Extended Data Fig. 8: Adaptive introgression at regulatory loci.
From: Dissecting human population variation in single-cell responses to SARS-CoV-2
a, Enrichment of eQTLs and reQTLs in introgressed haplotypes (mean and 2.5th −97.5th percentiles of observed/expected ratios across N = 10,000 resamplings). b, For each population and condition, the frequencies of introgressed haplotypes are compared according to their effects on gene expression (eQTL vs. non-eQTL; Benjamini-Hochberg-adjusted two-sided Wilcoxon’s rank-sum p-values < 0.01 are shown). The numbers of independent SNPs and eQTLs considered, n and neQTL respectively, are indicated. Middle line: median; notches: 95% CIs of median, box limits: upper and lower quartiles; whiskers: 1.5× interquartile range; points: outliers. Benjamini-Hochberg -adjusted two-sided Student’s t-test p-values < 0.01 are shown. For a and b, each population was downsampled to the same number of donors prior to eQTL mapping to avoid biases due to differences in statistical power. c, Adaptively introgressed eQTLs of host defence genes. From left to right: (i) effects of the introgressed allele on gene expression across immune lineages and stimulation conditions, (ii) clinical and functional annotations of associated genes, (iii) present-day population frequencies of the introgressed alleles, (iv) percentile of archaic allele frequency at the locus (CEU and CHS; dark shades: top 1%, light shades: top 5%), and (v) effects of the target allele on COVID-19 risk (infection, hospitalization, and critical state). Arrows indicate the increase/decrease in gene expression or disease risk with each copy of the introgressed allele. Opacity increases with significance (two-sided Student’s t-test -log10 p-value). In the leftmost panel, arrow colours indicate the stimulation condition (grey: NS, red: COV, blue: IAV). For each eQTL, the introgressed allele is defined as the allele segregating with the archaic haplotype in Eurasians.
