Identifying sex and individual from faecal DNA of the Asian elephant using a single multiplex PCR for population monitoring

Information on the sex- and individual-specific space use by a species elucidates demography, resource selection and individual life history. However, traditional field surveys often lack information on sex and individual identity, thereby not maximizing the potential of the effort put in. Recent advances in genetic non-invasive sampling provide cost-effective approaches to determine identity and sex from faecal DNA with high accuracy, which are advantageous for tracking individuals compared to field observations. Therefore, we describe the first single multiplex-based sex and individual identification protocol using faecal samples of the wild Asian elephant ( Elephas maximus ) collected from the vicinity of Rajaji Tiger Reserve, Uttarakhand, India. We co-amplified fluorescence-labelled microsatellites (n = 5) and a Y chromosome-linked sex marker in four replicates from faecal DNA extracts (n = 149). The mean per genotype allelic drop-out rate was 0.11 ± 0.02, while the false allele rate was 0.05 ± 0.01. The mean null allele frequency across the markers was 0.15 ± 0.02. We obtained 74.1% consensus genotypes across microsatellites and dropped samples with more than one-locus missing genotype from further analyses. The remaining dataset comprised 105 samples, 30.5% of which were females. We identified 51 unique individuals (25 males and 26 females) with a maximum of one-locus mismatch. With low genotyping error rates and adequate misidentification probabilities (P ID = 4.2 × 10 −4 ; P IDSib = 3.0 × 10 −2 ), the described panel provides a cost-effective method (US$ 18/sample) for molecular sexing and individual identification. Hence, the suggested multiplex panel would provide a thorough understanding of individual and sex-specific differences in habitat use across heterogeneous landscapes, facilitating effective conservation strategies.