Molecular Biology and Evolution, Vol 16, 218-233, Copyright © 1999 by Society for Molecular Biology and Evolution
AJ Roger, O Sandblom, WF Doolittle and H Philippe
Elongation factor 1 alpha (EF-1 alpha) is a highly conserved ubiquitous
protein involved in translation that has been suggested to have desirable
properties for phylogenetic inference. To examine the utility of EF-1 alpha
as a phylogenetic marker for eukaryotes, we studied three properties of
EF-1 alpha trees: congruency with other phyogenetic markers, the impact of
species sampling, and the degree of substitutional saturation occurring
between taxa. Our analyses indicate that the EF-1 alpha tree is congruent
with some other molecular phylogenies in identifying both the deepest
branches and some recent relationships in the eukaryotic line of descent.
However, the topology of the intermediate portion of the EF-1 alpha tree,
occupied by most of the protist lineages, differs for different
phylogenetic methods, and bootstrap values for branches are low. Most
problematic in this region is the failure of all phylogenetic methods to
resolve the monophyly of two higher-order protistan taxa, the Ciliophora
and the Alveolata. JACKMONO analyses indicated that the impact of species
sampling on bootstrap support for most internal nodes of the eukaryotic
EF-1 alpha tree is extreme. Furthermore, a comparison of observed versus
inferred numbers of substitutions indicates that multiple overlapping
substitutions have occurred, especially on the branch separating the
Eukaryota from the Archaebacteria, suggesting that the rooting of the
eukaryotic tree on the diplomonad lineage should be treated with caution.
Overall, these results suggest that the phylogenies obtained from EF-1
alpha are congruent with other molecular phylogenies in recovering the
monophyly of groups such as the Metazoa, Fungi, Magnoliophyta, and
Euglenozoa. However, the interrelationships between these and other protist
lineages are not well resolved. This lack of resolution may result from the
combined effects of poor taxonomic sampling, relatively few informative
positions, large numbers of overlapping substitutions that obscure
phylogenetic signal, and lineage- specific rate increases in the EF-1 alpha
data set. It is also consistent with the nearly simultaneous
diversification of major eukaryotic lineages implied by the "big-bang"
hypothesis of eukaryote evolution.
ORIGINAL ARTICLE
An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes
Department of Biochemistry Dalhousie University, Halifax, Nova Scotia, Canada. roger@evol5.mbl.edu
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