title: Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata.
abstract: There is growing interest in the use of alternative, more slowly-evolving RGCs (rare genomic changes). Recently, Rogozin and coauthors (Rogozin et al. 2007) proposed a novel phylogenetic method employing rare amino acid changes, RGC-CAMs (rare genomic changes-conserved amino acids-multiple substitutions). They applied their method to 694 sets of eukaryotic orthologs in order to distinguish the relationship between nematodes, arthropods and deuterostomes. They concluded that such rare amino acid changes were consistent with the Coelomata hypothesis, which groups arthropods and deuterostomes to the exclusion of nematodes. Here we use newly available genomic sequences from Nematostella vectensis, a basal metazoan, and from Brugia malayi, an additional nematode. We show that the apparent support for Coelomata is likely to be the result of the rapid rate of evolution leading to Caenorhabditis nematodes. Including the additional species paints a very different picture, with 13 remaining characters consistent with Ecdysozoa versus only 1 consistent with Coelomata.
authors.affiliation: Departament de Genètica, Universitat de Barcelona, Barcelona, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Irimia
authors.forename: Ignacio
authors.initials: I
authors.lastname: Maeso
authors.forename: David
authors.initials: D
authors.lastname: Penny
authors.forename: Jordi
authors.initials: J
authors.lastname: Garcia-Fernàndez
authors.forename: Scott William
authors.initials: SW
authors.lastname: Roy
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001181:Arthropods / Q000235:genetics*; D017173:Caenorhabditis elegans / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D009348:Nematoda / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics*; D010802:Phylogeny; D017386:Sequence Homology, Amino Acid