Figure 6: ML phylogeny for partitioned internal regions from recombinants in S. kudriavzevii, pure Tsu4 FLEs in S. mikatae, S. jurei, and S. uvarum, plus representatives of Ty4 elements.

Panel (A) shows the ML phylogeny for left-side internal region based on 357 distinct alignment sites; Panel (B) for middle internal region based on 367 distinct alignment sites; Panel (C) for right-side internal region based on 423 distinct alignment sites. In all three panels, internal regions from 47 Ty4 and Tsu4 FLEs are included. All trees are midpoint rooted, and visualized in the same tree scale which is shown in units of substitutions per site. Bootstrap supporting values are annotated for key nodes.