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Genetic Makeup of African-American Populations Influenced by Ancestry-Biased Migrations

NEW YORK (GenomeWeb) – Based on genetic data, a McGill University-led team has traced the movements of African-American populations in the US.

As they reported today in PLOS Genetics, McGill's Simon Gravel and his colleagues studied the migration history and genomic diversity of African Americans by drawing on a cohort of more than 3,700 African Americans who'd undergone genotyping. From this, the researchers estimated that about 82 percent of African Americans' ancestors could be traced to Africa and nearly 17 percent to Europe. Within the US, they found that mixing between African Americans' ancestors and European Americans largely took place in the pre-Civil War South. Ancestry-biased migrations from the South to the North and the West during the Great Migration between 1910 and 1970 then shaped regional differences in ancestry among African Americans.

"[It's thought that] massive migrations had tended to make all communities more similar to each other and one of the things that we show here is that this is not quite the case," Gravel told GenomeWeb. "There are communities that are more similar to each other along the transit routes that people used, but other than that, there is a still a lot of structure in the population."

Gravel and his colleagues analyzed data from three cohorts: the Health and Retirement Study, which includes 1,501 African Americans and 9,308 European Americans from urban and rural regions in all 50 states; the Southern Community Cohort Study, which includes 2,128 African Americans from the rural South; and a 1000 Genomes Project cohort of 97 African Americans from the Southwestern US.

Gravel noted that his team was lucky that these three cohorts were genotyped on either the Illumina Omni2.5M or Omni1M, which allowed the researchers to easily combine datasets.

Using the RFMix modeling approach and additional data from 1000 Genomes Project panels from Africa, Europe, and Asia, they identified the most likely continental ancestry for each locus for the individuals in their cohorts.

For the Health and Retirement Study cohort — which the researchers noted is widely representative of the entire African-American population — they estimated that African Americans in the South have 83 percent African ancestry, while African Americans in the North and West have slightly smaller percentages of African ancestry — some 80 percent and 79 percent, respectively.

Within the Southern Community Cohort Study, the researches noted a higher percentage of African ancestry among African Americans in Florida and South Carolina — 89 percent and 88 percent, respectively — and a lower portion of African ancestry among Louisianan African Americans at 75 percent.

Using the tract-length modeling tool Tracts, the researchers also traced the timing of admixture events among the African and European ancestors of African Americans. In the HRS cohort, a two-pulse model of an admixture event in about 1740 and a second in about 1863 appeared to be the best match, while admixture events in 1714 and 1854 best explained the SCCC cohort.

Though the researchers cautioned that these estimates are an "oversimplification" of historical occurrences, they nevertheless noted that these estimates suggest that most admixture events between the African and European ancestors of African Americans took place in the South during slavery and that there was limited admixture between 1930 and 1960.

Gravel and his colleagues also noted regional differences in ancestry among African Americans. In particular, they noticed that ancestry-biased migration appears to have occurred, meaning that African Americans who left the South had higher proportions of European ancestry, 16.5 percent, than those who remained behind, 15.3 percent. In addition, African Americans who moved North and West in the mid-20th century toward the end of the Great Migration had less European ancestry than the African Americans already living in those locales — 21 percent in Northern African Americans and 25 percent in Western African Americans.

"A lot of this difference is actually caused by the migration patterns," Gravel said. "Much of the admixture occurred in the South prior to the Civil War during slavery and it's individuals with more European ancestry that were more likely to migrate towards the North, so this would explain the regional differences between North and West and South."

This ancestry-biased migration, the researchers noted, could be due to increased social opportunities for African Americans with higher levels of European ancestry.

Through identity-by-descent analyses, Gravel and his colleagues also examined patterns of genetic relatedness among African Americans and found an increased relatedness with increased distance. While this pattern is uncommon in population genetics, they noted it is likely because ancestry-biased migration is also relatedness-biased migration. In addition, they said that the reduced relatedness between Northern European Americans and Northern African Americans could have also been further increased by recent European migrations to the Northern US.

These patterns of relatedness, Gravel and his team noted, could inform genetic studies. Because of the long-range IBD sharing they observed, they said it's more likely that rare monogenetic traits could be shared over long distances among African Americans. At the same time, however, the short-range distribution would still be structured.

Gravel said his team now plans to investigate the Old World origins of African Americans.

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