The success of our approach depends upon the quality of the eigenmap. In practice, the map can be constructed from the full sample of individuals available or a representative base sample. The base sample might include individuals from a broad range of ancestry or a fairly homogeneous sample. Once constructed, new individuals can be projected onto the ancestry map based on their genotypes using the Nystrom approximation [27]. To illustrate how the map varies depending upon the choice of base sample we use two public databases that have samples of people of European ancestry and sufficient demographic data to permit classification of each person to his country of origin. In the first sample, individuals were collected for the Human Genome Diversity Project (HGDP) to reflect the genetic diversity of current human populations, thereby enhancing studies of human evolutionary history [28]. This sample emphasizes distinct populations, including isolated and geographically well-separated peoples. In contrast the Population Reference Sample (POPRES) was assembled with the goal of bringing together a set of DNA samples that would support a variety of efforts related to
