Figure 1

(a) Flow chart of targeted gene selection, and (b) a schema of the SNP screening method. We first focused on 44 genes with allele frequencies highly differentiated among human populations, including the 27 genes listed in Table nine of the first HapMap paper [1] based on high F_st values for nonsynonymous SNPs and the 17 genes listed in Table S4 of Sabeti et al. (2006) in the category "population differentiation." A SNP site with a F_st value higher than the genome average represents higher population differentiation at this site [26], possibly driven by natural selection [27–30]. Secondly, from the 44 genes, we removed pseudogenes, genes with unclear annotation and genes without biological information in the database. Thirdly, we chose genes for which only a single gene was assigned as an ortholog in the medaka genome by searching the Ensembl database http://www.ensembl.org/index.html. After applying these selection criteria, 11 genes were subjected to the SNP screening (Table 1).