Barplots of ancestry proportions estimated using genome-wide data and using AIMs.

<p>In the first panel ancestry proportions were estimated using genome-wide data. The admixed study group (sac) is ordered by proportions of African San, African non-San, European, South Asian and East Asian ancestry. In the second panel ancestry proportions were estimated using 96 AIMs. Individuals appear in the same order as in the first panel.</p

Ancestry proportion distribution.

<p>Median and IQR of the ancestry proportions estimated using genome-wide data and AIMs, per admixed study group.</p

Source population data.

<p>Data sets used to represent the five source populations of the South African Coloured population. The sample size reflects the group size after relative pairs have been removed. Henn et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082224#pone.0082224-Henn1" target="_blank">[52]</a> merged the Juu San data from the Human Genome Diversity Project (HGDP) and Schuster et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082224#pone.0082224-Schuster1" target="_blank">[53]</a> and the African non-San data from Bryc et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0082224#pone.0082224-Bryc1" target="_blank">[54]</a>.</p

Admixture proportion correlation versus number of AIMs in set.

<p>Correlation between admixture proportions estimated using AIMs and proportions estimated using genome-wide data, using AIM sets of increasing size (increments of 25) for the Cape Town study group (n = 733). A proportion of the SNPs in each set of AIMs were selected using the multiple -statistic, indicated in each panel as a percentage, while the remaining SNPs were selected using the pairwise -statistic, as described in the Methods section.</p