Nature 464, 898-902 (8 April 2010) | doi:10.1038/nature08837; Received 1 September 2009; Accepted 19 January 2010; Published online 17 March 2010

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Bridgett M. vonHoldt1, John P. Pollinger1, Kirk E. Lohmueller2, Eunjung Han3, Heidi G. Parker4, Pascale Quignon4, Jeremiah D. Degenhardt2, Adam R. Boyko2, Dent A. Earl5, Adam Auton2, Andy Reynolds2, Kasia Bryc2, Abra Brisbin2, James C. Knowles1, Dana S. Mosher4, Tyrone C. Spady4, Abdel Elkahloun4, Eli Geffen6, Malgorzata Pilot7, Wlodzimierz Jedrzejewski8, Claudia Greco9, Ettore Randi9, Danika Bannasch10, Alan Wilton11, Jeremy Shearman11, Marco Musiani12, Michelle Cargill13, Paul G. Jones14, Zuwei Qian15, Wei Huang15, Zhao-Li Ding16, Ya-ping Zhang17, Carlos D. Bustamante2, Elaine A. Ostrander4, John Novembre1,18 & Robert K. Wayne1

  1. Department of Ecology and Evolutionary Biology, 621 Charles E. Young Drive South, University of California, Los Angeles, California 90095, USA
  2. Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853-2601, USA
  3. Department of Biostatistics, University of California, Los Angeles, California 14853, USA
  4. Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
  5. Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
  6. Department of Zoology, Tel Aviv University, Tel Aviv 69978, Israel
  7. Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warszawa, Poland
  8. Mammal Research Institute, Polish Academy of Sciences, 17-230 Bialowieza, Poland
  9. Instituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), 40064 Ozzano Emilia (B), Italy
  10. Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California 95616, USA
  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
  12. Faculty of Environmental Design, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
  13. Affymetrix Corporation, 3420 Central Expressway, Santa Clara, California 95051, USA
  14. The WALTHAM Centre for Pet Nutrition, Waltham on the Worlds, Leicestershire LE14 4RT, UK
  15. Affymetrix Asia Pacific, Scientific Affairs and Collaborations, 1233 Lujiazui Ring Road, AZIA Center, Suite 1508, Shanghai 200120, China
  16. Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China
  17. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
  18. Interdepartmental Program in Bioinformatics, 621 Charles E. Young Drive South, University of California, Los Angeles, California 90095, USA

Correspondence to: Robert K. Wayne1 Correspondence and requests for materials should be addressed to R.K.W. (Email: rwayne@ucla.edu).

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication1, 2. To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data3. Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.