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A protocol for the identification of ancestry informative markers (AIMs) fromgenome-wide single nucleotide polymorphism (SNP) data is proposed. The protocolconsists of three main steps: (a) identification of potential positiveselection regions via Fst extremity measurement, (b) SNP screening viatwo-stage attribute selection and (c) classification model construction using anaive Bayes classifier. The two-stage attribute selection is composed of anewly developed round robin symmetrical uncertainty ranking technique and awrapper embedded with a naive Bayes classifier. The protocol has been appliedto the HapMap Phase II data. Two AIM panels, which consist of 10 and 16 SNPsthat lead to complete classification between CEU, CHB, JPT and YRI populations,are identified. Moreover, the panels are at least four times smaller than thosereported in previous studies. The results suggest that the protocol could beuseful in a scenario involving a larger number of populations.

Small ancestry informative marker panels for complete classification between the original four HapMap populations