Archaeal Phylogeny: Reexamination of the Phylogenetic Position of Archaeoglohus fulgidus in Light of Certain Composition-induced Artifacts

Woese, Carl R.; Achenbach, Laurie A.; Rouvière, Pierre E.; Mandelco, Linda

doi:10.1016/s0723-2020(11)80311-5

Cited by 199 publications

(117 citation statements)

References 36 publications

Supporting

Mentioning

113

Contrasting

Order By: Relevance

“…The euryarchaeal sequences conform to accepted archaeal taxonomy (30,32,33), distinguished by a specific relationship between Methanococcoides burtonii and the genus Methanosarcina, in addition to well supported clusters of the Methanomicrobiales and Methanococcales. The clear sisterhood between the Methanomicrobiales and Archaeoglobus was previously established with rRNA (34,35), ribosomal protein, and transcription factor phylogenies (22,33). A recent analysis of environmental rRNA sequences from a group of anaerobic methane-oxidizing archaea (ANME-1) (31) supports the inclusion of ANME-1 in this group.…”

Section: Resultsmentioning

confidence: 82%

The evolutionary history of Cys-tRNA ^Cys formation

O’Donoghue

Sethi

Woese

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

100

View full text Add to dashboard Cite

The recent discovery of an alternate pathway for indirectly charging tRNA Cys has stimulated a re-examination of the evolutionary history of Cys-tRNA Cys formation. In the first step of the pathway, O-phosphoseryl-tRNA synthetase charges tRNA Cys with O-phosphoserine (Sep), a precursor of the cognate amino acid. In the following step, Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep to Cys in a tRNA-dependent reaction. The existence of such a pathway raises several evolutionary questions, including whether the indirect pathway is a recent evolutionary invention, as might be implied from its localization to the Euryarchaea, or, as evidence presented here indicates, whether this pathway is more ancient, perhaps already in existence at the time of the last universal common ancestral state. A comparative phylogenetic approach is used, combining evolutionary information from protein sequences and structures, that takes both the signature of horizontal gene transfer and the recurrence of the full canonical phylogenetic pattern into account, to document the complete evolutionary history of cysteine coding and understand the nature of this process in the last universal common ancestral state. Resulting from the historical study of tRNA Cys aminoacylation and the integrative perspective of sequence, structure, and function are 3D models of O-phosphoseryl-tRNA synthetase and SepCysS, which provide experimentally testable predictions regarding the identity and function of key active-site residues in these proteins. The model of SepCysS is used to suggest a sulfhydrylation reaction mechanism, which is predicted to occur at the interface of a SepCysS dimer.aminoacyl-tRNA synthetase ͉ cysteine ͉ methanogenic archaea ͉ O-phosphoserine ͉ structure and sequence-based phylogeny

show abstract

Section: Resultsmentioning

confidence: 82%

The evolutionary history of Cys-tRNA ^Cys formation

O’Donoghue

Sethi

Woese

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

100

View full text Add to dashboard Cite

show abstract

“…tree, indicating that the removal of the third codon positions renders MP less sensitive to the compositional bias. Case 3: The use of the slowly evolving transversions is known to avoid artifacts caused by the compositional signal [19], because the purine (and pyrimidine) content is generally homogeneous even when the GCC content is not ( Figure S2 in the supplementary material online). As expected, when the transversions at the first two codon positions are analyzed by MP, the same tree as that obtained with amino acid sequences is recovered ( Figure S5 in the supplementary material online).…”

Section: Congruence Among Phylogenetic Markersmentioning

confidence: 99%

Phylogenomics: the beginning of incongruence?

et al. 2006

View full text Add to dashboard Cite

International audienceUntil recently, molecular phylogenies based on a single or few orthologous genes often yielded contradictory results. Using multiple genes in a large concatenation was proposed to end these incongruences. Here we show that single-gene phylogenies often produce incongruences, albeit ones lacking statistically significant support. By contrast, the use of different tree reconstruction methods on different partitions of the concatenated supergene leads to well-resolved, but real (i.e. statistically significant) incongruences. Gathering a large amount of data is not sufficient to produce reliable trees, given the current limitation of tree reconstruction methods, especially when the quality of data is poor. We propose that selecting only data that contain minimal nonphylogenetic signals takes full advantage of phylogenomics and markedly reduces incongruence

show abstract

“…When nucleotides intentionally are recoded to a 3- or 2-state alphabet in order to focus on a subset of the possible types of substitutions (e.g., transversions [1-3]) or reduce compositional heterogeneity [4], it is no longer appropriate to use model-based phylogenetic methods that rely solely on time-reversible, 4-state Markov models. Instead, one needs to use a 3- or 2-state Markov model to approximate the evolutionary processes for the recoded sequence data.…”

Section: Introductionmentioning

confidence: 99%

“…This requirement was first realised by Phillips and Penny [5], who used a time-reversible 2-state Markov model [6] to analyse RY -recoded nucleotide sequences, and Gibson et al [7], who developed a time-reversible 3-state Markov model to analyse Y -recoded nucleotide sequences. Before these studies, other investigators had used RY -recoded nucleotide sequences to infer the evolutionary relationships among mammals [1-3] and among bacteria [4]. …”

Section: Introductionmentioning

confidence: 99%

Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics

et al. 2014

View full text Add to dashboard Cite

BackgroundUnder a Markov model of evolution, recoding, or lumping, of the four nucleotides into fewer groups may permit analysis under simpler conditions but may unfortunately yield misleading results unless the evolutionary process of the recoded groups remains Markovian. If a Markov process is lumpable, then the evolutionary process of the recoded groups is Markovian.ResultsWe consider stationary, reversible, and homogeneous Markov processes on two taxa and compare three tests for lumpability: one using an ad hoc test statistic, which is based on an index that is evaluated using a bootstrap approximation of its distribution; one that is based on a test proposed specifically for Markov chains; and one using a likelihood-ratio test. We show that the likelihood-ratio test is more powerful than the index test, which is more powerful than that based on the Markov chain test statistic. We also show that for stationary processes on binary trees with more than two taxa, the tests can be applied to all pairs. Finally, we show that if the process is lumpable, then estimates obtained under the recoded model agree with estimates obtained under the original model, whereas, if the process is not lumpable, then these estimates can differ substantially. We apply the new likelihood-ratio test for lumpability to two primate data sets, one with a mitochondrial origin and one with a nuclear origin.ConclusionsRecoding may result in biased phylogenetic estimates because the original evolutionary process is not lumpable. Accordingly, testing for lumpability should be done prior to phylogenetic analysis of recoded data.

show abstract

Archaeal Phylogeny: Reexamination of the Phylogenetic Position of Archaeoglohus fulgidus in Light of Certain Composition-induced Artifacts

Cited by 199 publications

References 36 publications

The evolutionary history of Cys-tRNA ^Cys formation

The evolutionary history of Cys-tRNA ^Cys formation

Phylogenomics: the beginning of incongruence?

Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics

Contact Info

Product

Resources

About

Archaeal Phylogeny: Reexamination of the Phylogenetic Position of Archaeoglohus fulgidus in Light of Certain Composition-induced Artifacts

Cited by 199 publications

References 36 publications

The evolutionary history of Cys-tRNA Cys formation

The evolutionary history of Cys-tRNA Cys formation

Phylogenomics: the beginning of incongruence?

Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics

Contact Info

Product

Resources

About

The evolutionary history of Cys-tRNA ^Cys formation

The evolutionary history of Cys-tRNA ^Cys formation