Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus)

Abstract

Background The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information at landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on 249 field-collected dhole faeces from five protected areas of the central Indian landscape in the state of Maharashtra, India. Results We tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57–88%), polymorphism (3–9 alleles), heterozygosity (0.23–0.63) and produced a cumulative misidentification rate or PID(unbiased) and PID(sibs) value of 4.7 × 10−10 and 1.5 × 10−4, respectively, indicating a high statistical power in individual discrimination from poor quality samples. Conclusion Our results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. This genetic approach would be useful in dhole population estimation across its range and will help in assessing population trends and other genetic parameters for this elusive, social carnivore.

Genetic Diversity of Historical and Modern Populations of Russian Cattle Breeds Revealed by Microsatellite Analysis

“…To determine the consensus genotypes, we used a modified multiple-tube approach, proposed by Mondol et al [ 48 ] and used by Modi et al [ 49 ]. After initial multiplex amplification of microsatellite loci in duplicates, we selected only the samples in which at least six loci were successfully amplified (positive multiplex PCRs) for further analysis.…”

Dhole pack size variation: Assessing the effect of Prey availability and Apex predator

“…In field studies, individual identification of dhole packs and their members is a challenge owing to their uniform pelage pattern (Modi et al, 2019). To overcome this challenge, we generated information on the spatial distribution of dhole packs in the study sites using a systematic camera trapping design optimized for large carnivores (Karanth & Nichols, 1998).…”

Dhole pack size variation: Assessing effect of Prey availability and Apex predator

“…In field studies individual identification of dholes is challenging because of their uniform pelage pattern (Modi, Habib, Ghaskadbi, Nigam, & Mondol, 2019), therefore we adhered to pack identification on the basis of activity centres (Stansbury et al, 2014). We surveyed study sites through camera trapping and identified activity centres on the basis of pack's activity hotspots and concentrated indirect signs.…”