Utilizing COI gene for the identification of Indian Rhesus macaque (Macaca mulatta) and determining their genetic relationship with other macaque species

Amplifying large fragments from degraded and non-invasive samples poses a significant challenge in species identification. Accurately identifying any species is crucial for understanding evolutionary history and species radiations from such samples. To address this challenge, we developed a novel mtDNA cytochrome c oxidase I (COI) primer for the Indian rhesus macaque, amplifying a 440 bp segment to identify non-invasive degraded fecal samples for effective conservation planning. Wild Indian rhesus macaque (Macaca mulatta) fecal samples were collected from seven states across India. We analyzed 47 sequences of Indian rhesus macaques alongside 120 sequences of the genus Macaca to see the genetic relationship. The phylogenetic tree was constructed using COI sequences. Our analysis suggests that, compared to other species in the cercopithecine subfamily, Indian macaques form a polyphyletic assemblage, comprising two potential lineages: one from Northern India and the other from Eastern India. These findings are crucial to aid in the conservation management and translocation process of Indian rhesus macaques.