MBE Advance Access published online on February 13, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm029
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Published by Oxford University Press 2007.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Research Article |
Ecdysozoan Clade Rejected by Genome-Wide Analysis of Rare Amino Acid Replacements
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD, USA
Address for correspondence and reprints: E.V.Koonin, NCBI/NLM/NIH, 8600 Rockville Pike, Bldg. 38A, Bethesda, MD 20894, USA. E-mail: koonin{at}ncbi.nlm.nih.gov, Fax: (301) 435-7793, Tel.: (301) 435-5913
Accepted for publication February 7, 2007.
As the number of sequenced genomes from diverse walks of life rapidly increases, phylogenetic analysis is entering a new era: reconstruction of the evolutionary history of organisms on the basis of full-scale comparison of their genomes. In addition to brute force, genome-wide analysis of alignments, rare genomic characters (RGCs) that are thought to comprise derived shared characters of individual clades are increasingly used in genome-wide phylogenetic studies. We propose a new type of RGCs designated RGC_CAMs (after Conserved Amino acids-Multiple substitutions), which are inferred using a genome-scale analysis of protein and underlying nucleotide sequence alignments. The RGC_CAM approach utilizes amino acid residues conserved in major eukaryotic lineages, with the exception of a few species comprising a putative clade, and selects for phylogenetic inference only those amino acid replacements that require 2 or 3 nucleotide substitutions, in order to reduce homoplasy. The RGC_CAM analysis was combined with a procedure for rigorous statistical testing of competing phylogenetic hypotheses. The RGC_CAM method is shown to be robust to branch length differences and taxon sampling. When applied to animal phylogeny, the RGC_CAM approach strongly supports the coelomate clade that unites chordates with arthropods as opposed to the ecdysozoan (molting animals) clade. This conclusion runs against the view of animal evolution that is currently prevailing in the evo-devo community. The final solution to the coelomate-ecdysozoa controversy will require a much larger set of complete genome sequences representing diverse animal taxa. It is expected that RGC_CAM and other RGC-based methods will be crucial for these future, definitive phylogenetic studies.
Key Words: Phylogenetic analysis • cladistics • rare genomic changes • coelomata • ecdysozoa • microsporidia
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