To see how the eigenspace varies depending on the choice of base sample, we estimate the eigenvectors using various base samples: (a) European HGDP data; (b) European POPRES; (c) HGDP and half of POPRES; and (d) the 330 individuals from HGDP and POPRES described above. The remaining data were projected onto the eigenspace to illustrate the estimated ancestry distribution (Figures 3(a)–(d)). Regardless of the choice of base, four of the HGDP populations (Adygei, French Basque, Sardinian and Russian) are distinct from other HGDP populations in the eigenspace. The other four populations (French, Northern Italian, Orcadian, and Tuscan), which are more similar to the POPRES sample, separate best in the eigenspace if at least some of the POPRES sample is included in the base (b, c, d). Overall the HGDP sample is more heterogeneous than the POPRES sample (a, c); however, this distinction is muted when the HGDP sample is not included in the base calculations (b). In essence, the eigenspace aims to separate clusters like those included in the base. As a result, when using HGDP as a base, the
