Age distribution of retrotransposon subclasses in D. melanogaster. Terminal branch lengths (measured as the number of substitutions per site) are shown as histograms for 279 LTR (dark grey) and 158 non-LTR (light grey) elements in 27 pseudogene-like retrotransposon families.

Fig. 3. Age distribution of LTR retrotransposons based on intra-element LTR-LTR comparisons. Intra-element LTR-LTR distances (measured as the number of substitutions per site) are shown as box plots for 17 LTR families (dark grey) ranked by decreasing median age. Numbers after family names indicate sample sizes of sequences in our alignments. Rectangles indicate the 25th and 75th percentiles, with the line horizontal line representing the median age, whiskers representing 1.5 times the interquartile range, and circles representing outliers beyond this range. The horizontal dashed line represents the estimated divergence time since the split of D. melanogaster and D. simulans from their common ancestor using the molecular clock estimate in ref. 1.

Fig. 4. Correlation of LTR element age estimates based on terminal branch lengths and intra-element LTR-LTR comparisons. Square root transformed distances for terminal branch lengths estimated from unique substitutions are shown on the abscissa and for intra-element LTR-LTR distances are shown on the ordinate. Age estimates based on these independent methods are highly correlated (Pearson's r² = 0.3491, P < 2 × 10^-16). The slope of the linear regression is shown as a solid line and the slope of perfect correlation is shown as a dotted line.

Fig. 5. Age distribution of retrotransposons in different genomic compartments. (A) Box plot of LTR and non-LTR retrotransposon ages in regions of high and low recombination as defined in ref. 1. (B) Box plot of LTR and non-LTR retrotransposon ages in genic and intergenic regions. See Fig. 1 in main text for details.