BTN3A2 CCND1 CDC25A CDKN2A GPX2 GPX3 GSTM3 GSTP1 HDAC1 HTR2A Il1A MICA SKP2 SMAD4 TGFB1 p (%) 0.108 0.090 0.023 0.027 0.110 0.121 0.068 0.200 0.051 0.117 0.050 0.062 0.005 0.003 0.109 S 14 13 7 8 16 11 6 13 12 18 3 15 2 2 9 k hom 9 0.43 11 0.38 7 0.67 7 0.65 17 0.27 10 0.36 7 0.33 12 0.30 11 0.34 13 0.30 4 0.33 17 0.14 3 0.90 2 0.97 9 0.38 1.76 (0.008) 1.61 (0.016) 1.57 (0.026) 1.88b (0.984) 1.21 (0.041) 1.41 2.75b (0.012) (0.048) Fay and Wu [2000]a H (p) 3.57 (0.050) 5.96 (0.009) 3.32 (0.013) 4.53 (0.036) Fu [1997] kexp Fs/(p) 8.4 ns 6.4 ns 2.7 5.15/(0.002) 3.5 3.45/(0.032) 8.9 6.37/(0.011) 9.4 ns 6.2 ns 12.9 ns 5.1 5.36/(0.0095) 9.0 ns 4.9 ns 6.8 9.84/(0.000) 1.5 2.41/(0.010) 1.3 ns 8.4 ns Observed values Tajima [1989] D (p) Fu and Li [1993] D/F (p) TABLE 2. NeutralityTests HUMAN MUTATION 28(5), 441^450, 2007 445 Chakraborty [1990] Ewens [1972]; Watterson [1978] Numbers in bold are the results that are signi¢cant after correction for multiple testing. aExceptionally, the values for the Fay and Wu [2000] test are based on a sample of 160 chromosomes. ns, not signi¢cant. simulations under a simple population model. The plot of haplotype allelic classes in CDC25A summarizes well the characteristics of this segment revealed by the negative Tajima’s and Fu Fs statistics as well as by Chakraborty’s test. Due to the excess of haplotypes originating in polymorphisms with low counts of the derived alleles, the distribution of haplotype allelic classes is skewed to the left as compared to the simulated curve. CDC25A is representative of a group of loci sharing similar characteristics (Table 2), namely CDKN2A, MICA, SKP2, SMAD4, and, to a much lesser extent, HDAC1 (Supplementary Fig. S2). On the other side of the spectrum are the segments with their major haplotypes removed by several mutations from the ancestral one, MZ3 (Table 1). As in CX3CR1 and GSTM3, in Figure 1 this time the observed distributions are skewed to the right relative to the simulated curve. As shown in Supplementary Figure S2, this group includes all segments already singled out by the Fay and Wu test and by the positive Fu and Li statistics (Table 2), i.e., BTN3A2, GPX3, GSTM3, GSTP1, and HTR2A, and in addition CX3CR1, which failed all these tests. Because recombinations were observed in some of these segments, we also simulated distributions of haplotype allelic classes assuming recombination at a rate 10 times the genomic average. It turned out that simulated distributions were relatively insensitive to crossovers, such that the observed distribution cannot be explained by the effect of recombinations at such intensity (dashed line in Fig. 1 for CX3CR1; see also Supplementary Fig. S2). Population Variance: Fst Over time, populations differentiate in allele frequencies, and the resulting geographic partitioning of this diversity can be measured by Fst [Wright, 1951]. We estimated fixation index (Fst) values [Weir and Cockerham, 1984] for each segment based on the contributing sites and for each polymorphic site separately. Over the segments, the average Fst was 6.675.4% in the total sample composed of five population groups, and 4.374.5% when four non-African population groups were considered (Table 1). In turn, when 254 polymorphisms were considered individually, the average Fst was 4.675.8% for all populations and 3.175.1% considering only four non-African groups. The individual Fst values can be evaluated by comparison to their empirical distributions obtained from larger data sets [Akey et al., 2002; Excoffier, 2005; Fullerton et al., 2002], and this approach was used to single out promoter polymorphisms that presumably evolved under natural selection [Hahn et al., 2004; Rockman et al., 2003, 2004; Wang et al., 2005]. As a reference, we used our set of the 254 Fst values for polymorphisms investigated here (Supplemen- tary Fig. S3). Several sites at the edge of the distribution exceeded the arbitrary threshold of the average Fst plus 2 SDs, either in the total five-population sample and/or in the non-African four- population sample (Supplementary Table S4). Among them, we find three sites in CX3CR1—rs2669846:G4T, rs11715522:A4C, rs11917223:C4G—that are characterized by relatively elevated (30–50%) new allele frequencies. Interestingly, the same sites were Human Mutation DOI 10.1002/humu kexp (p) 4.9 (0.031) 5.8 (0.014) 2.7 (0.005) 2.8 (0.005) 8.4 (0.001) 5.9 (0.042) 7.5 ns 7.7 (0.053) 6.6 (0.040) 7.5 (0.019) 6.7 (0.946) 15.2 ns 1.4 ns 1.1 ns 5.7 ns homexp (pw; ps) 0.28 ns 0.23 (ns; 0.970) 0.36 (0.970; ns) 0.36 (0.967; ns) 0.14 (0.986; 0.984) 0.25 ns 0.36 ns 0.21 (ns; 0.965) 0.23 (ns; 0.976) 0.19 (ns; 0.968) 0.55 (ns; 0.043) 0.14 ns 0.66 ns 0.80 ns 0.29 (ns; 0.982)