The gray wolf (Canis lupus) is a widely distributed top predator and ancestor of the domestic dog. To address questions about wolf relationships to each other and dogs, we assembled and analyzed a data set of 34 canine genomes. The divergence between New and Old World wolves is the earliest branching event and is followed by the divergence of Old World wolves and dogs, confirming that the dog was domesticated in the Old World. However, no single wolf population is more closely related to dogs, supporting the hypothesis that dogs were derived from an extinct wolf population. All extant wolves have a surprisingly recent common ancestry and experienced a dramatic population decline beginning at least ∼30 thousand years ago (kya). We suggest this crisis was related to the colonization of Eurasia by modern human hunter-gatherers, who competed with wolves for limited prey but also domesticated them, leading to a compensatory population expansion of dogs. We found extensive admixture between dogs and wolves, with up to 25% of Eurasian wolf genomes showing signs of dog ancestry. Dogs have influenced the recent history of wolves through admixture and vice versa, potentially enhancing adaptation. Simple scenarios of dog domestication are confounded by admixture, and studies that do not take admixture into account with specific demographic models are problematic.

This work was supported by National Science Foundation (NSF) grant EF-1021397 (R.K.W., R.M.S.), the National Key Technology R&D Program of China 2012BAC01B06 (Z.F., B.S.Y.), ICREA, EMBO YIP 2013 and MICINN BFU2014-55090-P (T.M.B.), National Human Genome Research Institute (NHGRI) grant R00HG005846 (J.X.), UC MEXUS-CONACYT doctoral fellowship 213627 (D.O.D.V.), the Chengdu Giant Panda Breeding Research Foundation CPF-yan-2012-10 (W.Z., Z.Z.), and the grant PRIC from Fundació Barcelona Zoo and Ajuntament de Barcelona (O.R.)