I’m in the middle of a longer post on a recent paper on the effects of genetics on gene expression differences in African-Americans, which has also been well-covered by p-ter at Gene Expression. I wanted to post this section separately to avoid detracting from the issues in that post.
This figure will not provide any big surprises for those who have been following developments in human genetics over the last five years – but it still provides a compelling illustration of the power of genetics to predict individual ancestry:
The figure shows the results obtained when the European, Nigerian and East Asian samples from HapMap and 100 African-American samples are clustered using principal component analysis based on data from ~600,000 genetic markers.
The European, Nigerian and East Asian samples form strong clusters that are extraordinarily well-separated, demonstrating how easy it is to distinguish between members of these groups with sufficiently large numbers of markers. However, it should be emphasised that adding additional populations from other parts of the world would fill most of the gaps between these clusters, since human geographic variation is largely continuous rather than discrete.
The most interesting aspect of the figure is the distribution of the African-Americans, who almost all fall on a remarkably clean line stretching between the European and Nigerian clusters, with some individuals being pulled towards the East Asian cluster (presumably due to admixture from
South or East Asia some population not well-captured by HapMap, e.g. Native Americans). Using these data each individual’s relative level of European and African ancestry can be estimated with high precision. After removing four outliers (the three samples falling furthest from the European-African line, and one individual falling very close to the European cluster) the European admixture levels of individual African-Americans fall between 1 and 62%, with an average of ~21% – a figure consistent with previous studies.
Alkes L. Price, Nick Patterson, Dustin C. Hancks, Simon Myers, David Reich, Vivian G. Cheung, Richard S. Spielman (2008). Effects of cis and trans Genetic Ancestry on Gene Expression in African Americans PLoS Genetics, 4 (12) DOI: 10.1371/journal.pgen.1000294