MBE Advance Access published online on June 2, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh182
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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1 Phylogénie, Bioinformatique et Génome, UMR 7622 CNRS, Université Pierre et Marie Curie, 9 quai St Bernard Bât. C - 75005 Paris - France
Resolving the relationships between Metazoa and other eukaryotic groups as well as between metazoan phyla is central to the understanding of the origin and evolution of animals. The current view is based on limited data sets, either a single gene with many species (e.g. ribosomal RNA) or many genes but with only a few species. Since a reliable phylogenetic inference simultaneously requires numerous genes and numerous species, we assembled a very large data set of 129 orthologous proteins ( Key Words:
molecular phylogeny, multi-gene analysis, missing data, choanoflagellata
Original Articles
Phylogenomics of Eukaryotes: The Impact of Missing Data on Large Alignments
2 School of Animal and Microbial Sciences, The University of Reading, Whiteknights PO Box 228, Reading RG6 6AJ, United Kingdom
3 Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
Abstract 
30,000 aligned amino acid positions) for 36 eukaryotic species. Included in the alignments are data from the choanoflagellate Monosiga ovata, obtained through the sequencing of about 1,000 cDNAs. We provide conclusive support for choanoflagellates as the closest relative of animals and for fungi as the second closest. The monophyly of Plantae and chromalveolates was recovered but without a strong statistical support. Within animals, in contrast to the monophyly of Coelomata observed in several recent large-scale analyses, we recovered a paraphyletic Coelamata, with nematodes and platyhelminths nested within it. To include a diverse sample of organisms, data from EST projects were used for several species, resulting in a large amount of missing data in our alignment (about 25%). Using different approaches, we verify that the inferred phylogeny is not very sensitive to these missing data. Therefore, this large data set provides a reliable phylogenetic framework for studying eukaryotic and animal evolution and will be easily extendable when large amounts of sequence information become available from a broader taxonomic range.
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