A Genotyping-in-Thousands by sequencing panel to inform invasive deer management using non-invasive fecal and hair samples

Studies in ecology, evolution, and conservation often rely on non-invasive samples, making it challenging to generate large amounts of high-quality genetic data for many elusive and at-risk species. We developed and optimized a Genotyping-in-Thousands by sequencing (GT-seq) panel using non-invasive samples to inform the management of invasive Sitka black-tailed deer (Odocoileus hemionus sitkensis) in Haida Gwaii (Canada). We validated our panel using paired high-quality tissue and non-invasive fecal and hair samples to simultaneously distinguish individuals, identify sex and reconstruct kinship among deer sampled across the archipelago, then provided a proof-of-concept application using field-collected feces on SGang Gwaay, an island of high ecological and cultural value. Genotyping success across 244 loci was high (90.3%) and comparable to that of high-quality tissue samples genotyped using restriction-site associated DNA sequencing (92.4%), while genotyping discordance between paired high-quality tissue and non-invasive samples was low (0.50%). The panel will be used to inform future invasive species management operations in Haida Gwaii by providing individual and population information before, during, and after deer eradications. More broadly, our GT-seq workflow that includes quality control analyses for targeted SNP selection and a modified protocol may be of wider utility for other studies and systems where non-invasive genetic sampling is employed.