Data from: 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.