Figure 3.

Evolutionary relationships of various families of enzymes illustrating the origin of eukaryotic versions within radiations of systems involved in inter- and intra-genomic conflicts. Reconstructed phylogenetic trees are shown for (A) The bacterial radiation of the SWI2/SNF2 ATPases. (B) MORC-like ATPases and (C) The Double-psi beta barrel containing RNA polymerases. Certain clades with multiple families such as the eukaryotic SWI2/SNF2 ATPases, the Topoisomerase ATPase subunits, the cellular DDRP and eukaryotic RdRPs are collapsed into triangles for clarity. Illustrative domain architectures or gene neighborhoods are shown next to the leaf. Genes in gene neighborhoods are shown in block arrows with the arrow head pointing from the 5′ to the 3′ gene. Proteins and gene neighborhoods are labeled by the gene name and species name separated by underscores. The trees represent only the overall topology because they were obtained by a combination of conventional phylogenetic tree construction and structure-based determination of higher-order relationships.