Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus) Shrushti Modi*, Bilal Habib*, Pallavi Ghaskadbi, Parag Nigam and Samrat Mondol Wildlife Institute of India, Chandrabani, Dehradun, Uttarakhand, India * These authors contributed equally to this work. 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. Subjects Conservation Biology, Genetics Keywords Dhole, Individual identification, Non-invasive sampling, Population parameters, Maharashtra tiger landscape How to cite this article Modi S, Habib B, Ghaskadbi P, Nigam P, Mondol S. 2019. Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus). PeerJ 7:e7453 DOI 10.7717/peerj.7453 Submitted 29 October 2018 Accepted 10 July 2019 Published 2 September 2019 Corresponding author Samrat Mondol, samrat@wii.gov.in Academic editor Antonio Amorim Additional Information and Declarations can be found on page 12 DOI 10.7717/peerj.7453 Copyright 2019 Modi et al. Distributed under Creative Commons CC-BY 4.0