Is shed hair the most effective non-invasive resource for estimating wild pedigrees?

Abstract

Wild pedigrees are critical for better understanding mating systems and inbreeding scenarios to inform conservation strategies for endangered species. To delineate pedigrees in wild populations, many identified individuals will have to be genotyped at thousands of loci, mostly from non-invasive samples. This requires us to quantify (a) the most common non-invasive sample available from identified individuals (b) the ability to acquire genome-wide data from such samples, and (c) the quality of such genome-wide data, and its ability to reconstruct relationships between animals within a population. We followed identified individuals from a wild endangered tiger population, and found that shed hair samples were most common compared to fecal samples, carcasses and opportunistic invasive samples. DNA extraction, library preparation and whole genome sequencing resulted in between 126,129 and 512,689 SNPs from across the genome for four such samples. Exploratory population genetic analyses revealed that these data were free of holistic biases, and could recover expected population structure and relatedness. Mitochondrial genomes recovered matrilineages as suggested by long-term monitoring data. Even with these few samples, we were able to uncover the matrilineage for an individual with unknown ancestry. In summary, we demonstrated that non-invasive shed hair samples yielded adequate quality/quantity DNA AND in conjunction with sensitive library preparation methods, provided reliable data from hundreds of thousands of SNPs across the genome. This makes shed hair are an effective resource for studying individual-based genetics of elusive endangered species.