COS 239-6 - GT-seq for genetic monitoring: recovery planning for threatened ground squirrel

Abstract: Northern Idaho ground squirrels (Urocitellus brunneus, hereafter NIDGS) are endemic to Idaho and federally listed as a threatened species. They persist within only a fraction of their former range due to habitat and population connectivity loss. Since 2002, we have collected genetic samples from this species and evaluated genetic diversity and gene flow using mitochondrial DNA sequencing and nuclear DNA microsatellites. More recently, we identified 2,663 single nucleotide polymorphism (SNP) loci and evaluated connectivity and adaptive diversity for 15 populations and 80 individuals. However, our SNP analyses were limited to samples with large amounts of high-quality DNA, and thus represent an incomplete sampling of individuals and populations. Further, the inconsistent sampling between past NIDGS genetic studies provides insufficient data to address research needs outlined by the United States Fish and Wildlife Service (USFWS) for species recovery. Therefore, there is a need for a genetic monitoring approach that can genotype large numbers of low-quality samples at a relatively low cost. The goals of our study were to design and optimize a set of SNP loci for a Genotyping-in-Thousands by sequencing (GT-seq) panel and then apply that panel to 1,092 archived NIDGS samples from 29 populations to evaluate connectivity and genetic diversity and structure at neutral and adaptive loci. The optimized NIDGS GT-seq panel consists of 224 neutral and 81 putatively adaptive SNPs, for a total of 305 SNPs. DNA collected from buccal swabs in 2016-2020 had a high average genotyping success rate of 85%, while samples collected from hair in 2002-2006 did not genotype successfully. We show evidence of movement between sites previously believed to have little to no dispersal, with central locations acting as a potential corridor for NIDGS gene flow. In conclusion, the GT-seq dataset provides insights into the extent to which NIDGS populations have had or continue to have genetic connectivity across the landscape and which populations are most important for species persistence. Additionally, the GT-seq panel is an effective and efficient genotyping tool that will aid in decision-making for future recovery decision making and monitoring.