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MBE Advance Access published online on November 24, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj068
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted November 15, 2005

Research Article

Comprehensive Multi-Gene Phylogenies of Excavate Protists Reveal the Evolutionary Positions of ‘Primitive’ Eukaryotes

Alastair G. B. Simpson 1 *, Yuji Inagaki 2, and Andrew J. Roger 3

1 Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4J1, Canada
2 Center for Computational Sciences and Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
3 Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 1X5, Canada

* To whom correspondence should be addressed.
Alastair G. B. Simpson, E-mail: alastair.simpson{at}dal.ca


  Abstract

Many of the protists thought to represent the deepest branches on the eukaryotic tree are assigned to a loose assemblage called the ‘excavates’. This includes the mitochondrion-lacking diplomonads and parabasalids (e.g. Giardia, Trichomonas), and the jakobids (e.g. Reclinomonas). We report the first multi-gene phylogenetic analyses to include a comprehensive sampling of excavate groups (six nuclear-encoded protein-coding genes, nine of the 10 recognized excavate groups). Excavates coalesce into three clades with relatively strong maximum likelihood bootstrap support. Only the phylogenetic position of Malawimonas is uncertain. Diplomonads, parabasalids and the free-living amitochondriate protist Carpediemonas are closely related to each other. Two other amitochondriate excavates, oxymonads and Trimastix, form the second monophyletic group. The third group is comprised of Euglenozoa (e.g. trypanosomes), Heterolobosea and jakobids. Unexpectedly, jakobids appear to be specifically related to Heterolobosea. This tree topology calls into question the concept of Discicristata as a super-group of eukaryotes united by discoidal mitochondrial cristae, and makes it implausible that jakobids represent an independent early-diverging eukaryotic lineage. The close jakobids-Heterolobosea-Euglenozoa connection demands complex evolutionary scenarios to explain the transition between the presumed ancestral bacterial-type mitochondrial RNA polymerase found in jakobids and the phage-type protein in other eukaryotic lineages, including Euglenozoa and Heterolobosea.

Keywords: Eukaryote Evolution; Giardia; Mitochondria; Protozoa; Tubulin.
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