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Sequencing Studies Point to Potential Dog Domestication by Pre-agricultural Humans

NEW YORK (GenomeWeb News) – Dog domestication from a still-to-be-determined group of wild wolf ancestors likely occurred through a series of dynamic processes that began before the advent of widespread agriculture by humans, according to a new PLOS Genetics study.

"Dog domestication is more complex than we originally thought," University of Chicago geneticist John Novembre said in a statement. "It makes the field of dog domestication very intriguing going forward."

Novembre and University of California at Los Angeles researcher Robert Wayne led a group of researchers who did genome sequencing on gray wolves from China, Croatia, and Israel — geographical regions representing locales previously proposed as potential centers for dog domestication.

The team also sequenced an Australian Dingo and an indigenous Basenji dog, believed to represent breeds from the base of the domestic dog tree, as well as the genome of a golden jackal, which belongs to a canine lineage that diverged prior to the dog-wolf split.

By analyzing the newly sequenced genomes, together with existing wolf and dog data, the researchers found that domestic dogs tend to cluster more closely with one another than with wolves, forming a single phylogenetic group with an apparent history of mixing with wolves.

Somewhat unexpectedly, they estimated that that domestication event took place as far back as 34,000-years-ago, probably preceding the advent of widespread human agriculture. But from patterns in the genomes, the study's authors argued that the source population of the domestic dog lineage was probably not any one of the wolf lineages currently found in the Middle East, Europe, or Asia.

"One possibility is there may have been other wolf lineages that these dogs diverged from that then went extinct," Novembre said in a statement.

"So now when you ask which wolves are dogs most closely related to, it's none of these three because these are wolves that diverged in the recent past," he explained. "It's something more ancient that isn't well represented by today's wolves."

Novembre, Wayne, and their colleagues used SOLiD and Illumina HiSeq sequencing, to generate high-quality genome sequences for six canines: three gray wolves, a Basenji, a Dingo, and a golden jackal.

The wolves selected for the study came from Israel, China, and Croatia, making it possible to test several dog domestication theories, including the so-called "regional domestication" hypothesis, which suggests dogs became domesticated independently in different parts of the world.

Under the regional domestication scheme, for example, the Basenji (an African breed) is expected to share closer ancestry with wolves from Israel, while sequences from the Dingo and Boxer breed (used to generate the dog reference genome) would theoretically show genetic ties to wolves from China and Croatia, respectively.

In contrast, though, the researchers' analysis of more than 10 million SNPs in the canine genomes indicated that domestic dogs cluster together in a group that's genetically separate from the wolves, which form their own genetic cluster.

Such findings are consistent with a single dog phylogeny, the researchers noted, though none of the modern-day wolves tested for the study appear to be descendants of the domestic dog source population.

The sequences held signs of earlier-than-anticipated dog domestication, too. Whereas past studies have argued that dogs became cozy with human populations after a shift to more agricultural lifestyles, the new analysis hints that domesticated dogs may have been around back when a hunting and gathering lifestyle was still more widespread amongst humans.

For instance, the team's look at sequence data from a dozen more domestic dog breeds revealed differences in representation by the gene coding for an amylase enzyme involved in starch digestion.

Past studies suggested that that gene had undergone expansions as wild dogs became domesticated. That, in turn, sparked speculation that agricultural human populations had a hand in domesticating dogs, sharing starch-rich food scraps with their furry companions.

Starch digestion and metabolism genes were also among those identified by researchers from the US, Sweden, and Norway who published a study in Nature early last year that highlighted dog genes showing signs of domestication-related selection.

In the current study, though, the researchers did not detect amylase gene expansions across the board in domestic pooches. The expansions were missing in Huskies and Dingoes, for example, though they did turn up in some wolf genomes, arguing against ties between dog domestication and human agricultural groups.

"In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds," researchers wrote, "suggesting the earliest dogs arose alongside hunter-gatherers rather than agriculturists."

The new sequence data also made it possible to retrace past population sizes for wolves and domestic dogs, pointing to dramatic population dips in both species following their divergence. That split was pegged at between 9,000 and 34,000 years ago, the team reported, while the golden jackal lineage appears to have diverged a few hundred thousand years ago.

At least one past study supports the notion that humans and dogs have been living in harmony for an extremely long time: a Chinese- and American-led team reporting in Nature Communications last year saw signs of human-influenced selection in dog genomes going back tens of thousands of years. That group estimated that dogs and wolves may have split from one another as many as 32,000 years ago.

Despite the details that the latest study offers on the timing and nature of dog domestication, those involved in the analysis noted that there are still questions about where this domestication took place as well as the ancestral wolf population involved.

"Our analysis suggests that none of the sampled wolf populations is more closely related to dogs than any others," they concluded, "and that dogs diverged from wolves at about the same time that the sampled wolf populations diverged from each other."

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