Our analyses provide guidelines for application especially with regards using the program STRUCTURE (Falush, et al., 2003; Pritchard, et al., 2000a). Other computational programs including ADMIXMAP (Hoggart, et al., 2004) can also be applied with very similar results (data not shown). In general, as indicated in the methods section, the performance of smaller AIM SNP sets in STRUCTURE analyses is only consistently reproducible when very large numbers of iterations are used. This is not a major limitation since the computational time is not a major problem when small sets of markers are used even with large sample sets; several thousand samples will require <24 hours for 100,000 replicates using STRUCTURE and 48 markers. However, smaller marker sets (especially those <64) provide a poorer ability to exclude subjects of disparate continental ancestry and will provide less precision in the individual ancestry assignment. For larger studies (sample sizes of several thousand) the precision of individual assignments will be less consequential than for smaller studies in which the investigation will be more dependent on the accurate assessment of ancestry of each individual. Thus
