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MBE Advance Access published online on October 20, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi023
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted October 8, 2004

Research Article

Root of the Eukaryota Tree as Inferred from Combined Maximum Likelihood Analyses of Multiple Molecular Sequence Data

Nobuko Arisue 1, Masami Hasegawa 1, and Tetsuo Hashimoto 2*

1 Department of Biosystems Science, Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa 240-0193, Japan; The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106-8569, Japan
2 Department of Biosystems Science, Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa 240-0193, Japan; The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106-8569, Japan; The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA; Institute of Biological Sciences, University of Tsukuba, Tsukuba 305-8572, Japan

* To whom correspondence should be addressed.
Tetsuo Hashimoto, E-mail: hashi{at}biol.tsukuba.ac.jp


  Abstract

Extensive studies aiming to establish the structure and root of the Eukaryota tree by phylogenetic analyses of molecular sequences resulted in no generally accepted tree so far. In order to re-examine the eukaryotic phylogeny using alternative genes, and to obtain a more robust inference for the root of the tree as well as the relationship among major eukaryotic groups, we sequenced the genes encoding isoleucyl- and valyl-tRNA synthetases, cytosolic-type heat shock protein 90, and the largest subunit of RNA polymerase II from several protists. Combined maximum-likelihood analyses of 22 protein coding genes including the above four genes clearly demonstrated that Diplomonadida and Parabasala shared a common ancestor in the rooted tree of Eukaryota, but only when the fast-evolving sites were excluded from the original data sets. The combined analyses, together with recent findings on the distribution of a fused dihydrofolate reductase-thymidylate synthetase gene, narrowed the possible position of the root of the Eukaryota tree on the branch leading to Opisthokonta or to the common ancestor of Diplomonadida/Parabasala. However, the analyses did not agree with the position of the root located on the common ancestor of Opisthokonta and Amoebozoa, which was argued by Stechmann and Cavalier-Smith [Curr. Biol. 13:R665-666, 2003] based on the presence or absence of a three gene fusion of pyrimidine biosynthetic pathway: carbamoyl-phosphate synthetase II, dihydroorotase, and aspartate carbamoyltransferase. The presence of the three gene fusion recently found in the Cyanidioschyzon merolae (Rhodophyta) genome sequence data supported our analyses against the Stechmann and Cavalier-Smith-rooting in 2003.

Keywords: Diplomonadida; Parabasala; eukaryote evolution; root; maximum likelihood; combined phylogeny.
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