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Study Suggests Early Start to Dog Domestication Followed by Parallel Evolution with Humans

NEW YORK (GenomeWeb News) – Humans and domestic dogs have likely shared close quarters for an extremely long stretch of time, a new study suggests, perhaps contributing to an apparent overlap in the sorts of genes under selection in each species.

As reported this week in Nature Communications, researchers from China, the US, and other parts of the world sequenced the genomes of four grey wolves from Russia and Inner Mongolia and half a dozen domestic dogs — including three representatives of indigenous dogs from China — as part of their effort to retrace early stages of dog domestication and evolution.

Comparing the genomes to one another and to an existing domestic dog reference sequence, they found genetic evidence for an earlier-than-anticipated split between wolves and Chinese indigenous dogs, hinting that the dog lineage has been subject to selection by humans for perhaps tens of thousands of years.

Consistent with a long, shared history between the species, study authors also detected overlap between the sorts of genes under selection in dogs and those believed to be under selection in the human genome.

"Our study on positive selection in humans and dogs found an extraordinary amount of parallel evolution, which was likely driven by their similar environments," corresponding authors Ya-ping Zhang, with the Chinese Academy of Sciences and the University of Chicago's Chung-I Wu, and colleagues wrote.

In particular, they noted that the "complex intimate interactions between dogs and humans might have also driven some of the striking parallelism seen in these two species."

The current model for dog domestication suggests a relatively gradual initial stage of domestication from wild dogs, the researchers noted, followed by a phase of more intense, selective breeding over the past few hundred years.

Several studies delved into genetic factors influencing some of the breed-specific traits that have cropped up over the latter stage of domestication. But beyond studies of mitochondrial or Y chromosome sequences, relatively little has been reported on the genetic shifts behind wild to domestic dog transitions.

For their part, authors of the new study reasoned that more in-depth analyses of China's indigenous dogs — which they called a potential "missing link in dog domestication" — might offer insights into the first phase of dog domestication, since targeted analyses in the past pointed to genetic diversity and closer-than-usual ties to grey wolves for 'ancient' or indigenous dog breeds from China and Southeast Asia.

With that in mind, the team used Illumina's GAIIx to sequence genomic DNA from four wolves (three from Russia's Bryansk, Altai, and Chukotka regions and one from Inner Mongolia), and six domestic dogs: representatives from the German shepherd, Belgian Malinois, and Tibetan Mastiff breeds and three indigenous dogs from sites in China's Shanxi, Yunnan, and Sichuan provinces.

Within resulting genomes (each sequenced to average depths of between around nine and 14-fold) and existing reference genome sequences for a dog from the Boxer breed, researchers tracked down nearly 14 million SNPs and more than three million small insertions and deletions.

Using these variants and data from almost 1,200 canines genotyped in the past, the group was able to look at wild and domestic dog relationships and demography.

Indeed, the researchers' results suggest that indigenous dogs and the Tibetan Mastiff breed, an ancient domestic breed, are slightly more genetically similar to wolves than are other domestic dogs, though all of the domestic dogs clustered broadly together.

Along with the genetic diversity present in indigenous dogs from China, the results support the notion that indigenous dogs are descended from ancestral animals involved in early stages of dog domestication, the study authors argued.

But the new data suggests that the split between ancestors of wolves and indigenous dogs may have occurred as far back as 32,000 years, followed by relatively relaxed population bottlenecks.

Among the 311 genes showing domestication-related signs of positive selection, the investigators saw over-representation by members of reproduction, digestion, metabolism, and neurological function-related pathways. In that respect, they said, the results overlap with selection studies of humans, which typically turn up contributors to many of the same processes.

And that, in turn, suggests that dogs could serve as a suitable stand-in for humans in studies aimed at understanding certain traits and diseases, the researchers noted.

"Parallel evolution happening in two species bestows on us an unprecedented opportunity to understand these traits by studying the evolution and the phenotypes in both species simultaneously," the study authors noted. "Our best friend in the animal kingdom might provide us with one of the most enchanting systems for illuminating our understandings of human evolution and disease."