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MBE Advance Access originally published online on October 20, 2004
Molecular Biology and Evolution 2005 22(3):409-420; doi:10.1093/molbev/msi023
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Molecular Biology and Evolution vol. 22 no. 3 © Society for Molecular Biology and Evolution 2004; all rights reserved.

Research Article

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

Nobuko Arisue*,{dagger},1, Masami Hasegawa*,{dagger} and Tetsuo Hashimoto*,{dagger},{ddagger},§

* Department of Biosystems Science, Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa, Japan; {dagger} The Institute of Statistical Mathematics, Minato-ku, Tokyo, Japan; {ddagger} The Rockefeller University; § Institute of Biological Sciences, University of Tsukuba, Tsukuba, Japan

E-mail: hashi{at}biol.tsukuba.ac.jp.

Extensive studies aiming to establish the structure and root of the Eukaryota tree by phylogenetic analyses of molecular sequences have thus far not resulted in a generally accepted tree. 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-tRNA 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 the 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.

Key Words: Diplomonadida • Parabasala • eukaryote evolution • root • maximum likelihood • combined phylogeny


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