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To identify transposable elements in all genomes, we used RepeatMasker version open-4.0.7 [95] using the crossmatch search engine and RepBase Release 20,170,127 [96]. For each species we ran RepeatMasker in the default mode, specifying the species’ scientific name (macaque, “Macaca mulatta”; narmoset, “Callithrix jacchus”; mouse, “Mus musculus”; rat, “Rattus norvegicus”; rabbit, “Oryctolagus cuniculus”; pig, “Sus scrofa”; dog, “Canis familiaris”; cat, “Felis catus”; horse, “Equus caballus”; opossum, “Monodelphis domestica”). For figures, we used DNA, LINE, LTR, and SINE categories from RepBase annotation. These correspond to different levels of transposable element classification hierarchies [23], but still represent exclusive non-overlapping sets of the hierarchy. Namely, DNA corresponds to the DNA transposons class, while all other groups belong to the retrotransposon classes. The LTRs are a subclass of retrotransposons, while the LINEs and SINEs are superfamilies of the non-LTR subclass of retrotransposons.

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