A genotyping‐in‐thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples
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 nonin...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Wiley
2022-06-01
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| Series: | Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/ece3.8993 |
| _version_ | 1811226894436139008 |
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| author | Brock T. Burgess Robyn L. Irvine Michael A. Russello |
| author_facet | Brock T. Burgess Robyn L. Irvine Michael A. Russello |
| author_sort | Brock T. Burgess |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T09:33:32Z |
| format | Article |
| id | doaj.art-615d02a4ea434a24b2aaa5b5b6adb061 |
| institution | Directory Open Access Journal |
| issn | 2045-7758 |
| language | English |
| last_indexed | 2024-04-12T09:33:32Z |
| publishDate | 2022-06-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj.art-615d02a4ea434a24b2aaa5b5b6adb0612022-12-22T03:38:18ZengWileyEcology and Evolution2045-77582022-06-01126n/an/a10.1002/ece3.8993A genotyping‐in‐thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samplesBrock T. Burgess0Robyn L. Irvine1Michael A. Russello2Department of Biology The University of British Columbia Kelowna CanadaEcosystem Conservation Team Protected Areas Establishment and Conservation Directorate Parks Canada Agency Gatineau CanadaDepartment of Biology The University of British Columbia Kelowna CanadaAbstract 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.https://doi.org/10.1002/ece3.8993conservation geneticsGT‐seqinvasive speciesmolecular ecologynoninvasive genetic samplingsingle nucleotide polymorphism |
| spellingShingle | Brock T. Burgess Robyn L. Irvine Michael A. Russello A genotyping‐in‐thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples Ecology and Evolution conservation genetics GT‐seq invasive species molecular ecology noninvasive genetic sampling single nucleotide polymorphism |
| title | A genotyping‐in‐thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples |
| title_full | A genotyping‐in‐thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples |
| title_fullStr | A genotyping‐in‐thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples |
| title_full_unstemmed | A genotyping‐in‐thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples |
| title_short | A genotyping‐in‐thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples |
| title_sort | genotyping in thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples |
| topic | conservation genetics GT‐seq invasive species molecular ecology noninvasive genetic sampling single nucleotide polymorphism |
| url | https://doi.org/10.1002/ece3.8993 |
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