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 Slatkin; Love Dalén; Beth Shapiro; Michael Hofreiter

doi:10.1038/s41559-018-0654-8

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

Department of Archaeology

Research output: Contribution to journal › Article › peer-review

Abstract

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 language	English
Pages (from-to)	1563-1570
Number of pages	8
Journal	Nature Ecology and Evolution
Volume	2
Issue number	10
DOIs	https://doi.org/10.1038/s41559-018-0654-8
State	Published - 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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41559-018-0654-8

Cite this

Barlow, A., Cahill, J. A., Hartmann, S., Theunert, C., Xenikoudakis, G., Fortes, G. G., Paijmans, J. L. A., Rabeder, G., Frischauf, C., Grandal-d’Anglade, A., García-Vázquez, A., Murtskhvaladze, M., Saarma, U., Anijalg, P., Skrbinšek, T., Bertorelle, G., Gasparian, B., Bar-Oz, G., Pinhasi, R., ... Hofreiter, M. (2018). Partial genomic survival of cave bears in living brown bears. Nature Ecology and Evolution, 2(10), 1563-1570. https://doi.org/10.1038/s41559-018-0654-8

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title = "Partial genomic survival of cave bears in living brown bears",

abstract = "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.",

author = "Axel Barlow and Cahill, {James A.} and Stefanie Hartmann and Christoph Theunert and Georgios Xenikoudakis and Fortes, {Gloria G.} and Paijmans, {Johanna L.A.} and Gernot Rabeder and Christine Frischauf and Aurora Grandal-d{\textquoteright}Anglade and Ana Garc{\'i}a-V{\'a}zquez and Marine Murtskhvaladze and Urmas Saarma and Peeter Anijalg and Toma{\v z} Skrbin{\v s}ek and Giorgio Bertorelle and Boris Gasparian and Guy Bar-Oz and Ron Pinhasi and Montgomery Slatkin and Love Dal{\'e}n and Beth Shapiro and Michael Hofreiter",

note = "Funding Information: This work was funded by European Research Council (ERC) consolidator grant {\textquoteleft}gene flow{\textquoteright} 310763 to M.H. G.G.F. and R.P. were supported by ERC starting grant 263441 to R.P. A.G.-d{\textquoteright}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{\textquoteright}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 Le{\'o}n, 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: {\textcopyright} 2018, The Author(s).",

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doi = "10.1038/s41559-018-0654-8",

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Barlow, A, Cahill, JA, Hartmann, S, Theunert, C, Xenikoudakis, G, Fortes, GG, Paijmans, JLA, Rabeder, G, Frischauf, C, Grandal-d’Anglade, A, García-Vázquez, A, Murtskhvaladze, M, Saarma, U, Anijalg, P, Skrbinšek, T, Bertorelle, G, Gasparian, B, Bar-Oz, G, Pinhasi, R, Slatkin, M, Dalén, L, Shapiro, B & Hofreiter, M 2018, 'Partial genomic survival of cave bears in living brown bears', Nature Ecology and Evolution, vol. 2, no. 10, pp. 1563-1570. https://doi.org/10.1038/s41559-018-0654-8

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AU - Barlow, Axel

AU - Cahill, James A.

AU - Hartmann, Stefanie

AU - Theunert, Christoph

AU - Xenikoudakis, Georgios

AU - Fortes, Gloria G.

AU - Paijmans, Johanna L.A.

AU - Rabeder, Gernot

AU - Frischauf, Christine

AU - Grandal-d’Anglade, Aurora

AU - García-Vázquez, Ana

AU - Murtskhvaladze, Marine

AU - Saarma, Urmas

AU - Anijalg, Peeter

AU - Skrbinšek, Tomaž

AU - Bertorelle, Giorgio

AU - Gasparian, Boris

AU - Bar-Oz, Guy

AU - Pinhasi, Ron

AU - Slatkin, Montgomery

AU - Dalén, Love

AU - Shapiro, Beth

AU - Hofreiter, Michael

N1 - 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).

PY - 2018/10/1

Y1 - 2018/10/1

N2 - 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.

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Partial genomic survival of cave bears in living brown bears

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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