Fig. 4.

—Schematic population-level evolutionary trajectories influenced by reverse-transcription-related recombination. Four hypothetical host lineages (A–D) are depicted, with the corresponding conjectural evolutionary trajectories of retrotransposon clans. Phyletic transformation may take place along a clan’s evolutionary trajectory (continuous and dotted black lines), speeded up by reverse-transcription-related recombination. Common ancestor clans are shown at host divergence points (gray triangles). Clan punctuated speciation may occur when an active founder variant emerge, which is unable to recombine back with the clan (gray circle). A hypothetical event of interspecies transfer is also shown (blue arrow). Note that phyletic transformation may eventually result in diversification, in this case depicted as the lack of recombination between the original clan line in (C) and the invasion clan line from (D). Clan extinction events are also assumed (red cross). For simplicity, the host speciation event for the clan denoted by the phyletic dotted line toward (C) is not shown.