Molecular Biology and Evolution, Vol 16, 234-245, Copyright © 1999 by Society for Molecular Biology and Evolution
D Moreira, H Le Guyader and H Philippe
The elongation factor 1 alpha (EF-1 alpha) has become widely employed as a
phylogenetic marker for studying eukaryotic evolution. However, a
disturbing problem, the artifactual polyphyly of ciliates, is always
observed. It has been suggested that the addition of new sequences will
help to circumvent this problem. Thus, we have determined 15 new ciliate
EF-1 alpha sequences, providing for a more comprehensive taxonomic sampling
of this phylum. These sequences have been analyzed together with a
representation of eukaryotic sequences using distance-, parsimony-, and
likelihood-based phylogenetic methods. Such analyses again failed to
recover the monophyly of Ciliophora. A study of the substitution rate
showed that ciliate EF-1 alpha genes exhibit a high evolutionary rate,
produced in part by an increased number of variable positions. This
acceleration could be related to alterations of the accessory functions
acquired by this protein, likely to those involving interactions with the
cytoskeleton, which is very modified in the Ciliophora. The high
evolutionary rate of these sequences leads to an artificial basal emergence
of some ciliates in the eukaryotic tree by effecting a long-branch
attraction artifact that produces an asymmetric topology for the basal
region of the tree. The use of a maximum- likelihood phylogenetic method
(which is less sensitive to long-branch attraction) and the addition of
sequences to break long branches allow retrieval of more symmetric
topologies, which suggests that the asymmetric part of the tree is most
likely artifactual. Therefore, the sole reliable part of the tree appears
to correspond to the apical symmetric region. These kinds of observations
suggest that the general eukaryotic evolution might have consisted of a
massive radiation followed by an increase in the evolutionary rates of
certain groups that emerge artificially as early branches in the asymmetric
base of the tree. Ciliates in the case of the EF-1 alpha genes would offer
clear evidence for this hypothesis.
ORIGINAL ARTICLE
Unusually high evolutionary rate of the elongation factor 1 alpha genes from the Ciliophora and its impact on the phylogeny of eukaryotes
Laboratoire de Biologie Cellulaire, Centre National de la Recherche Scientifique, Universite Paris-Sud, Orsay, France.
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