Genome sequencing highlights the dynamic early history of dogs.
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. In dogs, the domestication bottleneck involved at least a 16-fold reduction in population size, a much more severe bottleneck than estimated previously. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was substantially larger than represented by modern wolf populations. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11-16 thousand years ago, predating the rise of agriculture. In light of this finding, we expand upon previous work regarding the increase in copy number of the amylase gene (AMY2B) in dogs, which is believed to have aided digestion of starch in agricultural refuse. We find standing variation for amylase copy number variation in wolves and little or no copy number increase in the Dingo and Husky lineages. In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds, suggesting the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that, surprisingly, none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary.
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America.
Adam H
AH
Freedman
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America.
Ilan
I
Gronau
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America.
Rena M
RM
Schweizer
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America.
Diego
D
Ortega-Del Vecchyo
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America.
Eunjung
E
Han
CIBIO-UP, University of Porto, Vairão, Portugal.
Pedro M
PM
Silva
ISPRA, Ozzano dell'Emilia, Italy.
Marco
M
Galaverni
Key Laboratory of Bioresources and Ecoenvironment, Sichuan University, Chengdu, China.
Zhenxin
Z
Fan
Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, Hungary.
Peter
P
Marx
Institut de Biologia Evolutiva (CSIC-Univ Pompeu Fabra), Barcelona, Spain.
Belen
B
Lorente-Galdos
National Institutes of Health/NHGRI, Bethesda, Maryland, United States of America.
Holly
H
Beale
Institut de Biologia Evolutiva (CSIC-Univ Pompeu Fabra), Barcelona, Spain.
Oscar
O
Ramirez
Department of Computer Science, University of California, Los Angeles, Los Angeles, California, United States of America.
Farhad
F
Hormozdiari
Bilkent University, Ankara, Turkey.
Can
C
Alkan
Estación Biológia de Doñana EBD-CSIC, Sevilla, Spain.
Carles
C
Vilà
Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America.
Kevin
K
Squire
Department of Zoology, Tel Aviv University, Tel Aviv, Israel.
Eli
E
Geffen
University of Zagreb, Zagreb, Croatia.
Josip
J
Kusak
Department of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America.
Adam R
AR
Boyko
National Institutes of Health/NHGRI, Bethesda, Maryland, United States of America.
Heidi G
HG
Parker
Life Technologies, Foster City, California, United States of America.
Clarence
C
Lee
Life Technologies, Foster City, California, United States of America.
Vasisht
V
Tadigotla
Alan
A
Wilton
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America.
Adam
A
Siepel
Stanford School of Medicine, Stanford, California, United States of America.
Carlos D
CD
Bustamante
Life Technologies, Foster City, California, United States of America.
Timothy T
TT
Harkins
Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America.
Stanley F
SF
Nelson
National Institutes of Health/NHGRI, Bethesda, Maryland, United States of America.
Elaine A
EA
Ostrander
Institut de Biologia Evolutiva (CSIC-Univ Pompeu Fabra), Barcelona, Spain ; Institució Catalana de Recerca i Estudis Avançats (ICREA). 08010, Barcelona, Spain.
Tomas
T
Marques-Bonet
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America.
Robert K
RK
Wayne
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America.
John
J
Novembre
D000681:Amylases / Q000235:genetics*; D000818:Animals; D000829:Animals, Domestic / Q000235:genetics*; D056915:DNA Copy Number Variations / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics; D004032:Diet; D004285:Dogs; D019143:Evolution, Molecular; D014644:Genetic Variation; D010802:Phylogeny; D011156:Population Density; D019596:Wolves / Q000145:classification / Q000235:genetics
D004272:DNA, Mitochondrial; D000681:Amylases