The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny.

Abstract

The genes for the protein synthesis elongation factors Tu (EF-Tu) and G (EF-G) are the products of an ancient gene duplication, which appears to predate the divergence of all extant organismal lineages. Thus, it should be possible to root a universal phylogeny based on either protein using the second protein as an outgroup. This approach was originally taken independently with two separate gene duplication pairs, (i) the regulatory and catalytic subunits of the proton ATPases and (ii) the protein synthesis elongation factors EF-Tu and EF-G. Questions about the orthology of the ATPase genes have obscured the former results, and the elongation factor data have been criticized for inadequate taxonomic representation and alignment errors. We have expanded the latter analysis using a broad representation of taxa from all three domains of life. All phylogenetic methods used strongly place the root of the universal tree between two highly distinct groups, the archaeons/eukaryotes and the eubacteria. We also find that a combined data set of EF-Tu and EF-G sequences favors placement of the eukaryotes within the Archaea, as the sister group to the Crenarchaeota. This relationship is supported by bootstrap values of 60-89% with various distance and maximum likelihood methods, while unweighted parsimony gives 58% support for archaeal monophyly.The use of primordially duplicated proteins to root the tree of life was pioneered by Gogarten et al. (1) for the catalytic and regulatory subunits of the V-and F-type ATPases and by Iwabe et al. (2) for the elongation factors Tu (EF-Tu) and G (EF-G). These analyses divide all living organisms into two clades, one consisting of the true bacteria, or eubacteria, and the other consisting of the archaeons and eukaryotes. The ATPase analyses are now complicated by the discoveries of eukaryotic/archaeal (V-type) ATPases in some eubacteria and of a eubacterial (F-type) ATPase in at least one archaebacterium, raising the possibility of multiple horizontal gene transfers (3). The elongation factor analyses have also been criticized, for the limited size of the homologous region, for alignment errors, and for inadequate taxonomic sampling [two eukaryotes, two eubacteria, and one archaebacterium for EF-G; and a few additional animal/fungal and organellar sequences for EF-Tu (4)].We have reanalyzed the elongation factor rooting with the much larger and more broadly representative data base now available for both proteins. This joint analysis now includes three to five representatives of each of the two archaeal kingdoms and a broad sampling of both eukaryotes and eubacteria. We have also modified and expanded the alignment of Iwabe et al. (2) using consensus sequences and crystal structures for both proteins. We find that rooted phylogenies for both elongation factors strongly support the Iwabe/ Gogarten rooting for the universal tree.These analyses address a second major issue, the origin of eukaryotes. Most data argue for a monophyletic Archaea composed of two kingdoms, crenarchaeotes ...

The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods

“…Current versions of both hypotheses hold that the root of the tree of life is either on the branch separating the eubacteria from the archaebacteria and eukaryotes, in line with rooting studies using ancient paralogous genes (e.g. Baldauf et al 1996;Zhaxybayeva et al 2005), or it lies within the eubacteria based on the polarization of cladistic characters or indels (Cavalier-Smith 2006;Skophammer et al 2007). For the purpose of this paper we also follow the convention of a eubacterial root, while recognizing that there is still a healthy debate about its reliability (Philippe & Forterre 1999;Zhaxybayeva et al 2005;Lake et al 2008, and references therein).…”

“…The root of the tree is often considered to be on the branch leading to the eubacteria (e.g. Baldauf et al 1996) or within the eubacteria (Cavalier-Smith 2006;Skophammer et al 2007). Under any of those rootings, the three-domains tree has a monophyletic archaebacteria, where Euryarchaeota group with the Crenarchaeota/eocytes.…”

“…The main evidence for the two competing hypotheses comes from analyses of molecular sequences, often the same ones, at different times and using different methods (Lake 1988;Yang & Roberts 1995;Baldauf et al 1996;Barns et al 1996;Tourasse & Gouy 1999;Brown et al 2001;Katoh et al 2001;Harris et al 2003). It has been suggested that the strongest support for archaebacterial monophyly, and hence the three-domains tree, comes from the simplest methods (Tourasse & Gouy 1999;Katoh et al 2001); the inference being that archaebacterial monophyly might be a phylogenetic artefact of model mis-specification.…”

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

“…This part of the neomuran theory is identical to the original, except that the number of uniquely shared neomuran character suites has doubled since the theory was originally proposed (Cavalier-Smith, 1987b), placing the relationship between eukaryotes and archaebacteria beyond question. To save space, I refer readers to the original paper for more details of the basic rationale of the neomuran T. Cavalier-Smith theory, including the sister relationship of archaebacteria and eukaryotes (rather than an ancestor descendant one, as suggested by Van Valen & Maiorana, 1980 ;Rivera & Lake, 1992 ;Baldauf et al, 1996), the much more ancient ancestral character of eubacteria and the changeover from peptidoglycan to glycoproteins, as well as for diagrams summarizing the cellular transformations (Cavalier-Smith, 1987b). …”

“…In the absence of long-branch attraction, the neomuran theory would expect the EF-1α/EF-Tu clade (orange branches) to be at the base of the eubacterial radiation, as shown by the black arrowhead ; long-branch attraction between this clade and the neomuran clade of the EF-2/G subtree is so severe that it artefactually branches from the excessively long neomuran stem at position 2 instead. The inset shows how long-branch attraction by the neomuran stem will move the observed root into it (open circle) irrespective of whether the true root (closed circle) is in the eubacterial bush, as the fossil record indicates it to be (left), or among the eukaryotes, as Forterre (1995) postulated (right).EF-1α\Tu (Rivera & Lake, 1992 ;Baldauf et al, 1996), which the vast majority of other data does not corroborate. Making trees based on concatenated proteins does not solve the problem of systematic bias caused by quantum evolution if most of the included proteins are similarly biased, as is likely for the ribosomal proteins that probably dominate the trees of Teichmann & Mitchison (1999).…”