For more than two millennia, indigenous peoples in Mesoamerica have traded macaws and included their feathers in rituals. The birds held immense symbolic value and represented sun gods in both Maya and Aztec culture.

And for more than a thousand years, these birds were traded north into what is now the southwestern United States in exchange for turquoise. The ancient Pueblo great houses of Chaco Canyon (in what's now New Mexico) started importing scarlet macaws from farther south around 900 A.D., using the birds as status symbols and markers of political status. (Find out more about Chaco Canyon.)

But who was supplying Chaco Canyon with macaws, and how? To find out, a team led by Richard George, a Ph.D. student at Pennsylvania State University, sequenced the mitochondrial DNA of of scarlet macaw remains recovered in archaeological excavations at Chaco Canyon and at Mimbres, an ancient Pueblo site in New Mexico. If the researchers could trace these birds back to living populations, they reasoned, perhaps they could identify the original sources of this colorful commodity.

Instead, the DNA evidence revealed an unexpected result: the scarlet macaws sent north on trade networks between 900 to 1200 A.D weren't wild-caught but locally bred, pushing back known macaw breeding in the region by hundreds of years.

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The find, published today in the Proceedings of the National Academy of Sciences, implies that somewhere in northern Mexico, there's an undiscovered bird breeding center waiting to be found.

“We get to take a snapshot of what was going on with different aspects of trade, and complexity, and how different groups were interacting,” says George, a lead author of the study.

The Scarlet Surprise

Macaw breeding has ample precedent in the region. The site of Paquimé, in the northern Mexico state of Chihuahua, features ruins of a massive bird breeding facility. But Paquimé couldn't have bred the macaws that George's team examined, since the site was founded around 1250 A.D., decades to centuries after the study's macaws lived and died.

To conduct the study, George's colleagues visited museums to sample the remains of 20 scarlet macaws, many of which trace back to Pueblo Bonito, the Chaco Canyon great houses that the National Geographic Society excavated from 1920 to 1927. (Read how DNA is offering up clues to a mysterious crypt in Pueblo Bonito.)

“The main reason we have these macaws is National Geographic,” says study coauthor Stephen Plog, an anthropologist at the University of Virginia.

Back in the lab, George successfully isolated 14 of the macaws' mitochondrial DNA. He then compared these strands against a database of wild scarlet macaws' mitochondrial DNA, which study coauthor Kari Schmidt had assembled for her Ph.D. dissertation.

Schmidt's work revealed that scarlet macaws fall into seven distinct genetic populations, called haplogroups, that are spread across the Americas. Scarlet macaws' Haplogroup 4, for instance, dominates South America. Haplogroup 7 nests along Panama's eastern coast.

But to the researchers' shock, all 14 of the ancient macaws hailed from Haplogroup 6, a fairly rare macaw lineage found today in southern Mexico. What's more, 10 of the 14 macaw genomes were identical along key stretches of DNA, a strong sign that they were closely related on their mothers' side.

So how did these macaws wind up so closely related? The homogeneity is exactly what you'd expect to see if the birds had been bred from the same stock, descended from a small group of founding birds. George says that similar genetic signals appear among domesticated turkeys, pigs, and dogs.

“The paper is a very important piece of evidence for fleshing out the history of the ancient Southwest,” says archaeologist Steve Lekson, the curator of anthropology at the University of Colorado Museum of Natural History who was not involved with the study.

A More Complex Past

DNA isn't the only evidence supporting the idea of earlier breeding centers. While George was sequencing the macaws' DNA, University of New Mexico archaeologist Patricia Crown was independently reexamining the same record.

In a 2016 review published in KIVA, Crown noted that by the time macaw traders walked from southern Mexico to Mimbres, the birds they'd be carrying probably would be 11 to 12 weeks old. But some paintings on Mimbres pottery depict birds that appear eight to 10 weeks old.

Crown notes that there are several possible reasons for this age discrepancy, but one possibility is that traders arrived at Mimbres from somewhere closer—maybe a breeding center between macaws' northern range and the Pueblo great houses.