Figure 5

Change in repeat density over time compared with the timing of Abp gene duplications. The mouse genome is shown in (A) and the rat is in (B). Top panels show the approximate timing of Abp gene duplications. Fold-change in density of L1 (center) and ERVII (bottom) repeats are colored depending on whether they are contributed by unique (orange/violet) or shared (grey for both) repeat subfamilies. All are plotted along 1% divergence bins. Divergence for the two repeat families represents divergence from genome-wide consensus (i.e. approximate time when the element was inserted in the Abp region). Dating of the Abp gene duplications was based on the distribution of pairwise half distances between Abp genes using the Kimura 2-parameter mutation model. Given the pattern of unique and shared repeat subfamilies on the genome-wide scale for all repeat families, the mouse-rat split occurred around 20% of divergence from consensus (red line).