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Post by Admin on Jun 29, 2017 19:28:45 GMT
Mapping loci associated with skin and eye color We used information from 903,837 autosomal SNPs to carry out genotype- and ancestry-based association analyses for skin (n = 685) and eye (n = 625) color. For genotype-based association, four skin color loci (5p13.3, 11q14.3, 15q13.1, and 15q21.1) and two eye color loci (15q13.1 and 15q21.1) met genome-wide criteria for significance, P<5.7×10−8 (Table 1, Table S2). In analyses adjusted only for principal components and sex, the signals at 15q21.1 (for skin color, Figure 3a) and 15q13.1 (for eye color, Figure 3b), dominate the significance plots. As described below, these signals correspond to SLC24A5 for skin color and HERC2 (OCA2) for eye color; Figure 3c and 3d show P value distributions when genotypes at SLC24A5 and HERC2 (OCA2) are considered as covariates. No additional loci were found in conditional analyses that adjust for the most significant SNPs in the known loci (four for skin and two for eye color). After removing SNPs surrounding these six loci, the genomic control parameters were 1.02 and 1.00 for skin color and eye color, respectively. We also examined the six loci identified in the combined sample in each island separately (Table S1); the direction of effect is consistent across all groups, with the derived allele associated with lighter skin color or a lower T-index (Table 1). Taken together with similar results from EMMAX (Figure S1), these results suggest adequate correction for population structure. Figure 3. GWAS results for skin and eye color in the total Cape Verdean cohort. Results are shown as −log10(P value) for the genotyped SNPs. Plots are ordered by chromosomal position. (a,c) Genotype and admixture association scan results for skin color. (b,d) Genotype and admixture association scan results for eye color. (a,b) show the P values obtained in the initial scans and (c,d) the P values of the following scans adjusting for the strongest associated SNP (in SLC24A5 for skin color and in HERC2 for eye color). Dashed red lines correspond to the genome-wide significance threshold (P<5×10−8 in the genotype scan; P<7×10−6 in the ancestry scan [see Material and Methods]). The location and identity of candidate genes are colored to correspond with chromosomal location; individual SNPs are given in Table 1. Table 1. Major loci for skin and eye color. For ancestry-based mapping, we used SABER+, an extension of a Markov-Hidden Markov Model method [24], to assign African vs. European ancestral segments along each chromosome, and then carried out a genome-wide evaluation of local ancestry association with skin and eye color, using the same covariates as for the genotype-based analysis. Ancestry-based association yields broader peaks than genotype-based association, but the distribution of significant regions is strikingly consistent for the two approaches, uncovering the identical set of six loci (Figure 3, Table 1).
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Post by Admin on Jul 1, 2017 19:20:10 GMT
Refinement of pigmentation loci by imputation and conditional analysis To help evaluate potential causative loci and molecular variants for skin and eye color, we imputed SNP information from HapMap phase II [19], repeated the genotype-based association, and considered the results in the context of existing knowledge and haplotype structure. The 5p13.3 and 11q14.3 regions affect only skin color (Figure 4a, 4b), whereas the chromosome 15 regions (15q13.1 and 15q21.1, Figure 4c, 4d) affect both skin and eye color. As described below, the 15q21.1 region harbors coding sequence variation in SLC24A5 that affects skin and eye color similarly, but the 15q13.1 region harbors two distinct peaks of regulatory sequence variation that act separately on skin and eye color. Figure 4. Imputation, fine-mapping, and selective signature scores for skin and eye color loci. Each panel shows the genotype-association results and the distribution of Composite of Multiple Signals scores of positive selection (CMS scores) [38] for genotyped and imputed SNPs (dark and light blue points in the association plots, respectively) surrounding the candidate loci; identities of individual SNPs are given in Table 1. Dashed red lines correspond to the genome-wide significance thresholds. (a) 5p13.3 region containing the SLC45A2 gene. (b) 11q14.3 region containing the GRM5 and TYR genes. (c) 15q21.1 region containing the SLC24A5 gene. (d) 15q13.1 region containing the OCA2, HERC2 and APBA2 genes. The interval between HERC2 and APBA2 contains a cluster of segmental duplications and a paucity of SNPs [45], and is also a source of a frequent deletion breakpoint as described in the Discussion. Previously identified candidate causative non-synonymous variants [11], [13], [14] are denoted as red dots in the association plots of panels (a,b,c). The location and identity of candidate genes are colored to correspond with chromosomal location; individual SNPs are given in Table 1. For skin color, the most strongly associated SNPs at 5p13.3 and 15q21.1 represent missense alterations in two well-known pigmentary genes, SLC45A2 L374F (Figure 4a) and SLC24A5 A111T (Figure 4c), thought to encode membrane transport proteins that promote melanogenesis [13], [25]–[27]. Neither amino acid substitution is predicted to dramatically alter protein function; nonetheless, expression of both genes is pigment cell-specific, and null mutations dramatically impair melanin synthesis in model organisms [13], [28], [29]. Thus, the European alleles probably represent hypomorphic alterations that compromise melanogenesis, leading to decreased pigmentation. The two remaining skin color loci at 11q14.3 and 15q13.1 exhibit the strongest association signals within intronic regions of GRM5 (Figure 4b) and APBA2 (Figure 4d), neither of which is an obvious candidate to control normal variation in human skin color. However, GRM5 and APBA2 lie 396 kb upstream and 1025 kb upstream of TYR and OCA2, respectively, two well-known pigmentary genes for which a complete loss-of-function causes albinism in humans and in other animals [30]–[32]. Furthermore, a missense alteration in TYR, S192Y (rs1042602) [11] (Figure 4b), is in linkage disequilibrium with the most significant SNP in GRM5 (rs10831496) in this sample, and in analyses that consider TYR and GRM5 SNPs as covariates, both remain significant (P = 3.7×10−6 for rs10831496; P = 0.00012 for rs1042602). Thus, the effect of the 11q14.3 locus on skin color could be mediated by a combination of regulatory and coding variation. The same is not true, however, for the 15q13.1 locus, for which the peak of skin color association in APBA2 is separated from OCA2 by ∼1 Mb (Figure 4d). This distinction is especially apparent when considering the 15q13.1 association signal for eye color, which lies ∼50 kb upstream of OCA2 in an intronic region of HERC2 (Figure 4d), and has been well recognized to account for Mendelian-like inheritance of blue vs. brown eye color in populations of European ancestry [7], [8], [10]. We considered whether the skin color GWAS signal for APBA2 might simply reflect linkage disequilibrium with HERC2 and OCA2, but rejected that hypothesis for several reasons. The GWAS significance peaks for eye color and skin color at 15q13.1 appear distinct (Figure 4d), and linkage disequilibrium between the two significance peaks is weak (R∧2 = 0.112 in our sample). Skin and eye color are, themselves, correlated, but in conditional regression analyses where genotypes at both loci are included as covariates, HERC2 does not affect skin color if eye color is also included as a covariate (HERC2 P = 0.48, APBA2 P = 0.0009); conversely, APBA2 does not affect eye color if skin color is also included as a covariate (APBA2 P = 0.083, HERC2 P<2×10−16). Thus, the effects of HERC2 and APBA2 are genetically and statistically separable. Still, there is strong experimental evidence that the HERC2 region represents regulatory variation that acts via OCA2 [33], and therefore we refer to these loci as HERC2 (OCA2) and APBA2 (OCA2) to indicate both their proximity to a well-known pigmentation gene, and a likely molecular mechanism. In addition to the major eye color locus at HERC2 (OCA2), there is a second eye color locus at 15q21.1 whose position corresponds to the SLC24A5 A111T allele (Figure 4c). The association of HERC2 and SLC24A5 with eye color is also apparent in individuals who do not have blue or green eyes: In the subset of 592 Cape Verdeans whose T-index >0.15 (Figure 1, Figure 2), both loci remain highly significant (HERC2 rs12913832, P = 5.23×10−16; and SLC24A5 rs2470102, P = 1.12×10−10), indicating that variation at these loci affects different shades of brown eye color.
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Post by Admin on Jul 3, 2017 20:14:10 GMT
Power to detect additional loci Notably absent from the four skin color loci detected in this study are ASIP and KITLG, reported previously to affect skin color in populations with African-European admixture [12], [15], and IRF4, MC1R, SLC24A4, TYRP1, reported previously to affect skin color in populations of European ancestry [4], [6]. To estimate the power of our study, we carried out simulations based on the observed distributions of individual genomic ancestry and genotypes for SLC24A5, in which the ability to detect a candidate locus at different levels of significance was evaluated as a function of effect size. For a genome-wide significance level (P<5×10−8), the results of our simulations reveal >90% power to detect an effect size of 0.21 MM (Figure 5a), which is 4.1% of the total range of skin color observed in our sample, and close to that suggested previously for ASIP (0.24 MM [12]) and KITLG (0.19–0.26 MM [15]). Figure 5. Power and candidate gene analyses. (a) Power estimated at three different alpha levels, plotted as a function of effect size (number of MM units by which each copy of the derived allele lightens skin pigmentation). The results shown here are based on derived allele frequencies of 0.1 and 0.9 in the ancestral African and European populations, respectively. The effect sizes detected in Cape Verde for the four major skin color loci are shown in blue; effect sizes for ASIP and KITLG as estimated (see Material and Methods) from [12] and [15], respectively are shown in red. (b) Distribution of P values for SNPs in 47 candidate genes, 16 regions with strong signatures of selection, and random SNPs, all shown as a q-q plot of the −log10 (P) values. Observed −log10 (P) values specifically for ASIP and KITLG SNPs are shown above the plot. We also asked if SNPs close to candidate genes might be enriched for low P values. In addition to ASIP, IRF4, KITLG, MC1R, SLC24A4, and TYRP1, we chose 41 additional candidate genes with a potential role in human skin color based on their phenotypes in model organisms, or in humans affected with albinism (Table S4). To evaluate candidate genes with no known role in pigmentation but which nonetheless have undergone recent selection, we used the XP-EHH metric to identify 16 regions harboring highly frequent and extended haplotypes in European compared to African populations (Table S5). As shown in Figure 5b, the distribution of P values for SNPs in both types of candidate genes overlaps with that of randomly chosen genomic regions. As described further below, the failure to replicate previously reported effects could be due to a paucity of allelic variation in the Cape Verde ancestral populations (e.g. MC1R), incomplete correction for genomic ancestry with small panels of ancestry informative markers in the earlier studies (e.g. ASIP, KITLG), or real effects of these loci that are too small to detect in our study.
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Post by Admin on Jul 5, 2017 19:15:01 GMT
Genetic and evolutionary relationships of eye and skin color genes at 15q13.1 As indicated above, one of the major skin color loci, APBA2 (OCA2), lies close to but has effects that are genetically separable from, the major eye color locus, HERC2 (OCA2). Selective pressure for fair skin in European ancestors is thought to reflect the need for sunlight-induced vitamin D production [1], [2], but there is no analogous hypothesis for selection of pale eye color; thus, a derivative HERC2 (OCA2) allele may have hitchhiked on a derivative APBA2-bearing chromosome, or could have undergone independent selection for reasons that are distinct from those affecting APBA2 (OCA2). To explore these ideas, we first examined worldwide allele frequency distributions for the most strongly associated SNP at each locus, using information from the Human Genome Diversity Project (HGDP) [39] and HapMap III [19]. The derived APBA2 (OCA2) allele is present at low frequencies in most populations of African ancestry, and at high frequencies in most populations of Asian and European ancestry. By contrast, the derived HERC2 (OCA2) allele is absent from African and East Asian populations, and appears at high frequency only in Western and Northern Europe (Figure 6a, 6b). These results suggest that an APBA2 (OCA2) mutation conferring light skin arose before the spread of humans out of Africa, and that a HERC2 (OCA2) mutation conferring pale eye color arose much later. Figure 6. Allele frequency and haplotype analysis for eye and skin color loci at 15q13.1. (a,b) Allele frequency distributions for the SNPs most significantly associated with eye [HERC2 rs1291382; (a)] and skin [APBA2 rs4424881; (b)] in the HapmapIII [19] and HGDP [39] panels for the old world. Blue/orange shading corresponds to the frequency of the ancestral/derived alleles, as determined by comparison with the chimp reference sequence (assembly CGSC2.1/pan Tro2). Frequency values are presented in Table S3. c) Visual displays of the haplotypes extending from HERC2 to the second intron of APBA2 in Europeans from HapMap phase III (CEU) and HGDP (French, French Basque, North Italian, Tuscan, Sardinian, Orcadian, and Russian) panels. Haplotypes were inferred on the basis of 26 SNPs common to both datasets; blue and orange shades represent the ancestral and derived alleles, respectively. Haplotypes were ordered according to the ancestral/derived states at HERC2 rs1291382 and APBA2 rs4424881 (marked with red arrows), as follows: haplotypes bearing the ancestral alleles for both SNPs (Anc-Anc); haplotypes bearing the derived allele for HERC2 rs1291382 and the ancestral allele for APBA2 rs4424881 (Der-Anc); haplotypes bearing the ancestral allele for HERC2 rs1291382 and the derived allele for APBA2 rs4424881 (Anc-Der); and haplotypes bearing the derived allele for both SNPs (Der-Der). We then considered whether the light skin and pale eye color derived alleles were carried on the same haplotype in chromosomes of European ancestry, using information from HapMap CEU and European HGDP populations. Each derived allele is present on a single major extended haplotype (>160 kb in length for HERC2 (OCA2) and >90 kb in length for APBA2 [OCA2]), whereas the ancestral alleles are found on multiple, shorter, haplotypes. However, measures of linkage disequilibrium between the two loci are not significant (R∧2 = 0.036, D′ = 0.071 with Χ2 = 0.517), extended haplotypes for the derived alleles are separated by ∼800 kb, and approximately half of the European chromosomes we examined carry an ancestral HERC2 (OCA2) haplotype together with a derivative APBA2 (OCA2) haplotype, or vice versa (Figure 6c). These observations are consistent with the presence of discrete CMS peaks under the HERC2 (OCA2) and APBA2 (OCA2) regions (Figure 4d) and suggest that the loci may have undergone selection independently in European populations.
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Post by Admin on Aug 9, 2017 19:03:52 GMT
Figure 1: Mesolithic samples and their genetic affinities To investigate the postglacial colonization of Scandinavia, we explored four hypothetical migration routes (primarily based on natural geography) linked to WHGs and EHGs, respectively (Supplementary Information 11); a) a migration of WHGs from the south, b) a migration of EHGs from the east across the Baltic Sea, c) a migration of EHGs from the east and along the north-Atlantic coast, d) a migration of EHGs from the east and south of the Baltic Sea, and combinations of these four migration routes. These scenarios allow us to formulate expected genetic affinities for northern, western, eastern, and central SHGs (Supplementary Information 11). The SHGs from northern and western Scandinavia show a distinct and significantly stronger affinity to the EHGs compared to the central and eastern SHGs (Fig. 1). Conversely, the SHGs from eastern and central Scandinavia were genetically more similar to WHGs compared to the northern and western SHGs (Fig. 1). Using a model-based approach (15, 16), the EHG genetic component of northern and western SHGs was estimated to 55% on average (43-67%) and significantly different (Wilcoxon test, p=0.014) from the average 35% (22-44%) in eastern and south-central SHGs. This average is similar to eastern Baltic hunter-gatherers from Latvia (28) (average 33%, Fig. 1A, Supplementary Information 6). These patterns of genetic affinity within SHGs are in direct contrast to the expectation based on geographic proximity with EHGs and WHGs and do not correlate with age of the sample (Supplementary Information 11) Figure 2: Genetic diversity in prehistoric Europe The archaeological record in Scandinavia shows early evidence of human presence in northern coastal Atlantic areas (12). Stable isotope analysis of northern and western SHGs revealed an extreme marine diet, suggesting a maritime subsistence, in contrast to the more mixed terrestrial/aquatic diet of eastern and central SHGs (Supplementary Information 1). Combining these isotopic results with the patterns of genetic variation, we suggest an initial colonization from the south, likely by WHGs. A second migration of people who were related to the EHGs – that brought the new pressure blade technique to Scandinavia and that utilized the rich Atlantic coastal marine resources –entered from the northeast moving southwards along the ice-free Atlantic coast where they encountered WHG groups. The admixture between the two colonizing groups created the observed pattern of a substantial EHG component in the northern and the western SHGs, contrary to the higher levels of WHG genetic component in eastern and central SHGs (Fig. 1, Supplementary Information 11).
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