Fig. 4.—

Analysis of RIP-like mutations in Gypsy-like retrotransposons. (A) Distributions of the number of RIP-like mutations in sequences either belonging or not belonging to the strain-specific expansion in MvD-Vinadio. (B) Maximum-likelihood phylogeny of Gypsy-like TEs in MvD-Vinadio colored by inferred relative fitness based on local branching index. (C) Number of RIP-like mutations in extant sequences from MvD-Vinadio plotted against relative fitness rank (rank closer to 0 is higher fitness). (D) Number of RIP-like mutations in extant sequences in each quartile of relative fitness (quartile 1 is highest fitness). RIP-like mutations were determined by comparison with the ancestor of all extant sequences inferred by maximum-likelihood .