Email: 7 shrushti@wii.gov.in 8 bh@wii.gov.in 9 pallavi@wii.gov.in 10 nigamp@wii.gov.in 11 samrat@wii.gov.in 12 13 Abstract 27 Background 28 The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest 29 dwelling, social canid distributed across south and Southeast Asia. Severe pressures from 30 habitat loss, prey depletion, disease, human persecution and interspecific competition resulted 31 in global population decline in dholes. Despite a declining population trend, detailed 32 information on population size, ecology, demography and genetics is lacking. Generating 33 reliable information and landscape level for dholes is challenging due to their secretive 34 behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based 35tools can be used to monitor populations and individuals across large landscapes. In this 36 paper, we describe standardization and validation of faecal DNA-based methods for 37 individual identification of dholes. We tested this method on field-collected dhole faeces in 38 four tiger reserves of the central Indian landscape in the state of Maharashtra, India. Further, 39 we conducted preliminary analyses of dhole population structure and demography in the 40 study area.
41Results 42 We tested a total of 18 cross-species markers and developed a panel of 12 markers for 43 unambiguous individual identification of dholes. This marker panel identified 101 unique 44 individuals from faecal samples collected across our pilot field study area. These loci showed 45 varied level of amplification success (57-88%), polymorphism (3-9 alleles), heterozygosity 46 (0.23-0.63) and produced a cumulative probability of identity (unbiased) and probability of 47 identity (sibs) value of 4.7x10 -10 and 1.5x10 -4 , respectively. Our preliminary analyses of 48 population structure indicated four genetic subpopulations in dholes. Qualitative analyses of 49 population demography show signal of population decline.50 3Conclusion 51 Our results demonstrated that the selected panel of 12 microsatellite loci can conclusively 52 identify dholes from poor quality, non-invasive biological samples and help in exploring 53 various population parameters. Our methods can be used to estimate dhole populations and 54 assess population trends for this elusive, social carnivore. 55 56 57 The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, endangered, social canid 58 distributed in south and southeast Asia [1, 2] occupying a range of habitat types including 59 alpine, temperate, sub-tropical and tropical forests [2]. Driven by habitat loss, prey depletion, 60 disease transmission from domestic dog, human persecution and interspecific competition [3, 61 4], dholes are currently found in about 75% of their historical global range [2, 4]. Global 62 dhole population is roughly estimated to be about 4500-10500 with only 949-2215 mature 63 individuals, but accurate estimates and population trends are not available from any part of its 64 range [4]. They are consid...