FIG. 2.—

Ancient paralogs quartet analysis. (a) Ancient paralogs are defined as paralogous proteins that were duplicated in the common ancestor of archaebacteria and eubacteria. (b) For a phylogenetic tree of four OTUs (operational taxonomic units), there are three possible topologies. No LGT among the major taxa results in topology t_vert (in black), whereas evolution by LGT may result in any of the other two topologies (in gray). (c) Here, we tested two different rate models for the t_vert topology: in the r_global model all OTUs evolve in the same rates. In the r_lineage model, OTUs from the same lineage evolve in the same rate, which differs between the lineages.