Figure 10: Age distribution of interspersed repeats in the mouse and human genomes.

This is an update of Fig. 18 in the IHGC human genome paper¹. a, b, Distribution for mouse and human of copies of each repeat class in bins corresponding to 1% increments in substitution level calculated using Jukes–Cantor formula (K = -3/4 ln(1 - D_rest^*4/3)) (see Supplementary Information for definition). The first bin for mouse is artificially low because the WGS assembly used for mouse excludes a larger percentage of very recent repeats. c, d, Interspersed repeats grouped into bins of approximately equal time periods after adjusting for the different rates of substitution in the two genomes. On average, the substitution level has been twofold higher in the mouse than in the human lineage (Table 6), but the difference was initially less and has increased over time. The present rates may differ over fourfold. The activity of transposable elements in the mouse lineage has been quite uniform compared with the human lineage, where an overall decline was interrupted temporarily by a burst of Alu activity. The apparent absence of <2% diverged interspersed repeats in mouse is primarily due to the shotgun sequencing strategy; long, closely similar interspersed repeats very often were not assembled. This is supported by an up to tenfold higher concentration of young L1 and ERV elements at the edges of gaps. The gradually decreasing density of repeats beyond a 30% substitution level reflects in part the limits of the detection method.