A genotyping‐in‐thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples. Issue 6 (10th June 2022)

• Record Type: Journal Article
• Authors: Burgess, Brock T.; Irvine, Robyn L.; Russello, Michael A.
• Is Part Of: Ecology and evolution. Volume 12:Issue 6(2022)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2022-06-10
• Subjects: conservation genetics -- GT‐seq -- invasive species -- molecular ecology -- noninvasive genetic sampling -- single nucleotide polymorphism; Ecology -- Periodicals; Evolution -- Periodicals; 577.05
• DOI: 10.1002/ece3.8993
• Languages: English
• ISSNs: 2045-7758

Abstract

Abstract: Studies in ecology, evolution, and conservation often rely on noninvasive 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 noninvasive samples to inform the management of invasive Sitka black‐tailed deer ( Odocoileus hemionus sitkensis ) in Haida Gwaii (Canada). We validated our panel using paired high‐quality tissue and noninvasive 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 noninvasive samples was low (0.50%). The panel will be used to inform future invasive species operations 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 noninvasive genetic sampling is employed. Abstract : Molecular ecology employs noninvasive sampling that can pose challenges for massively parallel DNA sequencing, with current methods limited in data quality/applicability. We demonstrate a GT‐seq workflow that can be applied to fecal and hair samples with high sample retention and genotyping accuracy, and provide a proof‐of‐concept application to invasive species management.