NEW YORK (GenomeWeb News) – Middle Eastern grey wolves appear to represent the source of genetic diversity in domestic dog breeds, according to a genotyping study appearing online today in Nature, suggesting dogs originated in that part of the world.
An international research team, including investigators from Affymetrix, genotyped nearly 1,000 dogs from 85 breeds as well as hundreds of grey wolves from 11 populations. In contrast to past analyses of mitochondrial DNA suggesting dogs originated in East Asia, data from the nuclear genome tells a different story.
"In our analysis of the entire genome, we found that dogs share more unique markers with Middle Eastern wolves than with East Asian wolves," lead author Bridget vonHoldt, a graduate student in University of California at Los Angeles ecology and evolutionary biology researcher Robert Wayne's lab, said in a statement. "We used a genome-wide approach, which avoids the bias of single genome region."
Results from the study also provide new insights into how dog breeds cluster genetically. For instance, the team found clusters corresponding to dog breeds as well as specific dog functional groups and phenotypes. They also detected a split between modern dog breeds and breeds that appear to have descended from more ancient breeds.
"We're, I guess, surprised that there's such a distinct pattern in the tree itself," senior author Wayne told GenomeWeb Daily News. "There are these layered levels of divergence in the dogs."
The researchers used Affymetrix arrays to genotype 912 dogs from 85 American Kennel Club breeds and 225 grey wolves from 11 populations at 48,036 autosomal SNPs.
When they began analyzing this data, the researchers found that dogs clustered by breed and were genetically distinct from wolves.
Only a few breeds — such as basenjis, Akitas, and Siberian huskies — showed strong evidence of admixture with wolves. These and other admixed breeds fall into a group of so-called "ancient" breeds that diverge from "modern" dog breeds, the researchers noted.
"The limitation of evidence for admixture to only a few breeds is striking given that backcrossing between dogs and wolves is know to occur and dogs and wolves coexist widely," the researchers noted. "Given that modern breeds are the products of controlled breeding practices of the Victorian era … the lack of detectable admixture with wolves is consistent with the strict breeding regimes recently implemented by humans."
Overall, their phylogenetic analyses identified three divergent ancient breeds, making up Asian, Middle Eastern, and northern groups.
Contrary to mitochondrial DNA studies suggesting domestic dogs originated in East Asia, the researchers analyses indicated that Middle Eastern wolves provided the main source of genetic diversity for domestic dogs, though pockets of interbreeding with wolves occurred in other parts of the world — leading, for instance, to haplotype sharing between European wolves and greyhounds, whippets, and a few other breeds and haplotype sharing between Chinese wolves and dogs from the Akita and chow chow breeds.
The team also found that dog diversity didn't consistently vary with geography. Instead, genetic clusters tended to correlate with functional and phenotypic traits. For example, herding dogs clustered together, as did retrievers, sight hounds, and so on.
In addition, Wayne noted, even within different lineages, the same discrete mutations seem to underlie specific traits. That means many dog traits can be distilled down to a handful of key genes, he explained, noting that short dogs from different breeds share one mutation, while those with short limbs share another.
"Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages," the researchers wrote. "More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity."
In an accompanying paper in BMC Biology last month, members of the team provided a more detailed look at one such gene, the insulin-like growth factor IGF1, which contains a characteristic SINE element and SNP in small dog breeds.
Other research coming out in the future will include studies looking at how many genes are responsible for phenotypic differences in dogs as well as a study focusing on genetic patterns in wild dogs, such as wolves, Wayne said.