Fig. 5

Genome occurrence and evolutionary history of manually curated LINE families. RepeatMasker results obtained using our manually curated set of LINEs (see the “Manual curation of LINEs, SINEs, and DDE/D-related transposons” and “Genome annotation of LINEs and SINEs using manually curated libraries and phylogenetic inference of curated LINE families” sections). A Genome coverage of curated families for each LINE clade/type. B CpG-corrected Kimura distance of each insertion from its consensus sequence as a proxy for the time of the transposition event for each LINE superfamily. The X-axes range from 0 to 50 while the Y-axes are on different scales for each specie/superfamily and represent the relative genome coverage. Numbers above the graphs represent the number of families for each species that possess insertions both in recent time (divergence < 5) and in the past (divergence > 30) requiring at least 30 annotated insertions in the recent divergence bin and 5 in the old one. Only 3′-anchored insertions longer than 100 bp were considered for this latest purpose (see the “Genome annotation of LINEs and SINEs using manually curated libraries and phylogenetic inference of curated LINE families” section)