National Geographic News
People walk in a crowded street of Mexico City, on November 4, 2011.

Different indigenous groups didn't mix much, a new study shows, unlike people today, as shown here on a crowded street in Mexico City in 2011.


Karen Weintraub

for National Geographic

Published June 12, 2014

Though one country politically, the genetics of indigenous Mexicans shows that their ancestors were very distinct groups that mixed remarkably little. A study published today in Science found more genetic isolation than expected among these populations.

"You can clearly differentiate each of the native American groups one from the other," said Carlos Bustamante, a professor of genetics at Stanford who led the research. It was "kind of surprising," he said, that this "plays out even though there's been 500 years of admixture, huge amounts of population growth, and lots of migration and movement."

The study marks the first time that researchers looked at the genetic history of Mexico, taking samples from more than a thousand people representing 20 indigenous and 11 mestizo (a person of combined European and Native American descent) groups. The map they made from that data shows nine distinct groups—including Maya, Lacandon, Tojolabal, and Zapotec—with very little intermingling among them.

Medical Implications

The research helps better explain the settlement patterns of early Mexico and has medical implications for Mexicans and people of Mexican heritage, said Bustamante, who is also co-founding director of Stanford's Center for Computational, Evolutionary and Human Genomics, whose team also included researchers from the University of California, San Francisco, and the National Institute of Genomic Medicine in Mexico.

Tiny genetic changes can lead to medically relevant differences, putting some ethnic groups at more or less risk for different diseases. For instance, Bustamante and his team looked at a standard measure of lung function, in which "normal" is defined differently based on a person's ancestry.

The diversity of Mexico's heritage showed up in the lung functions of the mestizo people Bustamante studied—those with both European and native heritage—some of whom would have been defined as diseased when they were actually healthy.

"The fact that you have Maya versus northern Mexican ancestry actually impacted the measurements of lung function," Bustamante said.

Mexican Americans, by contrast, generally have more of a mix of ancestry, he said, including indigenous Mexican, European, and a bit of African.

But doctors need to be cautious, he said, about lumping people together based on a box they checked on a survey. The Mexican migration patterns are similar to ones all over the world, said Dr. Harry Ostrer, a professor of pathology, genetics, and pediatrics at the Albert Einstein College of Medicine in the Bronx. A few people venture far away from their homes and settle in a new area where they are isolated from others, he said. The next generations intermarry and stay put, so any genetic mutations they carry spread through the group.

"People lived very simple lives," he said. "There weren't cities. There was not necessarily a drive for migration to improve one's economic life."

Bustamante said he was surprised to find that so many of these groups remained distinct, though. In Europe, he said, genetics show the waves of powerful invaders who took over vast swaths of land; in Mexico, by contrast, the indigenous groups retained their distinct territories—at least until the Europeans arrived.

Comparing it to the United States, it would be as if you could take people from Massachusetts, North Carolina, and California, and they'd all be different from each other because of migration that happened centuries earlier, he said.

Laura Guerin
Laura Guerin

Interesting, as I have children that are 1/2 Guatemalan & Caucasian. One child has very specific health concerns that make sense if you think of him from Guatemala only. Time to look at this study & take it to my pediatrician.

Thank you for bringing this information out!

Jon Rehmert
Jon Rehmert

I read some years ago about a great medicine trail. Where trading between Various Native peoples took place. Including some from Mexico. I know a large number of ppl. that have Native American heritage in the central U. S.

Kit Grundstein
Kit Grundstein

Not sure what Dr. Ostrer classifies as a city, but Mexico had a couple of the largest in the world, even before Europeans arrived. It also had waves of invasions from some pre-Columbian societies to others. 

Teotihuacan was a culturally influential invader into Maya territory, according to research done at both The University of Pennsylvania and Harvard as well as other universities, several Mexican. 

The Aztecs described themselves as invaders, successful ones, who terrified their victims and the Spanish agreed. Their city, now Mexico City, was so large and clean that the Spanish invaders were amazed, reporting that it was larger than cities in Spain. 

Evidently, based on DNA as reported here, there was little intermingling between the peoples, but it wasn't because there were no cities or invasions. 

Marilyn Manning
Marilyn Manning

This is not surprising.  Look at the indigenous of North America (Canada) and  the the north Inuit (NWT).  All are descendents of one another, sharing beliefs and folklore and living conditions, YET, both remain in their own environment, not venturing forth to explore one another.  Hard to believe, but among their community's, there is a mistrust of strangers, ideas, abandonment, sickness, and eventually no identity  I empathy with those wishing to be left alone, but also, I fear ignorance will surely wipe them out. I share my thoughts with you, because I know first hand.  I AM ONE OF THOSE.

anne boad
anne boad

@Marilyn Manning is it certain that the people of canada that you mention are all descended from each other, and share a common original folklore and culture, as you suggest? It's an appealing idea, but is there a solid basis for it?


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