title: The deep roots of the rings of life.
abstract: Reconstructing early evolutionary events like the origins of informational and operational genes, membranes, and photophosphorylation is difficult because early evolutionary events can be masked by subsequent gene flows. Furthermore, as evolution progresses through both Darwinian survival of the fittest (tree-like evolution) and symbiotic/endosymbiotic cooperation (ring-like evolution), trees alone are not adequate to represent Earth's evolutionary history. Here, we reconstruct and root the New Rings of Life and use it as a framework for interpreting early events in the evolution of life. Unlike the three-domain hypothesis, the rings do not fit all life into one of three immutable categories, but rather accommodate new gene flows as novel organisms are discovered. A draft of the Rooted Rings of Life is reconstructed by analyzing the phylogenetic distributions of indels (insertions/deletions) and genes coding for fundamental molecular processes. Their phylogenetic distributions are inconsistent with all trees. Hypergeometric distribution analyses of them strongly localize the root of the rings to a segment of the deepest ring (P < 10(-21) and P < 10(-194)), and whole-genome analyses independently confirm the topology of the rooted rings (P < 7.1 × 10(-6)). The rings identify several large gene flows, including a flow of a thousand genes into the Halobacteria and the Eubacteria, the related photocyte flow, the flow of genes into the last common ancestor of the eocytes and the eukaryotes, and the informational and operational gene flows into the eukaryotes. The rooted rings also chronologically order steps in the evolution of extant taxa, that is, phototrophy evolved from Halobacteria (photophosphorylation) → Heliobacteria (photosynthesis) → Cyanobacteria (oxygenic photosynthesis).
authors.affiliation: Department of MCD Biology, University of California, Los Angeles.
authors.forename: James A
authors.initials: JA
authors.lastname: Lake
authors.forename: Janet S
authors.initials: JS
authors.lastname: Sinsheimer
mesh_terms: D019883:Alkyl and Aryl Transferases / Q000235:genetics; D000595:Amino Acid Sequence; D000619:Aminohydrolases / Q000235:genetics; D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D005075:Biological Evolution; D027081:DNA Gyrase / Q000235:genetics; D027101:DNA Topoisomerase IV / Q000235:genetics; D056890:Eukaryota / Q000235:genetics; D019143:Evolution, Molecular; D051456:Gene Flow; D016678:Genome / Q000235:genetics; D054643:INDEL Mutation; D008969:Molecular Sequence Data; D000069497:Origin of Life; D010788:Photosynthesis / Q000235:genetics; D010802:Phylogeny
chemical_list: D019883:Alkyl and Aryl Transferases; C083737:phosphoglycerol geranylgeranyltransferase; C087227:imidazole glycerol phosphate synthase; D000619:Aminohydrolases; D027101:DNA Topoisomerase IV; D027081:DNA Gyrase
keywords: ether lipids; genomes; hypergeometric distributions; indels; photosynthesis; sporulation