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

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.

[1]  R. Nielsen,et al.  Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA. , 1997, Systematic biology.

[2]  S. Morris.  The fossil record and the early evolution of the Metazoa , 1993, Nature.

[3]  Michael J. Sanderson,et al.  THE RELATIONSHIP BETWEEN HOMOPLASY AND CONFIDENCE IN A PHYLOGENETIC TREE , 1996 .

[4]  R. Gutell,et al.  Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994. , 1993, Nucleic acids research.

[5]  G. Olsen,et al.  Ribosomal RNA: a key to phylogeny , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[6]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[7]  D. Turner,et al.  Improved free-energy parameters for predictions of RNA duplex stability. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Chen,et al.  Precambrian sponges with cellular structures , 1998, Science.

[9]  J. W. Valentine,et al.  Developmental evolution of metazoan bodyplans: the fossil evidence. , 1996, Developmental biology.

[10]  Z. Yang,et al.  Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. , 1996, Molecular biology and evolution.

[11]  Yves Van de Peer,et al.  Evolutionary Relationships Among the Eukaryotic Crown Taxa Taking into Account Site-to-Site Rate Variation in 18S rRNA , 1997, Journal of Molecular Evolution.

[12]  W. Wheeler,et al.  Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications. , 1988, Molecular biology and evolution.

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

[14]  R. Raff,et al.  Deuterostome phylogeny and the sister group of the chordates: evidence from molecules and morphology. , 1994, Molecular biology and evolution.

[15]  A. Knoll,et al.  Three-dimensional preservation of algae and animal embryos in a Neoproterozoic phosphorite , 1998, Nature.

[16]  B. Runnegar.  A molecular‐clock date for the origin of the animal phyla , 1982 .

[17]  D. Erwin.  Metazoan phylogeny and the Cambrian radiation. , 1991, Trends in ecology & evolution.

[18]  A. H. Clark,et al.  Animal evolution , 1981 .

[19]  Z. Yang,et al.  Among-site rate variation and its impact on phylogenetic analyses. , 1996, Trends in ecology & evolution.

[20]  A. Smith.  RNA SEQUENCE DATA IN PHYLOGENETIC RECONSTRUCTION: TESTING THE LIMITS OF ITS RESOLUTION , 1989, Cladistics : the international journal of the Willi Hennig Society.

[21]  J. Felsenstein,et al.  A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. , 1994, Molecular biology and evolution.

[22]  Joseph Felsenstein,et al.  A likelihood approach to character weighting and what it tells us about parsimony and compatibility , 1981 .

[23]  A. Knoll,et al.  Calibrating rates of early Cambrian evolution. , 1993, Science.

[24]  D. Hillis,et al.  Ribosomal DNA: Molecular Evolution and Phylogenetic Inference , 1991, The Quarterly Review of Biology.

[25]  M. P. Cummings,et al.  PAUP* Phylogenetic analysis using parsimony (*and other methods) Version 4 , 2000 .

[26]  D. Ord,et al.  PAUP:Phylogenetic analysis using parsi-mony , 1993 .

[27]  M. Wills,et al.  The cambrian evolutionary ‘explosion’ recalibrated , 1997 .

[28]  W. Brown,et al.  Rates and patterns of base change in the small subunit ribosomal RNA gene. , 1993, Genetics.

[29]  R. Raff,et al.  USING DNA SEQUENCES TO UNRAVEL THE CAMBRIAN RADIATION OF THE ANIMAL PHYLA , 1994 .

[30]  C. Marshall,et al.  The Coming of Age of Molecular Systematics , 1998, Science.

[31]  D. Tautz,et al.  An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order Diptera. , 1997, Molecular biology and evolution.

[32]  A. Meyer,et al.  Evolutionary relationships of the coelacanth, lungfishes, and tetrapods based on the 28S ribosomal RNA gene. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[33]  R. Raff,et al.  Molecular phylogeny of the animal kingdom. , 1988, Science.

[34]  S. Morris.  Why molecular biology needs palaeontology , 1994 .

[35]  R. Doolittle,et al.  Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock , 1996, Science.

[36]  Jeffrey S. Levinton,et al.  Molecular Evidence for Deep Precambrian Divergences Among Metazoan Phyla , 1996, Science.

[37]  Anne Chenuil,et al.  Can the Cambrian explosion be inferred through molecular phylogeny , 1994 .

[38]  Robin Ray Gutell,et al.  Collection of small subunit (16S- and 16S-like) ribosomal RNA structures , 1993, Nucleic Acids Res..

[39]  H. Wada,et al.  Details of the evolutionary history from invertebrates to vertebrates, as deduced from the sequences of 18S rDNA. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[40]  M. Nei,et al.  Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. , 1994, Molecular biology and evolution.

[41]  P. W. Signor.  The Geologic History of Diversity , 1990 .

[42]  R. Gutell,et al.  Comparative anatomy of 16-S-like ribosomal RNA. , 1985, Progress in nucleic acid research and molecular biology.

[43]  C. Marshall.  Substitution bias, weighted parsimony, and amniote phylogeny as inferred from 18S rRNA sequences. , 1992, Molecular biology and evolution.