De novo SNP Discovery in the Spotted Hyena (Crocuta crocuta)

Abstract: Relatedness studies of wild populations using reliable high-quality genetic markers enhance our understanding of a species’ behavior and ecology. Spotted hyenas (Crocuta crocuta) have a matriarchal social structure, unique amongst carnivores. However, genetically based relatedness studies on this species have been limited, but SNPs now provide an opportunity to study kinship patterns in better detail. We have developed a panel of 74 SNP markers suitable for genotyping spotted hyenas in Zambia. High-throughput de novo sequencing of reduced representation libraries of 27 individuals generated millions of read pairs. Aligned reads were used as input for the Stacks pipeline, resulting in the discovery of 261,694 putative SNPs. Strict filtering criteria were applied to find high-quality SNP markers informative for individual identification and population level analyses. Validation by genotyping a set of 80 individuals resulted in the selection of 74 autosomal SNPs (77%). To obtain a fully functional panel, we recommend an additional targeted approach for the discovery of Y-chromosome and mitochondrial markers. This SNP panel is a promising tool to infer relatedness in spotted hyena populations and has the potential to yield valuable information to support management and conservation efforts.