Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication.
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.
Vonholdt
Bridgett M
BM
Department of Ecology and Evolutionary Biology, 621 Charles E. Young Drive South, University of California, Los Angeles, California 90095, USA.
Pollinger
John P
JP
Lohmueller
Kirk E
KE
Han
Eunjung
E
Parker
Heidi G
HG
Quignon
Pascale
P
Degenhardt
Jeremiah D
JD
Boyko
Adam R
AR
Earl
Dent A
DA
Auton
Adam
A
Reynolds
Andy
A
Bryc
Kasia
K
Brisbin
Abra
A
Knowles
James C
JC
Mosher
Dana S
DS
Spady
Tyrone C
TC
Elkahloun
Abdel
A
Geffen
Eli
E
Pilot
Malgorzata
M
Jedrzejewski
Wlodzimierz
W
Greco
Claudia
C
Randi
Ettore
E
Bannasch
Danika
D
Wilton
Alan
A
Shearman
Jeremy
J
Musiani
Marco
M
Cargill
Michelle
M
Jones
Paul G
PG
Qian
Zuwei
Z
Huang
Wei
W
Ding
Zhao-Li
ZL
Zhang
Ya-Ping
YP
Bustamante
Carlos D
CD
Ostrander
Elaine A
EA
Novembre
John
J
Wayne
Robert K
RK
D000818:Animals; D000829:Animals, Domestic / Q000145:classification / Q000235:genetics*; D000835:Animals, Wild / Q000145:classification / Q000235:genetics; D001947:Breeding; D019295:Computational Biology; D004285:Dogs / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D005202:Asia, Eastern / Q000208:ethnology; D016678:Genome / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics*; D008877:Middle East / Q000208:ethnology; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D019596:Wolves / Q000145:classification / Q000235:genetics