apadodharanan Subramanian

摘要

Background

Genetic diversity plays a crucial role in influencing evolution and adaptation. The order Primates is distinguished by advanced social structures, ecological adaptability, and extensive geographic distribution. These factors suggest that genetic variation within primate species is formed by both natural selection and historical population changes. Rhesus macaques (Macaca mulatta) occupy a broad range across India. Their extensive genomic variation reveals significant intra-specific differences among populations.

Methods and Results

We sequenced and analyzed approximately 565 bases of the mitochondrial DNA (mtDNA) control region from 236 fecal samples of wild Indian rhesus macaques, collected from 25 locations across 12 Indian states. We identified 66 haplotypes with overall haplotype and nucleotide diversity of 0.833 ± 0.023 and 0.0174 ± 0.0031, respectively. Among states, West Bengal_Sundarban showed the highest haplotype diversity (1.000 ± 0.126), while Delhi showed the lowest (0.182 ± 0.144). Phylogenetic analysis revealed two divergent clades. Clade 1 comprised North Indian cluster, including those from the Himalayan foothills, and Clade 2 comprised East Indian cluster. Genetic difference (Fst) of 80.05% observed between the two clades, indicating the presence of two deeply divergent mitochondrial lineages, suggesting the possible presence of two subspecies of rhesus macaques in India. However, this inference should be further validated using additional nuclear markers to confirm the taxonomic status. PCA plot and Median-joining (MJ) network analysis further revealed two haplogroups: Haplogroup I was primarily associated with North Indian cluster, while Haplogroup II from East Indian cluster. Interestingly, some individuals from the South Indian cluster, Telangana appeared in both Clade suggesting possible southward dispersal. Telangana, Manipur, Assam, West Bengal_Sundarban, and Odisha populations showed signatures of geographical and historical isolation. Demographic analyses indicated historical population contraction. The pronounced genetic structure and mtDNA divergence, when compared with rhesus macaques from other countries, further support the existence of two subspecies that can be confirmed with nuclear markers for robust taxonomic inference.

Conclusions

Our study contributes to understanding genetic connectivity, population structure and migration patterns, which will aid in the long-term monitoring of Indian rhesus macaques.