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 jack...

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Veröffentlicht in:PLoS genetics Jg. 10; H. 1; S. e1004016
Hauptverfasser: Freedman, Adam H., Gronau, Ilan, Schweizer, Rena M., Ortega-Del Vecchyo, Diego, Han, Eunjung, Silva, Pedro M., Galaverni, Marco, Fan, Zhenxin, Marx, Peter, Lorente-Galdos, Belen, Beale, Holly, Ramirez, Oscar, Hormozdiari, Farhad, Alkan, Can, Vilà, Carles, Squire, Kevin, Geffen, Eli, Kusak, Josip, Boyko, Adam R., Parker, Heidi G., Lee, Clarence, Tadigotla, Vasisht, Siepel, Adam, Bustamante, Carlos D., Harkins, Timothy T., Nelson, Stanley F., Ostrander, Elaine A., Marques-Bonet, Tomas, Wayne, Robert K., Novembre, John
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States Public Library of Science 01.01.2014
Public Library of Science (PLoS)
Schlagworte:
ADN mitocondrial
Amylases - genetics
Animal populations
Animals
Animals, Domestic - genetics
Biology
Diet
DNA Copy Number Variations - genetics
DNA sequencing
DNA, Mitochondrial - genetics
Dogs
Evolució molecular
Evolution, Molecular
Genes
Genetic aspects
Genetic research
Genetic Variation
Genomes
Genètica
Gossos
Llops
Nucleotide sequencing
Phylogeny
Population Density
Studies
Wolves
Wolves - classification
Wolves - genetics
Zoological research
United States
ISSN:1553-7404, 1553-7390, 1553-7404
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Beschreibung
Zusammenfassung: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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Current address: Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.
The authors have declared that no competing interests exist.
Conceived and designed the experiments: AHF CDB TTH SFN EAO TMB RKW JN. Performed the experiments: RMS BLG HB OR CV KS ARB HGP CL VT. Analyzed the data: AHF RMS IG EH DODV PMS MG ZF PM BLG OR FH CA VT AS JN. Contributed reagents/materials/analysis tools: CV EG JK EAO RKW. Wrote the paper: AHF RMS IG EH DODV PMS MG ZF PM HB AS TMB RKW JN.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1004016