Figure 4

Phylogenetic relationship from the full length multiple sequence alignment and the predicted region. (A) NJ phylogeny (MEGA3.0 [32]) from the reverse transcriptase full length sequence alignments clusters the genes from the same host: Osser, Tnt1, SIRE-1 and Opie-2 are from plant host, while Copia and 1731 are from Drosophila. Ty1 and Ty5 are from Saccharomyces cerevisiae. (B) Split cluster from the window length of 50 aa (position 166–215) in the predicted region 1 supports the functional subtype split. (C) Functional signal (measured by the bootstrap of node β in panel B), as well as the evolutionary background (measured by the bootstrap of node α in panel A), plotted against the window size. In the window length less than 90, the split-clustering supports the functional subtypes split and the bootstrap value reach the peak in window with length around 50 aa. A mixed topology is detected when window length is longer than 90 aa, measured by the bootstrap (γ) between two major subtrees. When more amino acid sites are included, the bootstrapping value converges to the node α in panel A.