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Genomic Analysis Traces Domestic Dog Origin to Southern East Asia

NEW YORK (GenomeWeb) – A team of researchers has traced the origin of domestic dogs to southern East Asia, based on a comparison of their genomes and the genomes of wolves.

The team led by Ya-Ping Zhang, the president of the Kunming Institute of Zoology at the Chinese Academy of Sciences, compared whole-genome sequences from 12 gray wolves, 27 primitive dogs from Asia and Africa, and 19 dogs of various breeds from around the world. Through their analyses, they found that dogs from southern East Asia have much higher genetic diversity than other dog populations and are the most basal group to gray wolves, as they reported today in Cell Research.

The researchers also traced the movement of dogs around the globe, noting that they spread after their origin some 33,000 years ago from Asia to the Middle East, Africa, and Europe. A few lineages subsequently moved back to Asia before mixing with lineages there and traveling to the Americas.

"Based on genome sequences from a worldwide collection of dogs … this study provides strong genetic evidence that the domestic dog originated in southern East Asia," Zhang and his colleagues wrote in their paper. "The analyses give a coherent picture, where the indigenous dogs in southern East Asia or East Asia in general stand out compared to other populations, with higher genetic diversity as a group, and occupying a basal position next to wolves. Other dog populations show progressive ancestry gradient away from wolves starting from southern East Asia."

The history of the domestic dog, they noted, has been murky. A number of locations have been suggested as its origin. A recent study drawing on both purebred and village dogs homed in on Central Asia as the likely source, though other studies have implicated China and Europe. Further, the domestication event, the researchers added, is thought to have occurred between 32,000 years and 10,000 years ago, though some reports place it even earlier.

Zhang and his colleagues collected and sequenced the genomes of 58 canids — including gray wolves, indigenous dogs, village dogs, and breed dogs from all over the world, including Afghan Hounds, Tibetan Mastiffs, and Chihuahuas, among others — to an average 15X coverage.

The genetic diversity of the canids, they reported, decreased from wolves to Chinese indigenous dogs and decreased again in breed dogs.

When the researchers clustered the canids using an expectation maximization algorithm, the approach first separated wolves from dogs, and then split the dogs into clusters: one representing indigenous dogs from southern East Asia and the other all other dogs. Additional partitioning of the third dog cluster split out African village dogs and breed dogs from the Eastern Artic, like Siberian Huskies.

A calculation of genetic diversity for these various groups indicated that dog breeds generally had lower diversity than Chinese indigenous dogs, though higher diversity than African indigenous dogs.

A principal component analysis, meanwhile, largely reflected the dogs' geographic origins. Though the dogs clustered much more closely together than the wolves, they spread along axes representing southern East Asia, Europe, and Africa. By adding in data from a previous SNP array study, the researchers further noted that southern Chinese indigenous dogs and a few other East Asian dogs are the most closely related to wolves.

Indeed, a phylogenetic analysis of the 58 canids placed East Asian dogs on both sides of the deep node connecting all dogs, suggesting to the researchers that East Asian dogs are the most basal lineages connected to gray wolves.

Zhang and his colleagues also timed the split of domestic dogs from gray wolves, reporting that they first began to diverge about 33,000 years ago. As dogs only experienced a mild population bottleneck, the researchers said that the dog domestication process may have been drawn out, starting from a group of wolves loosely associated with people that later underwent selection for phenotypes that favored stronger bonding with humans.

After the split, the researchers said that dogs radiated from southern East Asia about 15,000 years ago — possibly following human settlements — to spread to the Middle East and Africa, arriving in Europe about 10,000 years ago. One lineage, they noted, then migrated back to northern China where it admixed with endemic Asian lineages to yield northern Chinese indigenous dogs and the Artic breed dogs.

As many Central and Southern American dog breeds exhibit no signs of admixture while the Arctic breeds do, Zhang and his colleagues suggested that human colonization of the New World — with dogs in tow — may have occurred in several waves.