Researchers have discovered tremendous genetic diversity between Mexico’s local populations. The genomes of Mexicans with mixed ancestry reflect these differences, which have implications for many aspects of Latino health.

In the largest-ever genomic dataset on indigenous populations, researchers reveal how Mexican genomes were shaped by population dynamics of ancient Native Americans -- people who lived there before Europeans colonized the area. Despite the mixing associated with colonization events over the last five centuries, the genetic traces of indigenous people are still strong in modern populations. Additionally, some groups are as genetically different from one another as Europeans are from East Asians, suggesting how some groups have been isolated for hundreds of thousands of years. 

“We’re moving beyond blanket definitions like Mexican or Latino,” Stanford’s Andres Moreno-Estrada says in a news release. Mexico contains 65 different indigenous ethnic groups. “Now we’re putting finer details on that map. Those broad terms imply common ground among populations, but we’re finding that it’s much more like a mosaic.”

A huge international team led by University of California, San Francisco, and Stanford researchers evaluated genomic data from 511 native Mexican individuals from 20 indigenous groups representing most geographical regions in the country. They focused on 1 million DNA sequence variations called single nucleotide polymorphisms (SNPs). 

Then they characterized the genetics of populations in Mexico prior to European colonization, finding variations in distinct genetic makeups that were as extensive as those between Europeans and the Chinese: The Seri along the northern mainland coast of the Gulf of California and a Mayan people known as the Lacandon, near the Guatemalan border. That suggests how early populations were highly isolated within Mexico, possibly because of geologic features like mountains and deserts.

After Europeans arrived, population dynamics within Mexico changed significantly: Most Mexicans today have mixed ancestry. To investigate this further, the team combined data from native Mexican groups with 500 mestizo (ethnically-mixed) individuals from 10 Mexican states, as well as Mexicans living in ​Guadalajara and Los Angeles. 

Using an algorithm to estimate ancestry proportions in individuals, the researchers found that older, native patterns lingered in the modern populations. People from northern Mexican states like Sonora show the highest proportions of northern native genomic components; whereas someone from Yucatan was more likely to have a southern native component in their genome, namely Mayan. Meanwhile, Mexican-Americans didn’t show this pattern, and that’s consistent with the fact that they have arrived in the U.S. from all over Mexico. 

Pictured above: The genetic diversity of Mexican populations is reflected in the chromosomal composition of mixed ancestry throughout Mexico. Three major Native American components are distributed across northern, central/southern, and southeastern regions of the country. 

“Over thousands of years, there’s been a tremendous language and cultural diversity across Mexico, with large empires like the Aztec and Maya, as well as small, isolated populations,” UCSF’s Christopher Gignoux says in a news release. “Not only were we able to measure this diversity across the country, but we identified tremendous genetic diversity, with real disease implications based on where, precisely, your ancestors are from in Mexico.”

With lung diseases, such as asthma or emphysema, it matters what ancestry you have at specific locations on your genes. UCSF’s Esteban González Burchard adds: “In this study, we realized that for disease classification it also matters what type of Native American ancestry you have. In terms of genetics, it’s the difference between a neighborhood and a precise street address.” Their findings may help doctors better tailor and interpret medical genetics studies. 

The work was published in Science this week. 

[UCSF, Stanford via Nature, Science]

Image: Rubén A. Ramos Mendoza; photos: Karla Sandoval and Andres Moreno; DNA image: Sergey Nivens/Shutterstock; chromosome painting: Christopher Gignoux and Luisa Lente