![]() Enrichment in SIV-related, and VIP categories of candidate targets of positive selection across populations, tested using set_perm. We note that no category reaches significant enrichment (after correcting FDR values for the number of populations tested using a BH correction). Colours represent Benjamini and Hochberg corrected-FDR values (red as highest significance). Categories are separated by gene set tested: SIV responsive genes, SIV co-expression modules, VIPs and GO categories. Abbreviations indicate the populations tested: central-eastern ancestor + central (A+C), central-eastern ancestor + eastern (A+E), central-eastern ancestor + central + eastern (A+C+E). Enrichment in SIV-related, VIP and GO categories of candidate targets of positive selection across populations, tested using Gowinda. SNPs at chr12:6978193 (V55I SNP) and chr12:6978232 (P68T SNP) are missense variants with signatures of positive selection in centrals and the central-eastern ancestor respectively. SNP at chr12:6963043 represents a splice variant with signatures of positive selection in the central-eastern ancestor. These candidate SNPs correspond to those highlighted in Fig 4. DAF of the three candidate SNPs of interest in CD4 across chimpanzee subspecies. Stars indicate a significant enrichment in that 3P-CLR quantile. Grey represents instances where a GO category was undetected in that particular quantile. Colours represent FDR values (red as highest significance). Categories are separated by GO class: Biological Process, Cellular Component and Molecular Function. Only categories with a significant enrichment in at least one quantile (FDR<0.05) are shown. ![]() Enrichment of gene ontology (GO) categories across candidate genes at different 3P-CLR quantiles in the central-eastern ancestor. The X axis is limited to focus on high-frequency derived alleles B: Absolute DAF difference between central-eastern and Nigeria-Cameroon. A: Unfolded SFS for central, eastern and central and eastern combined. ![]() Allele frequencies of SNPs genome-wide and at different 3P-CLR tail thresholds. Site frequency spectrum of SNPs in candidate windows. The SFS are all indicative of selective sweeps. The central-eastern combined SFS was made by simply pooling all the samples as both subspecies have nearly identical sample sizes (central: 18, eastern: 19). Full unfolded SFS for the whole genome and each 3P-CLR tail threshold in centrals (top left), easterns (top right) and central-eastern combined (bottom). Each ROC curve was generated from 1000 neutral simulations and 1000 selection simulations for each s (s = 0.05, 0.1). Power of 3P-CLR in the ancestral central-eastern population. S1 Appendix: Supplementary Figures A-O and Tables A,B.
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