The Great Migration and African-American Genomic History

Over 45 million African-Americans share a recent common history largely shaped by “The Great Migration” (1910-1970) from out of the Southern United States. And yet, the admixture history of the African-American community, and its consequences for public health are little understood.

A history of slavery and of systemic discrimination led to increased social, economic, and health burdens in many African-American communities. Health disparities continue to be compounded by poverty, unequal access to care, and unequal representation in medical research. To reduce health disparity in research, many cohorts are currently being assembled to encompass more of the diversity within the US. These cohorts create opportunities in both medical and population genetics; they also require an understanding of genetic diversity within diverse cohorts.

In a commendable (first) effort to understand the complex genomic history of African-Americans, Baharian et al. (2016) analyze data from genotyping >13,000 individuals, of which >3,700 identified as African-Americans across three studies (Health and Retirement Study, Southern Community Cohort Study, and the 1000 Genomes Project cohort). Using data from >5 million high quality SNP’s, inferred continental ancestry patterns largely indicated that African Americans from all three cohorts contained anywhere between 75-85% of African continental ancestry, 14-21% European ancestry, and 1-3% of Native American ancestry. Across the cohorts, individuals genotyped from Southern states (especially South Carolina and Louisiana, p < 1e-4) were inferred to contain a greater degree of African ancestry, when compared to other regions.

Proportions of inferred continental ancestry from >3700 African-Americans across three genetic cohort studies. Image courtesy: Baharian et al. (2016) http://dx.doi.org/10.1371/journal.pgen.1006059

Proportions of inferred continental ancestry from >3700 African-Americans across three genetic cohort studies. Image courtesy: Baharian et al. (2016) http://dx.doi.org/10.1371/journal.pgen.1006059

Baharian et al. (2016) also infer times of admixture events by quantifying lengths of IBD tracts under two models – (1) model of two source populations – African and Non-African (to avoid confounding lengths from Native American ancestry) and a single admixture event, and (2) a two-pulse model of admixture. A single pulse model indicated that the time of admixture was around g = 5.8 generations ago, leading to an admixture year around 1808 (95% CI = 1805.5-1810.4). A two-pulse model on the other hand suggests a first admixture event around 1740, and a second event around 1863, both estimates pointing to admixture events occurring in the Southern ancestors of current African-Americans.

Additional analyses of IBD decay across populations with geographical distance indicate that African-Americans across the USA are related more to European-Americans from the South, than from the North or West. Similarly, using a quantitative model to describe Isolation by Distance during long-scale migrations, Baharian et al. (2016) estimate an average displacement of 15-16 km per generation, comparable with census estimates, but inconsistent with recent root mean square (RMS) estimates (989 km), which are often biased by single largest displacement event.

The observed patterns of relatedness have consequences for genetics research. Long IBD segments are often inherited from a recent common ancestor and are likely to carry shared but recent mutations. Such variants are more likely to be deleterious than older variants and are therefore prime targets for disease-mapping studies of rare traits.

Reference: Baharian, S., Barakatt, M., Gignoux, C.R., Shringarpure, S., Errington, J., Blot, W.J., Bustamante, C.D., Kenny, E.E., Williams, S.M., Aldrich, M.C. and Gravel, S., 2015. The Great Migration and African-American genomic diversity. PLoS Genetics http://dx.doi.org/10.1371/journal.pgen.1006059

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About Arun Sethuraman

I am a computational biologist, and I build statistical models and tools for population genetics. I am particularly interested in studying the dynamics of structured populations, genetic admixture, and ancestral demography.
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