Out of southern East Asia: the natural history of domestic dogs across the world

Abstract

The origin and evolution of the domestic dog remains a controversial question for the scientific community, with basic aspects such as the place and date of origin, and the number of times dogs were domesticated, open to dispute. Using whole genome sequences from a total of 58 canids (12 gray wolves, 27 primitive dogs from Asia and Africa, and a collection of 19 diverse breeds from across the world), we find that dogs from southern East Asia have significantly higher genetic diversity compared to other populations, and are the most basal group relating to gray wolves, indicating an ancient origin of domestic dogs in southern East Asia 33 000 years ago. Around 15 000 years ago, a subset of ancestral dogs started migrating to the Middle East, Africa and Europe, arriving in Europe at about 10 000 years ago. One of the out of Asia lineages also migrated back to the east, creating a series of admixed populations with the endemic Asian lineages in northern China before migrating to the New World. For the first time, our study unravels an extraordinary journey that the domestic dog has traveled on earth.

Figure 1

Population structure and genetic diversity of 58 canids. (A) Geographic locations of the 58 canids sequenced in this study. (B) Amount of of SNPs and small indels called in this study. (C) Genetic diversity for the 58 canids. AF, African village dogs; BEM, Belgian Malinois; CHI, Chihuahua; FIL, Finnish Lapphund; GAL, Galgo; GNE, Gray Norwegian Elkhound; GSD, German Shepherd Dog; JAM, Jamthund; LAH, Lapponian Herder; MEN, Mexican naked (hairless); PEN, Peruvian naked (hairless); SWL, Swedish Lapphund; AFG, Afghan Hound; SLO, Sloughi; SAM, Samoyed; ESL, East Siberian Laika; SIH, Siberian Husky; ALM, Alaska Malamute; GRD, Greenland dogs; TIM, Tibetian Mastiff. (D) Structure analysis of the 58 canids. (E) Genetic diversity of the different groups. AF, African village dogs; EB, European breeds; SI, southern Chinese indigenous dogs; W, wolves. (F) Linkage disequilibrium patterns for the different groups. (G) Principle component analysis of the 58 canids. Inset is for all individuals and the large panel is for dogs only. (H) Principle component plot for a large collection of canids together with our data. (I) A clock-like tree (UPGMA) for all the 58 individuals.

Figure 2

Demographic and migration histories for the domestic dog. (A) Tree topology inferred from TreeMix when no migratory tracts are allowed. The drift parameter is the amount of genetic drift along each population. Further inferred migratory tracts are shown in the bottom-left corner of the panel. The three important nodes are those that we have provided extensive dating information. (B) The PSMC plot for all the individuals. Gray lines plot the benthic δO¹⁸ levels, which are a proxy for global temperature. The span of the current ice age (Quaternary ice age, 2.58M-now) is shown with an arrow. The x-axis is time plotted in log scale and the y-axis is effective population size. (C) Inferred population demographic history between wolves and southern East Asian indigenous dogs using the joint site frequency spectra. (D) A proposed migratory history for domestic dogs across the world based on the evidence from our study. Solid arrows represent migratory tracts that we have dating information, while dashed arrows indicate those without accurate dating.