Patterns of Genetic Ancestry of Self-Reported European Americans
We find that many self-reported European Americans, predominantly those living west of the Mississippi River, carry Native American ancestry (Figure 3B). We estimate that European Americans who carry at least 2% Native American ancestry are found most frequently in Louisiana, North Dakota, and other states in the West. Using a less stringent threshold of 1%, our estimates suggest that as many as 8% of individuals from Louisiana and upward of 3% of individuals from some states in the West and Southwest carry Native American ancestry (Figure S7).
Consistent with previous anecdotal results,32 the frequency of European American individuals who carry African ancestry varies strongly by state and region of the US (Figure 3A). We estimate that a substantial fraction, at least 1.4%, of self-reported European Americans in the US carry at least 2% African ancestry. Using a less conservative threshold, approximately 3.5% of European Americans have 1% or more African ancestry (Figure S8). Individuals with African ancestry are found at much higher frequencies in states in the South than in other parts of the US: about 5% of self-reported European Americans living in South Carolina and Louisiana have at least 2% African ancestry. Lowering the threshold to at least 1% African ancestry (potentially arising from one African genealogical ancestor within the last 11 generations), European Americans with African ancestry comprise as much as 12% of European Americans from Louisiana and South Carolina and about 1 in 10 individuals in other parts of the South (Figure S8).
Most individuals who have less than 28% African ancestry identify as European American, rather than as African American (Figures 4 and 5A). Logistic regression of self-identified European Americans and African Americans reveals that the proportion of African ancestry predicts self-reported ancestry significantly, with a coefficient of 20.1 (95% CI: 18.0–22.2) (Table S6 and Figure S9). For a full characterization of terms and logistic models, see Table S6 and Figure S9.
Fitting a model of European and Native American admixture followed later by African admixture, we find the best fit with initial Native American and European admixture about 12 generations ago and subsequent African gene flow about 4 generations ago.
Non-European ancestry in European Americans follows a sex bias in admixture contributions from males and females, as seen in African Americans and Latinos. The ratio between X chromosome and genome-wide Native American ancestry estimates in European Americans shows greater Native American female and higher European male ancestry contributions (Tables 1 and S4). Though we do not observe evidence of a sex bias in African ancestry contributions in European Americans overall, analysis of only those individuals with at least 1% African ancestry reveals 15% higher African ancestry on the X chromosome relative to genome-wide estimates (p value 0.013). This increase suggests female-African and male-European sex bias in European Americans that follows the same direction as in African Americans and Latinos, with greater male European and female African and Native American contributions.
Finally, we estimate, for self-reported European Americans, proportions of British/Irish, Eastern European, Iberian, and Scandinavian ancestry (Figure 3) and other European subpopulation ancestries (Figure S10).