期刊
PLOS GENETICS
卷 10, 期 1, 页码 -出版社
PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pgen.1004016
关键词
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资金
- NSF [DBI-0905784, EF-1021397, DEB-0948510]
- Searle Foundation Scholar Award
- NIH [T32 HG002536]
- NIH (NIGMS) [GM102192]
- UC MEXUS-CONACYT [213627]
- Fundacao para a Ciencia e a Tecnologia (Portugal) [SFRH/BD/60549/2009]
- University of Bologna (Italy), XXIV cicle, Biodiversity and Evolution
- National Science and Technology Support Project of China [2012BAC01B06]
- Rosztoczy Foundation
- USHHS Ruth L. Kirschstein Institutional National Research Service Award [T32 CA009056]
- National Institute of Bioinformatics
- National Human Genome Research Institute
- JAEDOC-CSIC
- Marie Curie CIG, Programa de Captacion del Conocimiento para Andalucia-a for sequencing of Chinese wolf at BGI [PCIG10-GA-2011-303772]
- ERC [260372]
- MICINN (Spain) [BFU2011-28549]
- NATIONAL CANCER INSTITUTE [T32CA009056] Funding Source: NIH RePORTER
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [ZIAHG200377, T32HG002536] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM102192] Funding Source: NIH RePORTER
- Direct For Biological Sciences [1021397] Funding Source: National Science Foundation
- Directorate For Geosciences [0910272] Funding Source: National Science Foundation
- ICREA Funding Source: Custom
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.
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