Archaeal phylogeny:  reexamination of the phylogenetic position of Archaeoglobus fulgidus  in light of certain composition-induced artifacts.
A major and too little recognized source of artifact in phylogenetic analysis of molecular sequence data is compositional difference among sequences.  The problem becomes particularly acute when alignments contain ribosomal RNAs from both mesophilic and thermophilic species.  Among prokaryotes the latter are considerably higher in G + C content than the former, which often results in artificial clustering of thermophilic lineages and their being placed artificially deep in phylogenetic trees.  In this communication we review archaeal phylogeny in the light of this consideration, focusing in particular on the phylogenetic position of the sulfate reducing species Archaeoglobus fulgidus, using both 16S rRNA and 23S rRNA sequences.  The analysis shows clearly that the previously reported deep branching of the A. fulgidus lineage (very near the base of the euryarchaeal side of the archaeal tree) is incorrect, and that the lineage actually groups with a previously recognized unit that comprises the Methanomicrobiales and extreme halophiles.
Woese
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CR
Department of Microbiology, University of Illinois, Urbana 61801, USA.
Achenbach
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Rouviere
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Mandelco
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L
D001105:Archaea / Q000145:classification* / Q000235:genetics; D001483:Base Sequence; D005075:Biological Evolution; D017018:Methanomicrobiales / Q000145:classification / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D012329:RNA, Bacterial / Q000145:classification / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000145:classification / Q000235:genetics*; D012338:RNA, Ribosomal, 23S / Q000145:classification / Q000235:genetics*; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid
D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S