Figure 5.
Between-block variation (σ2b) in substitution rates within ancestral repeats (A) and flanking sequence (B). Substitution rates are estimated at all sites. Between-block variances are estimated fitting the chromosome as a fixed effect and the block as a random effect across different block sizes, from 25 kb to 125 Mb. Block sizes are plotted on a log10 scale. The 95% confidence intervals of the between-block variance were as estimated by the lme routine of the nlme package in R. The Akaike Information Criterion (AIC) is shown for each fitted model.
