Molecular Phylogeny and Population genetic structure of Himalayan Blue sheep (Pseudois nayaur) in Himalayan region

Abstract

The Himalayan blue sheep (Pseudois nayaur), commonly known as bharal, is a high-altitude caprine species endemic to the rugged terrains of the high Himalayas. Although classified as a species of "Least Concern" by the International Union for Conservation of Nature (JUCN), significant ambiguities persist regarding its taxonomic delineation and population structure. These uncertainties are further compounded by the paucity of comprehensive genetic data, particularly concerning populations within the Indian Himalayan Region (IHR), where geographical isolation and environmental heterogeneity may have promoted evolutionary divergence. The present study aims to elucidate the phylogenetic relationships, genetic diversity, and population structure of Pseudois nayaur across its Indian range, with a specific focus on populations inhabiting the eastern and western Himalayas. Employing a molecular phylogenetic approach, this investigation integrates mitochondrial DNA (mtDNA) markers-principally the cytochrome b gene, control region and the complete mitogenome-with nuclear microsatellite markers to assess lineage differentiation, historical demography, and gene flow. Non-invasive and ethically compliant sampling strategies were utilized to obtain biological material, ensuring minimal disturbance to wildlife. Laboratory analyses, including DNA extraction, polymerase chain reaction (PCR) amplification, and sequencing, were followed by bioinformatic assessments using tools such as DnaSP, Arlequin, STRUCTURE, BEAST, and PopART. Phylogenetic reconstructions revealed distinct mitochondrial haplotypes between eastern and western Himalayan populations, suggesting limited gene flow and historical isolation likely driven by topographic and climatic barriers. The genetic differentiation observed was consistent with the theory of allopatric divergence facilitated by the orogenic and glacial history of the Himalayas. Furthermore, the study confirms the phylogenetic placement of Pseudois nayaur within the subfamily Caprinae, identifying close evolutionary affinities with Ovis and Hemitragus species while supporting its unique lineage status. These findings have important implications for conservation biology, as they suggest the existence of evolutionarily significant units (ESUs) that merit region-specific management interventions. The bharal's role as a herbivore and primary prey for apex predators such as the snow leopard (Panthera uncia) further underscores its ecological significance in alpine ecosystems.