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PMID: 1602493 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Early evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences: phylogenetic coherence and structure of the archaeal domain.

Journal of molecular evolution ·Vol. 34 ·No. 5 ·1992-05-00 ·Pages 396-405

Cammarano P, Palm P, Creti R, Ceccarelli E, Sanangelantoni AM, Tiboni O

Abstract

Phylogenies were inferred from both the gene and the protein sequences of the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria). All treeing methods used (distance-matrix, maximum likelihood, and parsimony), including evolutionary parsimony, support the archaeal tree and disprove the "eocyte tree" (i.e., the polyphyly and paraphyly of the Archaea). Distance-matrix trees derived from both the amino acid and the DNA sequence alignments (first and second codon positions) showed the Archaea to be a monophyletic-holophyletic grouping whose deepest bifurcation divides a Sulfolobus branch from a branch comprising Methanococcus, Halobacterium, and Thermoplasma. Bootstrapped distance-matrix treeing confirmed the monophyly-holophyly of Archaea in 100% of the samples and supported the bifurcation of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 97% of the samples. Similar phylogenies were inferred by maximum likelihood and by maximum (protein and DNA) parsimony. DNA parsimony trees essentially identical to those inferred from first and second codon positions were derived from alternative DNA data sets comprising either the first or the second position of each codon. Bootstrapped DNA parsimony supported the monophyly-holophyly of Archaea in 100% of the bootstrap samples and confirmed the division of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 93% of the bootstrap samples. Distance-matrix and maximum likelihood treeing under the constraint that branch lengths must be consistent with a molecular clock placed the root of the universal tree between the Bacteria and the bifurcation of Archaea and Eukarya. The results support the division of Archaea into the kingdoms Crenarchaeota (corresponding to the Sulfolobus branch and Euryarchaeota). This division was not confirmed by evolutionary parsimony, which identified Halobacterium rather than Sulfolobus as the deepest offspring within the Archaea.

MeSH Terms
Amino Acid Sequence Animals Archaea/classification,genetics Bacteria/classification,genetics Bacterial Proteins/genetics Classification Cricetinae DNA/genetics Dictyostelium/classification,genetics Drosophila melanogaster/classification,genetics Likelihood Functions Mesocricetus/classification,genetics Molecular Sequence Data Peptide Elongation Factor 2 Peptide Elongation Factor G Peptide Elongation Factors/genetics Phylogeny Sequence Alignment Software Species Specificity
Chemicals
Bacterial Proteins Peptide Elongation Factor 2 Peptide Elongation Factor G Peptide Elongation Factors DNA
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Cammarano P
Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Biopatologia Umana, Università di Roma, La Sapienza, Roma, Italy.
Palm P
Creti R
Ceccarelli E
Sanangelantoni A M
Tiboni O
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Article Info
Journal
Journal of molecular evolution
Abbr.
J Mol Evol
ISSN
0022-2844
DOI
10.1007/BF00162996
Published
1992-05-00
Pages
396-405
Language
English
Region
Germany
NLM ID
0360051
Subset
IM
External Links
PubMed source DOI: 10.1007/BF00162996 View journal details
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