Analysis of Rare Amino Acid Replacements Supports the Coelomata Clade

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Abstract
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.

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