Understanding how genetic diversity is distributed across spatiotemporal scales in species of conservation or management concern is critical for identifying large-scale mechanisms affecting local conservation status and implementing large-scale biodiversity monitoring programs. However, cross-scale surveys of genetic diversity are often impractical within single studies, and combining datasets to increase spatiotemporal coverage is frequently impeded by using different sets of molecular markers. Recently developed molecular tools make surveys based on standardized SNP panels more feasible than ever but require existing genomic information. Here, we demonstrate the utility of genome-wide SNPs reflective of range-wide genetic diversity for surveying populations across the native species range. These data can be leveraged to design SNP panels that allow datasets to be combined for large-scale analyses. We develop this resource for brook trout (Salvelinus fontinalis). We performed restriction site-associated DNA sequencing for wild brook trout from 82 locations spanning much of the native range and domestic brook trout from 24 hatchery strains used in stocking efforts. We identified over 24,000 SNPs putatively representing neutral and adaptive regions of the brook trout genome. We explored the ability of these SNPs to resolve relationships across spatial scales, including population structure, hatchery admixture, and outlier loci. Our dataset captures a wide spectrum of genetic diversity in native brook trout, offering a valuable resource for developing SNP panels. We highlight potential applications of this resource with the goal of increasing the integration of genomic information into decision-making for brook trout and other species of conservation or management concern.

We performed restriction site-associated DNA sequencing (RADseq) on wild-caught brook trout (Salvelinus fontinalis) from 82 sites spanning much of the native species range and domestic brook trout representing 24 hatchery strains. RADseq libraries were prepared following the methods of Ali et al. (2016 Genetics) then underwent PE150 sequencing on an Illumina HiSeq 4000. We used resulting data to perform SNP discovery based on the Salvelinus sp. reference genome (Christensen et al. 2018, 2021 PLoS ONE). We then performed quality filtering to remove loci and individuals missing an excessive proportion of genotypes, genotypes with low quality scores or read depths, genotypes with poor allele balance, and loci with low minor allele counts. We also removed paralogous loci and loci rendered monomorphic by the filtering process. The resulting quality filtered dataset comprises genotypes for 24,337 SNPs in 201 wild-caught brook trout and 66 hatchery brook trout.