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Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage
Open accessAbstract
Recent studies have shown that the polar bear matriline (mitochondrial DNA) evolved from a brown bear lineage since the late Pleistocene, potentially indicating rapid speciation and adaption to arctic conditions. Here, we present a high-resolution data set from multiple independent loci across the nuclear genomes of a broad sample of polar, brown, and black bears. Bayesian coalescent analyses place polar bears outside the brown bear clade and date the divergence much earlier, in the middle Pleistocene, about 600 (338 to 934) thousand years ago. This provides more time for polar bear evolution and confirms previous suggestions that polar bears carry introgressed brown bear mitochondrial DNA due to past hybridization. Our results highlight that multilocus genomic analyses are crucial for an accurate understanding of evolutionary history.
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Cites
Inference of Population Structure Using Multilocus Genotype Data
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000) · Genetics · doi:10.1093/genetics/155.2.945 · Cited by 33,871
MRBAYES: Bayesian inference of phylogenetic trees.
Huelsenbeck, J. P., & Ronquist, F. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.8.754 · Cited by 21,937
Detecting the number of clusters of individuals using the software structure: a simulation study
Evanno, G., Regnaut, S., & Goudet, J. (2005) · Molecular Ecology · doi:10.1111/j.1365-294x.2005.02553.x · Cited by 21,540
Excoffier, L., & Lischer, H. E. L. (2010) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2010.02847.x · Cited by 16,266
DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
Librado, P., & Rozas, J. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp187 · Cited by 16,147
Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992) · Genetics · doi:10.1093/genetics/131.2.479 · Cited by 13,929
BEAST: Bayesian evolutionary analysis by sampling trees
Drummond, A. J., & Rambaut, A. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-214 · Cited by 13,104
Earl, D. A., & vonHoldt, B. M. (2011) · Conservation Genetics Resources · doi:10.1007/s12686-011-9548-7 · Cited by 12,389
jModelTest: Phylogenetic Model Averaging
Posada, D. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn083 · Cited by 10,578
TCS: a computer program to estimate gene genealogies
Clement, M., Posada, D., & Crandall, K. A. (2000) · Molecular Ecology · doi:10.1046/j.1365-294x.2000.01020.x · Cited by 9,844
EMBOSS: the European molecular biology open software suite.
Rice, P., Longden, I., & Bleasby, A. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02024-2 · Cited by 9,466
A Pliocene‐Pleistocene stack of 57 globally distributed benthic δ 18 O records
Lisiecki, L. E., & Raymo, M. E. (2005) · Paleoceanography · doi:10.1029/2004pa001071 · Cited by 8,584
A New Statistical Method for Haplotype Reconstruction from Population Data
Stephens, M., Smith, N. J. C., & Donnelly, P. (2001) · The American Journal of Human Genetics · doi:10.1086/319501 · Cited by 7,512
The genetic legacy of the Quaternary ice ages
Hewitt, G. M. (2000) · Nature · doi:10.1038/35016000 · Cited by 7,177
The interplay between habitat availability and population differentiation
Verkuil, Y. I., Piersma, T., Jukema, J., Zwarts, L., Baker, A. J., & Hooijmeijer, J. C. E. W. (2012) · Biological Journal of the Linnean Society · Cited by 6,547
Relaxed Phylogenetics and Dating with Confidence
Drummond, A. J., Ho, S. Y. W., Phillips, M. J., & Rambaut, A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040088 · Cited by 6,463
Jakobsson, M., & Rosenberg, N. A. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm233 · Cited by 6,309
A Comparison of Bayesian Methods for Haplotype Reconstruction from Population Genotype Data
Stephens, M., & Donnelly, P. (2003) · The American Journal of Human Genetics · doi:10.1086/379378 · Cited by 3,516
Bayesian inference of species trees from multilocus data
Heled, J., & Drummond, A. J. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msp274 · Cited by 2,453
Funk, D. J., & Omland, K. E. (2003) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev.ecolsys.34.011802.132421 · Cited by 2,254
Beerli, P., & Felsenstein, J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.081068098 · Cited by 1,701
Evidence for Ecological Speciation and Its Alternative
Schluter, D. (2009) · Science · doi:10.1126/science.1160006 · Cited by 1,538
A new method for calculating evolutionary substitution rates
Lanave, C., Preparata, G., Saccone, C., & Serio, G. (1984) · Journal of Molecular Evolution · doi:10.1007/bf02101990 · Cited by 1,417
The sequence and de novo assembly of the giant panda genome
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., et al. (2010) · Nature · doi:10.1038/nature08696 · Cited by 1,180
Wild mammals of North America: biology, management, and conservation
(2004) · Choice Reviews Online · doi:10.5860/choice.41-5307 · Cited by 1,146
Comparison of Bayesian and maximum-likelihood inference of population genetic parameters
Beerli, P. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti803 · Cited by 937
Mitochondrial DNA under siege in avian phylogeography
Zink, R. M., & Barrowclough, G. F. (2008) · Molecular Ecology · doi:10.1111/j.1365-294x.2008.03737.x · Cited by 932
THE HIDDEN SIDE OF INVASIONS: MASSIVE INTROGRESSION BY LOCAL GENES
Currat, M., Ruedi, M., Petit, R. J., & Excoffier, L. (2008) · Evolution · doi:10.1111/j.1558-5646.2008.00413.x · Cited by 816
Molecular and Evolutionary History of Melanism in North American Gray Wolves
Anderson, T. M., vonHoldt, B. M., Candille, S. I., Musiani, M., Greco, C., Stahler, D. R., Smith, D. W., Padhukasahasram, B., Randi, E., Leonard, J. A., et al. (2009) · Science · doi:10.1126/science.1165448 · Cited by 416
Self-citationSplign: algorithms for computing spliced alignments with identification of paralogs
Kapustin, Y., Souvorov, A. E., Tatusova, T. A., & Lipman, D. J. (2008) · Biology Direct · doi:10.1186/1745-6150-3-20 · Cited by 365
The million-year wait for macroevolutionary bursts
Uyeda, J. C., Hansen, T. F., Arnold, S. J., & Pienaar, J. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1014503108 · Cited by 358
Population genetics of Ice Age brown bears
Leonard, J. A., Wayne, R. K., & Cooper, A. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.040453097 · Cited by 310
Self-citationAncient Hybridization and an Irish Origin for the Modern Polar Bear Matriline
Edwards, C. J., Suchard, M. A., Lemey, P., Welch, J. J., Barnes, I., Fulton, T. L., Barnett, R., O’Connell, T. C., Coxon, P., Monaghan, N. T., et al. (2011) · Current Biology · doi:10.1016/j.cub.2011.05.058 · Cited by 282
Calibrating And Constraining Molecular Clocks
Benton, M. J., Donoghue, P. C. J., & Asher, R. J. (2009) · Oxford University Press eBooks · doi:10.1093/oso/9780199535033.003.0004 · Cited by 269
Genetic structure of the world’s polar bear populations
Paetkau, D., Amstrup, S. C., Born, E. W., Calvert, W., Derocher, A. E., Garner, G. W., Messier, F., Stirling, I., Taylor, M. K., Wiig, Ø., et al. (1999) · Molecular Ecology · doi:10.1046/j.1365-294x.1999.00733.x · Cited by 262
Ecological factors influence population genetic structure of European grey wolves
Pilot, M., Jędrzejewski, W., Branicki, W., Sidorovich, V. E., Jędrzejewska, B., Stachura-Skierczyńska, K., & Funk, S. M. (2006) · Molecular Ecology · doi:10.1111/j.1365-294x.2006.03110.x · Cited by 255
Cytonuclear genomic dissociation in African elephant species
Roca, A. L., Georgiadis, N., & O’Brien, S. J. (2004) · Nature Genetics · doi:10.1038/ng1485 · Cited by 239
Recombination-filtered genomic datasets by information maximization
Woerner, A. E., Cox, M. P., & Hammer, M. F. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm253 · Cited by 223
Ancient hybridization and mitochondrial capture between two species of chipmunks
Good, J. M., Hird, S. M., Reid, N. M., Demboski, J. R., Steppan, S. J., MARTIN‐NIMS, T. R., & Sullivan, J. M. (2008) · Molecular Ecology · doi:10.1111/j.1365-294x.2007.03640.x · Cited by 218
Mammalian Response to Cenozoic Climatic Change
Blois, J. L., & Hadly, E. A. (2009) · Annual Review of Earth and Planetary Sciences · doi:10.1146/annurev.earth.031208.100055 · Cited by 215
Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear
Lindqvist, C., Schuster, S. C., Sun, Y., Talbot, S. L., Qi, J., Ratan, A., Tomsho, L. P., Kasson, L., Zeyl, E., Aars, J., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914266107 · Cited by 193
PHYLOGENETIC RELATIONSHIPS OF NORTH AMERICAN URSIDS BASED ON ANALYSIS OF MITOCHONDRIAL DNA
Shields, G. F., & Kocher, T. D. (1991) · Evolution · doi:10.1111/j.1558-5646.1991.tb05279.x · Cited by 178
Davison, J., Ho, S. Y. W., Bray, S. C. E., Korsten, M., Tammeleht, E., Hindrikson, M., Østbye, K., Østbye, E., Lauritzen, S., Austin, J. J., et al. (2010) · Quaternary Science Reviews · doi:10.1016/j.quascirev.2010.11.023 · Cited by 167
Natural hybridization generates mammalian lineage with species characteristics
Larsen, P. A., Marchán-Rivadeneira, M. R., & Baker, R. J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000133107 · Cited by 161
Perini, F. A., Russo, C., & Schrago, C. G. (2009) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2009.01901.x · Cited by 144
Mammalian Evolution May not Be Strictly Bifurcating
Hallström, B. M., & Janke, A. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq166 · Cited by 136
Self-citationDecoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels
Dmitriev, D. A., & RAKITOV, R. A. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000113 · Cited by 134
Phylogeny of the bears (Ursidae) based on nuclear and mitochondrial genes
Li, Y., Li, Q., Ryder, O. A., & Zhang, Y. (2004) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2004.02.015 · Cited by 124
champuru 1.0: a computer software for unraveling mixtures of two DNA sequences of unequal lengths
Flot, J. (2007) · Molecular Ecology Notes · doi:10.1111/j.1471-8286.2007.01857.x · Cited by 112
Molecular distance and divergence time in carnivores and primates.
Wayne, R. K., Valkenburgh, B. V., & O’Brien, S. J. (1991) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040651 · Cited by 112
Kelly, B. P., Whiteley, A. R., & Tallmon, D. A. (2010) · Nature · doi:10.1038/468891a · Cited by 110
Combined analysis of fourteen nuclear genes refines the Ursidae phylogeny
Pagès, M., Calvignac‐Spencer, S., Klein, C., Paris, M., Hughes, S., & Hänni, C. (2007) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2007.10.019 · Cited by 94
The evolution of the Polar Bear, Ursus maritimus Phipps
Kurtén, B. (1964) · Työväentutkimus Vuosikirja · Cited by 88
Biomechanical Consequences of Rapid Evolution in the Polar Bear Lineage
Slater, G. J., Figueirido, B., Louis, L. D., Yang, P., & Valkenburgh, B. V. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013870 · Cited by 69
Phylogenetic Relationships of North American Ursids Based on Analysis of Mitochondrial DNA
Shields, G. F., & Kocher, T. D. (1991) · Evolution · doi:10.2307/2409495 · Cited by 65
Novel intron markers to study the phylogeny of closely related mammalian species
Igea, J., Javier Juste, B., & Castresana, J. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-369 · Cited by 58
Welch, A. J., YOSHIDA, A. A., & Fleischer, R. C. (2011) · Molecular Ecology · doi:10.1111/j.1365-294x.2011.05008.x · Cited by 40
Unequal Rates of Y Chromosome Gene Divergence during Speciation of the Family Ursidae
Nakagome, S., Pecon‐Slattery, J., & Masuda, R. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn086 · Cited by 38
A Genomic Approach to Examine the Complex Evolution of Laurasiatherian Mammals
Hallström, B. M., Schneider, A., Zoller, S., & Janke, A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028199 · Cited by 34
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- B. Li G. Zhang E. Willerslev J. Wang J. Wang Genomic data from the Polar Bear ( Ursus maritimus ) GigaScience doi:10.5524/100008.10.5524/100008 · DOI
- S. Rozen H. Skaletsky in Bioinformatics Methods and Protocols S. Krawetz S. Misener Eds. (Humana Totowa NJ 1999) pp. 365–386.
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Metadata
- Authors
- Hailer, F., Kutschera, V. E., Hallström, B. M., Klassert, D., Fain, S. R., Leonard, J. A., Arnason, U., & Janke, A.
- Affiliations
- Senckenberg - Leibniz Institution for Biodiversity and Earth System Research (DE)
- National Fish and Wildlife Forensic Laboratory, 1490 East Main Street, Ashland, OR, USA.
- Estación Biológica de Doñana (ES)
- Lund University Hospital, Box 117, 221 00 Lund, Sweden.
- Goethe University Frankfurt (DE)
- Corresponding author
- Hailer, Frank
- Janke, Axel
- Venue
- Science
- Published
- 2012-04-20
- Volume
- 336
- Issue
- 6079
- Pages
- 344-347
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2057692000
- Cited by
- 308
- References
- 58
- Citations by year
- 2026: 7 · 2025: 14 · 2024: 13 · 2023: 9 · 2022: 41 · 2021: 22 · 2020: 44 · 2019: 18 · 2018: 7 · 2017: 26 · 2016: 13 · 2015: 25 · 2014: 29 · 2013: 28 · 2012: 12
- FWCI
- 17.98
- Type
- journal article
- Language
- en
- Open access
- green
- hdl.handle.net
- Licence
- other-oa
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, other-oa)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- polar bear, brown bear, Ursus americanus, nuclear genome, divergence time estimation, speciation, Pleistocene, hybridization, introgression, mitochondrial DNA, Ursus, molecular phylogeny
- MeSH terms
- Animals, Bayes Theorem, Ursidae, Cell Nucleus, DNA, Mitochondrial, Biological Evolution, Haplotypes, Hybridization, Genetic, Molecular Sequence Data, Phylogeny, Genetic Variation, Genome, Genetic Speciation, Gene Flow, Multilocus Sequence Typing
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