  To identify genetic changes underlying dog domestication and reconstruct
their early evolutionary history, we analyzed novel high-quality genome
sequences of three gray wolves, one from each of three putative centers of dog
domestication, two ancient dog lineages (Basenji and Dingo) and a golden jackal
as an outgroup. We find dogs and wolves diverged through a dynamic process
involving population bottlenecks in both lineages and post-divergence gene
flow, which confounds previous inferences of dog origins. In dogs, the
domestication bottleneck was severe involving a 17 to 49-fold reduction in
population size, a much stronger bottleneck than estimated previously from less
intensive sequencing efforts. A sharp bottleneck in wolves occurred soon after
their divergence from dogs, implying that the pool of diversity from which dogs
arose was far larger than represented by modern wolf populations. Conditional
on mutation rate, we narrow the plausible range for the date of initial dog
domestication to an interval from 11 to 16 thousand years ago. This period
predates the rise of agriculture, implying that 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 are more closely related to dogs, and the
sampled wolves instead form a sister monophyletic clade. This result, in
combination with our finding of dog-wolf admixture during the process of
domestication, suggests a re-evaluation of past hypotheses of dog origin is
necessary. Finally, we also detect signatures of selection, including evidence
for selection on genes implicated in morphology, metabolism, and neural
development. Uniquely, we find support for selective sweeps at regulatory sites
suggesting gene regulatory changes played a critical role in dog domestication.
