Phylogenetic relationships among retrotransposons and the distribution of putative translational regulatory mechanisms. The four major clusters of retrotransposons are labeled Ty1/copia, Ty3/gypsy, BEL, and DIRS. Retrotransposons in the core data set are labeled with their names at the end of the branches. Retrotransposons in the expanded data set begin with an abbreviation for the host organism: Ath, A. thaliana; Dmel, D. melanogaster; Sp, S. pombe; Calb, C. albicans; Cer, C. elegans. Following the host species abbreviation are the chromosome number and nucleotide position for given insertions. Branch coloring indicates the gene organization of gag and pol: green, single ORF elements; blue, pol in the +1 frame; red, pol in the −1 frame; pink, a stop codon between gag and pol. Shading identifies the kingdom from which the retrotransposons originate. The clades labeled A–D are described in Figure 2.
