The tangle of questions regarding the ancestry of dog breeds indigenous to the Americas is slowly unraveling.

Unlike the poodles that populate many a household, native American dog breed lineages originated from East Asian canines, with little genetic influence from European breeds—formerly an open question, according to a new study.

It was already known that many dog breeds are descended from canines living in the Americas during pre-Columbian times—or the period before European colonization and influence.

When humans crossed the Bering Land Bridge, the strip of land connecting Alaska and Russia, about 15,000 to 10,000 years ago, they brought their dogs with them.

"Dogs have been here pretty much since humans have been here," said Adam Boyko, an evolutionary geneticist at Cornell University in Ithaca, New York, who was not involved in the study.

But a mystery remained as to how much original, pre-Columbian genetic stock remained in these native populations, said Peter Savolainen, an evolutionary geneticist at KTH Royal Institute of Technology in Sweden and a co-author of the study. (Read about how to build a dog in National Geographic magazine.)

Ancient Signal

"The breeds that we are looking at are almost totally pure," said Savolainen. The most exciting result, he said, is the genetic link between a modern Chihuahua sequence and an ancient one.

"We have a straight line back in time," he said. The modern Chihuahua is most definitely descended from pre-Columbian canines living in Mexico.

Savolainen and colleagues also looked at "free-ranging" or stray dog populations, including a group of canines in the southeastern U.S. called Carolina dogs.

When Savolainen and colleagues started this study, the evolutionary geneticist expected that any native DNA signals in stray dog populations would have been completely replaced by sequences from European dogs like German shepherds or poodles.

But it turns out that certain rural populations of these strays in Mexico, Bolivia, and the U.S. retain a small stamp of their ancient origins, the researchers report in a study published July 9 in the journal Proceedings of the Royal Society B.

Savolainen said, "What surprised me the most were the Carolina dogs," which look like dingoes or Asian village dogs. A previous researcher suggested the Carolina dog might be indigenous to America, but most people didn't believe him.

But the team's genetic analysis found that Carolina dogs share a unique genetic marker called A184 that hasn't been reported before. And A184 belongs to a group of genetic markers specific to East Asian canines.

Complications

The researchers were able to conduct this comparison between American, European, and East Asian dogs thanks to a large data set of mitochondrial DNA sequenced from thousands of dogs. They were also able to compare their modern sequences with 19 ancient dog genomes taken from remains found in Bolivia, Peru, Mexico, and Alaska.

Mitochondrial DNA comes from structures in cells called mitochondria, which function like battery packs, supplying energy for the cell's activities. They are inherited only from an organism's mother.

It's easier to compare genomes between individuals using mitochondrial DNA than using DNA from a cell's nucleus, explained Boyko, a National Geographic grantee.

Nuclear DNA comes from both the mother and the father, and the copies can swap pieces with each other in a process called recombination. This makes for an amazing variety of looks in the offspring, but creates enormous headaches for scientists trying to track down a population's origins.

"It gets complicated really quickly," Boyko said.

Buildup

The sheer scope of the canine genetic analysis is impressive, he said. Not only did the team look at breeds from the Old and New World, but they also looked at stray dogs in the Americas.

One hitch is the fact that the researchers were limited in the number of genetic markers they examined, Boyko said. The authors acknowledged as much in the paper, he added, and it shouldn't take anything away from the study.

Indeed, co-author Savolainen said he plans on looking at nuclear DNA in these dog populations to get a sense of how big the founding population might have been, and to pin down when their canine ancestors came over from East Asia.

The problem is that you need big data sets for the kinds of comparisons he wants to make, and there aren't many nuclear DNA data sets for dogs just lying around.

Researchers are working on building them, he said. "[But] I think it will be a couple of years before you can try this specifically on American dogs."