Population Histories of the United States Revealed through Fine-Scale Migration and Haplotype Analysis

Chengzhen L Dai; Mohammad M Vazifeh; Chen-Hsiang Yeang; Remi Tachet; R Spencer Wells; Miguel G Vilar; Mark J Daly; Carlo Ratti; Alicia R Martin

doi:10.1016/j.ajhg.2020.02.002

Population Histories of the United States Revealed through Fine-Scale Migration and Haplotype Analysis

Am J Hum Genet. 2020 Mar 5;106(3):371-388. doi: 10.1016/j.ajhg.2020.02.002.

Authors

Chengzhen L Dai¹, Mohammad M Vazifeh², Chen-Hsiang Yeang³, Remi Tachet², R Spencer Wells⁴, Miguel G Vilar⁵, Mark J Daly⁶, Carlo Ratti², Alicia R Martin⁷

Affiliations

¹ Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
² Senseable City Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
³ Institute of Statistical Science, Academia Sinica, Nankang, Taipei, Taiwan.
⁴ Insitome, Inc, Austin, TX 78701, USA.
⁵ Genographic Project, National Geographic Society, Washington, DC 20036, USA.
⁶ Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
⁷ Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address: armartin@broadinstitute.org.

Abstract

The population of the United States is shaped by centuries of migration, isolation, growth, and admixture between ancestors of global origins. Here, we assemble a comprehensive view of recent population history by studying the ancestry and population structure of more than 32,000 individuals in the US using genetic, ancestral birth origin, and geographic data from the National Geographic Genographic Project. 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. Examples of these patterns include substantial substructure 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. Taken together, our results provide detailed insights into the genetic structure and demographic history of the diverse US population.

Keywords: USA; birth records; demography; human genomics; human history; identity-by-descent; population genetics.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Cluster Analysis
Demography
Emigration and Immigration*
Genetics, Population*
Haplotypes*
Humans
United States

Grants and funding

K99 MH117229/MH/NIMH NIH HHS/United States