![]() ![]() ![]() Thermomicrobium, Dehalococcoides) and some apparently deeper-branching lineages known only from environmental DNA sequences and thus of unknown properties. Chlorobacteria comprise photosynthetic 'non-sulphur' green bacteria like Chloroflexus and Heliothrix, some little-studied heterotrophs (e.g. I show here that, in conjunction with palaeontology and sequence trees, the methods of transition analysis and congruence testing demonstrate that archaebacteria are the youngest bacterial phylum and that the root lies within eubacteria, specifically among negibacteria of the superphylum Eobacteria, probably between Chlorobacteria and all other living organisms (Table (Table1 1 summarizes the prokaryotic nomenclature used here, which is slightly revised from previously, primarily by excluding Eurybacteria from Posibacteria). I then apply these methods comprehensively to establish far more closely than ever before where the root of the tree of life actually is. Here I explain how this seemingly intractable problem can be solved by supplementing standard molecular phylogenetic methods with the very same conceptual methods that were originally used to establish 'known outgroups' in well-defined parts of the tree, long before sequencing was invented. However, outgroups for the entire tree are air, rocks and water, not other organisms, vastly increasing the problem, which uniquely involves the origin of life – not just transitions between known types of organism. Usually the root of a subtree is located by comparisons with known outgroups. Establishing the root of a small part of the tree is more straightforward, yet often surprisingly difficult for organisms without plentiful fossils. The wrong answer misleads profoundly in numerous ways. It is also most important to solve correctly because the result colours all interpretations of evolutionary history, influencing ideas of which features are primitive or derived and which branches are deeper and more ancient than others. ![]() It is probably the most difficult problem of all in phylogenetics, but not yet solved – contrary to widespread assumptions. Evolution of the negibacterial outer membrane places the root within Eobacteria (Hadobacteria and Chlorobacteria, both primitively without lipopolysaccharide): as all phyla possessing the outer membrane β-barrel protein Omp85 are highly probably derived, the root lies between them and Chlorobacteria, the only negibacteria without Omp85, or possibly within Chlorobacteria.Ĭorrectly placing the root of the evolutionary tree of all life would enable us to deduce rigorously the major characteristics of the last common ancestor of life. ![]() RNA polymerase and other insertions strongly favour the monophyly of Gracilicutes (Proteobacteria, Planctobacteria, Sphingobacteria, Spirochaetes). Posibacteria are derived from Eurybacteria and ancestral to neomura. Cell wall and flagellar evolution independently locate the root outside Posibacteria (Actinobacteria and Endobacteria), and thus among negibacteria with two membranes. Proteasome evolution shows that the universal root is outside a clade comprising neomura and Actinomycetales (proteates), and thus lies within other eubacteria, contrary to a widespread assumption that it is between eubacteria and neomura. I infer the first fully resolved prokaryote tree, with a basal stem comprising the new infrakingdom Glidobacteria (Chlorobacteria, Hadobacteria, Cyanobacteria), which is entirely non-flagellate and probably ancestrally had gliding motility, and two derived branches (Gracilicutes and Unibacteria/Eurybacteria) that diverged immediately following the origin of flagella. I analyze 13 major transitions within eubacteria, showing how they can all be congruently polarized. Transition analysis, involving comparative/developmental and selective arguments, can polarize major transitions and thereby systematically exclude the root from major clades possessing derived characters and thus locate it previously the 20 shared neomuran characters were thus argued to be derived, but whether the root was within eubacteria or between them and archaebacteria remained controversial. Palaeontology shows that eubacteria are much more ancient than eukaryotes, and, together with phylogenetic evidence that archaebacteria are sisters not ancestral to eukaryotes, implies that the root is not within the neomura. Protein paralogue trees can theoretically place the root, but are contradictory because of tree-reconstruction artefacts or poor resolution ribosome-related and DNA-handling enzymes suggested one between neomura (eukaryotes plus archaebacteria) and eubacteria, whereas metabolic enzymes often place it within eubacteria but in contradictory places. Despite great advances in clarifying the family tree of life, it is still not agreed where its root is or what properties the most ancient cells possessed – the most difficult problems in phylogeny. ![]()
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