The population structure analyses of different population groups are also influenced by which subjects are included. When the subject set is limited to only those individuals of particular self-identified backgrounds the results show more distinct cluster assignments. This is illustrated in Fig. 1d when East Asian and South Asian subjects are excluded from the analyses and the number of assumed population groups is defined as three (K=3). In addition, small numbers of markers chosen using other criteria may provide good distinction between two or three population groups but provide inaccurate information on other non-included population groups. The performance of subsets of markers selected using either European/West African informativeness or European/Amerindian informativeness is provided in Supplementary Table S3.
