Figure 4: Maximum likelihood (ML) phylogenetic trees of sampled reverse transcriptase (a), integrase (b), and chromodomains (c) from 39 LTR retrotransposons. The plant-specific clades: Reina, Galadriel, and Tekay, as well as the Tcn1 clade, are indicated. Statistical support was evaluated by bootstrapping (100 replications); bootstrap values within clades are not shown. The changing in position of SM1-Galahad and SM2-Galahad LTR retrotransposons from Selaginella are shown by a gray box for each tree. The results of selection tests are reported for the tested branches, as is the proportion of sites under particular selective regimes for clades/groups. The red color indicates branches where sites under positive selection at the cutoff posterior probability 90% were identified.