Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication (original) (raw)

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Acknowledgements

Grants from NSF and NIH (R.K.W.; C.D.B. and J.N.), the Polish Ministry of Science and Higher Education (M.P. and W.J.), European Nature Heritage Fund EURONATUR (W.J.), National Basic Research Program of China (Y.-p.Z.), and Chinese Academy of Sciences (Y.-p.Z.) supported this research. J.N. was supported by the Searle Scholars Program. B.M.vH. was supported by a NIH Training Grant in Genomic Analysis and Interpretation. K.E.L. was supported by a NSF Graduate Research Fellowship. E.A.O., D.S.M., T.C.S., A.E. and H.G.P. are supported by the intramural program of the National Human Genome Research Institute. M.P. was supported by the Foundation for Polish Science. Wolf samples from central and eastern Europe and Turkey were collected as a result of a continuing project on genetic differentiation in Eurasian wolves. We thank the project participants (B. Jedrzejewska, V. E. Sidorovich, M. Shkvyrya, I. Dikiy, E. Tsingarskaya and S. Nowak) for their permission to use 72 samples for this study. We acknowledge R. Hefner and the Zoological collection at Tel Aviv University for Israeli wolf samples. We thank the American Kennel Club (AKC) for the dog images reproduced in Fig. 1. We also gratefully acknowledge the dog owners who generously provided samples, the AKC Canine Health Foundation, and Affymetrix Corporation. We thank B. Van Valkenburgh, K.-P. Koepfli, D. Stahler and D. Smith for reviewing the manuscript.

Author Contributions Samples were contributed by E.G., M.P., W.J., C.G., E.R., D.B., A.W., J.S., M.M., E.A.O. and R.K.W. The experiment was designed and carried out with the help of B.M.vH., J.P.P., H.G.P., P.Q., D.S.M., T.C.S., A.E., A.W., J.S., M.C., P.G.J., Z.Q., W.H., Z.-L.D., Y.-p.Z., C.D.B., E.A.O. and R.K.W. The genotyping program was written by A.R.B., A.A., A.R., K.B., A.B. and C.D.B. and further programming was completed by K.E.L., J.D.D., D.A.E., E.H. and J.N. The analyses were conducted by B.M.vH., J.P.P., K.E.L., E.H., H.G.P., J.D.D., A.R.B., D.A.E., A.A., A.R., J.C.K. and J.N. The manuscript was written by B.M.vH., K.E.L., C.D.B., E.A.O., J.N. and R.K.W.

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Authors and Affiliations

1. Department of Ecology and Evolutionary Biology, 621 Charles E. Young Drive South, University of California, Los Angeles, California 90095, USA,
   Bridgett M. vonHoldt, John P. Pollinger, James C. Knowles, John Novembre & Robert K. Wayne
2. Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853-2601, USA,
   Kirk E. Lohmueller, Jeremiah D. Degenhardt, Adam R. Boyko, Adam Auton, Andy Reynolds, Kasia Bryc, Abra Brisbin & Carlos D. Bustamante
3. Department of Biostatistics, University of California, Los Angeles, California 14853, USA,
   Eunjung Han
4. Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA ,
   Heidi G. Parker, Pascale Quignon, Dana S. Mosher, Tyrone C. Spady, Abdel Elkahloun & Elaine A. Ostrander
5. Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA,
   Dent A. Earl
6. Department of Zoology, Tel Aviv University, Tel Aviv 69978, Israel
   Eli Geffen
7. Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warszawa, Poland ,
   Malgorzata Pilot
8. Mammal Research Institute, Polish Academy of Sciences, 17-230 Bialowieza, Poland
   Wlodzimierz Jedrzejewski
9. Instituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), 40064 Ozzano Emilia (B), Italy
   Claudia Greco & Ettore Randi
10. Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California 95616, USA,
    Danika Bannasch
11. School of Biotechnology and Biomolecular Sciences and Clive and Vera Ramaciotti Center for Gene Function Analysis, University of New South Wales, Sydney NSW 2052, Australia
    Alan Wilton & Jeremy Shearman
12. Faculty of Environmental Design, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada ,
    Marco Musiani
13. Affymetrix Corporation, 3420 Central Expressway, Santa Clara, California 95051, USA ,
    Michelle Cargill
14. The WALTHAM Centre for Pet Nutrition, Waltham on the Worlds, Leicestershire LE14 4RT, UK ,
    Paul G. Jones
15. Affymetrix Asia Pacific, Scientific Affairs and Collaborations, 1233 Lujiazui Ring Road, AZIA Center, Suite 1508, Shanghai 200120, China ,
    Zuwei Qian & Wei Huang
16. Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
    Zhao-Li Ding
17. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
    Ya-ping Zhang
18. Interdepartmental Program in Bioinformatics, 621 Charles E. Young Drive South, University of California, Los Angeles, California 90095, USA,
    John Novembre

Authors

1. Bridgett M. vonHoldt
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2. John P. Pollinger
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3. Kirk E. Lohmueller
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4. Eunjung Han
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5. Heidi G. Parker
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6. Pascale Quignon
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7. Jeremiah D. Degenhardt
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8. Adam R. Boyko
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9. Dent A. Earl
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10. Adam Auton
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11. Andy Reynolds
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12. Kasia Bryc
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13. Abra Brisbin
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14. James C. Knowles
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15. Dana S. Mosher
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16. Tyrone C. Spady
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17. Abdel Elkahloun
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18. Eli Geffen
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19. Malgorzata Pilot
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20. Wlodzimierz Jedrzejewski
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21. Claudia Greco
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22. Ettore Randi
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23. Danika Bannasch
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24. Alan Wilton
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25. Jeremy Shearman
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26. Marco Musiani
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27. Michelle Cargill
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28. Paul G. Jones
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29. Zuwei Qian
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30. Wei Huang
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31. Zhao-Li Ding
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32. Ya-ping Zhang
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33. Carlos D. Bustamante
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34. Elaine A. Ostrander
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35. John Novembre
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36. Robert K. Wayne
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Corresponding author

Correspondence toRobert K. Wayne.

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vonHoldt, B., Pollinger, J., Lohmueller, K. et al. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication.Nature 464, 898–902 (2010). https://doi.org/10.1038/nature08837

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• Received: 01 September 2009
• Accepted: 19 January 2010
• Published: 17 March 2010
• Issue Date: 08 April 2010
• DOI: https://doi.org/10.1038/nature08837