Partial genomic survival of cave bears in living brown bears (original) (raw)

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Acknowledgements

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.

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Author notes

1. These authors contributed equally: Axel Barlow, James A. Cahill.

Authors and Affiliations

1. Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
   Axel Barlow, Stefanie Hartmann, Georgios Xenikoudakis, Gloria G. Fortes, Johanna L. A. Paijmans & Michael Hofreiter
2. Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
   James A. Cahill & Beth Shapiro
3. Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
   Christoph Theunert & Montgomery Slatkin
4. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
   Christoph Theunert
5. Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
   Gloria G. Fortes & Giorgio Bertorelle
6. Institute of Palaeontology, University of Vienna, Vienna, Austria
   Gernot Rabeder & Christine Frischauf
7. Instituto Universitario de Xeoloxía, Universidade da Coruña, A Coruña, Spain
   Aurora Grandal-d’Anglade & Ana García-Vázquez
8. Ilia State University, Institute of Ecology, Tbilisi, Georgia
   Marine Murtskhvaladze
9. Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
   Urmas Saarma & Peeter Anijalg
10. Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
    Tomaž Skrbinšek
11. Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
    Boris Gasparian
12. Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
    Guy Bar-Oz
13. Earth Institute, University College Dublin, Dublin, Ireland
    Ron Pinhasi
14. Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
    Ron Pinhasi
15. Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
    Love Dalén

Authors

1. Axel Barlow
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2. James A. Cahill
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3. Stefanie Hartmann
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4. Christoph Theunert
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5. Georgios Xenikoudakis
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6. Gloria G. Fortes
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7. Johanna L. A. Paijmans
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8. Gernot Rabeder
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9. Christine Frischauf
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10. Aurora Grandal-d’Anglade
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11. Ana García-Vázquez
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12. Marine Murtskhvaladze
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13. Urmas Saarma
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14. Peeter Anijalg
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15. Tomaž Skrbinšek
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16. Giorgio Bertorelle
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17. Boris Gasparian
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18. Guy Bar-Oz
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19. Ron Pinhasi
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20. Montgomery Slatkin
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21. Love Dalén
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22. Beth Shapiro
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23. Michael Hofreiter
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Contributions

A.B. and M.H. conceived the study; A.B., G.X., G.G.F., L.D. and P.A. performed laboratory work; A.B., J.A.C., S.H., C.T. and J.L.A.P. performed data analysis; A.B., J.A.C., S.H., C.T., J.L.A.P., G.X., G.B., R.P., L.D., B.S., M.S. and M.H. interpreted the results; A.B., J.A.C., S.H., C.T., J.L.A.P., B.S., M.S. and M.H. provided theoretical discussion of methodological developments; M.H., B.S. and M.S. supervised work carried out in their respective research groups; A.B., J.A.C. and M.H. wrote the manuscript; G.R., C.F., A.G.-d’A., A.G.-V., M.M., U.S., P.A., T.S., B.G., G.B.-O. and R.P. selected samples; G.B. contributed data; M.H., R.P., B.S. and A.G.-d’A. obtained funding. All authors read, gave comments and helped to revise the final version of the manuscript.

Corresponding author

Correspondence toAxel Barlow.

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Supplementary information

Supplementary Tables and Figures

Supplementary information, figures and tables

Reporting Summary

Supplementary Data 1

D statistic tests for unequal allele sharing between two brown or polar bears and a cave bear candidate introgressor

Supplementary Data 2

D statistic tests for unequal allele sharing between two cave bears and a polar bear or brown bear candidate introgressor

Supplementary Data 3

D statistic tests inconsistent with the species tree as a measure of clade differentiation — comparisons within European cave bears and European cave bears relative to the Caucasus cave bear kudarensis

Supplementary Data 4

D statistic tests inconsistent with the species tree as a measure of clade differentiation — comparisons polar bears relative to brown bears, and brown bears relative to polar bears

Supplementary Data 5

f estimates of cave bear ancestry in brown relative polar bears, and among polar bears

Supplementary Data 6

f estimates of brown bear ancestry in European cave bears, relative to the Caucasus cave bear kudarensis

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Barlow, A., Cahill, J.A., Hartmann, S. et al. Partial genomic survival of cave bears in living brown bears.Nat Ecol Evol 2, 1563–1570 (2018). https://doi.org/10.1038/s41559-018-0654-8

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• Received: 31 March 2017
• Accepted: 27 July 2018
• Published: 27 August 2018
• Issue Date: October 2018
• DOI: https://doi.org/10.1038/s41559-018-0654-8