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. Pyjamas
Gernot Rabeder
Christine Frischauf
Aurora Grandal-d’Anglade
Marine Murtskhvaladze
Urmas Saarma
Peeter Anijalg
Giorgio Bertorelle
Boris Gasparian
Guy Bar-Oz
Ron Pinhasi
Montgomory Slatkin
Love Dalén
Beth Shapiro
Michael Hofreiter


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.