Fig. 2: Selective sweeps for CEU-LCE1A-SMCP and CEU-IVL out-of-Africa.
From: Selective sweep for an enhancer involucrin allele identifies skin barrier adaptation out of Africa
a Phasing reveals CEU-LCE1A-SMCP and CEU-IVL haplotypes (green bars) in CEU based on SNPs in linkage disequilibrium (r2 > 0.8) with the high CMS/iSAFE (red; rs12022319, rs4845490 [bolded], rs4845491, & rs3737861) and iSAFE (orange; rs4845327 [bolded], rs1854779, rs7539232, rs11205132, rs2229496, rs7535306, & rs7545520) SNPs (lollipops). CEU-IVL includes IVL and the epidermis-specific 923 enhancer, whereas CEU-LCE1A-SMCP includes LCE1A, LCE6A, and SMCP. b Direct and positive correlations between the frequencies of rs4845490-A & rs4845327-G, and Northern latitudes reveal associations of the CEU-LCE1A-SMCP and CEU-IVL selective sweeps with out-of-Africa migration (ρ = 1.7E-5 and 2.2E-5), respectively. Black line indicates a linear relationship (Pearson’s correlation) between allele frequency and geographic latitude, two-sided t-test (9 degrees of freedom) with gray area surrounding the regression line representing 95% confidence intervals for the group mean values of the latitude for each allele frequency. Pie charts of rs4845327-G allele frequency for each population are indicated on the map. c Violin plots for rs4845327-G for CEU-IVL, an eQTL for increased IVL and decreased LCE1D and LCE1E expressions shown in not sun-exposed skin (GTEx [V8]). Box in violin plot represents interquartile range with median (white line). Numbers in parenthesis indicate number of individuals for each genotype. Norm. Exp., normalized expression; TPM, transcripts per million. Chi-Square p-value was calculated based on Mahalanobis distance and Bonferroni corrected.
