Loss of genetic diversity and inbreeding in Kashmir red deer (Cervus elaphus hanglu) of Dachigam National Park, Jammu & Kashmir, India

Abstract

BackgroundHangul (Cervus elaphus hanglu), the eastern most subspecies of red deer, is now confined only to the mountains in the Kashmir region of Jammu & Kashmir State of India. It is of great conservation significance as this is the last and only hope for Asiatic survivor of the red deer species in India. Wild population of free ranging hangul deer inhabiting in and around Dachigam National Park was genetically assessed in order to account for constitutive genetic attributes of hangul population using microsatellite markers.ResultsIn a pool of 36 multi-locus genotypes, 30 unique individuals were identified based on six microsatellite loci. The estimated cumulative probability of identity assuming all individuals were siblings (PID sibs) was 0.009 (9 in 1000). Altogether, 49 different alleles were observed with mean (± s.e.) allelic number of 8.17 ± 1.05, ranging from 5 to 11 per locus. The observed heterozygosity ranged between 0.08 and 0.83, with mean 0.40 ± 0.11 and the inbreeding coefficient ranged between −0.04 and 0.87 with mean 0.38 ± 0.15. Majority of loci (5/6) were found to be informative (PIC value > 0.5). All loci deviated from Hardy-Weinberg equilibrium except Ca-38 (P > 0.05) and none of the pairs of loci showed significant linkage disequilibrium except the single pair of Ca-30 and Ca-43 (P < 0.05).ConclusionsThe preliminary findings revealed that hangul population is significantly inbred and exhibited a low genetic diversity in comparison to other deer populations of the world. We suggest prioritizing the potential individuals retaining high heterozygosity for ex situ conservation and genetic monitoring of the hangul population should be initiated covering the entire distribution range to ensure the long term survival of hangul. We speculate further ignoring genetics attributes may lead to a detrimental effect which can negatively influence the reproductive fitness and survivorship of the hangul population in the wild.

Insights into the evolutionary history ofCervus(Cervidae, tribe Cervini) based on Bayesian analysis of mitochondrial marker sequences, with first indications for a new species

“…Mitochondrial markers had never been studied so far in this population, and their phylogenetic relationships were totally unknown. A microsatellite-based study has been published recently, revealing low genetic variability and high inbreeding for the population of Dachigam National Park, the last surviving nucleus of Kashmir red deer (Mukesh et al 2013). Based on our genetic results, this deer clearly belongs to the species C. hanglu (our nomenclature), although being distinct from Cervus hanglu bactrianus/Cervus hanglu yarkandensis (that are clearly synonyms), as suggested by a highly resolved node in the CR tree.…”

Species identification and molecular sexing from feces of Kashmir stag (Cervus elaphus hanglu)

“…Out of 37 samples, 21 unique individuals were identified following Mukesh et al (2013b) where 7 females and 14 males were identified. Thus, all samples of known or unknown sexes were correctly assigned to their respective sexes.…”

“…Despite the rigorous conservation efforts of the Department of Wildlife Protection in Jammu & Kashmir (J&K), the hangul population has experienced a severe decline in numbers and range contraction in the past few decades (Charoo et al 2010;Mukesh et al 2013b). The hangul population once abundant in the past has now largely confined to the Dachigam landscape, with a recent population estimate of 218 individuals (±13.96) in 2011 (Mukesh et al 2013b). It is listed under Schedule-I of the Indian Wildlife (Protection) Act, 1972 and J&K Wildlife (Protection) Act, 1978 and has also been categorized among the top 15 species of high conservation priority by the Government of India.…”

“…For many wildlife population studies, non-invasive sampling and modern molecular genetics tools augment and sometimes replace traditional field methods in unveiling the important characteristics like species identification (Waits and Paetkau 2005;Silva et al 2014), population genetic fitness (Paetkau and Strobeck 1994), sex discrimination (Mukesh et al 2013a), individual identification (Mukesh et al 2013b) and evolutionary history (Taberlet and Bouvet 1992) of elusive, rare and/or endangered species which are otherwise difficult to study. Genomic DNA can be easily obtained from the remnants epithelial cells often encase the fecal pellets without harming or even observing the animals for generating species-specific sequences (Chancellor et al 2012) and individual-specific genotypes (Bellemaina et al 2007).…”

Pragmatic Perspective on Conservation Genetics and Demographic History of the Last Surviving Population of Kashmir Red Deer (Cervus elaphus hanglu) in India

“…In total, we collected 160 individual tufts of pneumatic hairs from different locations of the Dachigam NP. Details of sample collection and DNA extraction from hair samples have been presented elsewhere [ 15 ].…”