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. Author manuscript; available in PMC: 2020 Jan 29.
Published in final edited form as: Nat Ecol Evol. 2019 Jul 29;3(8):1253–1264. doi: 10.1038/s41559-019-0947-6

Fig. 4. Evidence of selection driving population differences in immune response.

Fig. 4.

(A) This density plot shows the distribution of the percent of SNPs with extreme values of FST (e.g. in the 95th percentile) for a set of randomly sampled cis-SNPs equally-sized sets of SNPs matched for allele frequencies with high-ΔPVE SNPs. 10,000 iterations were run to obtain the distribution for each condition. The red point on each graph shows the percentage of high-ΔPVE SNPs in the 95th percentile. High-ΔPVE variants in all conditions had significantly more SNPs in the 95th Percentile (FST comparison Chi-Squared Statistic; CTL P. value = 2.2−16, LPSP. value = 2.2−16, GARD P. value = 2.2−16). (B) A tree diagram illustrating the mean values of the population branch statistic for the HG-Batwa, AG-Bakiga, and a cohort from Great Britain as an outgroup. This figure illustrates a greater mean PBS score in the HG-Batwa population among high-ΔPVE variants. (C) The distribution of the ratio of mean PBS in the HG-Batwa to the AG-Bakiga for a set of randomly sampled cis-SNPs equally-sized sets of SNPs matched for allele frequencies with high-ΔPVE SNPs. 100,000 iterations were run to obtain the distribution and to calculate the P. value. The red point shows the ratio of mean PBS values represented as the branch lengths in the tree graph. (D) A bar graph illustrating the percentage of high-ΔPVE SNPs that have an iHS value in the 95th percentile compared to a background of all top cis-SNPs. For iHS, only values in the GARD-stimulated cells in the HG-Batwa population had significantly more SNPs in the 95th percentile (HG-Batwa iHS comparison Chi-Squared Statistic; CTL P. value = 0.446, LPS P. value = 0.080, GARD P. value = 0.002; AG-Bakiga iHS comparison Chi-Squared Statistic; CTL P. value = 0.586, LPS P. value = 0.929, GARD P. value = 0.210). (E) PBS values for selection between populations graphed against absolute iHS values showing selection within each. population for high-ΔPVE variants. Pink (AG-Bakiga) and Red (AG-Batwa) dots represent high-ΔPVE SNPs in the 95th percentile of both PBS and iHS. Among this group points are labeled with the corresponding gene name.