Development of a Genotyping‐in‐Thousands by Sequencing (GT‐Seq) Panel for Identifying Individuals and Estimating Relatedness Among Alaska Black Bears (Ursus americanus)
ABSTRACT The management and conservation of large mammals, such as black bears (Ursus americanus), have long been informed by genetic estimates of population size and individual dispersal. Amplicon sequencing methods, also known as ‘genotyping‐in‐thousands‐by sequencing’ (GT‐seq), now enable the eff...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2025-04-01
|
| Series: | Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/ece3.71273 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850119750851493888 |
|---|---|
| author | Eleni L. Petrou Colette D. Brandt Timothy J. Spivey Kristen M. Gruenthal Cherie M. McKeeman Sean D. Farley David Battle Cory Stantorf Andrew M. Ramey |
| author_facet | Eleni L. Petrou Colette D. Brandt Timothy J. Spivey Kristen M. Gruenthal Cherie M. McKeeman Sean D. Farley David Battle Cory Stantorf Andrew M. Ramey |
| author_sort | Eleni L. Petrou |
| collection | DOAJ |
| description | ABSTRACT The management and conservation of large mammals, such as black bears (Ursus americanus), have long been informed by genetic estimates of population size and individual dispersal. Amplicon sequencing methods, also known as ‘genotyping‐in‐thousands‐by sequencing’ (GT‐seq), now enable the efficient and cost‐effective genotyping of hundreds of loci and individuals in the same sequencing run. Here, we develop a GT‐seq panel for individual identification and kinship inference in Alaska black bears. Using genomic data from restriction site‐associated DNA sequencing of hunter‐harvested bears from Southcentral Alaska (n = 85), we identified 170 microhaplotype and single nucleotide polymorphism (SNP) loci that were highly heterozygous in local populations. To enable sexing of individuals, we also included a previously published sex‐linked locus in the GT‐seq panel. We empirically validated the GT‐seq panel using samples collected at different spatial scales. These samples included tissues (n = 82) obtained from bears within a small geographic area in Anchorage, Alaska, which were likely to be relatives as well as the hunter‐harvested samples collected from geographically widespread locations throughout Southcentral Alaska. Empirical validation indicated high genotyping success and genotype reproducibility across replicate subsamples. Computer simulations demonstrated that the GT‐seq panel had ample statistical power for distinguishing distinct individuals and first‐order relatives (parent‐offspring and full‐sibling pairs) from unrelated individuals. As a final proof of concept, the panel was used to identify individual bears and close kin sampled from urban and wild habitats in Anchorage, Alaska. We anticipate that the GT‐seq panel will be a useful genomic resource for the monitoring and management of Alaska black bear populations. |
| format | Article |
| id | doaj-art-e98e2817244d4101b68c29df04a53d61 |
| institution | OA Journals |
| issn | 2045-7758 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj-art-e98e2817244d4101b68c29df04a53d612025-08-20T02:35:33ZengWileyEcology and Evolution2045-77582025-04-01154n/an/a10.1002/ece3.71273Development of a Genotyping‐in‐Thousands by Sequencing (GT‐Seq) Panel for Identifying Individuals and Estimating Relatedness Among Alaska Black Bears (Ursus americanus)Eleni L. Petrou0Colette D. Brandt1Timothy J. Spivey2Kristen M. Gruenthal3Cherie M. McKeeman4Sean D. Farley5David Battle6Cory Stantorf7Andrew M. Ramey8U.S. Geological Survey, Alaska Science Center 4210 University Drive Anchorage Alaska USAU.S. air Force, Joint Base Elmendorf‐Richardson JBER Alaska USAAlaska Department of Fish and Game Anchorage Alaska USAAlaska Department of Fish and Game Anchorage Alaska USAU.S. Geological Survey, Alaska Science Center 4210 University Drive Anchorage Alaska USAAlaska Department of Fish and Game Anchorage Alaska USAAlaska Department of Fish and Game Anchorage Alaska USAAlaska Department of Fish and Game Anchorage Alaska USAU.S. Geological Survey, Alaska Science Center 4210 University Drive Anchorage Alaska USAABSTRACT The management and conservation of large mammals, such as black bears (Ursus americanus), have long been informed by genetic estimates of population size and individual dispersal. Amplicon sequencing methods, also known as ‘genotyping‐in‐thousands‐by sequencing’ (GT‐seq), now enable the efficient and cost‐effective genotyping of hundreds of loci and individuals in the same sequencing run. Here, we develop a GT‐seq panel for individual identification and kinship inference in Alaska black bears. Using genomic data from restriction site‐associated DNA sequencing of hunter‐harvested bears from Southcentral Alaska (n = 85), we identified 170 microhaplotype and single nucleotide polymorphism (SNP) loci that were highly heterozygous in local populations. To enable sexing of individuals, we also included a previously published sex‐linked locus in the GT‐seq panel. We empirically validated the GT‐seq panel using samples collected at different spatial scales. These samples included tissues (n = 82) obtained from bears within a small geographic area in Anchorage, Alaska, which were likely to be relatives as well as the hunter‐harvested samples collected from geographically widespread locations throughout Southcentral Alaska. Empirical validation indicated high genotyping success and genotype reproducibility across replicate subsamples. Computer simulations demonstrated that the GT‐seq panel had ample statistical power for distinguishing distinct individuals and first‐order relatives (parent‐offspring and full‐sibling pairs) from unrelated individuals. As a final proof of concept, the panel was used to identify individual bears and close kin sampled from urban and wild habitats in Anchorage, Alaska. We anticipate that the GT‐seq panel will be a useful genomic resource for the monitoring and management of Alaska black bear populations.https://doi.org/10.1002/ece3.71273amplicon sequencingGT‐seqindividual identificationparentagepopulation structureUrsus americanus |
| spellingShingle | Eleni L. Petrou Colette D. Brandt Timothy J. Spivey Kristen M. Gruenthal Cherie M. McKeeman Sean D. Farley David Battle Cory Stantorf Andrew M. Ramey Development of a Genotyping‐in‐Thousands by Sequencing (GT‐Seq) Panel for Identifying Individuals and Estimating Relatedness Among Alaska Black Bears (Ursus americanus) Ecology and Evolution amplicon sequencing GT‐seq individual identification parentage population structure Ursus americanus |
| title | Development of a Genotyping‐in‐Thousands by Sequencing (GT‐Seq) Panel for Identifying Individuals and Estimating Relatedness Among Alaska Black Bears (Ursus americanus) |
| title_full | Development of a Genotyping‐in‐Thousands by Sequencing (GT‐Seq) Panel for Identifying Individuals and Estimating Relatedness Among Alaska Black Bears (Ursus americanus) |
| title_fullStr | Development of a Genotyping‐in‐Thousands by Sequencing (GT‐Seq) Panel for Identifying Individuals and Estimating Relatedness Among Alaska Black Bears (Ursus americanus) |
| title_full_unstemmed | Development of a Genotyping‐in‐Thousands by Sequencing (GT‐Seq) Panel for Identifying Individuals and Estimating Relatedness Among Alaska Black Bears (Ursus americanus) |
| title_short | Development of a Genotyping‐in‐Thousands by Sequencing (GT‐Seq) Panel for Identifying Individuals and Estimating Relatedness Among Alaska Black Bears (Ursus americanus) |
| title_sort | development of a genotyping in thousands by sequencing gt seq panel for identifying individuals and estimating relatedness among alaska black bears ursus americanus |
| topic | amplicon sequencing GT‐seq individual identification parentage population structure Ursus americanus |
| url | https://doi.org/10.1002/ece3.71273 |
| work_keys_str_mv | AT elenilpetrou developmentofagenotypinginthousandsbysequencinggtseqpanelforidentifyingindividualsandestimatingrelatednessamongalaskablackbearsursusamericanus AT colettedbrandt developmentofagenotypinginthousandsbysequencinggtseqpanelforidentifyingindividualsandestimatingrelatednessamongalaskablackbearsursusamericanus AT timothyjspivey developmentofagenotypinginthousandsbysequencinggtseqpanelforidentifyingindividualsandestimatingrelatednessamongalaskablackbearsursusamericanus AT kristenmgruenthal developmentofagenotypinginthousandsbysequencinggtseqpanelforidentifyingindividualsandestimatingrelatednessamongalaskablackbearsursusamericanus AT cheriemmckeeman developmentofagenotypinginthousandsbysequencinggtseqpanelforidentifyingindividualsandestimatingrelatednessamongalaskablackbearsursusamericanus AT seandfarley developmentofagenotypinginthousandsbysequencinggtseqpanelforidentifyingindividualsandestimatingrelatednessamongalaskablackbearsursusamericanus AT davidbattle developmentofagenotypinginthousandsbysequencinggtseqpanelforidentifyingindividualsandestimatingrelatednessamongalaskablackbearsursusamericanus AT corystantorf developmentofagenotypinginthousandsbysequencinggtseqpanelforidentifyingindividualsandestimatingrelatednessamongalaskablackbearsursusamericanus AT andrewmramey developmentofagenotypinginthousandsbysequencinggtseqpanelforidentifyingindividualsandestimatingrelatednessamongalaskablackbearsursusamericanus |