Characterizing regions of ambiguous alignment caused by the expansion and contraction of hairpin-stem loops in ribosomal RNA molecules

Molecular Phylogenetics and Evolution

Volumn 33, Issue 3, 2004, Pages 936-943

  Gillespie, Joseph J ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; RIBOSOME RNA; RNA;

ANIMAL; ARTICLE; BEETLE; CHEMISTRY; CONFORMATION; GENETIC PROCEDURES; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY;

ANIMALS; BASE SEQUENCE; BEETLES; DNA, RIBOSOMAL; GENETIC TECHNIQUES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA; RNA, RIBOSOMAL; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 7444256051     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2004.08.004     Document Type: Article

References (70)

1. B.G. Baldwin, M.J. Sanderson, J.M. Porter, M.F. Wojciechowski, C.C. Campbell, and M.J. Donoghue The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny Ann. Mo. Bot. Gard. 82 1995 257 277
2. B. Billboud, M.-A. Geurrucci, M. Masselot, and B. Misof Cirripede phylogeny using a novel approach: Molecular morphometrics Mol. Biol. Evol. 17 2000 1435 1445
3. Cannone, J.J., Subramanian, S., Schnare, M.N., Collett, J.R., D'Souza, L.M., Du, Y., Feng, B., Lin, N., Madabusi, L.V., Muller, K.M., Pande, N., Shang, Z., Yu, N., Gutell, R.R., 2002. The comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BioMed Central Bioinformatics 3, 2. (Correction: BioMed Central Bioinformatics 3, 15). Available from: 〈http://www.rna.icmb.utexas. edu/〉
4. L.J. Collins, V. Moulton, and D. Penny Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP J. Mol. Evol. 51 2000 194 204
5. K.A. Crandall, and J.J. Fitzpatrick Crayfish molecular systematics: Using a combination of procedures to estimate phylogeny Syst. Biol. 45 1996 1 26
6. T.J. Crease, and D.J. Taylor 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 1998 1430 1446
7. C.O. Cunningham, H. Aliesky, and C.M. Collins Sequence and secondary structure variation in the Gyrodactylus (Platyhelminthes: Monogenea) ribosomal RNA gene array J. Parasitol. 86 2000 567 576
8. P. DeRijk, Y. Van de Peer, I. Van den Broeck, and R. De Wachter Evolution according to large ribosomal subunit RNA J. Mol. Evol. 41 1995 366 375
9. M.T. Dixon, and D.M. Hillis Ribosomal secondary structure: compensatory mutations and implications for phylogenetic analysis Mol. Biol. Evol. 10 1993 256 267
10. E. Douzery, and F.M. Catzeflis Molecular evolution of the mitochondrial 12S rRNA in Ungulata (Mammalia) J. Mol. Evol. 41 1995 622 636
11. O. Flores-Villela, K.M. Kjer, M. Benabib, and J.W. Sites Multiple data sets, congruence, and hypothesis testing for the phylogeny of basal groups of the lizard genus Sceloporus (Squamata, Phrynosomatidae) Syst. Biol. 49 2000 713 739
12. J. Gatesy, C. Hayashi, R. DeSalle, and E. Vrba Rate limits for pairing and compensatory change: the mitochondrial ribosomal DNA of antelopes Evolution 48 1994 188 196
13. J.J. Gillespie, K.M. Kjer, C.N. Duckett, and D.W. Tallamy Convergent evolution of cucurbitacin feeding in spatially isolated rootworm taxa (Coleoptera: Chrysomelidae; Galerucinae, Luperini) Mol. Phylogenet. Evol. 29 2003 161 175
14. J.J. Gillespie, K.M. Kjer, E.R. Riley, and D.W. Tallamy The evolution of cucurbitacin pharmacophagy in rootworms: Insight from Luperini paraphyly P.H. Jolivet J.A. Santiago-Blay M. Schmitt New Developments in the Biology of Chrysomelidae 2004 Kluwer Academic Publishers Boston, MA 37 57
15. Gillespie, J.J., Cannone, J.J., Gutell, R.R., Cognato, A.I., 2004. A secondary structural model of the 28S rRNA expansion segments D2 and D3 from rootworms and related leaf beetles (Coleoptera: Chrysomelidae; Galerucinae). Insect Mol. Biol. (in press)
16. L.R. Goertzen, J.J. Cannone, R.R. Gutell, and R.K. Jansen ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae Mol. Phylogenet. Evol. 29 2003 216 234
17. P. Gonzalez, and J. Labarere Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains Microbiology 146 2000 209 221
18. R.R. Gutell, N. Larsen, and C.R. Woese Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective Microbiol. Rev. 58 1994 10 26
19. R.R. Gutell Comparative sequence analysis and the structure of 16S and 23S rRNA A.E. Dahlberg E.A. Zimmerman Ribosomal RNA Structure, Evolution, Processing and Function in Protein Sysnthesis 1996 CRC Press Boca Raton, FL 111 129
20. J.M. Hancock, and A.P. Vogler How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: implications for phylogeny reconstruction Mol. Phylogenet. Evol. 14 2000 366 374
21. D.S. Hibbet, Y. Fukumasa-Nakai, A. Tsuneda, and M.J. Donoghue Phylogenetic diversity in shiitake inferred from nuclear ribosomal DNA Mycologia 87 1995 618 638
22. R.E. Hickson, C. Simon, A. Cooper, G.S. Spicer, J. Sullivan, and D. Penny Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA Mol. Biol. Evol. 13 1996 150 169
23. R.E. Hickson, C. Simon, and S.W. Perrey The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence Mol. Biol. Evol. 17 2000 530 539
24. P.G. Higgs RNA secondary structure: physical and computational aspects Q. Rev. Biophys. 33 2000 199 253
25. D.M. Hillis, and M.T. Dixon Ribosomal DNA: molecular evolution and phylogenetic inference Q. Rev. Biol. 66 1991 411 453
26. I.L. Hofacker, W. Fontana, P.F. Stadler, L.S. Bonhoeffer, M. Tacker, and P. Schuster Fast folding and comparison of RNA secondary structures Monatsh. Chem. 125 1994 167 188
27. C. Hudelot, V. Gowri-Shankar, H. Jow, M. Rattray, and P.G. Higgs RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences Mol. Phylogenet. Evol. 28 2003 241 252
28. S.K. Hwang, and J.G. Kim Secondary structure and phylogenetic implications of nuclear large subunit ribosomal RNA in the ectomycorrhizal fungus Tricholoma matsutake Curr. Microbiol. 40 2000 250 256
29. U.I. Hwang, W. Kim, D. Tautz, and M. Friedrich Molecular phylogenetics at the Felsenstein zone: approaching the Strepsiptera problem using 5.8S and 28S rDNA sequences Mol. Phylogenet. Evol. 9 1998 470 480
30. H. Jow, C. Hudelot, M. Rattray, and P.G. Higgs Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution Mol. Biol. Evol. 19 2002 1591 1601
31. S.J. Kim, K.M. Kjer, and C.N. Duckett Comparison between molecular and morphological-based phylogenies of galerucine/alticine leaf beetles (Coleoptera, Chrysomelidae: Galerucinae) Insect Syst. Evol. 34 2003 53 64
32. M. Kimura DNA and the neutral theory Philos. Trans. Roy. Soc. Lond. B312 1986 343 354
33. K.M. Kjer, G.D. Baldridge, and A.M. Fallon Mosquito large subunit ribosomal RNA: simultaneous alignment of primary and secondary structure Biochim. Biophys. Acta 1217 1994 147 155
34. K.M. Kjer Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs Mol. Phylogenet. Evol. 4 1995 314 330
35. K.M. Kjer An alignment template for amphibian 12S rRNA, domain III: conserved primary and secondary structural motifs J. Herpetol. 31 1997 599 604
36. K.M. Kjer, R.J. Blahnik, and R.W. Holzenthal Phylogeny of Trichoptera (Caddisflies): characterization of signal and noise within multiple datasets Syst. Biol. 50 2001 781 816
37. F. Kraus, L. Jarecki, M. Miyamoto, S. Tanhauser, and P. Laipis Mispairing and compensational changes during the evolution of mitochondrial ribosomal RNA Mol. Biol. Evol. 9 1992 770 774
38. A. Kretzer, Y. Li, T. Szaro, and T.D. Bruns Internal transcribed spacer sequences from 38 recognized species of Suillus sensu lato: phylogenetic and taxonomic implications Mycologia 88 1996 776 785
39. M.S.Y. Lee Unalignable sequences and molecular evolution Trends Ecol. Evol. 16 2001 681 685
40. F. Lutzoni, P. Wagner, and V. Reeb Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses using unequivocal coding and optimal character-state weighting Syst. Biol. 49 2000 628 651
41. C. Lydeard, W.E. Holznagel, M.N. Schnare, and R.R. Gutell Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures Mol. Phylogenet. Evol. 15 2000 83 102
42. P.S. Manos Systematics of Nothofagus (Nothofagaceae) based on rDNA spacer sequences (ITS): taxonomic congruence with morphology and plastid sequences Am. J. Bot. 84 1997 1137 1155
43. M. Manuel, C. Borchiellini, E. Alivon, Y. Le Parco, J. Vacelet, and N. Boury-Esnault Phylogeny and evolution of calcareous sponges: monophyly of Calcinea and Calcaronea, high level of morphological homoplasy, and the primitive nature of axial symmetry Syst. Biol. 52 2003 311 333
44. C.R. Marshall Substitution biases, weighted parsimony, and amniote phylogeny as inferred from 18S-ribosomal-RNA sequences Mol. Biol. Evol. 9 1992 370 373
45. G.J. Mitchison A probabilistic treatment of phylogeny and sequence alignment J. Mol. Evol. 49 1999 11 22
46. L. Morin Long branch attraction effects and the status of "basal eukaryotes": phylogeny and structural analysis of the ribosomal RNA gene cluster of the free-living diplomonad Trepomonas agilis J. Eukaryot. Microbiol. 47 2000 167 177
47. D.A. Morrison, and J.T. Ellis Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of Apicomplexa Mol. Biol. Evol. 14 1997 428 441
48. N.B. Mugridge, D.A. Morrison, A.M. Johnson, K. Luton, J. Dubey, J. Votypka, and A.M. Tenter Phylogenetic relationships of the genus Frenkelia: a review of its history and new knowledge gained from comparison of large subunit ribosomal ribonucleic acid gene sequences Int. J. Parasitol. 29 1999 957 972
49. M.A. Nedbal, M.W. Allard, and R.L. Honeycutt Molecular systematics of hystricognath rodents: evidence from the mitochondrial 12S rRNA gene Mol. Phylogenet. Evol. 3 1994 206 220
50. C. Notredame, E.A. O'Brien, and D.G. Higgins RAGA: RNA sequence alignment by genetic algorithm Nucleic Acids Res. 25 1997 4570 4580
51. D. Ouvrard, B.C. Campbell, T. Bourgoin, and K.L. Chan 18S rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta, Hemiptera) Mol. Phylogenet. Evol. 16 2000 403 417
52. R.D.M. Page, R. Crulckshank, and K.P. Johnson Louse (Insecta: Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable Insect Mol. Biol. 11 2002 361 369
53. G. Petersen, O. Seberg, L. Aagesen, and S. Frederiksen An empirical test of the treatment of indels during optimization alignment based on the phylogeny of the genus Secale (Poaceae) Mol. Phylogenet. Evol. 30 2004 733 742
54. F. Rousset, M. Pelandakis, and M. Solignac Evolution of compensatory substitutions through GU intermediate state in Drosophila rRNA Proc. Natl. Acad. Sci. USA 88 1991 10032 10036
55. N.J. Savill, D.C. Hoyle, and P.G. Higgs RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum likelihood methods Genetics 157 2001 399 411
56. M.N. Schnare, S.H. Damberger, M.W. Gray, and R.R. Gutell Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23S-like) ribosomal RNA J. Mol. Biol. 256 1996 701 719
57. E.A. Schultes, P.T. Hraber, and T.H. LaBean Estimating the contributions of selection and self-organization in RNA secondary structure J. Mol. Evol. 49 1999 76 83
58. B.A. Shapiro, and K. Zhang Comparing multiple RNA secondary structures using tree comparisons CABIOS 6 1990 309 318
59. M.S. Springer, and E. Douzery Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules J. Mol. Evol. 43 1996 357 373
60. M.S. Springer, L.J. Hollar, and A. Burk Compensatory substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals Mol. Biol. Evol. 12 1995 1138 1150
61. Swofford, D.L., 1999. PAUP*: phylogenetic analysis using parsimony (* and other methods), version 4. Computer program distributed by Sinauer
62. D.L. Swofford PAUP 3: Phylogenetic Analysis Using Parsimony. User manual 1993 University of Illinois Urbana
63. T.A. Titus, and D.R. Frost Molecular homology assessment and phylogeny in the lizard family Opluridae (Squamata: Iguania) Mol. Phylogenet. Evol. 6 1996 49 62
64. H. Uchida, K. Kitae, K.I. Tomizawa, and A. Yokota Comparison of the nucleotide sequence and secondary structure of the 5.8S ribosomal RNA gene of Chlamydomonas tetragama with those of green algae DNA Seq. 8 1998 403 408
65. Y. Van de Peer, J.M. Neeps, P. DeRijk, and R. De Wachter Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: calibration of the molecular clock J. Mol. Evol. 37 1993 221 232
66. L. Vawter, and W.M. Brown Rates and patterns of srDNA change Genetics 134 1993 597 608
67. W.C. Wheeler, and R.L. Honeycutt Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications Mol. Biol. Evol. 5 1988 90 96
68. W.C. Wheeler Fixed character states and the optimization of molecular sequence data Cladistics 15 1999 379 385
69. X. Xia Phylogenetic relationship among horseshoe crab species: the effect of substitution models on phylogenetic analyses Syst. Biol. 49 2000 87 100
70. X. Xia, Z. Xie, and K.M. Kjer 18S ribosomal RNA and tetrapod phylogeny Syst. Biol. 52 2003 283 295