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>.