We conjecture that eigenmaps are most successful when the base sample is a diverse but representative sample. If our conjecture is correct we predict that analysis of worldwide samples will highlight continental differentiation, but obscure fine-scale ancestral differentiation. To examine this prediction we construct an eigenmap using the full sample of 51 populations from HGDP. Using this base, we identified 12 significant dimensions of ancestry. In clustering individuals based on this 12 dimensional space, we successfully clustered individuals by continent, but lost the ability to identify many of the individual populations within continents that were apparent at the continental level (Supplementary Figures 1 and 5). For example, the six formerly distinct African populations now cluster together; the six regionally distinct clusters of East Asians now cluster into a southern and northern component; and all Europeans cluster together.
