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Indian Rhesus Macaques Formed Two Deep Mitochondrial Lineages Across 12 States

Rhesus macaque in Sundarbans National Park, West Bengal, India
Research · Genetics & genomics

A nationwide genetic study of wild rhesus macaques (Macaca mulatta) in India identified two deeply divergent mitochondrial lineages. The researchers analysed DNA from 236 faecal samples collected at 25 locations in 12 states and found a northern lineage, including populations from the Himalayan foothills, and an eastern lineage. Mitochondrial DNA (mtDNA) is inherited through the maternal line, so these lineages trace maternal ancestry rather than the whole genome.

The team analysed the mtDNA control region and identified 66 haplotypes—distinct variants of the mitochondrial sequence. Haplotype diversity was highest in the Sundarbans population in West Bengal and lowest in Delhi. Here, high haplotype diversity means that a population contains many different mitochondrial maternal lineages, whereas low diversity means that fewer such lineages are represented. The Sundarbans population therefore retained greater maternal-line variation than Delhi.

Two deep maternal lineages divided northern and eastern India

The two main clades showed strong genetic differentiation, separating a mainly North Indian haplogroup from an East Indian one. Samples from Telangana occurred in both clades, while populations from Telangana, Manipur, Assam, the West Bengal Sundarbans and Odisha showed signatures consistent with geographical or historical isolation.

The possible taxonomic split still needs nuclear-genome testing

The authors suggest that the deep mitochondrial split could indicate two subspecies within Indian rhesus macaques, but state that this interpretation requires testing with additional nuclear markers before the taxonomic status can be confirmed. Their demographic analyses also indicated historical population contraction.

Sources and image credit

  1. Sharon, E. A., Bhaskar, R., & Subramanian, K. A. (2026). Assessment of genetic diversity and population structure of wild populations of Indian Rhesus macaque (Macaca mulatta) using mitochondrial DNA control region sequences. Molecular Biology Reports, 53(1), 564. https://doi.org/10.1007/s11033-026-11694-1Primary research article published 31 March 2026. Approximately 565 bp of mitochondrial control-region DNA were analysed from 236 faecal samples collected at 25 locations in 12 Indian states. The study identified 66 haplotypes and two deeply divergent mitochondrial clades, broadly representing northern and eastern Indian populations. The authors suggest that the split could indicate two subspecies but explicitly state that nuclear markers are needed to confirm the taxonomic interpretation.

Image: Tisha Mukherjee / Wikimedia Commons — rhesus macaque photographed in Sundarbans National Park, West Bengal, India, on 13 March 2026; representative image from one of the sampled states, not an identified study animal. · CC BY-SA 4.0 · Source

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