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MBE Advance Access originally published online on October 5, 2007
Molecular Biology and Evolution 2007 24(12):2594-2597; doi:10.1093/molbev/msm218
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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.

Letter

Analysis of Rare Amino Acid Replacements Supports the Coelomata Clade

Igor B. Rogozin, Yuri I. Wolf, Liran Carmel and Eugene V. Koonin

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland

E-mail: koonin{at}ncbi.nlm.nih.gov.

Accepted for publication September 27, 2007.

The recent analysis of a novel class of rare genomic changes, RGC_CAMs (after conserved amino acids—multiple substitutions), supported the Coelomata clade of animals as opposed to the Ecdysozoa clade (Rogozin et al. 2007). A subsequent reanalysis, with the sequences from the sea anemone Nematostella vectensis included in the set of outgroup species, suggested that this result was an artifact caused by reverse amino replacements and claimed support for Ecdysozoa (Irimia et al. 2007). We show that the internal branch connecting the sea anemone to the bilaterian animals is extremely short, resulting in a weak statistical support for the Coelomata clade. Direct estimation of the level of homoplasy, combined with taxon sampling with different sets of outgroup species, reinforces the support for Coelomata, whereas the effect of reversals is shown to be relatively minor.

Key Words: phylogenetic analysis • cladistics • rare genomic changes • coelomata • ecdysozoa

Lauren McIntyre, Associate Editor


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