Partial genomic survival of cave bears in living brown bears

Axel Barlow, James A. Cahill, Stefanie Hartmann, Christoph Theunert, Georgios Xenikoudakis, Gloria G. Fortes, Johanna L.A. Paijmans, Gernot Rabeder, Christine Frischauf, Aurora Grandal-d’Anglade, Ana García-Vázquez, Marine Murtskhvaladze, Urmas Saarma, Peeter Anijalg, Tomaž Skrbinšek, Giorgio Bertorelle, Boris Gasparian, Guy Bar-Oz, Ron Pinhasi, Montgomery SlatkinLove Dalén, Beth Shapiro, Michael Hofreiter

Research output: Contribution to journalArticlepeer-review


Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.

Original languageEnglish
Pages (from-to)1563-1570
Number of pages8
JournalNature Ecology and Evolution
Issue number10
StatePublished - 1 Oct 2018

Bibliographical note

Funding Information:
This work was funded by European Research Council (ERC) consolidator grant ‘gene flow’ 310763 to M.H. G.G.F. and R.P. were supported by ERC starting grant 263441 to R.P. A.G.-d’A. and A.G.-V. were supported by research project CGL2014-57209-P of the Spanish Ministry of Economy and Competitiveness to A.G.-d’A. J.A.C. and B.S. were supported by a grant from the Gordon and Betty Moore Foundation (GBMF-3804) and NSF ARC-1417036 to B.S. U.S. was supported by grant IUT20-32 from the Estonian Ministry of Education and Research, and P.A. by the Estonian Science Foundation DoRa programme. We thank the regional governments of Asturias and Castilla y León, in Spain, for providing tissue samples of Cantabrian bears. The authors would like to acknowledge support from Science for Life Laboratory, the National Genomics Infrastructure (NGI), Sweden, the Knut and Alice Wallenberg Foundation and UPPMAX for providing assistance in massively parallel DNA sequencing and computational infrastructure.

Publisher Copyright:
© 2018, The Author(s).

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Ecology


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