Mike the Mad Biologist, whose bailiwick is the domain of the small, asks in the comments:
I don't mean to bring up a tangential point to the post, but why does the field of human genetics use PCA to visualize relationships? When I see plots like those shown here that have a 'geometric pattern' to them (the sharp right angles; another common pattern is a Y-shape), that tells me that there are lots of samples with zeros for many of the Y-variables (i.e., alleles that are unique to certain populations). Thus, the spatial arrangement of the points is largely an artifact of an inappropriate method: how does one calculate a correlation matrix when many of things one is correlating have values of zero? If one really was keen on using PCA, one could calculate a pairwise distance matrix and then use that instead of the correlation matrix (Principal Coordinates Analysis).
Since I know some human geneticists do read this weblog, I thought it was worth throwing the question out there.
