DOI: 10.5683/sp3/yxu2ua
title: Data from: A genotyping-in-thousands by sequencing panel to inform invasive deer management using non-invasive fecal and hair samples

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;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 (&lt;em&gt;Odocoileus hemionus sitkensis&lt;/em&gt;) 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.&lt;/p&gt;
description: &lt;b&gt;Methods&lt;/b&gt;&lt;br /&gt;&lt;p&gt;Genotyping-in-Thousands by sequencing (GT-seq) following Campbell et al. (2015) &lt;em&gt;Molecular Ecology Resources&lt;/em&gt; as modified in Schmidt et al. (2020) &lt;em&gt;Molecular Ecology Resources&lt;/em&gt; and the associated work.&lt;/p&gt;
description: &lt;b&gt;Usage notes&lt;/b&gt;&lt;br /&gt;&lt;p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;"&gt;gtseq244_nis_genepop.txt: genepop file of genotypic data at 244 SNPs collected with GT-seq for non-invasive (fecal and hair) samples.&lt;/p&gt;
&lt;p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;"&gt; &lt;/p&gt;
&lt;p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;"&gt;gtseq244_tissue_genepop.txt: genepop file of genotypic data at 244 SNPs collected with GT-seq for paired tissue samples.&lt;/p&gt;
&lt;p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;"&gt; &lt;/p&gt;
&lt;p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;"&gt;radseq244_final.vcf: vcf file of genotypic data at 244 SNPs collected with RAD-seq for tissue samples.&lt;/p&gt;
&lt;p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;"&gt; &lt;/p&gt;
&lt;p class="MsoNormal" style="margin:0in;font-size:12pt;font-family:Calibri , sans-serif;"&gt;metadata.csv: text file containing individual metadata for all samples used including sample identifiers, location, year, and sample type.&lt;/p&gt;
description: <b>Dryad version number:</b> 4
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> https://datadryad.org/stash/share/ZzTmqQvMJYc9yzeG-VK3H38x1vrk_Q2vhzRgJFpuLWA
<b>Storage size:</b> 1224521
<b>Visibility:</b> public