Using the balanced sample we compare the HGDP populations with particular subsets of the POPRES data (Figures 4(a)–(d)). The HGDP-French correspond well with the bulk of the POPRES-French sample (a). Likewise the core of the POPRES-British & Irish sample corresponds well with HGDP-Orcadian population (b). The POPRES-Italian sample is more heterogeneous, spanning the range of the HGDP-Northern Italians and HGDP-Tuscans (c). The HGDP-French-Basque map midway between the POPRES-French and POPRES-Spanish/Portuguese samples on the first dimension, but separate in the second dimension (d). The POPRES sample is not well represented by individuals from eastern Europe, hence there is no natural comparison group for the HGDP-Russian and Adygei samples. Similarly none of the populations sampled in POPRES overlaps with the HGDP-Sardinian population. In total the similarity of the populations of like ancestry suggests that the eigenmap based on ancestrally balanced samples is providing a meaningful representation of ancestry that can be used to match cases and controls of unknown ancestry in practice.
