The American Journal of Human Genetics, Volume 96 Supplemental Data Katarzyna Bryc, Eric Y. Durand, J. Michael Macpherson, David Reich, and Joanna L. Mountain geom proportions of self-reported African American individualsancestry, from and these Georgia states had are displayed theRestricted using highest to mean states African for which ancestry.ferences we The in had distribution at African of least ancestry the 50and distributions individuals, ancestry only in D.C. those had African European the Americans Americans lowestHistogram that from mean have of California African at and African least Georgia. 2% (C)(B) African and ancestry. in Native (E) European Qualitative Americans American dif- (red (D)fine-scale bars), differences ancestry Latinos among (gold in cohorts. bars), African and Histogramcestry Americans, African of fall Americans African Latinos, (blue within ancestry bars). (A) each andindividuals ancestry Native from bin. American each Note self-reportedLatino, that cohort and the that European y-axis are American isFigure individuals. estimated shown S1: to in have a proportion log African scale to an- illustrate Frequency of ancestry proportion Frequency of ancestry proportion CD within population (%) within population (%) AB 100.0 100.0 10.0 50.0 10.0 50.0 0.1 0.5 1.0 5.0 0.1 0.5 1.0 5.0 density 0 % 0 % 2 % 2 % 4 % 4 % 6 % 6 % 8 % 8 % 10 % 10 % Histogram of ancestry, in bins of 2%, in self-reported African American, 12 % 12 % 14 % 14 % 16 % 16 % 18 % 18 % 20 % 20 % 22 % 22 % 24 % 24 % in 26 % 26 % 28 % 28 % Proportion African ancestry 30 % Proportion African ancestry 30 % 32 % 32 % ggplot2 34 % 34 % 36 % 36 % E 38 % 38 % 40 % 40 % 42 % 42 % 44 % 44 % density 46 % 46 % 3 4 0 1 2 48 % 48 % 50 % 50 % 0.00 52 % 52 % 54 % 54 % 56 % 56 % 58 % 58 % 60 % 60 % 62 % Europeans with>2%African ancestry Latino African American 62 % from 64 % 64 % 66 % 66 % 68 % 68 % 0.25 70 % 70 % 72 % 72 % 74 % 74 % African_ancestry 76 % 76 % R 78 % 78 % 80 % 80 % . 82 % 82 % 84 % 84 % African American Latino European 0.50 86 % 86 % 88 % 88 % 90 % 90 % 92 % 92 % 94 % 94 % 96 % 96 % 98 % 98 % 0.75 1 Frequency of ancestry proportion Frequency of ancestry proportion The vertical bars represent the proportion of within population (%) within population (%) 100.0 100.0 10.0 50.0 10.0 50.0 0.5 1.0 5.0 0.5 1.0 5.0 0.1 0.1 1.00 0 % 0 % State 2 % 2 % 4 % 4 % 6 % 6 % georgia district_of_columbia 8 % 8 % 10 % 10 % 12 % 12 % 14 % 14 % 16 % 16 % 18 % 18 % 20 % 20 % 22 % 22 % 24 % 24 % 26 % 26 % Proportion American ancestry 28 % Proportion American ancestry 28 % 30 % 30 % 32 % 32 % 34 % 34 % 36 % 36 % 38 % 38 % 40 % 40 % 42 % 42 % 44 % 44 % 46 % 46 % 48 % 48 % 50 % 50 % 52 % 52 % 54 % 54 % 56 % 56 % 58 % 58 % 60 % 60 % 62 % Europeans with>2%African ancestry Latino African American 62 % 64 % 64 % 66 % 66 % 68 % 68 % 70 % 70 % 72 % 72 % 74 % 74 % 76 % 76 % 78 % 78 % 80 % 80 % 82 % 82 % 84 % 84 % African American Latino European 86 % 86 % 88 % 88 % 90 % 90 % 92 % 92 % 94 % 94 % 96 % 96 % 98 % 98 % Self−reported African Americans Self−reported African Americans with > 2% Native American ancestry with > 1% Native American ancestry Percent of Percent of African African Americans Americans 10 20 5 10 0 Figure S2: Frequency of self-reported African American individuals with at least 2% (left) and 1% (right) Native American ancestry across states with at least 20 individu- als. The geographic distribution of self-reported African Americans with Native American ancestry. States with fewer than 20 individuals are excluded and shaded in gray. The proportion of individuals with Native American ancestry, out of the total number of African Americans per state, is shown by shade of green. African American ancestry tract lengths Latino ancestry tract lengths European American ancestry tract lengths ! ! 1000 ! ! ! ! ! ! !! ! ! ! ! ! !!!!! !! !!! !!!!! !!!!!!!! !!!! 500 10000 !!!!!!! !!!!! ! ! !!!!!!!!!! !!!! ! ! !!!!!!!!! !!!! !!! ! !!!!!!!! !!! !! !! !!!!!! !!!!! !!!!! ! !!!! !!!!! !!!!! !!!! ! ! !!!!!!! !!!! !!!! !! !!! !!!!! !!!!!!! !!!! ! ! ! !! !!! !!!!!! !! !! !!!!!!! ! !! !!! !!!!! ! ! !!!! !! !!! ! !!!!!!! !! !!!!! 10000 !! !! !!! !!!! !!!!!!!!! !!!!!!!! !!! !!!!! !!! ! !! !!!! !! !! !!! ! !! !! !!!!!! !! !! !!!! !! ! !! !! !! ! !! !!!!!! ! !!! !! ! ! !!!!! !! ! !!! !! !! !! ! !!!!! ! !!! ! !! !!! ! ! ! !! !!!!!! ! ! !!! ! ! !!!!!!! ! !!! !!!!!! !! !!! !!! !! ! ! ! ! ! !! !! !!!! ! ! !!! !!! !!! !!! !! !! !! !!!! !! !! !!!!! ! ! ! ! !! !!! !!!!!!! ! !! !!!! ! ! !!!!!! !!! !! !! !! !!! !!! ! ! !! ! ! 1000 !! !!!! ! !!! ! ! !!!!! 100 ! ! !! ! !!! !!!!! !!! !!! !!!! !! !! ! ! !! !!!!! !! ! !!!!! ! ! ! !! !!! !!!! !!!!! !! !!!!! !!! ! ! ! !!!!! !!!! !! !!!!! ! ! ! !! !!! ! !! !!!!! !!! ! ! !!! !!!!! !! ! !! !!!!!!! !!! !! !! ! !!! !!!!!!! !! !!! !!!!! ! !!!!!!!!! !! !! ! !!!!! !! !!!! !!! !!! ! ! !!!!! !! ! !!! !!!! !! ! ! !!! 50 ! !! ! ! ! ! !!! ! ! !!!!! !!! !! !!!!!! !! ! !!!! ! !!!! ! ! !! !!! ! ! ! ! ! !! !! !!! ! ! !!!!!!!! ! ! !! ! Ancestry !! !!! ! !!!! !!! !!!!! !! ! ! ! !!! ! !!! !!! !!!! ! !! !! ! !! !!! !!! !!! !!!! !!! ! ! ! !! !! ! !!!! !! !! !!!!!!!! !! ! !!! !! !!! !!! ! !! ! ! ! ! ! !! !!!! !! !!! !! !!!!! ! ! !!!!!!! !!! !!! ! !!! !!!!! ! ! 100 ! ! !! !!!! !!! !!!! !! ! !! ! american ! !!!!! ! !!! !!!!! !!! !!! !! ! !! ! !!! !! ! !!!!! ! ! ! ! ! !! ! ! !!!! !!! !!! !!! !! ! !!! !!! !!!! !! !! ! ! !!!! ! !! !! !! ! ! ! ! ! ! !!!! 100 !!!!!!!! !!!!! ! !!!! !!! ! ! ! ! !!! ! ! !! !! !! ! ! ! !! ! ! !! ! ! european ! !! ! !! !! !!!!! ! ! ! !!!!!! !! ! ! !!!!!!! ! ! !! !! ! ! !! ! ! !!! ! !! ! !! ! !!!!!!!! ! ! !!! !! ! ! ! ! !!! !!!!! ! ! !! ! 10 ! !!!! ! !!! !!!! ! ! !! !!!! ! !! ! ! ! !!!!! ! !!!! ! !!!!!! !!! !! ! ! !!!! ! ! !!!! african !! ! !! !! ! ! ! !!!!!!! ! ! ! !! ! !! ! !! ! !! ! ! ! !! !! !!!!!!!! !!!!!!! ! !! ! ! !! ! ! !! !!!!!!! !! !! !! ! ! !! ! !!! ! ! !! !! !! !! !!!!!!!! ! !!!!!!!! !! !! !! ! ! ! ! !!!!!!!!!! !! ! !! ! ! ! !!! !! !! Number of tracts !! ! !!! !!! !! !!!! !!!! Number of tracts ! !!!!!! !! !!!!!! ! Number of tracts ! !! ! !!! !!!!!!!! !! ! 5 10 ! ! ! ! ! ! !! ! ! !!!!! ! ! !!!! ! ! ! !!!! !!! !!!! ! !!! !!! !! ! !! ! !!!!!!! ! !!! ! ! ! ! ! ! ! !! !! ! ! ! ! ! !! ! !!!!!!! !! ! !!!!!!! !! ! !! ! !!!! ! ! ! ! ! ! ! ! !!!! ! ! !!! !! ! !! !!! !!!! ! ! ! ! !! !!!!! !!! !!!! !! ! !! !!!!! !!!!!!!!!! !!!!!! ! !!!!!!!!!!!! ! ! ! ! ! !!!! !!!!! !! ! !!!! ! !!!!! !! !!!!! ! !!!!!!!!!!!!!!!! !! ! ! !! ! 1 ! !!!!!! !!!!!! !!! !! ! ! !!! !!!!! !!! !! 1 ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!! !!!!!!!!!!! !!! 1 !!!!!!!!!!!!!!!!!!!!!!!!! !!! ! !! ! ! ! ! 0 50 100 150 200 250 300 0 50 100 150 200 250 300 0 50 100 150 200 250 300 Length of ancestry tract (cM) Length of ancestry tract (cM) Length of ancestry tract (cM) Figure S3: Distribution of the lengths of ancestry segments for African Americans, Lati- nos, and Europeans with at least 2% African ancestry. The lengths of segments, or tracts, of ancestry, and the frequency of those tracts is shown by points, colored by population. The num- ber of ancestry tracts is shown on a log scale. Counts are shown self-reported African Amer- icans, Latinos, and European Americans. The number of tracts of Native American (gold), European (red) and African (blue) ancestry tracts is shown for each bin of 1Mb of segment length. 2 African Americans Latinos European Americans African African African Eur. N.Am. Eur. N.Am. Eur. N.Am. Figure S4: Ternary plots of African, European, and Native American ancestry in self- reported African American, Latino, and European American individuals. Each point rep- resents a self-reported individual and is positioned within the triangle reflecting the amount of ancestry estimated from each population. Note that each individual is plotted as a semi- transparent point to convey density of individuals. Only a random sample of 10,000 of the European Americans are shown for plotting purposes. 3 Mexican Puerto Rican Cuban African African African Eur. N.Am. Eur. N.Am. Eur. N.Am. Dominican Central American South American African African African Eur. N.Am. Eur. N.Am. Eur. N.Am. White Black African African Eur. N.Am. Eur. N.Am. Figure S5: Ancestry of self-reported Latinos by secondary self-reported subpopulation. Each individual is shown projected onto the triangle by their genome-wide proportions of African, European, and Native American ancestry, by their self-reported Hispanic sub-identity. Proportion of ancestry can be computed for an individual from the distance in dropping a per- pendicular line from the point to the edge opposite the vertex. 4 Self-reported European Americans Self-reported African Americans Self-reported Latinos Proportion Proportion Proportion British\ British\ British\ Irish Irish Irish of European of European of European ancestry ancestry ancestry 0.400 0.5 0.4 0.375 0.3 0.4 0.350 0.2 0.3 0.325 0.300 0.1 Proportion Proportion Proportion Iberian Iberian Iberian of European of European of European ancestry ancestry ancestry 0.03 0.04 0.30 0.03 0.25 0.02 0.02 0.20 0.01 0.15 0.01 0.10 0.00 0.00 Proportion Proportion Proportion French French French German German German of European of European of European ancestry ancestry ancestry 0.16 0.125 0.06 0.14 0.100 0.04 0.12 0.075 0.10 0.02 0.050 0.08 0.00 0.025 Figure S6: Differences in the European subpopulation Ancestry Composition among self- reported European Americans, African Americans, and Latinos from different states. The relative amoung of European ancestry, out of the total mean European ancestry, estimated for each state. Shown for inferred British/Irish ancestry, inferred Iberian ancestry, and inferred