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Genetic Analysis Traces Origins of Ancient American Dog Lineage to Siberia

NEW YORK (GenomeWeb) – Ancient dogs that lived in the Americas can trace their origins to Siberia, a new study has found. This suggests dogs followed humans who migrated from Asia to North America.

Researchers led by Laurent Frantz at Queen Mary University of London sequenced the mitochondrial genomes of 71 dogs and, to low coverage, the nuclear genomes of seven dogs, all of whose remains were uncovered at archaeological sites in North America and Siberia that pre-dated European colonization. Dogs have been present in the Americas for nearly 10,000 years, but the origin and destiny of these native dogs has been unclear.

As they reported in Science today, the researchers found that the ancient American dogs belong to their own clade that likely originated in Siberia before dispersing in the Americas. Additionally, they found that modern American dogs inherited little from native dogs.

"It is fascinating that a population of dogs that inhabited many parts of the Americas for thousands of years, and that was an integral part of so many Native American cultures, could have disappeared so rapidly," Frantz said in a statement. "Their near-total disappearance is likely due to the combined effects of disease, cultural persecution, and biological changes, starting with the arrival of Europeans."

The researchers compared the 71 mitochondrial genomes they generated to 145 other modern and ancient canid mitochondrial genomes and constructed a phylogenetic tree. This tree placed all the American, pre-European contact dogs in a single monophyletic group within haplogroup A. In addition, all pre-contact dogs shared a common ancestor that lived about 14,600 years ago.

This placement on the phylogenetic tree, the researchers noted, suggests a close relationship between the pre-contact dogs and a 9,000-year-old population of dogs that lived on Zhokov Island in Siberia. The two groups shared a common ancestor that lived about 15,600 years ago.

Similarly, the low-coverage nuclear genome data placed the pre-contact dogs in their own monophyletic group. The most closely related sister clade to the native dogs included modern Arctic dogs from the Americas and Eurasia, such as Alaskan malamutes, Alaskan huskies, and Siberian huskies, the researchers noted. This suggests that pre-contact dogs were not domesticated in the Americas from North American wolves, but instead were introduced by people moving into the Americas from Beringia.

While modern Arctic dogs are closely related to pre-contact dogs, the researchers said they are not their direct descendants, but are sister taxons. In fact, many modern American dogs inherited little from pre-contact dogs.

In their analysis of genomic data collected from 5,000 modern dogs, including American village dogs, they found that although American Arctic dogs harbored between 7 percent and 20 percent pre-contact dog ancestry, this could reflect ancient population substructure rather than admixture.

Additionally, North America-derived breeds like hairless dogs and Catahoulas harbored no trace of pre-contact dogs ancestry. Within a set of 590 additional village and breed dogs from the Americas, most had no pre-contact dog ancestry, though one Chihuahua and one mixed-breed dog from Nicaragua had less than 2 percent pre-contact dog ancestry. This indicated to the researchers that European dogs almost completely replaced native dogs.

But the pre-contact dogs' lineage may have left a mark on modern dogs in the form of a transmissible cancer. This cancer arose in a dog that lived more than 8,000 years ago and still harbors much of the founder dog's genome. The cancer's genome suggests that the founder dog was closely related to pre-contact dogs, though the researchers suspected that the cancer arose in an Asian dog closely related to the pre-contact American dogs.

To further tease out the story of pre-contact dogs, Linda Goodman and Elinor Karlsson from the Broad Institute wrote in an accompanying Science commentary that more genomic data from more dogs is needed. "More complete genomes, both nuclear and mitochondrial, from both ancient and modern dogs will reveal new details about the pre-contact dog populations that were an integral part of Native American life," they wrote.

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