Journal of Molecular Evolution

, Volume 47, Issue 4, pp 394–405

Limitations of Metazoan 18S rRNA Sequence Data: Implications for Reconstructing a Phylogeny of the Animal Kingdom and Inferring the Reality of the Cambrian Explosion

  • Ehab  Abouheif
  • Rafael  Zardoya
  • Axel  Meyer

DOI: 10.1007/PL00006397

Cite this article as:
Abouheif, E., Zardoya, R. & Meyer, A. J Mol Evol (1998) 47: 394. doi:10.1007/PL00006397

Abstract.

We document the phylogenetic behavior of the 18S rRNA molecule in 67 taxa from 28 metazoan phyla and assess the effects of among-site rate variation on reconstructing phylogenies of the animal kingdom. This empirical assessment was undertaken to clarify further the limits of resolution of the 18S rRNA gene as a phylogenetic marker and to address the question of whether 18S rRNA phylogenies can be used as a source of evidence to infer the reality of a Cambrian explosion. A notable degree of among-site rate variation exists between different regions of the 18S rRNA molecule, as well as within all classes of secondary structure. There is a significant negative correlation between inferred number of nucleotide substitutions and phylogenetic information, as well as with the degree of substitutional saturation within the molecule. Base compositional differences both within and between taxa exist and, in certain lineages, may be associated with long branches and phylogenetic position. Importantly, excluding sites with different degrees of nucleotide substitution significantly influences the topology and degree of resolution of maximum-parsimony phylogenies as well as neighbor-joining phylogenies (corrected and uncorrected for among-site rate variation) reconstructed at the metazoan scale. Together, these data indicate that the 18S rRNA molecule is an unsuitable candidate for reconstructing the evolutionary history of all metazoan phyla, and that the polytomies, i.e., unresolved nodes within 18S rRNA phylogenies, cannot be used as a single or reliable source of evidence to support the hypothesis of a Cambrian explosion.

Key words: 18S rRNA — Molecular phylogeny — Metazoan phylogeny — Cambrian explosion — Among-site rate variation

Copyright information

© Springer-Verlag New York Inc. 1998

Authors and Affiliations

  • Ehab  Abouheif
    • 1
  • Rafael  Zardoya
    • 1
  • Axel  Meyer
    • 1
  1. 1.Department of Ecology and Evolution, State University of New York, Stony Brook, New York 11794-5245, USAUS