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

These GEITP pages, from time-to-time, have discussed issues of human evolution and global migration; this topic represents one of the latter group. The U.S. population represents tremendous diversity of global ancestries — shaped by migration from distant continents, plus admixture of recent migrants and Native Americans. Admixture (i.e. interbreeding) between groups, which have historically been genetically and geographically distinct — has resulted in individuals with complex ancestries; in addition, within-country migration has led to genetic differentiation (accumulation of differences in allelic frequencies between completely, or partially, isolated populations — due to evolutionary forces such as selection or genetic drift). An in-depth understanding of population history is important for learning about human evolution and demographic history, as well as for adequate study design when associating genotypes (DNA sequence; genetic make-up) with phenotypes (traits). 😊

Earlier population-genetic studies in the U.S. broadly characterized this structure, usually using a limited set of ancestry-informative markers or uni-parental mtDNA (mitochondrial DNA) and Y-chromosome DNA data. Because the cost of genetic technologies has dropped, more recent studies have inferred population history with more complete genome-wide data — typically using >100,000 single-nucleotide variants (SNVs) ascertained via sequencing or genotyping. Also, previous genetic studies of the U.S. population have sought to infer genetic ancestry and population history primarily in European Americans, African Americans, and/or Hispanics/Latinos. European-American ancestry is characterized by substantial mixing between different ancestral European populations and, to a lesser extent, admixture with non-European populations.

Isolation among certain European populations (e.g. Ashkenazi-Jewish, French-Canadian, and Finnish populations) have also resulted in founder effects (i.e. decreased genetic diversity resulting from a population derived from a small number of colonizing ancestors). The mixing of European settlers with Native Americans has contributed to large variations in the admixture proportions of different Hispanic/Latino populations. Among Hispanics/Latinos — Mexicans and Central Americans have more Native-American ancestry; Puerto Ricans and Dominicans have more African ancestry; and Cubans have more European ancestry. In African Americans — proportions of African, European, and Native-American ancestry were shown to vary across the country — reflecting migration routes, slavery, and patterns of segregation between states.

Although much effort has been made to understand genetic diversity in the U.S. — fine-scale patterns of demography,

migration, isolation, and founder effects are still being uncovered with the growing scale of genetic data — particularly for Latin-American and African descendants having complex admixture histories. At the same time, there has been little research on the population structure of individuals with East-Asian, South-Asian, and Mid-Eastern ancestry in the U.S.

Authors [see attached article] studied the ancestry and population structure of >32,000 individuals in the U.S. — using genetic, ancestral birth origin, and geographic data from the National Geographic Genographic Project (NGGP). Authors could identify migration routes, and barriers, that reflect historical demographic events. They also uncovered spatial patterns of relatedness in subpopulations — through the combination of haplotype clustering (recall that ‘haplotype’ describes the combination of alleles, or a set of SNVs found on the same chromosome — indicating they arose from one parent or more distant ancestor), ancestral birth origin analysis, and local ancestry inference. Examples of these patterns included substantial substructure and heterogeneity in Hispanics/Latinos, isolation-by-distance in African Americans, higher levels of relatedness and homozygosity in Asian immigrants, and fine-scale structure in European descents. Taken together, these data offer detailed insights into the genetic structure and demographic history of the diverse U.S. population.


Am J Hum Genet 5 Mar 2020; 106: 371–388

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