Accounting for Evolutionary Rate Variation among Sequence Sites Consistently Changes Universal Phylogenies Deduced from rRNA and Protein-Coding Genes

Phylogenetic analyses of gene and protein sequences have led to two major competing views of the universal phylogeny, the evolutionary tree relating the three kinds of living organisms, Bacteria, Archaea, and Eukarya. In the first scheme, called “the archaebacterial tree,” organisms of the same type...

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Bibliographic Details
Published in:Molecular phylogenetics and evolution 1999-10, Vol.13 (1), p.159-168
Main Authors: Tourasse, Nicolas J., Gouy, Manolo
Format: Article
Language:English
Subjects:
Animals
Archaea
Archaea - genetics
Bacteria - genetics
DNA-Directed RNA Polymerases - genetics
Evolution, Molecular
evolutionary distance
Genes
Humans
Life Sciences
Likelihood Functions
long-branch attraction
maximum-likelihood
Other
Phylogeny
Proteins - genetics
ribosomal RNA
RNA, Ribosomal - genetics
Space life sciences
substitution rate variation among sites
universal phylogeny
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Summary:Phylogenetic analyses of gene and protein sequences have led to two major competing views of the universal phylogeny, the evolutionary tree relating the three kinds of living organisms, Bacteria, Archaea, and Eukarya. In the first scheme, called “the archaebacterial tree,” organisms of the same type are clustered together. In the second scenario, called “the eocyte tree,” the archaeal phylum of Crenarchaeota is more closely related to eukaryotes than are other Archaea. A major property of the evolution of functional ribosomal and protein-encoding genes is that the rate of nucleotide and amino acid substitution varies across sequence sites. Here, using distance-based and maximum-likelihood methods, we show that universal phylogenies of ribosomal RNAs and RNA polymerases built by ignoring this variation are biased toward the archaebacterial tree because of attraction between long branches. In contrast, taking among-site rate variability into account gives support for the eocyte tree.
ISSN:1055-7903
1095-9513
DOI:10.1006/mpev.1999.0675