Multiple linear regression of the difference (Δ) between self-perceived and genetically estimated ancestry for the three continental components.

<p>NOTE: Δ refers to self-perception (bands 1 to 5, see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004572#s4" target="_blank">Methods</a>) minus continental ancestry proportions (0–100%) estimated from the genetic data. Sex and country of sampling were incorporated in the analyses as factors while the other variables were treated as quantitative. For ease of interpretation, the regression coefficient and p-value for Δ AMERICA (*) refer to Native American (not European) ancestry.</p><p>Multiple linear regression of the difference (Δ) between self-perceived and genetically estimated ancestry for the three continental components.</p

Sample size, proportion of women, age, estimated admixture proportions and phenotypic features of the study sample.

<p>Note: Values shown are medians except for categorical traits where the numbers indicate percentages in that category. Data for women is shown in the numerator (except for Male pattern baldness). For the regression analyses (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004572#pgen-1004572-t002" target="_blank">Tables 2</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004572#pgen-1004572-t003" target="_blank">3</a> below) categorical phenotypes 15–17 were considered ordinal variables with 4 or 5 ordered integer levels as specified here (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004572#s4" target="_blank">Methods</a>). Individual ancestry histograms for each country are presented in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004572#pgen.1004572.s011" target="_blank">Text S1</a>.</p><p>Sample size, proportion of women, age, estimated admixture proportions and phenotypic features of the study sample.</p

Bar plots contrasting skin pigmentation (Melanin Index) to proportion of European genetic ancestry across four self-identified ethno/racial categories in samples from Brazil, Chile, Colombia, México and Perú.

<p>Sample sizes and all estimates of pigmentation and ancestry, are presented in Table S4. In Perú no individual self-identified as “Black”.</p

Geographic distribution of Native American (blue), African (green) and European (red) ancestry based on individual estimates for samples from (A) Brazil, (B) Chile, (C) Colombia, (D) México and (E) Perú.

<p>To facilitate comparison, color intensity transitions occur at 10% ancestry intervals for all maps. The birthplace of individuals are indicated by purple dots on the African ancestry map. Sampling density is shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004572#pgen.1004572.s004" target="_blank">Figure S4</a>. Maps were obtained using Kriging interpolation as detailed in the text.</p

Multiple linear regression of physical appearance traits on European and African ancestry.

<p>Note: All regressions account for age, sex, country, education and wealth. Regressions for facial features (traits 13 to 18) also account for BMI and height. %R² refers to trait variance explained by a regression model incorporating European and African ancestry (being proportions, European, African and American ancestries sum up to 1 and since in this sample African ancestry is very low (median of 7%), we use Native American ancestry as a baseline). %Δ R² refers to the difference in variance explained by this full model and a model without ancestry as a predictor. P-Values <10⁻³ are shown in bold italic. The facial features (traits 13 to 18) refer to morphogeometric summaries of face variation derived from 3D landmark coordinates (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004572#s4" target="_blank">Methods</a>). PC = Principal Components of the procrustes 3D landmark coordinates (% in parenthesis refer to variance explained by that PC).</p><p>Multiple linear regression of physical appearance traits on European and African ancestry.</p

Vertical histograms (pyramid plots) showing the distribution of genetic ancestry for each of the five self-perceived ancestry categories.

<p>As reference, (A) shows the theoretical case of agreement between self-perceived and genetically estimated ancestry. For this plot random values were drawn from a beta distribution such that, for each self-perception band, the median ancestry lies at the centre of a 0.2 interval containing 75% of the simulated ancestry values. The number of simulated values was fixed at our sample size. Panels (B), (C) and (D) show respectively, the observed distributions for European, Native American and African ancestries. The red diagonal line indicates the midpoint, on the genetic ancestry scale, of each self-perceived ancestry category. Distributions are coded in three shades of orange: the darkest shade denotes the central quartiles (the median shown as a brown line), the medium-shade indicates the 5%–95% range, and the lightest shade refers to samples outside this range. For European ancestry, self-perception tends to underestimate genetic ancestry (the distributions are mostly above the diagonal). By contrast, self-perception tends to overestimate African ancestry (the distributions are mostly below the diagonal). At increasing levels of Native American genetic ancestry self-perception first underestimates then overestimates genetic ancestry (the distributions are on both sides of the diagonal). Simulations and plots were carried out using MATLAB <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004572#pgen.1004572-TheMathWorks1" target="_blank">[61]</a>.</p