Figure 3

Comparison of LINE ages at the three rodent V1Ra/V1Rb clusters to the mouse genome at large. The percentage of total LINE repeat content likely to be lineage-specific with respect to the musculus-spretus split (annotated in RepeatMasker with <2% substitution) or with respect to the mouse-rat split (annotated in RepeatMasker with <10% substitution), as well as older LINE content (>20% substitution), is compared between Mus spretus (sp.V1R, light gray), Mus musculus (mm.V1R, dark gray), and rat (rn.V1R, black), as well as to the Mus musculus genome at large (wider, open rectangles). The assumption that LINE repeats integrating since the mouse-rat split would exhibit <10% substitution is based on an estimate of neutral substitution levels of <20% among orthologous sequences (20% substitution between orthologs = 10% substitution along both lineages since the ancestral node). These data indicate that the majority of dense populations of LINE repeats at these rodent V1R loci integrated around the time of the mouse-rat split (but not since the musculus-spretus split) and that rodent V1R loci have younger LINE repeat content as compared to the genome at large.