Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication.
Bridgett M. Vonholdt
(1)
,
John P. Pollinger
(1)
,
Kirk E. Lohmueller
(2)
,
Eunjung Han
(3)
,
Heidi G. Parker
(4)
,
Pascale Quignon
(4)
,
Jeremiah D. Degenhardt
(2)
,
Adam R. Boyko
(2)
,
Dent A. Earl
(5)
,
Adam Auton
(2)
,
Andy Reynolds
(2)
,
Kasia Bryc
(2)
,
Abra Brisbin
(2)
,
James C. Knowles
(1)
,
Dana S. Mosher
(4)
,
Tyrone C. Spady
(4)
,
Abdel G. Elkahloun
(4)
,
Eli Geffen
(6)
,
Malgorzata Pilot
(7)
,
Wlodzimierz Jedrzejewski
(8)
,
Claudia Greco
(9)
,
Ettore Randi
(9)
,
Danika Bannasch
(10)
,
Alan Wilton
(11)
,
Jeremy Shearman
(11)
,
Marco Musiani
(12)
,
Michelle Cargill
(13)
,
Paul G. Jones
(14)
,
Zuwei Qian
(15)
,
Wei Huang
(15)
,
Zhao-Li Ding
(16)
,
Ya-Ping Zhang
(17)
,
Carlos D. Bustamante
(2, 13)
,
Elaine A. Ostrander
(4)
,
John Novembre
(18)
,
Robert K. Wayne
(1)
1
Department of Ecology and Evolutionary Biology
2 Department of Biological Statistics and Computational Biology
3 Department of Biostatistics
4 Cancer Genetics Branch
5 Department of Biomolecular Engineering
6 Department of Zoology
7 Institute of Zoology
8 Mammal Research Institute
9 ISPRA - Instituto Superiore per la Protezione e la Ricerca Ambientale
10 Department of Population Health and Reproduction
11 School of Biotechnology and Biomolecular Sciences
12 Faculty of Environmental Design
13 Affymetrix
14 The WALTHAM Centre for Pet Nutrition
15 Affymetrix Asia Pacific
16 Laboratory for Conservation and Utilization of Bio-resources
17 State Key Laboratory of Genetic Resources and Evolution
18 Interdepartmental Program in Bioinformatics
2 Department of Biological Statistics and Computational Biology
3 Department of Biostatistics
4 Cancer Genetics Branch
5 Department of Biomolecular Engineering
6 Department of Zoology
7 Institute of Zoology
8 Mammal Research Institute
9 ISPRA - Instituto Superiore per la Protezione e la Ricerca Ambientale
10 Department of Population Health and Reproduction
11 School of Biotechnology and Biomolecular Sciences
12 Faculty of Environmental Design
13 Affymetrix
14 The WALTHAM Centre for Pet Nutrition
15 Affymetrix Asia Pacific
16 Laboratory for Conservation and Utilization of Bio-resources
17 State Key Laboratory of Genetic Resources and Evolution
18 Interdepartmental Program in Bioinformatics
Pascale Quignon
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- PersonId : 868167
- ORCID : 0000-0001-7769-8978
Robert K. Wayne
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- PersonId : 868168
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Résumé
Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication. 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 data. 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.