Phylogenomic based functional prediction

Original submitted version of Figure 2 from Eisen et al. 1997. 

Phylogenomic based functional prediction - general concept and applied to MutS family.  Four different scenarios are shown.  A) Hypothetical ancient duplication in a gene family with divergence into two distinct functions.  B) More recent duplication (as compared to A).  C) Ancient duplication followed by gene loss. D) Inferred history of the evolution of MiutS genes.  Column 1 shows model for evolution of gene family (skinny red and blue lines) embedded inside the species tree (thick gray lines).  Column 2 shows gene family phylogeny (i.e., the gene tree extracted from the species tree). For the tree in D) MutS-like protein sequences were aligned and a tree of these sequences was generated using molecular phylogenetic methods. The tree of MutS-like proteins (thin lines) is shown embedded within the species tree (thick grey lines). The gene duplication event (marked by an asterisk) occurred prior to the divergence of these bacterial species and led to the presence of two paralogous MutS-like subgroups (distinguished by different colors and gene subscripts a or b). Gene loss in some lineages is indicated when the MutS tree stops within the species tree. right, The MutS tree is extracted from the species tree and untwisted to better show the relaitonships among the different MutS forms. Only one lineage (labeled in blue) includes genes with established roles in mismatch repair. The genes in the second lineage (in red) have no known function. Because the H. pylori gene is a member of this second lineage, it should not be assigned the MutS function.