Molecular Biology and Evolution, Vol 16, 817-825, Copyright © 1999 by Society for Molecular Biology and Evolution
H Brinkmann and H Philippe
The 54-kDa signal recognition particle and the receptor SR alpha, two
proteins involved in the cotranslational translocation of proteins, are
paralogs. They originate from a gene duplication that occurred prior to the
last universal common ancestor, allowing one to root the universal tree of
life. Phylogenetic analysis using standard methods supports the generally
accepted cluster of Archaea and Eucarya. However, a new method increasing
the signal-to-noise ratio strongly suggests that this result is due to a
long-branch attraction artifact, with the Bacteria evolving fastest. In
fact, the Archaea/Eucarya sisterhood is recovered only by the fast-evolving
positions. In contrast, the most slowly evolving positions, which are the
most likely to retain the ancient phylogenetic signal, support the
monophyly of prokaryotes. Such a eukaryotic rooting provides a simple
explanation for the high similarity of Archaea and Bacteria observed in
complete-genome analysis, and should prompt a reconsideration of current
views on the origin of eukaryotes.
ORIGINAL ARTICLE
Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies
Phylogenie et Evolution Moleculaires (UPRES-A 8080 CNRS), Universite Paris-Sud, Orsay, France.
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