@article {308964,
	title = {Genome sequencing highlights the dynamic early history of dogs.},
	journal = {PLoS Genet},
	volume = {10},
	year = {2014},
	note = {http://www.plosgenetics.org/article/info\%3Adoi\%2F10.1371\%2Fjournal.pgen.1004016},
	month = {2014 Jan},
	pages = {e1004016},
	abstract = {<p>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.</p>},
	keywords = {Amylases, Animals, Animals, Domestic, Diet, DNA Copy Number Variations, DNA, Mitochondrial, Dogs, Evolution, Molecular, Genetic Variation, Phylogeny, Population Density, Wolves},
	issn = {1553-7404},
	doi = {10.1371/journal.pgen.1004016},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/24453982},
	author = {Freedman, Adam H and Gronau, Ilan and Schweizer, Rena M and Ortega-Del Vecchyo, Diego and Han, Eunjung and Silva, Pedro M and Galaverni, Marco and Fan, Zhenxin and Marx, Peter and Lorente-Galdos, Belen and Beale, Holly and Ramirez, Oscar and Hormozdiari, Farhad and Alkan, Can and Vil{\`a}, Carles and Squire, Kevin and Geffen, Eli and Kusak, Josip and Boyko, Adam R and Parker, Heidi G and Lee, Clarence and Tadigotla, Vasisht and Wilton, Alan and Siepel, Adam and Bustamante, Carlos D and Harkins, Timothy T and Nelson, Stanley F and Ostrander, Elaine A and Marques-Bonet, Tomas and Wayne, Robert K and Novembre, John}
}
