Universal trees based on large combined protein sequence data sets

Brown, James R.; Douady, Christophe J.; Italia, Michael J.; Marshall, William E.; Stanhope, Michael J.

doi:10.1038/90129

Cited by 356 publications

(328 citation statements)

References 28 publications

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“…(b) Support for alternative trees of life based on protein-coding genes It has been demonstrated previously (Brown et al 2001;Cox et al 2008) that equally weighted MP analyses of concatenated proteins across the tree of life support the traditional three-domains hypothesis. With our expanded eocyte sampling, this remained the case with both standard amino acid coding (86% BS for a monophyletic archaebacteria-table 3, row A; electronic supplementary material, figure S10) and Dayhoff-recoded data (88% BS-table 3, row G; electronic supplementary material, figure S11).…”

Section: Resultsmentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

Foster

Cox

Embley

2009

Phil. Trans. R. Soc. B

103

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The three-domains tree, which depicts eukaryotes and archaebacteria as monophyletic sister groups, is the dominant model for early eukaryotic evolution. By contrast, the 'eocyte hypothesis', where eukaryotes are proposed to have originated from within the archaebacteria as sister to the Crenarchaeota (also called the eocytes), has been largely neglected in the literature. We have investigated support for these two competing hypotheses from molecular sequence data using methods that attempt to accommodate the across-site compositional heterogeneity and across-tree compositional and rate matrix heterogeneity that are manifest features of these data. When ribosomal RNA genes were analysed using standard methods that do not adequately model these kinds of heterogeneity, the three-domains tree was supported. However, this support was eroded or lost when composition-heterogeneous models were used, with concomitant increase in support for the eocyte tree for eukaryotic origins. Analysis of combined amino acid sequences from 41 protein-coding genes supported the eocyte tree, whether or not composition-heterogeneous models were used. The possible effects of substitutional saturation of our data were examined using simulation; these results suggested that saturation is delayed by among-site rate variation in the sequences, and that phylogenetic signal for ancient relationships is plausibly present in these data.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Foster

Cox

Embley

2009

Phil. Trans. R. Soc. B

103

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“…This stepwise procedure was criticized as potentially biasing the results towards a three-domains topology but also, when the individual alignments were combined, to have introduced alignment errors between domains 19 . Brown et al 45 also inferred trees from a concatenation of a subset of 14 universally conserved proteins, but in this study the tree recovered depended on the phylogenetic method used; the three-domains topology was recovered using maximum parsimony, but model-based methods recovered an eocyte topology.…”

Section: Challenges Of Reconstructing Ancient Relationshipsmentioning

confidence: 97%

An archaeal origin of eukaryotes supports only two primary domains of life

Williams

Foster

Cox

et al. 2013

Nature

443

376

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The discovery of the Archaea and the proposal of the three-domains 'universal' tree, based on ribosomal RNA and core genes mainly involved in protein translation, catalysed new ideas for cellular evolution and eukaryotic origins. However, accumulating evidence suggests that the three-domains tree may be incorrect: evolutionary trees made using newer methods place eukaryotic core genes within the Archaea, supporting hypotheses in which an archaeon participated in eukaryotic origins by founding the host lineage for the mitochondrial endosymbiont. These results provide support for only two primary domains of life-Archaea and Bacteria-because eukaryotes arose through partnership between them.S ince their discovery by Carl Woese and his co-workers in 1977, the Archaea have figured prominently in hypotheses for eukaryotic origins 1,2 . Although similar to Bacteria in terms of cell structure, molecular phylogenies for ribosomal RNA and a small core of genes, that mainly have essential roles in protein translation 3 , suggested that the Archaea were more closely related to the eukaryotic nuclear lineage; that is, to the host cell that acquired the mitochondrion 4 . The idea that Archaea and eukaryotes are more closely related to each other than either is to Bacteria depends on analyses suggesting that the root of the tree should be placed on the bacterial stem, or within the Bacteria 5-12 , implying that the prokaryotes-cells that lack a nucleus-are a paraphyletic group 13 . The main question now debated is whether core components of the eukaryotic nuclear lineage descend from a common ancestor shared with Archaea, as in the three-domains tree 14 (Fig. 1), which is also often called the 'universal tree' or 'tree of life' 15-17 , or from within the Archaea, as proposed by archaeal-host hypotheses for eukaryotic origins 2 . The archaeal-host scenario with the greatest phylogenetic support is the eocyte hypothesis 18 , which proposes a sister-group relationship between eukaryotes and the eocytes (or Crenarchaeota 14 ), one of the major archaeal divisions (Fig. 1). However, the three-domains-eocyte debate remains controversial because different phylogenetic methods have delivered different results, often from the same data 19 . This disagreement is due, at least in part, to the difficulties associated with resolving ancient divergences in phylogenetic trees. Challenges of reconstructing ancient relationshipsA major issue in reconstructing ancient relationships is the strength and quality of historical signal remaining after the millions of years since the divergence of Archaea and eukaryotes. The earliest fossils identified as eukaryotic appeared by about 1.8 billion years ago 20 ; over this enormous span of time, the accumulation of multiple substitutions in DNA and protein sequences might have erased any signal that would allow the relationship between archaeal and eukaryotic core genes to be established 21 . However, more recent simulations and empirical studies suggest that there are reasons to be cautiously optimistic ...

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“…In addition, there is some evidence of gene transfer with eukaryotic organisms (Bond & Francklyn, 2000;Brown et al, 2001). It is highly likely therefore that the treponemes as a taxon will have evolved a range of unique characteristics.…”

Section: Introductionmentioning

confidence: 99%

“…Treponemes are members of the phylum Spirochaetes, a clade often grouped separately from both Gram-positive and Gram-negative bacteria, and believed to have undergone extensive horizontal gene transfer with Archaea (Brown et al, 2001;Ibba et al, 1997;Wolf et al, 2001). In addition, there is some evidence of gene transfer with eukaryotic organisms (Bond & Francklyn, 2000;Brown et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

Treponema denticola biofilm-induced expression of a bacteriophage, toxin–antitoxin systems and transposases

et al. 2010

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Treponema denticola is an oral spirochaete that has been strongly associated with chronic periodontitis. The bacterium exists as part of a dense biofilm (subgingival dental plaque) accreted to the tooth. To determine T. denticola gene products important for persistence as a biofilm we developed a continuous-culture biofilm model and conducted a genome-wide transcriptomic analysis of biofilm and planktonic cells. A total of 126 genes were differentially expressed with a fold change of 1.5 or greater. This analysis identified the upregulation of putative prophage genes in the T. denticola 35405 genome. Intact bacteriophage particles were isolated from T. denticola and circular phage DNA was detected by PCR analysis. This represents the first, to our knowledge, functional bacteriophage isolated from T. denticola, which we have designated Qtd1. In biofilm cells there was also an upregulation of genes encoding several virulence factors, toxinantitoxin systems and a family of putative transposases. Together, these data indicate that there is a higher potential for genetic mobility in T. denticola when growing as a biofilm and that these systems are important for the biofilm persistence and therefore virulence of this bacterium.

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Universal trees based on large combined protein sequence data sets

Cited by 356 publications

References 28 publications

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

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

An archaeal origin of eukaryotes supports only two primary domains of life

Treponema denticola biofilm-induced expression of a bacteriophage, toxin–antitoxin systems and transposases

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