Structural rRNA characters support monophyly of raptorial limbs and paraphyly of limb specialization in water fleas

Proceedings of the Royal Society B: Biological Sciences

Volumn 270, Issue 1518, 2003, Pages 887-896

  Swain, Timothy D ^a,b   Taylor, Derek J ^a  

^a UNIVERSITY AT BUFFALO   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

Author keywords

Arthropod limb evolution; Molecular morphometrics; Phylogeny; rRNA secondary structure

Indexed keywords

RIBOSOME RNA; WATER;

ARTHROPOD; EVOLUTION; LIMB; PHYLOGENY;

ARTICLE; BODY BUILD; ECOLOGICAL SPECIALIZATION; FLEA; GENE SEQUENCE; LIMB; MOLECULAR BIOLOGY; MONOPHYLY; MORPHOMETRICS; PARAPHYLY; PHYLOGENY; PRIORITY JOURNAL; RAPTOR; RNA ANALYSIS; RNA STRUCTURE; STRUCTURE ANALYSIS;

ARTHROPODA; CLADOCERA; RAPTORES; SIPHONAPTERA (FLEAS);

EID: 0038703751     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2002.2297     Document Type: Article

References (41)

1. Alonso, M. 1996 Crustacea, Branchiopoda. Fauna Iberica. Madrid: Museo Nacional de Ciencas Naturales CSIC.
2. Billoud, B., Guerrucci, M. A., Masselot, M. & Deutsch, J. S. 2000 Cirripede phylogeny using a novel approach: molecular morphometrics. Mol. Biol. Evol. 17, 1435-1445.
3. Braband, A., Richter, S., Hiesel, R. & Scholtz, G. 2002 Phylogenetic relationships within the Phyllopoda (Crustacea, Branchiopoda) based on mitochondrial and nuclear markers. Mol. Phylogenet. Evol. 25, 229-244.
4. Caetano-Anolles, G. 2001 Novel strategies to study the role of mutation and nucleic acid structure in evolution. Plant Cell Tissue Organ Cult. 67, 115-132.
5. Caetano-Anolles, G. 2002a Evolved RNA secondary structure and the rooting of the universal tree of life. J. Mol. Evol. 54, 333-345.
6. Caetano-Anolles, G. 2002b Tracing the evolution of RNA structure in ribosomes. Nucleic Acids Res. 30, 2575-2587.
7. Cisne, J. L. 1974 Evolution of world fauna of aquatic free-living arthropods. Evolution 28, 337-366.
8. Collins, L. J., Moulton, V. & Penny, D. 2000 Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP. J. Mol. Evol. 51, 194-204.
9. Crease, T. J. & Colbourne, J. K. 1998 The unusually long small-subunit ribosomal RNA of the crustacean, Daphnia pulex: sequence and predicted secondary structure. J. Mol. Evol. 46, 307-313.
10. Crease, T. J. & Taylor, D. J. 1998 The origin and evolution of variable-region helices in V4 and V7 of the small-subunit ribosomal RNA of branchiopod crustaceans. Mol. Biol. Evol. 15, 1430-1446.
11. De Rijk, P. & De Wachter, R. 1993 DCSE, an interactive tool for sequence alignment and secondary structure research. Comput. Applic. Biosci. 9, 735-740.
12. De Rijk, P. & De Wachter, R. 1997 RnaViz, a program for the visualisation of RNA secondary structure. Nucleic Acids Res. 25, 4679-4684.
13. De Rijk, P., Wuyts, J., Van De Peer, Y., Winkelmans, T. & De Wachter, R. 2000 The European large subunit ribosomal RNA database. Nucleic Acids Res. 28, 177-178.
14. Doyle, J. J. & Doyle, J. L. 1987 A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11-15.
15. Galant, R. & Carroll, S. B. 2002 Evolution of a transcriptional repression domain in an insect Hox protein. Nature 415, 910-913.
16. Gutell, R. R., Lee, J. C. & Cannone, J. J. 2002 The accuracy of ribosomal RNA comparative structure models. Curr. Opin. Struct. Biol. 12, 301-310.
17. Hall, T. A. 1999 BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Series 41, 95-98.
18. Hanner, R. & Fugate, M. 1997 Branchiopod phylogenetic reconstruction from 12S rDNA sequence data. J. Crust. Biol. 17, 174-183.
19. Hillis, D. M., Bull, J. J., White, M. E., Badgett, M. R. & Molineux, I. J. 1992 Experimental phylogenetics: generation of a known phylogeny. Science 255, 589-592.
20. Huelsenbeck, J. P. & Ronquist, F. 2001 MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
21. Kerfoot, C. W. & Lynch, M. 1987 Branchiopod communities: associations with planktivorous fish in space and time. In Predation: direct and indirect impacts on aquatic communities (ed. W. C. Kerfoot & A. Sih), pp. 367-378. Hanover: University Press of New England.
22. Lankester, E. R. 1904 The structure and classification of the Arthropoda. Q. J. Microsc. Sci. 47, 523-582.
23. Martin, J. W. & Cash-Clark, C. E. 1995 The external morphology of the Onychopod cladoceran genus Bythotrephes (Crustacea, Branchiopoda, Onychopoda, Cercopagididae), with notes on the morphology and phylogeny of the order Onychopoda. Zool. Scripta 24, 61-90.
24. Mathews, D. H., Sabina, J., Zuker, M. & Turner, D. H. 1999 Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940.
25. Olesen, J., Richter, S. & Scholtz, G. 2001 The evolutionary transformation of phyllopodous to stenopodous limbs in the Branchiopoda (Crustacea) - is there a common mechanism for early limb development in arthropods? Int. J. Devl Biol. 45, 869-876.
26. Omilian, A. R. & Taylor, D. J. 2001 Rate acceleration and long-branch attraction in a conserved gene of cryptic daphniid (Crustacea) species. Mol. Biol. Evol. 18, 2201-2212.
27. Posada, D. & Crandall, K. A. 1998 MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818.
28. Richter, S., Braband, A., Aladin, N. & Scholtz, G. 2001 The phylogenetic relationships of 'predatory water-fleas' (Cladocera: Onychopoda, Haplopoda) inferred from 12S rDNA. Mol. Phylogenet. Evol. 19, 105-113.
29. Roessler, E. W. 1995 Review of Colombian Conchostraca (Crustacea) - ecological aspects and life-cycles - family Cyclestheriidae. Hydrobiologia 298, 113-124.
30. Ronshaugen, M., McGinnis, N. & McGinnis, W. 2002 Hox protein mutation and macroevolution of the insect body plan. Nature 415, 914-917.
31. Sanderson, M. J. & Shaffer, H. B. 2002 Troubleshooting molecular phylogenetic analyses. A. Rev. Ecol. Syst. 33, 49-72.
32. Schwenk, K., Sand, A., Boersma, M., Brehm, M., Mader, E., Offerhaus, D. & Spaak, P. 1998 Genetic markers, genealogies and biogeographic patterns in cladocera. Aquat. Ecol. 32, 37-51.
33. Shiga, Y., Yasumoto, R., Yamagata, H. & Hayashi, S. 2002 Evolving role of Antennapedia protein in arthropod limb patterning. Development 129, 3555-3561.
34. Spears, T. & Abele, L. G. 2000 Branchiopod monophyly and interordinal phylogeny inferred from 18S ribosomal DNA. J. Crust. Biol. 20, 1-24.
35. Swofford, D. L. 2000 PAUP*: phylogenetic analysis using parsimony (* and other methods) v. 4.0b4a. Sunderland, MA: Sinauer.
36. Tamura, K. & Nei, M. 1993 Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512-526.
37. Taylor, D. J., Crease, T. J. & Brown, W. M. 1999 Phylogenetic evidence for a single long-lived clade of crustacean cyclic parthenogens and its implications for the evolution of sex. Proc. R. Soc. Lond. B266, 791-797. (DOI 10.1098/rspb.1999.0707.)
38. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. 1997 The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882.
39. Van de Peer, Y., De Rijk, P., Wuyts, J., Winkelmans, T. & De Wachter, R. 2000 The European small subunit ribosomal RNA database. Nucleic Acids Res. 28, 175-176.
40. Williams, T. A. & Nagy, L. M. 1995 Arthropod evolution: brine shrimp add salt to the stew. Curr. Biol. 5, 1330-1333.
41. Zuker, M., Mathews, D. H. & Turner, D. H. 1999 Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In RNA biochemistry and biotechnology (ed. J. Barciszewski & B. F. C. Clark), pp. 11-43. Dordrecht, The Netherlands: Kluwer.