Figure 4. The proportion of D attributable to the indel decreases after the indel event.

The indels found in comparisons between highly similar strains have a higher proportion of the nucleotide diversity attributable to the indel effect than sets of indels uncovered by pairwise comparisons of progressively more diverged strains for (A) E. coli (Pearson's correlation coefficient, r = −0.769, p = 0.00933), (B) S. paradoxus (Pearson's correlation coefficient, r = −0.963, p = 0.008), and (C) Drosophila (Pearson's correlation coefficient, r = −0.980, p = 0.128). Note that the pair D. simulans/D. sechelia is less diverged than the D. melanogastor/D. melanogastor comparisons because strains used for the latter were inbred with balancer chromosomes, allowing the accumulation of a large amount of mutations (see Materials and Methods).