Molecular Biology and Evolution 19:289-301 (2002)
© 2002 Society for Molecular Biology and Evolution
Testing the New Animal Phylogeny: First Use of Combined Large-Subunit and Small-Subunit rRNA Gene Sequences to Classify the Protostomes
School of Biological Sciences, Washington State University
Although the small-subunit ribosomal RNA (SSU rRNA) gene is widely used in the molecular systematics, few large-subunit (LSU) rRNA gene sequences are known from protostome animals, and the value of the LSU gene for invertebrate systematics has not been explored. The goal of this study is to test whether combined LSU and SSU rRNA gene sequences support the division of protostomes into Ecdysozoa (molting forms) and Lophotrochozoa, as was proposed by Aguinaldo et al. (1997) (Nature 387:489) based on SSU rRNA sequences alone. Nearly complete LSU gene sequences were obtained, and combined LSU + SSU sequences were assembled, for 15 distantly related protostome taxa plus five deuterostome outgroups. When the aligned LSU + SSU sequences were analyzed by tree-building methods (minimum evolution analysis of LogDet-transformed distances, maximum likelihood, and maximum parsimony) and by spectral analysis of LogDet distances, both Ecdysozoa and Lophotrochozoa were indeed strongly supported (e.g., bootstrap values >90%), with higher support than from the SSU sequences alone. Furthermore, with the LogDet-based methods, the LSU + SSU sequences resolved some accepted subgroups within Ecdysozoa and Lophotrochozoa (e.g., the polychaete sequence grouped with the echiuran, and the annelid sequences grouped with the mollusc and lophophorates)—subgroups that SSU-based studies do not reveal. Also, the mollusc sequence grouped with the sequences from lophophorates (brachiopod and phoronid). Like SSU sequences, our LSU + SSU sequences contradict older hypotheses that grouped annelids with arthropods as Articulata, that said flatworms and nematodes were basal bilateralians, and considered lophophorates, nemerteans, and chaetognaths to be deuterostomes. The position of chaetognaths within protostomes remains uncertain: our chaetognath sequence associated with that of an onychophoran, but this was unstable and probably artifactual. Finally, the benefits of combining LSU with SSU sequences for phylogenetic analyses are discussed: LSU adds signal, it can be used at lower taxonomic levels, and its core region is easy to align across distant taxa—but its base frequencies tend to be nonstationary across such taxa. We conclude that molecular systematists should use combined LSU + SSU rRNA genes rather than SSU alone.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. Paps, J. Baguna, and M. Riutort Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes Proc R Soc B, April 7, 2009; 276(1660): 1245 - 1254. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Helmkampf, I. Bruchhaus, and B. Hausdorf Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept Proc R Soc B, August 22, 2008; 275(1645): 1927 - 1933. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. J Telford, S. J Bourlat, A. Economou, D. Papillon, and O. Rota-Stabelli The evolution of the Ecdysozoa Phil Trans R Soc B, April 27, 2008; 363(1496): 1529 - 1537. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. H. Struck and F. Fisse Phylogenetic Position of Nemertea Derived from Phylogenomic Data Mol. Biol. Evol., April 1, 2008; 25(4): 728 - 736. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Stoeck, S. Jost, and J. Boenigk Multigene phylogenies of clonal Spumella-like strains, a cryptic heterotrophic nanoflagellate, isolated from different geographical regions Int J Syst Evol Microbiol, March 1, 2008; 58(3): 716 - 724. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Q. Matus, K. M. Halanych, and M. Q. Martindale The Hox gene complement of a pelagic chaetognath, Flaccisagitta enflata Integr. Comp. Biol., December 1, 2007; 47(6): 854 - 864. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Hausdorf, M. Helmkampf, A. Meyer, A. Witek, H. Herlyn, I. Bruchhaus, T. Hankeln, T. H. Struck, and B. Lieb Spiralian Phylogenomics Supports the Resurrection of Bryozoa Comprising Ectoprocta and Entoprocta Mol. Biol. Evol., December 1, 2007; 24(12): 2723 - 2729. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Zheng, I. B. Rogozin, E. V. Koonin, and T. M. Przytycka Support for the Coelomata Clade of Animals from a Rigorous Analysis of the Pattern of Intron Conservation Mol. Biol. Evol., November 1, 2007; 24(11): 2583 - 2592. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. B. Rogozin, Y. I. Wolf, L. Carmel, and E. V. Koonin Ecdysozoan Clade Rejected by Genome-Wide Analysis of Rare Amino Acid Replacements Mol. Biol. Evol., April 1, 2007; 24(4): 1080 - 1090. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Valles and J. L. Boore Lophotrochozoan mitochondrial genomes Integr. Comp. Biol., August 1, 2006; 46(4): 544 - 557. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Giribet, A. Okusu, A. R. Lindgren, S. W. Huff, M. Schrodl, and M. K. Nishiguchi Evidence for a clade composed of molluscs with serially repeated structures: Monoplacophorans are related to chitons PNAS, May 16, 2006; 103(20): 7723 - 7728. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Giribet and G. D Edgecombe Conflict between datasets and phylogeny of centipedes: an analysis based on seven genes and morphology Proc R Soc B, March 7, 2006; 273(1586): 531 - 538. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. H. Struck, G. Purschke, and K. M. Halanych Phylogeny of Eunicida (Annelida) and Exploring Data Congruence Using a Partition Addition Bootstrap Alteration (PABA) Approach Syst Biol, February 1, 2006; 55(1): 1 - 20. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. G. Collins, P. Cartwright, C. S. McFadden, and B. Schierwater Phylogenetic Context and Basal Metazoan Model Systems Integr. Comp. Biol., August 1, 2005; 45(4): 585 - 594. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. V. Lavrov and B. F. Lang Poriferan mtDNA and Animal Phylogeny Based on Mitochondrial Gene Arrangements Syst Biol, August 1, 2005; 54(4): 651 - 659. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-x. Luan, J. M. Mallatt, R.-d. Xie, Y.-m. Yang, and W.-y. Yin The Phylogenetic Positions of Three Basal-Hexapod Groups (Protura, Diplura, and Collembola) Based on Ribosomal RNA Gene Sequences Mol. Biol. Evol., July 1, 2005; 22(7): 1579 - 1592. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. J. Peterson, M. A. McPeek, and D. A. D. Evans Tempo and mode of early animal evolution: inferences from rocks, Hox, and molecular clocks Paleobiology, June 1, 2005; 31(2_Suppl): 36 - 55. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Philippe, N. Lartillot, and H. Brinkmann Multigene Analyses of Bilaterian Animals Corroborate the Monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia Mol. Biol. Evol., May 1, 2005; 22(5): 1246 - 1253. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. K. Philip, C. J. Creevey, and J. O. McInerney 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 Mol. Biol. Evol., May 1, 2005; 22(5): 1175 - 1184. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J Telford, M. J Wise, and V. Gowri-Shankar Consideration of RNA Secondary Structure Significantly Improves Likelihood-Based Estimates of Phylogeny: Examples from the Bilateria Mol. Biol. Evol., April 1, 2005; 22(4): 1129 - 1136. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. W. Roy and W. Gilbert Resolution of a deep animal divergence by the pattern of intron conservation PNAS, March 22, 2005; 102(12): 4403 - 4408. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Papillon, Y. Perez, X. Caubit, and Y. Le Parco Identification of Chaetognaths as Protostomes Is Supported by the Analysis of Their Mitochondrial Genome Mol. Biol. Evol., November 1, 2004; 21(11): 2122 - 2129. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Bertrand, F. G. Brunet, H. Escriva, G. Parmentier, V. Laudet, and M. Robinson-Rechavi Evolutionary Genomics of Nuclear Receptors: From Twenty-Five Ancestral Genes to Derived Endocrine Systems Mol. Biol. Evol., October 1, 2004; 21(10): 1923 - 1937. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Philippe, E. A. Snell, E. Bapteste, P. Lopez, P. W. H. Holland, and D. Casane Phylogenomics of Eukaryotes: Impact of Missing Data on Large Alignments Mol. Biol. Evol., September 1, 2004; 21(9): 1740 - 1752. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. A. Gontcharov, B. Marin, and M. Melkonian Are Combined Analyses Better Than Single Gene Phylogenies? A Case Study Using SSU rDNA and rbcL Sequence Comparisons in the Zygnematophyceae (Streptophyta) Mol. Biol. Evol., March 1, 2004; 21(3): 612 - 624. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. N. Austad On Herrera and Jagadeeswaran's "Annual Fish as a Genetic Model for Aging" J. Gerontol. A Biol. Sci. Med. Sci., February 1, 2004; 59(2): B99 - 100. [Full Text] [PDF]
|
|
|
|
 |
|
 Y. I. Wolf, I. B. Rogozin, and E. V. Koonin Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic Analysis Genome Res., January 1, 2004; 14(1): 29 - 36. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Balavoine and A. Adoutte The Segmented Urbilateria: A Testable Scenario Integr. Comp. Biol., February 1, 2003; 43(1): 137 - 147. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Ruiz-Trillo, J. Paps, M. Loukota, C. Ribera, U. Jondelius, J. Baguna, and M. Riutort A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians PNAS, August 20, 2002; 99(17): 11246 - 11251. [Abstract] [Full Text] [PDF]
|
|