Data from: Phylogeographic analyses of American black bears (Ursus americanus) suggest four glacial refugia and complex patterns of post-glacial admixture
Studies of species with continental distributions continue to identify intraspecific lineages despite continuous habitat. Lineages may form due to isolation by distance, adaptation, divergence across barriers, or genetic drift following range expansion. We investigated lineage diversification and ad...
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Data Archiving and Networked Services (DANS)
2016
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Online Access: | https://doi.org/10.5061/dryad.dc02b |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::9d7ab4980d65e2e744eccf440aa00401 2023-05-15T18:48:52+02:00 Data from: Phylogeographic analyses of American black bears (Ursus americanus) suggest four glacial refugia and complex patterns of post-glacial admixture Puckett, Emily E. Etter, Paul D. Johnson, Eric A. Eggert, Lori S. 2016-05-04 https://doi.org/10.5061/dryad.dc02b undefined unknown Data Archiving and Networked Services (DANS) http://dx.doi.org/10.5061/dryad.dc02b https://dx.doi.org/10.5061/dryad.dc02b lic_creative-commons oai:easy.dans.knaw.nl:easy-dataset:89374 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:89374 10.5061/dryad.dc02b 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f re3data_____::r3d100000044 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 Life sciences medicine and health care microsatellites mitochondrial genome admixture phylogeography lineage divergence Ursus americanus SNPs American black bear Holocene species distribution modeling Pleistocene North America envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2016 fttriple https://doi.org/10.5061/dryad.dc02b 2023-01-22T17:23:52Z Studies of species with continental distributions continue to identify intraspecific lineages despite continuous habitat. Lineages may form due to isolation by distance, adaptation, divergence across barriers, or genetic drift following range expansion. We investigated lineage diversification and admixture within American black bears (Ursus americanus) across their range using 22 k single nucleotide polymorphisms and mitochondrial DNA sequences. We identified three subcontinental nuclear clusters which we further divided into nine geographic regions: Alaskan (Alaska-East), eastern (Central Interior Highlands, Great Lakes, Northeast, Southeast), and western (Alaska-West, West, Pacific Coast, Southwest). We estimated that the western cluster diverged 67 ka, before eastern and Alaskan divergence 31 ka; these divergence dates contrasted with those from the mitochondrial genome where clades A and B diverged 1.07 Ma, and clades A-east and A-west diverged 169 ka. We combined estimates of divergence timing with hindcast species distribution models to infer glacial refugia for the species in Beringia, Pacific Northwest, Southwest, and Southeast. Our results show a complex arrangement of admixture due to expansion out of multiple refugia. The delineation of the genomic population clusters was inconsistent with the ranges for 16 previously described subspecies. Ranges for U. a. pugnax and U. a. cinnamomum were concordant with admixed clusters, calling into question how to order taxa below the species level. Additionally, our finding that U. a. floridanus has not diverged from U. a. americanus also suggests that morphology and genetics should be reanalyzed to assess taxonomic designations relevant to the conservation management of the species. Puckett_etal-MaxEntInputGeographic coordinates used as input in MaxEnt species distribution model.Puckett_etal-mtDNA_HaplotypeListList of samples and the identified mitochondrial haplotype. See GenBank accessions: AY334363–AY334367 (Onorato et al 2004), FJ619652–FJ619659 (Van Den ... Dataset Alaska Beringia Unknown Pacific |
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Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care microsatellites mitochondrial genome admixture phylogeography lineage divergence Ursus americanus SNPs American black bear Holocene species distribution modeling Pleistocene North America envir geo |
spellingShingle |
Life sciences medicine and health care microsatellites mitochondrial genome admixture phylogeography lineage divergence Ursus americanus SNPs American black bear Holocene species distribution modeling Pleistocene North America envir geo Puckett, Emily E. Etter, Paul D. Johnson, Eric A. Eggert, Lori S. Data from: Phylogeographic analyses of American black bears (Ursus americanus) suggest four glacial refugia and complex patterns of post-glacial admixture |
topic_facet |
Life sciences medicine and health care microsatellites mitochondrial genome admixture phylogeography lineage divergence Ursus americanus SNPs American black bear Holocene species distribution modeling Pleistocene North America envir geo |
description |
Studies of species with continental distributions continue to identify intraspecific lineages despite continuous habitat. Lineages may form due to isolation by distance, adaptation, divergence across barriers, or genetic drift following range expansion. We investigated lineage diversification and admixture within American black bears (Ursus americanus) across their range using 22 k single nucleotide polymorphisms and mitochondrial DNA sequences. We identified three subcontinental nuclear clusters which we further divided into nine geographic regions: Alaskan (Alaska-East), eastern (Central Interior Highlands, Great Lakes, Northeast, Southeast), and western (Alaska-West, West, Pacific Coast, Southwest). We estimated that the western cluster diverged 67 ka, before eastern and Alaskan divergence 31 ka; these divergence dates contrasted with those from the mitochondrial genome where clades A and B diverged 1.07 Ma, and clades A-east and A-west diverged 169 ka. We combined estimates of divergence timing with hindcast species distribution models to infer glacial refugia for the species in Beringia, Pacific Northwest, Southwest, and Southeast. Our results show a complex arrangement of admixture due to expansion out of multiple refugia. The delineation of the genomic population clusters was inconsistent with the ranges for 16 previously described subspecies. Ranges for U. a. pugnax and U. a. cinnamomum were concordant with admixed clusters, calling into question how to order taxa below the species level. Additionally, our finding that U. a. floridanus has not diverged from U. a. americanus also suggests that morphology and genetics should be reanalyzed to assess taxonomic designations relevant to the conservation management of the species. Puckett_etal-MaxEntInputGeographic coordinates used as input in MaxEnt species distribution model.Puckett_etal-mtDNA_HaplotypeListList of samples and the identified mitochondrial haplotype. See GenBank accessions: AY334363–AY334367 (Onorato et al 2004), FJ619652–FJ619659 (Van Den ... |
format |
Dataset |
author |
Puckett, Emily E. Etter, Paul D. Johnson, Eric A. Eggert, Lori S. |
author_facet |
Puckett, Emily E. Etter, Paul D. Johnson, Eric A. Eggert, Lori S. |
author_sort |
Puckett, Emily E. |
title |
Data from: Phylogeographic analyses of American black bears (Ursus americanus) suggest four glacial refugia and complex patterns of post-glacial admixture |
title_short |
Data from: Phylogeographic analyses of American black bears (Ursus americanus) suggest four glacial refugia and complex patterns of post-glacial admixture |
title_full |
Data from: Phylogeographic analyses of American black bears (Ursus americanus) suggest four glacial refugia and complex patterns of post-glacial admixture |
title_fullStr |
Data from: Phylogeographic analyses of American black bears (Ursus americanus) suggest four glacial refugia and complex patterns of post-glacial admixture |
title_full_unstemmed |
Data from: Phylogeographic analyses of American black bears (Ursus americanus) suggest four glacial refugia and complex patterns of post-glacial admixture |
title_sort |
data from: phylogeographic analyses of american black bears (ursus americanus) suggest four glacial refugia and complex patterns of post-glacial admixture |
publisher |
Data Archiving and Networked Services (DANS) |
publishDate |
2016 |
url |
https://doi.org/10.5061/dryad.dc02b |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Alaska Beringia |
genre_facet |
Alaska Beringia |
op_source |
oai:easy.dans.knaw.nl:easy-dataset:89374 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:89374 10.5061/dryad.dc02b 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f re3data_____::r3d100000044 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 |
op_relation |
http://dx.doi.org/10.5061/dryad.dc02b https://dx.doi.org/10.5061/dryad.dc02b |
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lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.dc02b |
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1766242188212043776 |