Developing a GTseq panel and evaluating population structure for native and transplanted Sitka black-tailed deer populations

Population size estimation is critical for managing harvested species. Spatial capture-recapture via non-invasive genetic sampling is one method employed to estimate population size and is especially useful in habitats where aerial or other survey techniques are not possible. Developments in DNA sequencing technologies have led to the application of amplicon-based genotyping-in-thousands by sequencing (GTseq) for genotyping tissue and non-invasive genetic samples. Here we develop and assess the power of a GTseq single nucleotide polymorphism (SNP) panel for individual identification and population structure analysis of Sitka black-tailed deer ( Odocoileus hemionus sitkensis ) across native and transplanted populations in Alaska and British Columbia. Our panel contains 248 SNPs and has enough power for individual identification with as few as 30 loci across all sampled populations. We identified population structure aligned with island geography and translocation histories. To select panel SNPs, we sampled our initial genomic data from one population resulting in ascertainment bias. We highlight that this ascertainment bias led to lower locus variability in more differentiated populations, and we make recommendations for future panel applications.