Worldwide patterns of genomic variation and admixture in gray wolves

Abstract

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.

Ancient European dog genomes reveal continuity since the Early Neolithic

“…Unlike the SNP-based analysis described above, single-sample genotype calling was performed with no particular ascertainment scheme, and we restricted our analysis to eight canid genomes with coverage ranging from 8 to 24 × . When we included only modern dogs, we observed that wolf populations appeared to diverge rapidly, concordant with previous studies2627, whereas the branching of the main dog lineages took place over a much longer period of time. We found that the (uncalibrated) dog–wolf divergence time in units of expected numbers of mutations per site (0.5247 × 10 −4 ) was similar to that reported in Freedman et al 26…”

Combining phylogenetic and demographic inferences to assess the origin of the genetic diversity in an isolated wolf population

“…In contrast, haplotypes in clade A have more limited distributions centered in southern-central European countries. This pattern, together with archaeological, morphological and genetic findings, suggest that extant Old and New World wolf populations expanded during or right after the last glacial period, balancing the local extinction of ancient wolf ecomorphs [53,56,65–68]. However, it is not known if the turnover of wolf populations has been the consequence of a generalized megafaunal extinction wave due to climate changes or to hunting pressure and/or competition with expanding modern human populations [69–71].…”

Dogs And Mankind: Coevolution on the Move – An Update

“…(Wayne 1986;1993;Vilà et al, 1997;Fan et al, 2016). Thirty years research, with unbelievable progress in methods, and broadening of the database have confirmed this statement in many ways.…”

“…Now we accept that western Eurasians carry a significant percentage of Neandertal genes, and in the Far East, Denisovan genes indicate the importance of regional adaptations (e.g., Pagani et al, 2016). Our dogs' ancestry is no longer that ideal pedigree, fit to be endorsed by the American Kennel Club, but more like a brushwood, lines of decent changing with every new study (e.g., Vilà et al, 1997;Freedman et al 2014;Frantz et al 2016;Fan et al 2016). The exchange of genes between dogs and wolves continues till today, and wolves are split into numerous clades, with specific traits (e.g., tundra wolves vs. forest wolves.…”