A third issue is that our methods require that divergence is small, and that allele frequencies are divergent primarily because of drift. We attempted to apply our methods to an African-American dataset genotyped on a panel of ancestry-informative markers [34]. The Tracy–Widom theory breaks down here with dozens of “significant” axes that we do not believe have genetic meaning. Perhaps this is to be expected, as on our informative panel FST is big (.58) and the theory could be expected to perform poorly. In addition our methods are here not dealing adequately with LD caused by large admixture blocks.
