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To estimate the age of LINEs, we used the percent mutations from RepBase consensus sequences of each element as reported by RepeatMasker (Repeat masking and classification of transposable elements). We extracted all LINE L2 and L1 matches in the genome and characterized them as regulatorily inactive if they did not overlap a regulatory region we identified in this project, as recently evolved regulatory region if they were recently evolved (The recently evolved and maintained regulomes across species (Fig. (Fig.3a)),3a)), and evolutionarily dynamic regulatory signature if we had found them to align to a regulatory region of another signature (Evolutionary dynamic regulatory signatures (Fig. (Fig.4b4b and Figure S5)). For Fig. Fig.5d,5d, we plotted the mutations for all species combined, while Additional file 1: Figure S10A shows the same data but split by the species it was identified in. The p values were calculated with the ggpubr package in R [94], using the stat_compare_means function and a one-sided Wilcoxon test between all pairs of categories (regulatorily inactive, recently evolved, and evolutionarily dynamic regulatory region).

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