Fig. 2

HT of BovB retrotransposons. a Representative BovB tree inferred using nucleotide centroid sequences, where the centroid was the longest intact BovB sequence for each species (min cut-off length 2 kb, max cut-off length 4 kb for species with chimeric BovBs). MUSCLE [50] was used to align sequences, Gblocks [51] was used to extract conserved blocks, FastTree [52] was used to infer a maximum likelihood phylogeny. FastTree branch support values are shown and branches are coloured taxonomically. RTE sequence from Schistosoma mansoni was included as an expected outgroup. b BovB subgroups in bats and frogs. All bat, frog, horse and rhino BovB nucleotide sequences in the range of 2–4 kb were grouped into a file. As above, MUSCLE [50] was used to align sequences, Gblocks [51] was used to extract conserved blocks, FastTree [52] was used to infer a maximum likelihood phylogeny and branches are coloured taxonomically. The Xenopus laevis subgroup (left) contains sequences from Perissodactyla (horses and rhino) and Chiroptera (bats). The Xenopus tropicalis subgroup (right) forms a distinct clade, clustering with the majority of the bat BovB sequences