The study looked at the genetic characteristics of 84 individual dogs from more than a dozen sites in North and South America, and is the largest analysis so far of ancient dogs in the Americas.
"Dogs are one of the earliest organisms to have migrated with humans to every continent, and I think that says a lot about the relationship dogs have had with humans," said University of Illinois graduate student Kelsey Witt.
The study focused on mitochondrial DNA, but included a much larger sample of dogs than had been analysed before.
The Janey B Goode site is located near the ancient city Cahokia, the largest and first known metropolitan area in North America.
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Dozens of dogs were ceremonially buried at Janey B Goode, suggesting that people there had a special reverence for dogs. While most of the dogs were buried individually, some were placed back-to-back in pairs.
The researchers found four never-before-seen genetic signatures in the new samples, suggesting greater ancient dog diversity in the Americas than previously thought.
They also found unusually low genetic diversity in some dog populations, suggesting that humans in those regions may have engaged in dog breeding.
In some samples, the team found significant genetic similarities with American wolves, indicating that some of the dogs interbred with or were domesticated anew from American wolves.
The findings appear in the Journal of Human Evolution.