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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ftzenodo:oai:zenodo.org:4965469 2024-09-15T18:41:28+00:00 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 unknown Zenodo https://doi.org/10.1093/molbev/msv114 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.dc02b oai:zenodo.org:4965469 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode mitochondrial genome lineage divergence SNPs Holocene info:eu-repo/semantics/other 2016 ftzenodo https://doi.org/10.5061/dryad.dc02b10.1093/molbev/msv114 2024-07-25T09:10:34Z 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-MaxEntInput Geographic coordinates used as input in MaxEnt species distribution model. Puckett_etal-mtDNA_HaplotypeList List of samples and the identified mitochondrial haplotype. See GenBank accessions: AY334363–AY334367 (Onorato et al 2004), FJ619652–FJ619659 (Van Den ... Other/Unknown Material Alaska Beringia Zenodo |
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mitochondrial genome lineage divergence SNPs Holocene |
spellingShingle |
mitochondrial genome lineage divergence SNPs Holocene 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 |
mitochondrial genome lineage divergence SNPs Holocene |
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-MaxEntInput Geographic coordinates used as input in MaxEnt species distribution model. Puckett_etal-mtDNA_HaplotypeList List of samples and the identified mitochondrial haplotype. See GenBank accessions: AY334363–AY334367 (Onorato et al 2004), FJ619652–FJ619659 (Van Den ... |
format |
Other/Unknown Material |
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 |
Zenodo |
publishDate |
2016 |
url |
https://doi.org/10.5061/dryad.dc02b |
genre |
Alaska Beringia |
genre_facet |
Alaska Beringia |
op_relation |
https://doi.org/10.1093/molbev/msv114 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.dc02b oai:zenodo.org:4965469 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.dc02b10.1093/molbev/msv114 |
_version_ |
1810485866022305792 |