Epistasis mediates the role of negative frequency-dependent selection in bacterial strain structure
Fig 4
Observed patterns of linkage disequilibrium in several populations.
(a) shows, according to the KEGG annotation of a focal gene, the probability to be in strong linkage disequilibrium (|D’| > 0.6) with any given gene. An asterisk on the diagonal signifies that there is significantly more linkage for that combination (two genes with a shared KEGG category) compared to the rest of the row/column (one gene of that category with genes of different categories). See Fig R in S1 File Supplementary Information for the extension of this figure to all genes, without the 100kb distance filtering. In (b,c), we study the distributions of absolute difference of LD across populations. We show for gene pairs highly linked in the Massachusetts dataset (|D’| > 0.6) the distribution of change in linkage compared to (b) the Southampton dataset or (c) the MaeLa dataset. The observed changes distributions are shown in green and the purple distributions show the changes in the simulated population. Note how there are fewer pairs of genes being shown for the simulated populations, consistent with the observation that there is overall less LD in the simulated than the real dataset (Fig P in S1 File Supplementary Information). See Fig S in S1 File Supplementary Information for all the population pairwise comparisons.