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Population histories of the United States revealed through fine-scale migration and haplotype analysis

By Chengzhen Dai, Mohammad M Vazifeh, Chen-Hsiang Yeang, Remi Tachet, Miguel G Vilar, Mark Daly, Carlo Ratti, Alicia R Martin

Posted 14 Mar 2019
bioRxiv DOI: 10.1101/577411

The population of the United States is shaped by centuries of migration, isolation, growth, and admixture between populations of global origins. Here, we assemble a comprehensive view of recent population history by studying the ancestry and population structure of over 32,000 individuals in the US using genetic, ancestral birth origin, and geographic data. We identify migration routes and barriers that reflect historical demographic events. We also uncover the spatial patterns of relatedness in subpopulations through the combination of haplotype clustering, ancestral birth origin analysis, and local ancestry inference. These patterns include substantial structure and heterogeneity in Hispanics/Latinos, isolation-by-distance in African Americans, elevated levels of relatedness and homozygosity in Asian immigrants, and fine-scale structure in European descents. Furthermore, quantification of familial birthplaces recapitulates historical immigration waves at high resolution. Taken together, our results provide detailed insights into the genetic structure and demographic history of the diverse US population.

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