Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution
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Despite extensive genetic analysis, the evolutionary relationship between polar bears (Ursus maritimus) and brown bears (U. arctos) remains unclear. The two most recent comprehensive reports indicate a recent divergence with little subsequent admixture or a much more ancient divergence followed by extensive admixture. At the center of this controversy are the Alaskan ABC Islands brown bears that show evidence of shared ancestry with polar bears. We present an analysis of genome-wide sequence data for seven polar bears, one ABC Islands brown bear, one mainland Alaskan brown bear, and a black bear (U. americanus), plus recently published datasets from other bears. Surprisingly, we find clear evidence for gene flow from polar bears into ABC Islands brown bears but no evidence of gene flow from brown bears into polar bears. Importantly, while polar bears contributed <1% of the autosomal genome of the ABC Islands brown bear, they contributed 6.5% of the X chromosome. The magnitude of sex-biased polar bear ancestry and the clear direction of gene flow suggest a model wherein the enigmatic ABC Island brown bears are the descendants of a polar bear population that was gradually converted into brown bears via male-dominated brown bear admixture. We present a model that reconciles heretofore conflicting genetic observations. We posit that the enigmatic ABC Islands brown bears derive from a population of polar bears likely stranded by the receding ice at the end of the last glacial period. Since then, male brown bear migration onto the island has gradually converted these bears into an admixed population whose phenotype and genotype are principally brown bear, except at mtDNA and X-linked loci. This process of genome erosion and conversion may be a common outcome when climate change or other forces cause a population to become isolated and then overrun by species with which it can hybridize.
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The major direction of introgression has historically been from polar bears into North American brown bears.
“These results suggest that the major direction of introgression has historically been from polar bears into North American brown bears, in agreement with (Cahill et al., 2013).”
From Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears (2014) · cites this paper as Cahill et al., 2013
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works
A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,216 · see citing works
A draft sequence of the Neandertal genome
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318 · see citing works
Self-citationIllumina Sequencing Library Preparation for Highly Multiplexed Target Capture and SequencingPreprint
Meyer, M., & Kircher, M. (2010) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot5448 · Cited by 2,233 · see citing works
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 · see citing works
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 · see citing works
Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania
Reich, D., Patterson, N., Kircher, M., Delfin, F., Nandineni, M. R., Pugach, I., Ko, A. M.-S., Ko, Y.-C., Jinam, T. A., Phipps, M. E., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.09.005 · Cited by 656 · see citing works
A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing
Green, R. E., Malaspinas, A., Krause, J., Briggs, A. W., Johnson, P. L. F., Uhler, C., Meyer, M., Good, J. M., Maričić, T., Stenzel, U., et al. (2008) · Cell · doi:10.1016/j.cell.2008.06.021 · Cited by 601 · see citing works
Self-citationDynamics of Pleistocene Population Extinctions in Beringian Brown Bears
Barnes, I., Matheus, P. E., Shapiro, B., Jensen, D., & Cooper, A. (2002) · Science · doi:10.1126/science.1067814 · Cited by 400 · see citing works
Self-citationMiller, W., Schuster, S. C., Welch, A. J., Ratan, A., Bedoya-Reina, O. C., Zhao, F., Kim, H. L., Burhans, R. C., Drautz, D. I., Wittekindt, N. E., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1210506109 · Cited by 353 · see citing works
Gene flow between insular, coastal and interior populations of brown bears in Alaska
Paetkau, D., Shields, G. F., & Strobeck, C. (1998) · Molecular Ecology · doi:10.1046/j.1365-294x.1998.00440.x · Cited by 344 · see citing works
Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage
Hailer, F., Kutschera, V. E., Hallström, B. M., Klassert, D., Fain, S. R., Leonard, J. A., Arnason, U., & Janke, A. (2012) · Science · doi:10.1126/science.1216424 · Cited by 308 · see citing works
Krause, J., Unger, T., Noçon, A., Malaspinas, A., Kolokotronis, S., Stiller, M., Soibelzon, L. H., Spriggs, H. F., Dear, P. H., Briggs, A. W., et al. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-220 · Cited by 285 · see citing works
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 278 · see citing works
Self-citationAnalysis of High-Throughput Ancient DNA Sequencing Data
Kircher, M. (2012) · Methods in Molecular Biology · doi:10.1007/978-1-61779-516-9_23 · Cited by 236 · see citing works
Phylogeography of Brown Bears (Ursus arctos) of Alaska and Paraphyly within the Ursidae
Talbot, S. L., & Shields, G. F. (1996) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1996.0044 · Cited by 203 · see citing works
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 · see citing works
A rapid column‐based ancient DNA extraction method for increased sample throughput
Rohland, N., Siedel, H., & Hofreiter, M. (2009) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2009.02824.x · Cited by 191 · see citing works
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 161 · see citing works
An Ice Age Refugium for Large Mammals in the Alexander Archipelago, Southeastern Alaska
Heaton, T. H., Talbot, S. L., & Shields, G. F. (1996) · Quaternary Research · doi:10.1006/qres.1996.0058 · Cited by 136 · see citing works
Interspecific and intraspecific mitochondrial DNA variation in North American bears (Ursus)
Cronin, M. A., Amstrup, S. C., Garner, G. W., & Vyse, E. R. (1991) · Canadian Journal of Zoology · doi:10.1139/z91-421 · Cited by 128 · see citing works
Carrara, P. E., Ager, T. A., & Baichtal, J. F. (2007) · Canadian Journal of Earth Sciences · doi:10.1139/e06-081 · Cited by 124 · see citing works
Extent and timing of the Last Glacial Maximum (LGM) in Britain and Ireland: a review
Chiverrell, R. C., & Thomas, G. S. P. (2010) · Journal of Quaternary Science · doi:10.1002/jqs.1404 · Cited by 110 · see citing works
The evolution of the Polar Bear, Ursus maritimus Phipps
Kurtén, B. (1964) · Työväentutkimus Vuosikirja · Cited by 88 · see citing works
Inǵólfsson, Ó., & Wiig, Ø. (2008) · Polar Research · doi:10.1111/j.1751-8369.2008.00087.x · Cited by 77 · see citing works
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 · see citing works
Polar bears: the natural history of a threatened species
(2012) · Choice Reviews Online · doi:10.5860/choice.49-2671 · Cited by 52 · see citing works
Bear-hybrids: behaviour and phenotype
Preuß, A., Gansloßer, U., Purschke, G., & Magiera, U. (2009) · Der Zoologische Garten · doi:10.1016/j.zoolgart.2009.08.005 · Cited by 18 · see citing works
Genomic data from the polar bear (Ursus maritimus).
Li, B., Zhang, G., Willersleve, E., Wang, J., & Wang, J. (2011) · GigaDB · doi:10.5524/100008 · Cited by 12 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [19]Heaton TH, Grady F (2003) The Late Wisconsin vertebrate history of Prince of Wales Island, southeast Alaska. In: Schubert BW, Mead JI, Graham RW, editors. Ice Age Cave Fauna of North America: Indiana University Press. pp. 17–53.
Cited by
Sorted by citations
Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears
Liu, S., Lorenzen, E. D., Fumagalli, M., Li, B., Harris, K., Xiong, Z., Zhou, L., Korneliussen, T. S., Somel, M., Babbitt, C., et al. (2014) · Cell · doi:10.1016/j.cell.2014.03.054 · Cited by 411 · see citing works
Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth
Palkopoulou, E., Mallick, S., Skoglund, P., Enk, J. M., Rohland, N., Li, H., Omrak, A., Vartanyan, S., Poinar, H. N., Götherström, A., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.04.007 · Cited by 370 · see citing works
Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series
Fages, A., Hanghøj, K., Khan, N., Gaunitz, C., Seguin‐Orlando, A., Leonardi, M., Constantz, C. M., Gamba, C., Al‐Rasheid, K. A. S., Albizuri, S., et al. (2019) · Cell · doi:10.1016/j.cell.2019.03.049 · Cited by 328 · see citing works
Self-citationPrehistoric genomes reveal the genetic foundation and cost of horse domestication
Schubert, M., Jónsson, H., Chang, D., Der Sarkissian, C., Ermini, L., Ginolhac, A., Albrechtsen, A., Dupanloup, I., Foucal, A., Petersen, B., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1416991111 · Cited by 324 · see citing works
Self-citationPhylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)Preprint
Li, G., Davis, B. W., Eizirik, E., & Murphy, W. J. (2015) · Genome Research · doi:10.1101/gr.186668.114 · Cited by 322 · see citing works
Conservation Paleobiology: Leveraging Knowledge of the Past to Inform Conservation and Restoration
Dietl, G. P., Kidwell, S. M., Brenner, M., Burney, D. A., Flessa, K. W., Jackson, S. T., & Koch, P. L. (2015) · Annual Review of Earth and Planetary Sciences · doi:10.1146/annurev-earth-040610-133349 · Cited by 286 · see citing works
Speciation and introgression between Mimulus nasutus and Mimulus guttatus
Brandvain, Y., Kenney, A. M., Flagel, L., Coop, G., & Sweigart, A. L. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004410 · Cited by 259 · see citing works
Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species
Koepfli, K., Pollinger, J. P., Godinho, R., Robinson, J. A., Lea, A. J., Hendricks, S. A., Schweizer, R. M., Thalmann, O., Silva, P., Fan, Z., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.06.060 · Cited by 231 · see citing works
Self-citationAncient genomic changes associated with domestication of the horse
Librado, P., Gamba, C., Gaunitz, C., Sarkissian, C. S. I. D., Pruvost, M., Albrechtsen, A., Fages, A., Khan, N., Schubert, M., Jagannathan, V., et al. (2017) · Science · doi:10.1126/science.aam5298 · Cited by 222 · see citing works
A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA
Shapiro, B., & Hofreiter, M. (2014) · Science · doi:10.1126/science.1236573 · Cited by 220 · see citing works
Self-citationEaton, D. A. R., Hipp, A. L., González‐Rodríguez, A., & Cavender-Bares, J. M. (2015) · Evolution · doi:10.1111/evo.12758 · Cited by 212 · see citing works
The evolutionary history of bears is characterized by gene flow across species
Kumar, V., Lammers, F., Bidon, T., Pfenninger, M., Kolter, L., Nilsson, M. A., & Janke, A. (2017) · Scientific Reports · doi:10.1038/srep46487 · Cited by 209 · see citing works
Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse
Sarkissian, C. S. I. D., Ermini, L., Schubert, M., Yang, M. A., Librado, P., Fumagalli, M., Jónsson, H., Bar‐Gal, G. K., Albrechtsen, A., Vieira, F. G., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.08.032 · Cited by 198 · see citing works
Self-citationFrom promise to practice: pairing non-invasive sampling with genomics in conservation
Russello, M. A., Waterhouse, M. D., Etter, P. D., & Johnson, E. A. (2015) · PeerJ · doi:10.7717/peerj.1106 · Cited by 178 · see citing works
Kutschera, V. E., Bidon, T., Hailer, F., Rodi, J. L., Fain, S. R., & Janke, A. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu186 · Cited by 176 · see citing works
Partial genomic survival of cave bears in living brown bears
Barlow, A., Cahill, J. A., Hartmann, S. A., Theunert, C., Xenikoudakis, G., Fortes, G. G., Paijmans, J. L. A., Rabeder, G., Frischauf, C., Grandal‐d'Anglade, A., et al. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0654-8 · Cited by 164 · see citing works
Self-citationGenomic evidence of geographically widespread effect of gene flow from polar bears into brown bears
Cahill, J. A., Stirling, I., Kistler, L., Salamzade, R., Ersmark, E., Fulton, T. L., Stiller, M., Green, R. E., & Shapiro, B. (2014) · Molecular Ecology · doi:10.1111/mec.13038 · Cited by 163 · see citing works
Self-citationWhat to eat now? Shifts in polar bear diet during the ice‐free season in western Hudson Bay
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Cahill, J. A., Heintzman, P. D., Harris, K., Teasdale, M. D., Kapp, J. D., Soares, A. E. R., Stirling, I., Bradley, D. G., Edwards, C. J., Graim, K. S., et al. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy018 · Cited by 114 · see citing works
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Laidre, K. L., Stirling, I., Estes, J. A., Kochnev, A. A., & Roberts, J. (2018) · Frontiers in Ecology and the Environment · doi:10.1002/fee.1963 · Cited by 107 · see citing works
Self-citationReview and meta-analysis of natural selection in mitochondrial complex I in metazoans
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Hybridization in human evolution: Insights from other organisms
Ackermann, R., Arnold, M. L., Baiz, M. D., Cahill, J. A., Cortés‐Ortiz, L., Evans, B. J., Grant, B. R., Grant, P. R., Hallgrímsson, B., Humphreys, R. A., et al. (2019) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21787 · Cited by 101 · see citing works
Self-citationUsing Ancient DNA to Understand Evolutionary and Ecological Processes
Orlando, L., & Cooper, A. (2014) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-120213-091712 · Cited by 100 · see citing works
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Bidon, T., Janke, A., Fain, S. R., Eiken, H. G., Hagen, S. B., Saarma, U., Hallström, B. M., Lecomte, N., & Hailer, F. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu109 · Cited by 94 · see citing works
Dufresnes, C., Nicieza, A. G., Litvinchuk, S. N., Rodrigues, N., Jeffries, D. L., Vences, M., Perrin, N., & Martínez-Solano, Í. (2020) · Molecular Ecology · doi:10.1111/mec.15368 · Cited by 92 · see citing works
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Recent Hybridization between a Polar Bear and Grizzly Bears in the Canadian Arctic
Pongracz, J., Paetkau, D., Branigan, M., & Richardson, E. (2017) · ARCTIC · doi:10.14430/arctic4643 · Cited by 82 · see citing works
Novak, B. J. (2018) · Genes · doi:10.3390/genes9110548 · Cited by 80 · see citing works
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Self-citationLaidre, K. L., Supple, M. A., Born, E. W., Regehr, E. V., Wiig, Ø., Ugarte, F., Aars, J., Dietz, R., Sonne, C., Hegelund, P., et al. (2022) · Science · doi:10.1126/science.abk2793 · Cited by 71 · see citing works
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Cabrera, A. A., & Palsbøll, P. J. (2017) · Molecular Ecology Resources · doi:10.1111/1755-0998.12696 · Cited by 70 · see citing works
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Werhahn, G., Liu, Y., Meng, Y., Cheng, C., Lü, Z., Atzeni, L., Deng, Z., Shi, K., Shao, X., Lu, Q., et al. (2020) · Journal of Biogeography · doi:10.1111/jbi.13824 · Cited by 69 · see citing works
Cahill, J. A., Soares, A. E. R., Green, R. E., & Shapiro, B. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0138 · Cited by 69 · see citing works
Self-citationRange-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence
de Jong, M., Niamir, A., Wolf, M., Kitchener, A. C., Lecomte, N., Seryodkin, I. V., Fain, S. R., Hagen, S. B., Saarma, U., & Janke, A. (2023) · Communications Biology · doi:10.1038/s42003-023-04514-w · Cited by 65 · see citing works
admixturegraph: an R package for admixture graph manipulation and fitting
Leppälä, K., Nielsen, S. V., & Mailund, T. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx048 · Cited by 65 · see citing works
Welch, A. J., Bedoya-Reina, O. C., Carretero‐Paulet, L., Miller, W., Rode, K. D., & Lindqvist, C. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu025 · Cited by 61 · see citing works
Peacock, E., Sonsthagen, S. A., Obbard, M. E., Boltunov, A. N., Regehr, E. V., Ovsyanikov, N., Aars, J., Atkinson, S. N., Sage, G. K., Hope, A. G., et al. (2015) · PLoS ONE · doi:10.1371/journal.pone.0112021 · Cited by 61 · see citing works
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Self-citationMalenfant, R. M., Coltman, D. W., & Davis, C. S. (2014) · Molecular Ecology Resources · doi:10.1111/1755-0998.12327 · Cited by 54 · see citing works
Bell, R. C., Drewes, R. C., & Zamudio, K. R. (2015) · Evolution · doi:10.1111/evo.12623 · Cited by 54 · see citing works
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Hassanin, A. (2015) · Comptes Rendus Biologies · doi:10.1016/j.crvi.2015.04.008 · Cited by 52 · see citing works
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Morris, M. R. J., Bowles, E., Allen, B. E., Jamniczky, H. A., & Rogers, S. M. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1228-8 · Cited by 51 · see citing works
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Ersmark, E., Klütsch, C. F. C., Chan, Y. L., Sinding, M. S., Fain, S. R., Illarionova, N. A., Oskarsson, M. C. R., Uhlén, M., Zhang, Y., Dalén, L., et al. (2016) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2016.00134 · Cited by 50 · see citing works
Firneno, T. J., O’Neill, J. R., Portik, D. M., Emery, A. H., Townsend, J. H., & Fujita, M. K. (2020) · Molecular Ecology · doi:10.1111/mec.15496 · Cited by 50 · see citing works
van Heteren, A. H., MacLarnon, A. M., Soligo, C., & Rae, T. C. (2015) · Organisms Diversity & Evolution · doi:10.1007/s13127-015-0238-2 · Cited by 48 · see citing works
Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome
Brealey, J. C., Leitão, H. G., van der Valk, T., Xu, W., Bougiouri, K., Dalén, L., & Guschanski, K. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa135 · Cited by 47 · see citing works
Salis, A. T., Bray, S. C. E., Lee, M. S. Y., Heiniger, H., Barnett, R., Burns, J. A., Doronichev, V. B., Fedje, D. W., Golovanova, L. V., Harington, C. R., et al. (2021) · Molecular Ecology · doi:10.1111/mec.16267 · Cited by 47 · see citing works
Welinder, K. G., Hansen, R., Overgaard, M. T., Brohus, M., Sønderkær, M., von Bergen�, M., Rolle-Kampczyk, U. E., Otto, W., Lindahl, T. L., Arinell, K., et al. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.742916 · Cited by 46 · see citing works
Insights into bear evolution from a Pleistocene polar bear genome
Lan, T., Leppälä, K., Tomlin, C., Talbot, S. L., Sage, G. K., Farley, S. D., Shideler, R. T., Bachmann, L., Wiig, Ø., Albert, V. A., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2200016119 · Cited by 42 · see citing works
Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons
Sørensen, E. F., Harris, R. A., Zhang, L., Raveendran, M., Kuderna, L. F. K., Walker, J. A., Storer, J. M., Kuhlwilm, M., Fontsere, C., Seshadri, L., et al. (2023) · Science · doi:10.1126/science.abn8153 · Cited by 42 · see citing works
Xenikoudakis, G., Ersmark, E., Tison, J.-L., Waits, L. P., Kindberg, J., Swenson, J. E., & Dalén, L. (2015) · Molecular Ecology · doi:10.1111/mec.13239 · Cited by 42 · see citing works
A polar bear paleogenome reveals extensive ancient gene flow from polar bears into brown bears
Wang, M., Murray, G. G. R., Mann, D. H., Groves, P., Vershinina, A. O., Supple, M. A., Kapp, J. D., Corbett-Detig, R. B., Crump, S. E., Stirling, I., et al. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01753-8 · Cited by 41 · see citing works
Self-citationLeavitt, D. H., Marion, A. B., Hollingsworth, B. D., & Reeder, T. W. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.02.010 · Cited by 41 · see citing works
Pagano, A. M., & Williams, T. M. (2021) · Journal of Experimental Biology · doi:10.1242/jeb.228049 · Cited by 41 · see citing works
Analyses of genetic ancestry enable key insights for molecular ecology
Gompert, Z., & Buerkle, C. A. (2013) · Molecular Ecology · doi:10.1111/mec.12488 · Cited by 40 · see citing works
Pereira, R. J., Martínez-Solano, Í., & Buckley, D. (2016) · Molecular Ecology · doi:10.1111/mec.13575 · Cited by 40 · see citing works
Zou, T., Kuang, W., Yin, T., Frantz, L., Zhang, C., Liu, J., Wu, H., & Yu, L. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2120307119 · Cited by 40 · see citing works
Krofel, M., Elfström, M., Ambarlı, H., Bombieri, G., González-Bernardo, E., Jerina, K., Laguna, A., Penteriani, V., Phillips, J. P., Selva, N., et al. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108692571 · Cited by 39 · see citing works
Genome-Wide Search Identifies 1.9 Mb from the Polar Bear Y Chromosome for Evolutionary Analyses
Bidon, T., Schreck, N., Hailer, F., Nilsson, M. A., & Janke, A. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv103 · Cited by 38 · see citing works
Land to sea transitions in vertebrates: the dynamics of colonization
Vermeij, G. J., & Motani, R. (2018) · Paleobiology · doi:10.1017/pab.2017.37 · Cited by 38 · see citing works
Qian, Y., Meng, M., Zhou, C., Liu, H., Jiang, H., Xu, Y., Chen, W., Ding, Z., Liu, Y., Gong, X., et al. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad129 · Cited by 37 · see citing works
Frantz, L., Madsen, O., Megens, H., Groenen, M. A. M., & Lohse, K. (2014) · Molecular Ecology · doi:10.1111/mec.12958 · Cited by 36 · see citing works
Barlow, A., Hartmann, S. A., González, J., Hofreiter, M., & Paijmans, J. L. A. (2020) · Genes · doi:10.3390/genes11010050 · Cited by 33 · see citing works
Mao, X., & Rossiter, S. J. (2020) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2020.106886 · Cited by 32 · see citing works
Phuong, M. A., Bi, K., & Moritz, C. C. (2017) · Molecular Ecology · doi:10.1111/mec.14238 · Cited by 31 · see citing works
Sharko, F. S., Boulygina, E. S., Tsygankova, S. V., Slobodova, N. V., Alekseev, D. A., Krasivskaya, A. A., Rastorguev, S. M., Tikhonov, A. N., & Nedoluzhko, A. V. (2021) · Nature Communications · doi:10.1038/s41467-021-22567-5 · Cited by 31 · see citing works
An evaluation of DNA extraction methods on historical and roadkill mammalian specimen
Molbert, N., Ghanavi, H. R., Johansson, T., Mostadius, M., & Hansson, M. C. (2023) · Scientific Reports · doi:10.1038/s41598-023-39465-z · Cited by 30 · see citing works
Trigo, T. C., Tirelli, F. P., de Freitas, T. R. O., & Eizirik, E. (2014) · PLoS ONE · doi:10.1371/journal.pone.0108469 · Cited by 29 · see citing works
Krofel, M., Elfström, M., Ambarlı, H., Bombieri, G., González-Bernardo, E., Jerina, K., Laguna, A., Penteriani, V., Phillips, J. P., Selva, N., et al. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108692571.016 · Cited by 27 · see citing works
Evolution of the Mutation Spectrum Across a Mammalian Phylogeny
Beichman, A. C., Robinson, J. A., Lin, M., Moreno‐Estrada, A., Nigenda‐Morales, S. F., & Harris, K. (2023) · Molecular Biology and Evolution · doi:10.1093/molbev/msad213 · Cited by 26 · see citing works
Philosophy and ethics of de-extinction
Odenbaugh, J. (2023) · Cambridge Prisms Extinction · doi:10.1017/ext.2023.4 · Cited by 26 · see citing works
The Role of Genomics in Conservation and Reproductive Sciences
Johnson, W. E., & Koepfli, K. (2014) · Advances in experimental medicine and biology · doi:10.1007/978-1-4939-0820-2_5 · Cited by 25 · see citing works
Chavez, A. S., Maher, S. P., Arbogast, B. S., & Kenagy, G. J. (2013) · Evolution · doi:10.1111/evo.12336 · Cited by 24 · see citing works
Genetic architecture and evolution of color variation in American black bears
Puckett, E. E., Davis, I. S., Harper, D. C., Wakamatsu, K., Battu, G., Belant, J. L., Beyer, D. E., Carpenter, C. P., Crupi, A. P., Davidson, M., et al. (2022) · Current Biology · doi:10.1016/j.cub.2022.11.042 · Cited by 23 · see citing works
Whales, fish and Alaskan bears: interest-relative taxonomy and kind pluralism in biology
Taylor, H. (2019) · Synthese · doi:10.1007/s11229-019-02284-9 · Cited by 22 · see citing works
Cronin, M. A., Rincón, G., Meredith, R. W., MacNeil, M. D., Islas‐Trejo, A., Cánovas, Á., & Medrano, J. F. F. (2014) · Journal of Heredity · doi:10.1093/jhered/est133 · Cited by 21 · see citing works
Brown Bear (Ursus arctos; Eurasia)
Swenson, J. E., Ambarlı, H., Arnemo, J. M., Миронович, Б. Л., Ciucci, P., Danilov, P. I., Delibes, M., Elfström, M., Evans, A. L., Groff, C., et al. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108692571.013 · Cited by 21 · see citing works
Monson, T. A., Boisserie, J., Brasil, M. F., Clay, S. M., Dvoretzky, R. R., Ravindramurthy, S., Schmitt, C. A., Souron, A., Takenaka, R., Ungar, P. S., et al. (2019) · Ecology and Evolution · doi:10.1002/ece3.5309 · Cited by 21 · see citing works
Mao, X., Tsagkogeorga, G., Thong, V. D., & Rossiter, S. J. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.106551 · Cited by 21 · see citing works
Endo, Y., Osada, N., Mano, T., & Masuda, R. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab195 · Cited by 19 · see citing works
Armstrong, E. E., Perry, B. W., Huang, Y., Garimella, K. V., Jansen, H. T., Robbins, C. T., Tucker, N. R., & Kelley, J. L. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac125 · Cited by 19 · see citing works
Experiences in integrated data and research object publishing using GigaDB
Edmunds, S., Li, P., Hunter, C., Zhe, X. S., Davidson, R., Nogoy, N., & Goodman, L. (2016) · International Journal on Digital Libraries · doi:10.1007/s00799-016-0174-6 · Cited by 18 · see citing works
Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska
Coelho, F. A. D. S., Gill, S., Tomlin, C., Papavassiliou, M., Farley, S. D., Cook, J. A., Sonsthagen, S. A., Sage, G. K., Heaton, T. H., Talbot, S. L., et al. (2023) · Molecular Ecology · doi:10.1111/mec.16960 · Cited by 18 · see citing works
Evolution of advertisement calls in an island radiation of African reed frogs
Gilbert, C. M., & Bell, R. C. (2017) · Biological Journal of the Linnean Society · doi:10.1093/biolinnean/blx129 · Cited by 18 · see citing works
Genomic basis for skin phenotype and cold adaptation in the extinct Steller’s sea cow
Duc, D. L., Velluva, A., Cassatt‐Johnstone, M., Olsen, R., Baleka, S., Lin, C.-C., Lemke, J. R., Southon, J. R., Burdin, A. M., Wang, M., et al. (2022) · Science Advances · doi:10.1126/sciadv.abl6496 · Cited by 18 · see citing works
Self-citationAmerican Black Bear (Ursus americanus)
Clark, J. D., Beckmann, J. P., Boyce, M. S., Leopold, B. D., Loosen, A. E., & Pelton, M. R. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108692571.012 · Cited by 16 · see citing works
Brown Bear (Ursus arctos; North America)
Haroldson, M. A., Clapham, M., Costello, C. M., Gunther, K. A., Kendall, K. C., Miller, S. D., Pigeon, K. E., Proctor, M. F., Rode, K. D., Servheen, C. W., et al. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108692571.014 · Cited by 16 · see citing works
Biological response to climate change in the Arctic Ocean: the view from the past
Cronin, T. M., & Cronin, M. A. (2015) · arktos · doi:10.1007/s41063-015-0019-3 · Cited by 16 · see citing works
Gormezano, L. J., Ellis‐Felege, S. N., Iles, D. T., Barnas, A. F., & Rockwell, R. F. (2017) · American Museum Novitates · doi:10.1206/3885.1 · Cited by 16 · see citing works
Using ancient DNA and coalescent-based methods to infer extinction
Chang, D., & Shapiro, B. (2016) · Biology Letters · doi:10.1098/rsbl.2015.0822 · Cited by 15 · see citing works
Self-citationSpeciation through the looking-glass
Vaux, F., Trewick, S. A., & Morgan‐Richards, M. (2016) · Biological Journal of the Linnean Society · doi:10.1111/bij.12872 · Cited by 15 · see citing works
Decoding Coalescent Hidden Markov Models in Linear Time
Harris, K., Sheehan, S., Kamm, J., & Song, Y. S. (2014) · Lecture notes in computer science · doi:10.1007/978-3-319-05269-4_8 · Cited by 15 · see citing works
- Authors
- Cahill, J. A., Green, R. E., Fulton, T. L., Stiller, M., Jay, F., Ovsyanikov, N., Salamzade, R., St. John, J., Stirling, I., Slatkin, M., & Shapiro, B.
- Affiliations
- University of California, Santa Cruz (US)
- University of California, Berkeley (US)
- University of Alberta (CA)
- Corresponding author
- Shapiro, Beth
- ORCID
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-03-14
- Volume
- 9
- Issue
- 3
- Pages
- e1003345
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC3597504
- OpenAlex
- W2099428625
- Cited by
- 221
- References
- 30
- Citations by year
- 2026: 6 · 2025: 18 · 2024: 13 · 2023: 16 · 2022: 18 · 2021: 8 · 2020: 45 · 2019: 10 · 2018: 10 · 2017: 16 · 2016: 14 · 2015: 24 · 2014: 18 · 2013: 5
- FWCI
- 13.48
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- National Science Foundation (ARC-09090456)
- Smithsonian Institution
- National Institutes of Health
- U.S. Fish and Wildlife Service
- National Institute of General Medical Sciences (R01GM040282, R01‑GM40282)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- polar bear, brown bear, Ursus americanus, hybridization, gene flow, sex-biased admixture, population isolation, last glacial period, genome erosion
- MeSH terms
- Animals, Ursidae, DNA, Mitochondrial, Biological Evolution, Female, Male, Phylogeny, X Chromosome, Genome, Gene Flow, Climate Change
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