A panel of microsatellites to individually identify leopards and its application to leopard monitoring in human dominated landscapes

Samrat Mondol,Kartik Sunagar,Uma Ramakrishnan,Velu Mani Selvaraj,Navya R,Vidya Athreya

doi:10.1186/1471-2156-10-79

Samrat Mondol, Kartik Sunagar + Show 4 more

Open Access

https://doi.org/10.1186/1471-2156-10-79

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Abstract

BackgroundLeopards are the most widely distributed of the large cats, ranging from Africa to the Russian Far East. Because of habitat fragmentation, high human population densities and the inherent adaptability of this species, they now occupy landscapes close to human settlements. As a result, they are the most common species involved in human wildlife conflict in India, necessitating their monitoring. However, their elusive nature makes such monitoring difficult. Recent advances in DNA methods along with non-invasive sampling techniques can be used to monitor populations and individuals across large landscapes including human dominated ones. In this paper, we describe a DNA-based method for leopard individual identification where we used fecal DNA samples to obtain genetic material. Further, we apply our methods to non-invasive samples collected in a human-dominated landscape to estimate the minimum number of leopards in this human-leopard conflict area in Western India.ResultsIn this study, 25 of the 29 tested cross-specific microsatellite markers showed positive amplification in 37 wild-caught leopards. These loci revealed varied levels of polymorphism (four-12 alleles) and heterozygosity (0.05-0.79). Combining data on amplification success (including non-invasive samples) and locus specific polymorphisms, we showed that eight loci provide a sibling probability of identity of 0.0005, suggesting that this panel can be used to discriminate individuals in the wild. When this microsatellite panel was applied to fecal samples collected from a human-dominated landscape, we identified 7 individuals, with a sibling probability of identity of 0.001. Amplification success of field collected scats was up to 72%, and genotype error ranged from 0-7.4%.ConclusionOur results demonstrated that the selected panel of eight microsatellite loci can conclusively identify leopards from various kinds of biological samples. Our methods can be used to monitor leopards over small and large landscapes to assess population trends, as well as could be tested for population assignment in forensic applications.

Highlights

Leopards are the most widely distributed of the large cats, ranging from Africa to the Russian Far East
We have developed a set of methodological tools for the genetic individual identification of leopards aimed at larger landscapes, where higher numbers of leopards are likely to be present (Athreya et al unpublished)
Standardization of Individual identification Microsatellite amplification We initially tested a total of 29 microsatellites using leopard blood DNA to determine the most polymorphic loci. 25 loci showed amplification (Table 1) while four did not (FCA069, FCA311, FCA466 and F27)

Summary

Introduction

Leopards are the most widely distributed of the large cats, ranging from Africa to the Russian Far East. High human population densities and the inherent adaptability of this species, they occupy landscapes close to human settlements. As a result, they are the most common species involved in human wildlife conflict in India, necessitating their monitoring. Noninvasive genetic typing of DNA extracted from animal hair or scats have been used for individual identification of rare, endangered or cryptic species [9,10,11,12,13,14,15,16] Such methods would be ideal for monitoring leopards in human-dominated landscapes

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