Analysis of rare amino acid replacements supports the Coelomata clade.

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.

[1]  A. Oskooi.  Molecular Evolution and Phylogenetics , 2008 .

[2]  M. Rausher,et al.  Relaxed constraint and evolutionary rate variation between basic helix-loop-helix floral anthocyanin regulators in Ipomoea. , 2007, Molecular biology and evolution.

[3]  J. Garcia-Fernández,et al.  Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata. , 2007, Molecular biology and evolution.

[4]  Liran Carmel,et al.  Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements. , 2007, Molecular biology and evolution.

[5]  S. Carroll,et al.  Bushes in the Tree of Life , 2006, PLoS biology.

[6]  S. Carroll,et al.  Animal Evolution and the Molecular Signature of Radiations Compressed in Time , 2005, Science.

[7]  H. Philippe,et al.  Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. , 2005, Molecular biology and evolution.

[8]  J. McInerney,et al.  The Opisthokonta and the Ecdysozoa may not be clades: stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa. , 2005, Molecular biology and evolution.

[9]  J. Dopazo,et al.  Genome-scale evidence of the nematode-arthropod clade , 2005, Genome Biology.

[10]  Richard R. Copley,et al.  Animal Phylogeny: Fatal Attraction , 2005, Current Biology.

[11]  Michael W. Berry,et al.  An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage , 2004, BMC Bioinformatics.

[12]  Patrick Aloy,et al.  Systematic searches for molecular synapomorphies in model metazoan genomes give some support for Ecdysozoa after accounting for the idiosyncrasies of Caenorhabditis elegans , 2004, Evolution & development.

[13]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[14]  E. Koonin,et al.  Coelomata and not Ecdysozoa: evidence from genome-wide phylogenetic analysis. , 2003, Genome research.

[15]  Jodie J. Yin,et al.  A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes , 2004, Genome Biology.

[16]  S. Carroll,et al.  Conflicting phylogenetic signals at the base of the metazoan tree , 2003, Evolution & development.

[17]  T. Gojobori,et al.  Bmc Evolutionary Biology the Evolutionary Position of Nematodes , 2022 .

[18]  P. Holland,et al.  Rare genomic changes as a tool for phylogenetics. , 2000, Trends in ecology & evolution.

[19]  N. Lartillot,et al.  The new animal phylogeny: reliability and implications. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Leo X. Liu,et al.  Large-scale taxonomic profiling of eukaryotic model organisms: a comparison of orthologous proteins encoded by the human, fly, nematode, and yeast genomes. , 1998, Genome research.

[21]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[22]  R. Raff,et al.  Evidence for a clade of nematodes, arthropods and other moulting animals , 1997, Nature.