supplemental tables and figures - biorxiv.org · supplemental tables and figures for bryc et al.,...

Supplemental Tables and FiguresFor Bryc et al., “The genetic ancestry of African, Latino, and European Americans across theUnited States.”

39

Table S1: Introduction text to the ethnicity survey. We note that the text clearly states thatthe survey will be used in ancestry-related research.

Medical researchers in the United States regularly assess research participants race andethnicity to ensure that inclusion in their research is fair and equitable. The definitionsof race and ethnicity used in research are the same as the US Census categories, meaningmedical researchers define race and ethnicity socially rather than biologically.

If you were born or live in the United States, this survey seeks to understand how youidentify yourself in terms of these socially-defined categories. Whether or not you are fromthe United States, the survey asks about your geographic roots.

Your answers will help 23andMe understand the genetic diversity of these categories.Your responses to this survey may be used in both health-related and ancestry-related re-search and in summarizing the ethnic breakdown of participants for some of our federally-funded studies, such as those funded by the National Institutes of Health (NIH). Over timeyour responses will enable 23andMe to improve its health and ancestry reports. Want tohelp improve 23andMes health and ancestry features? Tell us how you identify in termsof ethnic and racial categories. Tell us what you know about your geographic roots. Youranswers may lead not only to new research findings, but also to new 23andMe health andancestry reports. This survey is about how you identify yourself in terms of the socially-defined categories of ethnicity and race, and about your geographic roots. Your responsesto this survey may be used in both health-related and ancestry-related research, and in sum-marizing the ethnic breakdown of participants for some of our federally-funded studies,such as those funded by the National Institutes of Health (NIH).

Estimated time to complete: Less than 5 minutes

40

Table S2: Mean ancestry proportions and sample sizes of 23andMe African Americans,European Americans, and Latinos. To protect participant privacy, ancestries have beenrounded, and states with fewer than 10 individuals from a cohort are not reported. Samplesizes between 10 and 49 individuals are denoted by (*), between 50 and 99 individuals by (**)and 100 or more individuals as (***). Mean levels of European (Eur.), African (Af.) and NativeAmerican (N. Am.) ancestry are reported for each state.

African Americans European Americans LatinosState Af. N.Am. Eur. Size Af. N.Am. Eur. Size Af. N.Am. Eur. SizeAlabama 81% 0.7% 17% * 0.5% 0.1% 98.9% *** - - - -Alaska - - - - 0.2% 0.4% 98.5% *** - - - -Arizona - - - - 0.1% 0.1% 99.2% *** 4% 18% 69% **Arkansas 80% 0.5% 18% * 0.2% 0.1% 99.3% *** 5% 10% 80% *California 73% 0.8% 24% *** 0.2% 0.3% 98.1% *** 4% 19% 65% ***Colorado 72% 0.8% 25% * 0.2% 0.1% 99.2% *** 4% 18% 67% **Connecticut 77% 0.5% 21% * 0.1% 0.0% 99.0% *** 10% 9% 75% *DC 70% 0.6% 28% ** 0.1% 0.1% 99.2% *** 14% 9% 64% *Delaware - - - - 0.2% 0.1% 99.5% *** - - - -Florida 81% 0.5% 17% * 0.3% 0.1% 98.7% *** 6% 7% 80% ***Georgia 81% 0.6% 17% ** 0.4% 0.1% 99.3% *** 16% 8% 71% *Hawaii - - - - 0.2% 0.1% 97.6% *** 4% 5% 57% *Idaho - - - - 0.2% 0.3% 98.7% *** - - - -Illinois 74% 0.5% 24% *** 0.1% 0.1% 99.1% *** 8% 19% 63% ***Indiana 73% 0.6% 25% * 0.1% 0.1% 99.3% *** 5% 8% 83% *Iowa - - - - 0.1% 0.1% 99.5% *** 6% 5% 79% *Kansas 69% 0.5% 29% * 0.2% 0.1% 99.5% *** 4% 14% 75% *Kentucky 69% 0.4% 29% * 0.3% 0.1% 99.3% *** 4% 4% 90% *Louisiana 75% 0.8% 23% ** 0.6% 0.3% 98.5% *** 22% 4% 70% *Maine - - - - 0.1% 0.1% 99.6% *** - - - -Maryland 72% 0.6% 26% * 0.1% 0.1% 99.2% *** 10% 7% 76% *Massachusetts 73% 0.5% 25% * 0.1% 0.1% 98.1% *** 11% 10% 73% *Michigan 75% 0.7% 23% ** 0.1% 0.1% 98.9% *** 15% 9% 69% *Minnesota - - - - 0.0% 0.1% 99.4% *** 12% 10% 70% *Mississippi 80% 0.6% 18% * 0.3% 0.2% 99.1% *** - - - -Missouri 76% 0.5% 22% ** 0.2% 0.1% 99.4% *** 14% 8% 76% *Montana - - - - 0.1% 0.3% 99.2% *** - - - -Nebraska - - - - 0.1% 0.1% 99.3% *** - - - -Nevada - - - - 0.2% 0.3% 98.2% *** - - - -New Hampshire - - - - 0.1% 0.0% 99.5% *** - - - -New Jersey 72% 1.1% 25% ** 0.2% 0.0% 98.3% *** 9% 10% 73% **New Mexico - - - - 0.2% 0.4% 98.7% *** 3% 20% 67% **New York 75% 0.9% 22% *** 0.1% 0.1% 97.8% *** 15% 8% 69% ***North Carolina 74% 0.6% 23% ** 0.4% 0.1% 98.9% *** 17% 5% 75% *North Dakota - - - - 0.1% 0.3% 98.8% *** - - - -Ohio 73% 0.6% 24% ** 0.2% 0.0% 99.1% *** 11% 7% 78% *Oklahoma 73% 0.9% 25% * 0.3% 0.2% 99.1% *** 8% 11% 72% *Oregon - - - - 0.2% 0.2% 98.8% *** 3% 11% 74% *Pennsylvania 72% 0.6% 26% *** 0.1% 0.0% 99.0% *** 15% 8% 72% **Rhode Island - - - - 0.1% 0.1% 98.7% *** - - - -South Carolina 83% 0.7% 15% * 0.5% 0.2% 99.0% *** - - - -South Dakota - - - - 0.0% 0.0% 99.8% *** - - - -Tennessee 77% 0.5% 21% ** 0.3% 0.1% 99.1% *** 2% 6% 89% *Texas 78% 0.7% 20% *** 0.2% 0.3% 98.9% *** 5% 21% 64% ***Utah - - - - 0.1% 0.2% 98.9% *** 1% 13% 78% *Vermont - - - - 0.1% 0.2% 99.1% *** - - - -Virginia 74% 0.6% 23% ** 0.4% 0.1% 98.9% *** 13% 10% 71% *Washington 66% 0.9% 30% * 0.1% 0.2% 99.0% *** 7% 9% 76% *West Virginia 64% 0.2% 34% * 0.2% 0.1% 98.9% *** - - - -Wisconsin 71% 0.5% 27% * 0.1% 0.1% 99.4% *** 11% 14% 68% *Wyoming - - - - 0.1% 0.1% 99.6% *** - - - -

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Table S3: Mean ancestry proportions and sample sizes of 23andMe African Americans, byregion. Sample sizes between 100 and 499 individuals are denoted by (*), between 500 and 999individuals by (**) and 1000 or more individuals as (***). Mean levels of European, Africanand Native American ancestry are reported for each subpopulation.

Region Africanances-try

Europeanances-try

NativeAmer-icanancestry

Samplesize

(States included in region)

West 72.6% 24.3% 0.9% * New Mexico, Hawaii, California, Montana,Oregon, Utah, Arizona, Idaho, Nevada,Wyoming, Alaska, Washington, Colorado

Midwest 73.6% 24.1% 0.6% * Missouri, Nebraska, Ohio, Kansas, Michi-gan, Wisconsin, Indiana, Illinois, Minnesota,Iowa, North Dakota, South Dakota

Northeast 73.2% 24.3% 0.8% ** Rhode Island, Pennsylvania, Vermont, NewYork, New Hampshire, Massachusetts, Con-necticut, New Jersey, D.C., Maine

South 77.1% 21.9% 0.6% ** Alabama, Texas, Kentucky, Florida, Geor-gia, Virginia, Louisiana, Maryland, NorthCarolina, Arkansas, South Carolina, WestVirginia, Oklahoma, Mississippi, Tennessee,Delaware

Table S4: Mean ancestry proportions and sample sizes of 23andMe Latinos by subpopu-lation. Mean proportions of ancestry among Latino individuals that selected “Hispanic” whoalso chose to select another identity, or selected one or more other ethnicities are provided. Toprotect participant privacy, ancestries have been rounded to the nearest percent. Sample sizesbetween 100 and 499 individuals are denoted by (*), between 500 and 999 individuals by (**)and 1000 or more individuals as (***). Mean levels of European, African and Native Americanancestry are reported for each subpopulation.

Subpopulation European African Native American Sample SizeCentral American 53% 9% 26% *Mexican 61% 3% 24% ***South American 69% 5% 17% **White 73% 5% 14% ***Cuban 84% 6% 4% *Puerto Rican 69% 14% 8% *Dominican 56% 28% 7% *Black 46% 42% 6% *

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Table S5: Logistic regression model results for predicting European American versusAfrican American self-reported identity. Logistic regression was performed using python’smodule statsmodels. The three models shown below include the full model, a model in-cluding only the most significant parameters, and a simple model using proportion Africanancestry and intercept.

Logit Regression Results==============================================================================Dep. Variable: 0 No. Observations: 161460Model: Logit Df Residuals: 161454Method: MLE Df Model: 5Date: Mon, 12 May 2014 Pseudo R-squ.: 0.9416Time: 15:10:22 Log-Likelihood: -1357.8converged: True LL-Null: -23269.

LLR p-value: 0.000============================================================================================

coef std err z P>|z| [95.0% Conf. Int.]--------------------------------------------------------------------------------------------ancestry 20.0753 1.069 18.775 0.000 17.980 22.171age 4.148e-05 0.005 0.009 0.993 -0.009 0.010sex 0.2906 0.168 1.730 0.084 -0.039 0.620age-ancestry-interaction 0.0472 0.020 2.308 0.021 0.007 0.087sex-ancestry-interaction -2.3224 0.768 -3.024 0.002 -3.828 -0.817intercept -7.1956 0.261 -27.600 0.000 -7.707 -6.685============================================================================================


LLR p-value: 0.000============================================================================================

coef std err z P>|z| [95.0% Conf. Int.]--------------------------------------------------------------------------------------------ancestry 19.6822 0.865 22.745 0.000 17.986 21.378age-ancestry-interaction 0.0476 0.016 2.887 0.004 0.015 0.080sex-ancestry-interaction -1.5871 0.639 -2.485 0.013 -2.839 -0.335intercept -7.0514 0.084 -84.239 0.000 -7.216 -6.887============================================================================================


LLR p-value: 0.000==============================================================================

coef std err z P>|z| [95.0% Conf. Int.]------------------------------------------------------------------------------ancestry 21.0602 0.375 56.096 0.000 20.324 21.796intercept -7.0477 0.084 -84.331 0.000 -7.212 -6.884==============================================================================

43

Table S6: Estimates of admixture from ADMIXTOOLS f4 test. Estimates of admixture fromAfricans into European Americans, stratified by our estimates of African ancestry, are shown.Populations used for validation include 1000 Genomes populations from Italy, Great Britain,and Yoruba from Nigeria.

X (test) A O (outgroup) B (control) C alpha stderrEuropean Americans 0.01-0.02 African TSI Chimp GBR YRI 0.972757 0.002220European Americans >0.02 African TSI Chimp GBR YRI 0.942362 0.002508

Table S7: Rates of mtDNA haplogroups A, B, C and D in African Americans and EuropeanAmericans with Native American ancestry. Estimates of the number of individuals that carryNative American mtDNA haplogroups corresponds, as expected, with the estimate of genome-wide Native American ancestry. Individuals from each cohort with Native American ancestrywere stratified by their estimated amount of Native American ancestry, and the number of A,B, C or D mtDNA haplogroups, and the rate of these Native American specific haplogroups isshown for each estimated amoung of Native American ancestry.

Cohort Prop N. Am. ancestry N. Am. haplogroups Total N RateEuropean Americans 0.01–0.02 96 1,278 7.5%European Americans > 0.02 774 2,697 28.7%African Americans 0.01–0.02 16 838 1.9%African Americans > 0.02 34 305 11.1%4GP Europeans all countries 21 15,651 0.13%4GP Europeans excl. Spain 7 15,021 0.047%

44

A B

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Figure S1: Histogram of ancestry, in bins of 2%, in self-reported African American,Latino, and European American individuals. The vertical bars represent the proportion ofindividuals from each self-reported cohort that are estimated to have proportion African an-cestry fall within each ancestry bin. Note that the y-axis is shown in a log scale to illustratefine-scale differences among cohorts. Histogram of African ancestry (A) and Native American(B) in European Americans (red bars), Latinos (gold bars), and African Americans (blue bars).Histogram of African (C) and Native American (D) ancestry in African Americans, Latinos,and only those European Americans that have at least 2% African ancestry. (E) Qualitative dif-ferences in African ancestry distributions in African Americans from California and Georgia.Restricted to states for which we had at least 50 individuals, D.C. had the lowest mean Africanancestry, and Georgia had the highest mean African ancestry. The distribution of the ancestryproportions of self-reported African American individuals from these states are displayed usinggeom density in ggplot2 from R.

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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 Americanancestry. States with fewer than 20 individuals are excluded and shaded in gray. The proportionof individuals with Native American ancestry, out of the total number of African Americans perstate, is shown by shade of green.

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Ancestryamericaneuropeanafrican

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, ofancestry, 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 segmentlength.

46

African

Eur. N.Am.

African AmericansAfrican

Eur. N.Am.

LatinosAfrican

Eur. N.Am.

European Americans

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 amountof 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 theEuropean Americans are shown for plotting purposes.

47

African

Eur. N.Am.

MexicanAfrican

Eur. N.Am.

Puerto RicanAfrican

Eur. N.Am.

Cuban

African

Eur. N.Am.

DominicanAfrican

Eur. N.Am.

Central AmericanAfrican

Eur. N.Am.

South American

African

Eur. N.Am.

WhiteAfrican

Eur. N.Am.

Black

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 ofAfrican, 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.

48

Self-reported European Americans Self-reported African Americans Self-reported Latinos

0.3

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ProportionBritishIrishof Europeanancestry

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0.100.150.200.250.30


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0.025

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0.125


Figure S6: Differences in the European subpopulation Ancestry Composition among self-reported European Americans, African Americans, and Latinos from different states. Therelative amoung of European ancestry, out of the total mean European ancestry, estimated foreach state. Shown for inferred British/Irish ancestry, inferred Iberian ancestry, and inferredItalian ancestry. The proportion of sub-population ancestry, normalized by the total estimatedEuropean ancestry, for each state is shown by shade of red.

49

Self-reported European Americans

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MeanSardinianancestry

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MeanScandinavianancestry

Figure S7: Differences in the European subpopulation ancestry among self-reported Eu-ropean Americans from different states. Shown for all European subpopulations that arecarried at greater than 1% frequency in some state. The mean ancestry proportion among self-reported European Americans from each state is shown by shade of red. Ancestries that do notachieve at least 1% mean average ancestry in any state are not shown.

50

0

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Self−reported European Americanswith > 2% Native American ancestry

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Figure S8: Frequency of self-reported European Americans with at least 2% Native Amer-ican ancestry (left) and 1% Native American ancestry (right). The geographic distributionof self-reported European Americans with Native American ancestry. States with fewer than 20individuals are excluded and shaded in gray. The proportion of individuals with Native Amer-ican ancestry, out of the total number of European Americans per state, is shown by shade ofgreen.

51

012345


Self−reported European Americans with > 2% African ancestry

2.55.07.510.012.5


Self−reported European Americanswith > 1% African ancestry

Figure S9: Frequency of self-reported European Americans with at least 2% African an-cestry (left) and 1% African ancestry (right). The geographic distribution of self-reportedEuropean Americans with African ancestry. States with fewer than 20 individuals are excludedand shaded in gray. The proportion of individuals with African ancestry, out of the total numberof European Americans per state, is shown by shade of green.

52

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10 20 30 40 50State population density of African Americans in 2010

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American ancestry in African Americans

Figure S10: Correlations of African and Native American ancestry components of AfricanAmericans with population density of African Americans and Latinos by state. The x-axis show the state estimated population density of African Americans (top row) and Latinos(bottom row), and the y-axis show the mean state ancestry proportions. Each point representsa state and is labeled by the two-letter state abbreviation, for states with at least 10 individuals.The blue line shows a regression fit between the two variables, and the 95% confidence intervalfor the line fit is shown in gray. Each state is colored by region.

53

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0 10 20 30 40 50State population density of African Americans in 2010

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Figure S11: Correlations of African and Native American ancestry components of Euro-pean Americans with population density of African Americans and Latinos by state.Thex-axis show the state estimated population density of African Americans (top row) and Latinos(bottom row), and the y-axis show the mean state ancestry proportions. Each point representsa state and is labeled by the two-letter state abbreviation, for states with at least 10 individuals.The blue line shows a regression fit between the two variables, and the 95% confidence intervalfor the line fit is shown in gray. Each state is colored by region.

54

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Figure S12: Correlations of African and Native American ancestry components of Latinoswith population density of African Americans and Latinos by state.The x-axis show thestate estimated population density of African Americans (top row) and Latinos (bottom row),and the y-axis show the mean state ancestry proportions. Each point represents a state and islabeled by the two-letter state abbreviation, for states with at least 10 individuals. The blue lineshows a regression fit between the two variables, and the 95% confidence interval for the linefit is shown in gray. Each state is colored by region.

55

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European AmericansLatinosAfrican Americans

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1.0

European AmericansLatinosAfrican Americans

Figure S13: Relationship between the amount of African ancestry and African Americanversus European American self-reported identity. (A) Using ancestry data jointly fromboth African Americans and European Americans, we show the probability of self-reportingas African American by proportion of African ancestry. The probability for each bin of 1%ancestry is shown (points), and the gray area is shaded to emphasize the transition region. (B)Proportion of individuals that self-report as European American, African American, and Latino,by proportion of African ancestry. (C) The proportion of individuals that self-report as EuropeanAmerican, African American, and Latino by the proportion of Native American ancestry.56

A

0−2

%2−

4 %

4−6

%6−

8 %

8−10

%10−1

2 %

12−1

4 %

14−1

6 %

16−1

8 %

18−2

0 %

20−2

2 %

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4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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2 %

42−4

4 %

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6 %

46−4

8 %

48−5

0 %

50−5

2 %

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4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

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8 %

68−7

0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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2 %

92−9

4 %

94−9

6 %

96−9

8 %

98−1

00 %


Freq

uenc

y of

anc

estry

pro

porti

on w

ithin

pop

ulat

ion

(%)

0

2

4

6

8

10

0−2

%2−

4 %

4−6

%6−

8 %

8−10

%10−1

2 %

12−1

4 %

14−1

6 %

16−1

8 %

18−2

0 %

20−2

2 %

22−2

4 %

24−2

6 %

26−2

8 %

28−3

0 %

30−3

2 %

32−3

4 %

34−3

6 %

36−3

8 %

38−4

0 %

40−4

2 %

42−4

4 %

44−4

6 %

46−4

8 %

48−5

0 %

50−5

2 %

52−5

4 %

54−5

6 %

56−5

8 %

58−6

0 %

60−6

2 %

62−6

4 %

64−6

6 %

66−6

8 %

68−7

0 %

70−7

2 %

72−7

4 %

74−7

6 %

76−7

8 %

78−8

0 %

80−8

2 %

82−8

4 %

84−8

6 %

86−8

8 %

88−9

0 %

90−9

2 %

92−9

4 %

94−9

6 %

96−9

8 %

98−1

00 %


Freq

uenc

y of

anc

estry

pro

porti

on w

ithin

pop

ulat

ion

(%)

0

2

4

6

8

10African Americans

B

0−2

%2−

4 %

4−6

%6−

8 %

8−10

%10−1

2 %

12−1

4 %

14−1

6 %

16−1

8 %

18−2

0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

36−3

8 %

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0 %

40−4

2 %

42−4

4 %

44−4

6 %

46−4

8 %

48−5

0 %

50−5

2 %

52−5

4 %

54−5

6 %

56−5

8 %

58−6

0 %

60−6

2 %

62−6

4 %

64−6

6 %

66−6

8 %

68−7

0 %

70−7

2 %

72−7

4 %

74−7

6 %

76−7

8 %

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0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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2 %

92−9

4 %

94−9

6 %

96−9

8 %

98−1

00 %


Freq

uenc

y of

anc

estry

pro

porti

on w

ithin

pop

ulat

ion

(%)

0

10

20

30

40

50

60

0−2

%2−

4 %

4−6

%6−

8 %

8−10

%10−1

2 %

12−1

4 %

14−1

6 %

16−1

8 %

18−2

0 %

20−2

2 %

22−2

4 %

24−2

6 %

26−2

8 %

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0 %

30−3

2 %

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4 %

34−3

6 %

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8 %

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0 %

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2 %

42−4

4 %

44−4

6 %

46−4

8 %

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0 %

50−5

2 %

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4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

66−6

8 %

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0 %

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2 %

72−7

4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

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8 %

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0 %

90−9

2 %

92−9

4 %

94−9

6 %

96−9

8 %

98−1

00 %


Freq

uenc

y of

anc

estry

pro

porti

on w

ithin

pop

ulat

ion

(%)

0

10

20

30

40

50

60Europeans with > 2% African ancestry

C

0−2

%2−

4 %

4−6

%6−

8 %

8−10

%10−1

2 %

12−1

4 %

14−1

6 %

16−1

8 %

18−2

0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

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8 %

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0 %

60−6

2 %

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4 %

64−6

6 %

66−6

8 %

68−7

0 %

70−7

2 %

72−7

4 %

74−7

6 %

76−7

8 %

78−8

0 %

80−8

2 %

82−8

4 %

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6 %

86−8

8 %

88−9

0 %

90−9

2 %

92−9

4 %

94−9

6 %

96−9

8 %

98−1

00 %


Freq

uenc

y of

anc

estry

pro

porti

on w

ithin

pop

ulat

ion

(%)

0.1

0.5

1.0

5.0

10.0

50.0

100.0

0−2

%2−

4 %

4−6

%6−

8 %

8−10

%10−1

2 %

12−1

4 %

14−1

6 %

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8 %

18−2

0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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2 %

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4 %

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6 %

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8 %

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0 %

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2 %

92−9

4 %

94−9

6 %

96−9

8 %

98−1

00 %


Freq

uenc

y of

anc

estry

pro

porti

on w

ithin

pop

ulat

ion

(%)

0.1

0.5

1.0

5.0

10.0

50.0

100.0African AmericansEuropeans with > 2% African ancestry

Figure S14: Distribution of African ancestry in African Americans and European Ameri-cans. (A) Histogram of African ancestry proportions of self-reported African Americans. (B)Histogram of those European Americans that are estimated to have at least 2% African ances-try. (C) Combined histogram of African Americans and European Americans that carry at least2% African ancestry. Note that histogram C is shown on a log-scale to allow visualization offine-scale differences between populations. Bins representing less than 0.1% of individuals arenot shown.

57

Figure S15: Comparison of Ancestry Composition estimates with 1000 genomes consensusestimates on four recently admixed populations from the 1000 genomes project: ASW(African Americans), CLM (Colombians), MXL (Mexicans) and PUR (Puerto Ricans).For each of the four populations, we plot the European, African and Native American admixtureproportions estimated by Ancestry Composition versus the 1000 genomes consensus estimates.We note that 5 individuals from the ASW population show large amounts of Native Americanancestry that was predicted as European by the 1kG consensus method. Ancestry Compositiontends to underestimates the proportion of Native American ancestry in CLM, MXL and PURcompared to the 1kG consensus method (Conservative estimates), unless we allow estimates ofgeneral East Asian/Native American ancestry (Speculative estimates).

58

Starting positions for ancestry segments inEuropean Americans, for each 1cM bin of genetic position

Native American segmentsAfrican segmentsEuropean segments

chr1

0102030

chr2

0102030

chr3

0102030

chr4

0102030

chr5

0102030

chr6

050

100150200250

chr7

0102030

chr8

0102030

chr9

0102030

chr1

0

0102030

chr1

1

0102030

chr1

2

0102030

chr1

3

0102030

chr1

4

0102030

chr1

5

0102030

chr1

6

0102030

chr1

7

0102030

chr1

8

0102030

chr1

9

0102030

chr2

0

0102030

chr2

1

0102030

chr2

2

0102030

chrX−n

par

0102030

Figure S16: Distribution of ancestry segment start positions across the genome in self-reported European Americans. The number of segments that start within a 1cM positionalong the genome, for each chromosome, are shown by a vertical bar, colored corresponding toAfrican (blue), European (red) or Native American (green) ancestry. Since the vast majority ofsegments start at the left-most part of each chromsome, the first 5cM of each chromosome areomitted from each plot.

59

Starting positions for ancestry segments inLatinos, for each 1cM bin of genetic position


chr1

0200400600

chr2

0200400600

chr3

0200400600

chr4

0200400600

chr5

0200400600

chr6

0500

10001500

chr7

0200400600

chr8

0200400600

chr9

0200400600

chr1

0

0200400600

chr1

1

0200400600

chr1

2

0200400600

chr1

3

0200400600

chr1

4

0200400600

chr1

5

0200400600

chr1

6

0200400600

chr1

7

0200400600

chr1

8

0200400600

chr1

9

0200400600

chr2

0

0200400600

chr2

1

0200400600

chr2

2

0200400600

chrX−n

par

0200400600

Figure S17: Distribution of ancestry segment start positions across the genome in self-reported Latinos.The number of segments that start within a 1cM position along the genome,for each chromosome, are shown by a vertical bar, colored corresponding to African (blue),European (red) or Native American (green) ancestry. Since the vast majority of segments startat the left-most part of each chromsome, the first 5cM of each chromosome are omitted fromeach plot.

60

Starting positions for ancestry segments inAfrican Americans, for each 1cM bin of genetic position


chr1

0100200300

chr2

0100200300

chr3

0100200300

chr4

0100200300

chr5

0100200300

chr6

0100200300400

chr7

0100200300

chr8

0100200300

chr9

0100200300

chr1

0

0100200300

chr1

1

0100200300

chr1

2

0100200300

chr1

3

0100200300

chr1

4

0100200300

chr1

5

0100200300

chr1

6

0100200300

chr1

7

0100200300

chr1

8

0100200300

chr1

9

0100200300

chr2

0

0100200300

chr2

1

0100200300

chr2

2

0100200300

chrX−n

par

0100200300

Figure S18: Distribution of ancestry segment start positions across the genome in self-reported African Americans.The number of segments that start within a 1cM position alongthe genome, for each chromosome, are shown by a vertical bar, colored corresponding toAfrican (blue), European (red) or Native American (green) ancestry. Since the vast majorityof segments start at the left-most part of each chromsome, the first 5cM of each chromosomeare omitted from each plot.

61

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