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23andMe Study Shows Diverse Genetic Ancestry within Three Major US Population Groups

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NEW YORK (GenomeWeb) – The genetic ancestry of European Americans, Latinos, and African Americans in the United States is more diverse than some might have assumed and regional differences in genetic ancestry reflect historical events, according to a new study by 23andMe and collaborators at Harvard Medical School.

The study, published in the American Journal of Human Genetics today, is based on data from 23andMe customers who described themselves as belonging to one of three groups — about 148,800 European Americans, 8,700 Latinos, and 5,300 African Americans.

These are the largest self-identified population groups in the US, and the ones the company had the most data for, Kasia Bryc, a population geneticist at 23andMe and the study's lead author, told GenomeWeb. "You really see ancestries from Africa, the Americas, and Europe in all of these cohorts," she said.

The findings can help inform medical genetic studies of complex diseases in the US. For example, "if you're conducting a study in European Americans, it's important to recognize that there may be segments of African or Native American ancestry in those groups, which you would need to correct for if you're doing, for example, a GWAS or a sequencing study — it would impact what variants you are discovering," explained Joanna Mountain, senior director of research at 23andMe and the senior study author.

Latinos are the most genetically mixed of the three groups, the researchers found, with "nearly all possible combinations of African, Native American, and European ancestries." On average, 65 percent of the genetic ancestry of Latinos is European, 18 percent is Native American, and 6.2 percent is African.

Latinos from states in the Southwest, especially those bordering Mexico, have the highest levels of Native American ancestry, and those from the South have the highest levels of African ancestry. The scientists estimated that Native Americans and Europeans first started mixing about 11 generations ago, and that African ancestry first appeared seven generations ago in the Latino group. More male than female Europeans contributed to the European ancestry in Latinos.

Overall, African Americans carry 73 percent African ancestry within their genomes, which also contains 24 percent European and 0.8 percent Native American ancestry, according to the study. African Americans born in the South, in particular, South Carolina and Georgia, had the highest levels of African ancestry, and those born in the West and Southwest had higher proportions of Native American ancestry. The researchers also found that more European men than women account for the European ancestry in African Americans.

Individuals usually self-identified as African Americans if their African ancestry made up the majority of their genetic ancestry. This runs counter to the common expectation that someone with even a small amount of African ancestry would call himself African American. "We don’t find that everybody with some African ancestry identifies as African American," said Mountain.

"Our results provide empirical support that over recent centuries, many individuals with partial African and Native American ancestry have 'passed' into the white community," the authors wrote.

On the other hand, individuals with just 5 percent Native American ancestry usually called themselves Latino, "suggesting differences in sociological or historical factors associated with identifying with these groups."

European Americans are the least admixed group, with 98.6 percent European ancestry, 0.19 percent African ancestry, and 0.18 Native American ancestry on average. However, because they represent a large percent of the US population, an estimated 6 million European Americans carry African ancestry and about 5 million carry Native American ancestry. About 10 percent of European Americans living in the South carry at least 1 percent African American ancestry. A larger part of African and Native American ancestry in European Americans stems more women than from men.

Some of the findings likely reflect historical events. For example, more than 14 percent of African Americans in Oklahoma carry at least 2 percent Native American ancestry, which probably results from the encounter of the two groups after the "Trail of Tears" forced relocation of Native Americans to the area in the 19th century.

The high levels of African ancestry in European Americans from Louisiana — about 12 percent carry some African ancestry — corresponds to historical accounts of intermarriage in the New Orleans area, the authors noted.

Latinos and European Americans in Florida, Louisiana, California, and Nevada receive much of their European ancestry from the Iberian peninsula — Spain and Portugal — which likely reflects the early Spanish rule in these states.

And Scandinavian ancestry in European Americans is highly concentrated in Minnesota and the Dakotas, where immigrants from these countries mainly settled.

Going forward, the researchers would like to expand their study to include other US populations, for example, South Asians, East Asians, Southeast Asians, and Middle Eastern individuals. As the number of customers keeps growing — from 500,000 at the time of the study to more than 800,000 now — and ethnic minorities are better represented, this will become more feasible, Bryc said.

They would also like to trace ancestry in greater detail, especially sub-Saharan African and Native American ancestry. For example, "it would be great to get better reference data within Africa to start to disentangle the different components of African ancestry," she said.

Mountain cautioned that there might be limits, though. For African ancestry, "I think we can take it further, maybe not to individual tribes or cultural groups, but we can refine it, and that's one of our goals," she said. Native American tribes, however, are genetically not very different. "Even if we had reference datasets from different tribes within the US, I'm not sure that we would be able to differentiate them," she said. 

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