mtDNA analysis confirms the endangered Kashmir musk deer extends its range to Nepal

Abstract

Musk deer Moschus spp. are endemic to the high mountain forests of central Asia. The taxonomic status of musk deer in the central and western Himalayas is poorly understood. We investigated the phylogenetic relationship of musk deer from the central and western Himalayas based on mitochondrial genomic data of Cytochrome b (380 bps) and D-loop (1000 bps). Our results distinguished two divergent lineages using higher bootstrap support (bs) values from the Maximum likelihood and Bayesian posterior probabilities (bpp). Both the Manang and Kaski lineages from central Nepal are confirmed as Himalayan musk deer Moschus leucogaster and represent a species complex widespread throughout the central and eastern Himalayan region. The musk deer Mustang lineage was confirmed as Kashmir musk deer Moschus cupreus and has wide distribution in the western Himalayas (from central Nepal to Afghanistan). Our analysis validates that Kashmir musk deer is a genetically distinct species and it clarifies that Himalayan musk deer and Kashmir musk deer are confirmed instead of Alpine musk deer Moschus chrysogaster which has been previously described from the southern parts of Himalayas of Nepal, India and Pakistan.

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features

“…The contraction gene families were most prominent in olfactory transduction pathway (Additional file 1: Figure S4). It might be attributed possibly to musk deer adaptation to the cold and highaltitude environment (1000-4200 m) where food sources and odorants are limited and diffused slowly, and the interactions between odorants and receptors weakened [79,80]. Similar results have been obtained in some high plateau animal genome studies, such as avian [81], wild boars [82], hot-spring snake [83] and Tibetan chicken [84].…”

mtDNA confirms the presence of Moschus leucogaster (Ruminantia, Moschidae) in Gaurishankar Conservation Area, Nepal

“…As musk deer are shy and nocturnal it is difficult to detect them in daytime (Green, 1986). Additionally, if they are seen in daytime they hide in the shrub understory, and even if they are encountered in forest and open areas they are visible only for a few seconds (Singh et al, 2019). Furthermore, it is not easy to identify the species of musk deer from their physical appearance and morphological characteristics (Groves et al, 1995;Singh et al, 2019).…”

“…Additionally, if they are seen in daytime they hide in the shrub understory, and even if they are encountered in forest and open areas they are visible only for a few seconds (Singh et al, 2019). Furthermore, it is not easy to identify the species of musk deer from their physical appearance and morphological characteristics (Groves et al, 1995;Singh et al, 2019). Singh et al (2019) A. americana, O. aries and T. kanchil were selected as outgroups.…”

“…All available nucleotide sequences of the cyt-b gene of Moschus species were downloaded from the NCBI GenBank database and the data source made available by Pan et al (2015) and Singh et al (2019) (table 1). The sequences of Alces alces americana, Ovis aries and Tragulus kanchil were also downloaded to be used as outgroups.…”

“…Although all the three species of musk deer found in Nepal are categorized as Endangered by IUCN (IUCN, 2013), only M. chrysogaster is enlisted as a protected mammal by the National Park and Wildlife Conservation Act 1973 due to lack of documentation on the confirmation of species of musk deer (Jnawali et al, 2011). There are only a few studies on taxonomic and phylogenetic analysis of musk deer in the context of Nepal (Singh et al, 2019). The Gaurishankar Conservation Area (GCA) is the newly established conservation area where molecular studies confirming the species presence are crucial for its conservation and management in the future.…”