Genetic Diversity, Geographical Structure, and Demographic History of the Kashmir Gray Langur (Semnopithecus ajax)

Genetic diversity allows species to survive in a dynamic environment where selective criteria are ever-changing. As a result, the long-term survival of a species can be affected by its levels of genetic diversity. The Kashmir gray langur, Semnopithecus ajax, is an Endangered primate species endemic to the northwestern Himalaya. It has a fragmented distribution, is exposed to severe anthropogenic and climatic pressures, and has received little scientific attention. We investigated patterns of genetic diversity, population structure, and demographic history in wild populations of the Kashmir gray langur in the Kashmir Himalaya. We sampled 15 langur groups by using noninvasive sampling for scat collection and also obtained a tissue sample from a dead langur for whole-genome sequencing. We sequenced a mt-DNA fragment encompassing part of the noncoding D-loop region (728 bp) for 63 samples and protein-coding Cytochrome b (775 bp) for 37 samples. We generated whole-genome data by using PCR-free shotgun sequencing. We also reconstructed the demographic history of the Kashmir gray langur through coalescent analysis using MSMC2. We observed (± SD) lower haplotype (Hd = 0.207 ± 0.088) and nucleotide (π = 0.00126 ± 0.00077) diversity in Cytochrome b (693 bp) gene sequences than in noncoding partial D-loop (625 bp) gene sequences (Hd = 0.878 ± 0.026 and π = 0.00735 ± 0.002). Concatenated alignment (Cytochrome b and D-loop, 1318 bp) defined 21 unique haplotypes with haplotype diversity of 0.935 ± 0.024 and nucleotide diversity of 0.00532 ± 0.00193. The haplotype network and maximum likelihood phylogenetic tree revealed strong signatures of genetic differentiation among geographic populations, with the Jhelum River appearing to be a prominent barrier to gene flow between these populations. We found no evidence of isolation-by-distance. Mean genome-wide heterozygosity was very low (0.00034). We estimated the long-term effective population size to be 8,702 individuals; however, the most recent estimate indicated a lower value of 1,844 individuals. Our study emphasizes the need for habitat connectivity to mitigate the negative impacts of habitat loss and fragmentation on the genetic diversity of terrestrial and arboreal animals inhabiting the Himalayan ecosystems, particularly habitat specialist species.