Figure 5.

The tree of life. All 10 bacterial phyla that I currently recognize are shown, with Posibacteria split into subphyla Endobacteria and Actinobacteria (for more detailed classification see Cavalier-Smith 2002a, 2006a). It is uncertain whether Actinobacteria are paraphyletic ancestors of neomura, as shown, or their holophyletic sisters; evidence for this otherwise fully resolved bacterial phylogeny is detailed in Cavalier-Smith (2006a). Bars mark major innovations. Cortical alveoli (CA) unite Plantae and chromalveolates as corticates (Cavalier-Smith 2003b); the bikont basal trifurcation remains unresolved. Ancestrally photosynthetic taxa are in green or purple (it is likely, but not certain, that Chlorobacteria were ancestrally photosynthetic; claims for lateral transfer of photosynthesis among bacteria are unsound; see Cavalier-Smith 2006a). Chlorarachnea within Rhizaria and many euglenoids within Excavata have chloroplasts acquired by green algal enslavement; whether this happened independently (asterisks) or, as I think more likely, in a putative common ancestor of Rhizaria and Excavata (Cavalier-Smith 1999) is uncertain. For clarity, the line connecting cyanobacteria to the ancestral plastid is omitted; dashed lines show the implantation of a red algal slave (R) into the ancestral chromalveolate and mitochondria into the protoeukaryote. Secondary losses of the murein wall within Endobacteria (generating Mollicutes) and Planctobacteria are not shown: nor are more numerous losses of flagella and photosynthesis within phyla. Two hyperthermophilic eubacterial groups (Thermotogales, Aquificales) often misplaced on sequence trees, probably by long-branch attraction to the ancestrally hyperthermophilic archaebacteria, are in red. In addition to characters discussed by Cavalier-Smith (2006a), gene arrangements support the grouping Gracilicutes (including Aquifex) and exclusion of Thermotoga (Kunisawa 2006). Blue blobs mark the four taxa that include species able to make sterols. Phylogenetic arrows are not to scale—either of time or magnitude of change; only topology and the position of the root are significant. Contrary to their misleading name, Archaebacteria is the youngest bacterial phylum by many hundreds of millions of years; methanogenesis arose even later. Glycerol 1-P dehydrogenase probably evolved slightly earlier than indicated as it is also present in the eurybacterium Thermotoga.