A polar bear paleogenome reveals extensive ancient gene flow from polar bears into brown bears | Panda Anku

  • Hewitt, G. The genetic legacy of the Quaternary ice ages. Nature 405, 907–913 (2000).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Muhlfeld, C. C. et al. Invasive hybridization in a threatened species is accelerated by climate change. Nat. Clim. Change 4, 620–624 (2014).

    Article 

    Google Scholar 

  • Taylor, S. A. et al. Climate-mediated movement of an avian hybrid zone. Curr. Biol. 24, 671–676 (2014).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Cahill, J. A. et al. Genomic evidence of widespread admixture from polar bears into brown bears during the last ice age. Mol. Biol. Evol. 35, 1120–1129 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Mao, Y., Economo, E. P. & Satoh, N. The roles of introgression and climate change in the rise to dominance of Acropora corals. Curr. Biol. 28, 3373–3382.e5 (2018).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Vianna, J. A. et al. Genome-wide analyses reveal drivers of penguin diversification. Proc. Natl Acad. Sci. USA 117, 22303–22310 (2020).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Racimo, F., Sankararaman, S., Nielsen, R. & Huerta-Sánchez, E. Evidence for archaic adaptive introgression in humans. Nat. Rev. Genet. 16, 359–371 (2015).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • McKelvey, K. S. et al. Patterns of hybridization among cutthroat trout and rainbow trout in northern Rocky Mountain streams. Ecol. Evol. 6, 688–706 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kim, B. Y., Huber, C. D. & Lohmueller, K. E. Deleterious variation shapes the genomic landscape of introgression. PLoS Genet. 14, e1007741 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wu, D.-D. et al. Pervasive introgression facilitated domestication and adaptation in the Bos species complex. Nat. Ecol. Evol. 2, 1139–1145 (2018).

    Article 
    PubMed 

    Google Scholar 

  • Wang, M.-S. et al. Ancient hybridization with an unknown population facilitated high-altitude adaptation of canids. Mol. Biol. Evol. 37, 2616–2629 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Meier, J. I. et al. Ancient hybridization fuels rapid cichlid fish adaptive radiations. Nat. Commun. 8, 14363 (2017).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Haig, S. M., Mullins, T. D., Forsman, E. D., Trail, P. W. & Wennerberg, L. I. V. Genetic identification of spotted owls, barred owls, and their hybrids: legal implications of hybrid identity. Conserv. Biol. 18, 1347–1357 (2004).

    Article 

    Google Scholar 

  • vonHoldt, B. M. et al. Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf. Sci. Adv. 2, e1501714 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Liu, S. et al. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell 157, 785–794 (2014).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kumar, V. et al. The evolutionary history of bears is characterized by gene flow across species. Sci. Rep. 7, 46487 (2017).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Preuß, A., Gansloßer, U., Purschke, G. & Magiera, U. Bear-hybrids: behaviour and phenotype. Zool. Gart. 78, 204–220 (2009).

    Article 

    Google Scholar 

  • Cahill, J. A. et al. Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. PLoS Genet. 9, e1003345 (2013).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Cahill, J. A. et al. Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Mol. Ecol. 24, 1205–1217 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pongracz, J. D., Paetkau, D., Branigan, M. & Richardson, E. Recent hybridization between a polar bear and grizzly bears in the Canadian Arctic. Arctic 70, 151–160 (2017).

    Article 

    Google Scholar 

  • Pugach, I., Matveyev, R., Wollstein, A., Kayser, M. & Stoneking, M. Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biol. 12, R19 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Farquharson, L. et al. Alaskan marine transgressions record out-of-phase Arctic Ocean glaciation during the last interglacial. Geology 46, 783–786 (2018).

    Article 

    Google Scholar 

  • Kapp, J. D., Green, R. E. & Shapiro, B. A fast and efficient single-stranded genomic library preparation method optimized for ancient DNA. J. Hered. 112, 241–249 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616–14621 (2007).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445–449 (2014).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Schiffels, S. & Durbin, R. Inferring human population size and separation history from multiple genome sequences. Nat. Genet. 46, 919–925 (2014).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Pease, J. B. & Hahn, M. W. Detection and polarization of introgression in a five-taxon phylogeny. Syst. Biol. 64, 651–662 (2015).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Barlow, A. et al. Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears. Curr. Biol. 31, 1771–1779.e7 (2021).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Barlow, A. et al. Partial genomic survival of cave bears in living brown bears. Nat. Ecol. Evol. 2, 1563–1570 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wang, K., Mathieson, I., O’Connell, J. & Schiffels, S. Tracking human population structure through time from whole genome sequences. PLoS Genet. 16, e1008552 (2020).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Polyak, L. et al. History of sea ice in the Arctic. Quat. Sci. Rev. 29, 1757–1778 (2010).

    Article 

    Google Scholar 

  • Dutton, A. et al. Sea-level rise due to polar ice-sheet mass loss during past warm periods. Science 349, aaa4019 (2015).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Salonen, J. S. et al. Abrupt high-latitude climate events and decoupled seasonal trends during the Eemian. Nat. Commun. 9, 2851 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Guarino, M.-V. et al. Sea-ice-free Arctic during the Last Interglacial supports fast future loss. Nat. Clim. Change 10, 928–932 (2020).

    Article 

    Google Scholar 

  • Rode, K. D., Robbins, C. T., Nelson, L. & Amstrup, S. C. Can polar bears use terrestrial foods to offset lost ice-based hunting opportunities? Front. Ecol. Environ. 13, 138–145 (2015).

    Article 

    Google Scholar 

  • Laidre, K. L., Stirling, I., Estes, J. A., Kochnev, A. & Roberts, J. Historical and potential future importance of large whales as food for polar bears. Front. Ecol. Environ. 16, 515–524 (2018).

    Article 

    Google Scholar 

  • Miller, S., Wilder, J. & Wilson, R. R. Polar bear–grizzly bear interactions during the autumn open-water period in Alaska. J. Mammal. 96, 1317–1325 (2015).

    Article 

    Google Scholar 

  • Steyaert, S. M. J. G., Endrestøl, A., Hackländer, K., Swenson, J. E. & Zedrosser, A. The mating system of the brown bear Ursus arctos. Mamm. Rev. 42, 12–34 (2012).

    Article 

    Google Scholar 

  • Stirling, I., Spencer, C. & Andriashek, D. Behavior and activity budgets of wild breeding polar bears (Ursus maritimus). Mar. Mamm. Sci. 32, 13–37 (2016).

    Article 

    Google Scholar 

  • Méheust, M., Stein, R., Fahl, K. & Gersonde, R. Sea-ice variability in the subarctic North Pacific and adjacent Bering Sea during the past 25 ka: new insights from IP25 and Uk′37 proxy records. Arktos 4, 1–19 (2018).

    Article 

    Google Scholar 

  • Brigham-Grette, J. & Hopkins, D. M. Emergent marine record and paleoclimate of the last interglaciation along the northwest Alaskan coast. Quat. Res. 43, 159–173 (1995).

    Article 

    Google Scholar 

  • Boessenkool, S. et al. Combining bleach and mild predigestion improves ancient DNA recovery from bones. Mol. Ecol. Resour. 17, 742–751 (2017).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, pdb.prot5448 (2010).

    Article 
    PubMed 

    Google Scholar 

  • Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Rohland, N. & Reich, D. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 22, 939–946 (2012).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. & Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Prüfer, K. snpAD: an ancient DNA genotype caller. Bioinformatics 34, 4165–4171 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Green, R. E. et al. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134, 416–426 (2008).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA–MEM. Preprint at https://doi.org/10.48550/arXiv.1303.3997 (2013).

  • McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kumar, S., Stecher, G., Peterson, D. & Tamura, K. MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis. Bioinformatics 28, 2685–2686 (2012).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kumar, S., Stecher, G. & Tamura, K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870–1874 (2016).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Vihtakari, M. PlotSvalbard: User Manual. Github https://mikkovihtakari.github.io/PlotSvalbard/articles/PlotSvalbard.html (2020).

  • Yu, G., Smith, D. K., Zhu, H., Guan, Y. & Lam, T. T. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol. Evol. 8, 28–36 (2017).

    Article 

    Google Scholar 

  • Yu, G. Using ggtree to visualize data on tree-like structures. Curr. Protoc. Bioinformatics 69, e96 (2020).

    Article 
    PubMed 

    Google Scholar 

  • Yu, G., Lam, T. T., Zhu, H. & Guan, Y. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Mol. Biol. Evol. 35, 3041–3043 (2018).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wang, L.-G. et al. Treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Mol. Biol. Evol. 37, 599–603 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Lindqvist, C. et al. Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc. Natl Acad. Sci. USA 107, 5053–5057 (2010).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Browning, B. L. & Browning, S. R. Genotype imputation with millions of reference samples. Am. J. Hum. Genet. 98, 116–126 (2016).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Kelleher, J., Etheridge, A. M. & McVean, G. Efficient coalescent simulation and genealogical analysis for large sample sizes. PLoS Comput. Biol. 12, e1004842 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Palkopoulou, E. et al. Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth. Curr. Biol. 25, 1395–1400 (2015).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Vershinina, A. O. et al. Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge. Mol. Ecol. 30, 6144–6161 (2021).

    Article 
    PubMed 

    Google Scholar 

  • Chen, L., Wolf, A. B., Fu, W., Li, L. & Akey, J. M. Identifying and interpreting apparent Neanderthal ancestry in African individuals. Cell 180, 677–687.e16 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lisiecki, L. E. & Raymo, M. E. A Pliocene-Pleistocene stack of 57 globally distributed benthic δ18O records. Paleoceanography 20, PA1003 (2005).

    Google Scholar 

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