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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 (<em>Odocoileus hemionus sitkensis</em>) 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 operations (culls or eradications) in Haida Gwaii by providing individual and population information to inform management. 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.</p>; <b>Methods</b><br />

Genotyping-in-Thousands by sequencing (GT-seq) following Campbell et al. (2015) <em>Molecular Ecology Resources</em> as modified in Schmidt et al. (2020) <em>Molecular Ecology Resources</em> and the associated work.</p>; <b>Usage notes</b><br /><p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;">gtseq244_nis_genepop.txt: genepop file of genotypic data at 244 SNPs collected with GT-seq for non-invasive (fecal and hair) samples.</p> <p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;"> </p> <p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;">gtseq244_tissue_genepop.txt: genepop file of genotypic data at 244 SNPs collected with GT-seq for paired tissue samples.</p> <p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;"> </p> <p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;">radseq244_final.vcf: vcf file of genotypic data at 244 SNPs collected with RAD-seq for tissue samples.</p> <p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;"> </p> <p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;">metadata.csv: text file containing individual metadata for all samples used including sample identifiers, location, year, and sample type.</p>