Predicted secondary structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): Impact on sequence alignment and phylogeny estimation

Journal of Molecular Evolution

Volumn 61, Issue 1, 2005, Pages 114-137

  Gillespie, Joseph J ^a   Yoder, Matthew J ^a   Wharton, Robert A ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

18S; 28S; Braconidae; Expansion segment; Homology; Hymenoptera; Ichneumonidae; Multiple alignment; Phylogeny; Ribosome; rRNA; Secondary structure; Variable regions

Indexed keywords

RNA 18S; RNA 28S;

ARTICLE; HYMENOPTERA; INSECT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PREDICTION; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ALIGNMENT; TAXON;

ANIMALS; BASE PAIRING; BASE SEQUENCE; BAYES THEOREM; HYMENOPTERA; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; PROTEIN STRUCTURE, SECONDARY; RNA, RIBOSOMAL, 18S; RNA, RIBOSOMAL, 28S; SEQUENCE ALIGNMENT; SOFTWARE;

APOCRITA; BRACONIDAE; HEXAPODA; HYMENOPTERA; ICHNEUMONIDAE; ICHNEUMONOIDEA; INSECTA;

EID: 23944456829     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-0246-x     Document Type: Article

References (137)

1. D Amako O-Y Kwon H Ishikawa 1996 Nucleotide sequence and presumed secondary structure of the 28S rRNA of pea aphid: Implication for diversification of insect rRNA J Mol Evol 4 469 475
2. SW Applebaum RP Ebstein GR Wyatt 1966 Dissociation of ribosomal ribonucleic acid from silkmoth pupae by heat and dimethylsulfoxide: Evidence for specific cleavage points J Mol Biol 21 29 41
3. I Bakke S Johansen 2002 Characterization of mitochondrial ribosomal RNA genes in gadiformes: Sequence variations, secondary structural features, and phylogenetic implications Mol Phylogenet Evol 25 87 100
4. I Balazas M Agosin 1968 Isolation and characterization of ribonucleic acid from Musca domestica (L) Comp Biochem Physiol 27 227 237
5. R Belshaw DLJ Quicke 1997 A molecular phylogeny of the Aphidiinae (Hymenoptera: Braconidae) Mol Phylogenet Evol 7 281 293
6. R Belshaw DLJ Quicke 2002 Robustness of ancestral state estimates: Evolution of life history strategy in ichneumonoid parasitoids Syst Biol 51 450 477
7. R Belshaw M Fitton E Herniou C Gimeno DLJ Quicke 1998 A phylogenetic reconstruction of the Ichneumonoidea (Hymenoptera) based on the D2 variable region of 28 ribosomal RNA Syst Biol 23 109 123
8. R Belshaw M Dowton DLJ Quicke AD Austin 2000 Estimating ancestral geographical distributions: a Gondwanan origin for aphid parasitoids? Proc R Soc Lond B 267 491 496
9. JJ Cannone S Subramanian MN Schnare JR Collett LM D'Souza Y Du B Feng N Lin LV Madabusi KM Müller N Pande Z Shang N Yu RR Gutell 2002 The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs BMC Bioinformatics 3 2 [Correction: BMC Bioinformatics 3:15]
10. CO Cunningham H Aliesky CM Collins 2000 Sequence and secondary structure variation in the Gyrodactylus (Platyhelminthes: Monogenea) ribosomal RNA gene array J Parasitol 86 567 576
11. G De Lanversin B Jacq 1989 Sequence and secondary structure of the central domain of Drosophila 26S rRNA: A universal model for the central domain of the large rRNA containing the region in which the central break may happen J Mol Evol 28 403 417
12. P DeRijk Y Van de Peer S Chapelle R De Wachter 1994 Database on the structure of large ribosomal subunit RNA Nucleic Acids Res 22 3495 3501
13. P DeRijk Y Van de Peer I Van den Broeck R De Wachter 1995 Evolution according to large ribosomal subunit RNA J Mol Evol 41 366 375
14. P DeRijk Y Van de Peer R De Wachter 1997 Database on the structure of the large ribosomal RNA Nucleic Acids Res 25 117 123
15. MT Dixon DM Hillis 1993 Ribosomal secondary structure: Compensatory mutations and implications for phylogenetic analysis Mol Biol Evol 10 256 267
16. EA Doherty RT Batey B Masquida JA Doudna 2001 A universal mode of packing in RNA Nat Struct Biol 8 339 343
17. KJ Doshi JJ Cannone CW Cobaugh RR Gutell 2004 Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction BMC Bioinformatics 5 105
18. E Douzery FM Catzeflis 1995 Molecular evolution of the mitochondrial 12S rRNA in Ungulata (Mammalia) J Mol Evol 41 622 636
19. M Dowton AD Austin 2001 Simultaneous analysis of 16S, 28S, COI and morphology in the Hymenoptera: Apocrita-evolutionary transitions among parasitic wasps Biol J Linn Soc 74 87 111
20. T Elgavish JJ Cannone JC Lee SC Harvey RR Gutell 2001 AA.AG@Helix.Ends: A:A and A:G base-pairs at the ends of 16S and 23S rRNA helices J Mol Biol 310 735 753
21. DS Fields RR Gutell 1996 An analysis of large rRNA sequences folded by a thermodynamic method Fold Des 1 419 430
22. H Fujiwara H Ishikawa 1986 Molecular mechanisms of introduction of the hidden break into the 28S rRNA of insects: Implication based on structural studies Nucleic Acids Res 14 6393 6401
23. PP Gardner R Giegerich 2004 A comprehensive comparison of comparative RNA structure prediction approaches BMC Bioinformatics 5 140
24. J Gatesy C Hayashi R DeSalle E Vrba 1994 Rate limits for pairing and compensatory change: The mitochondrial ribosomal DNA of antelopes Evolution 48 188 196
25. ID Gauld 2002 The Ichneumonidae of Costa Rica, 4 Mem Am Ent Inst 66 1 768
26. SA Gerbi 1985 Evolution of ribosomal DNA RJ Maclntyre Molecular evolutionary genetics Plenum New York 419 517
27. JJ Gillespie 2004 Characterizing regions of ambiguous alignment caused by the expansion and contraction of hairpin-stem loops in ribosomal RNA molecules Mol Phylogenet Evol 33 936 943
28. JJ Gillespie KM Kjer CN Duckett DW Tallamy 2003 Convergent evolution of cucurbitacin feeding in spatially isolated rootworm taxa (Coleoptera: Chrysomelidae; Galerucinae, Luperini) Mol Phylogenet Evol 29 161 175
29. JJ Gillespie KM Kjer ER Riley DW Tallamy 2004a The evolution of cucurbitacin pharmacophagy in rootworms: Insight from Luperini paraphyly PH Jolivet JA Santiago-Blay M Schmitt New developments on the biology of Chrysomelidae Kluwer Academic Boston, MA 37 58
30. JJ Gillespie JJ Cannone RR Gutell AI Cognato 2004b 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 13 495 518
31. JJ Gillespie J Munro J Heraty M Yoder A Owen A Carmichael 2005 A secondary structural model of the 28S rRNA expansion segments D2 and D3 for chalcidoid wasps (Hymenoptera: Chalcidoidea) Mol Biol Evol 22 1593 1608
32. Gladstein DS, Wheeler WC (1997) POY: The optimization of alignment characters. Program and documentation. Available at: ftp.amnh.org/pub/molecular
33. JR Greenberg 1969 Synthesis and properties of ribosomal RNA in Drosophila J Mol Biol 46 85 98
34. P Gonzalez J Labarere 2000 Phylogenetic relationships of Pleurotus species according to the sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains Microbiology 146 209 221
35. RR Gutell 1992 Evolutionary characteristics of 16S and 23S rRNA structures H Hartman K Matsuno The origin and evolution of prokaryotic and eukaryotic cells World Scientific Hackensack, NJ 243 309
36. RR Gutell 1993 Collection of Small Subunit (16S- and 16S-like) ribosomal RNA structures Nucleic Acids Res 21 3051 3054
37. RR Gutell 1994 Collection of Small Subunit (16S- and 16S-like) ribosomal RNA structures: 1994 Nucleic Acids Res 22 3502 3507
38. RR Gutell 1996 Comparative sequence analysis and the structure of 16S and 23S rRNA AE Dahlberg RA Zimmerman Ribosomal RNA: Structure, evolution, processing and function in protein synthesis CRC Press Boca Raton, FL 111 128
39. RR Gutell GE Fox 1988 A compilation of large subunit RNA sequences presented in a structural format Nucleic Acids Res 16S r175 r269
40. RR Gutell B Weiser CR Woese HF Noller 1985 Comparative anatomy of 16S-like ribosomal RNA Prog Nucleic Acid Res Mol Biol 32 155 216
41. RR Gutell MN Schnare MW Gray 1990 A compilation of large subunit (23S-like) ribosomal RNA sequences presented in a secondary structure format Nucleic Acids Res 188 2319 2330
42. RR Gutell A Power G Hertz E Putz G Stormo 1992a Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods Nucleic Acids Res 20 5785 5795
43. RR Gutell MN Schnare MW Gray 1992b A compilation of large subunit (23S- and 23S-like) ribosomal RNA structures Nucleic Acids Res 21S 3055 3074
44. RR Gutell MW Gray MN Schnare 1993 A compilation of large subunit (23S- and 23S-like) ribosomal RNA structures Nucleic Acids Res 20S 2095 2109
45. RR Gutell N Larsen CR Woese 1994 Lessons from an evolving rRNA: 168 and 23S rRNA structures from a comparative perspective Microbiol Rev 58 10 26
46. RR Gutell JJ Cannone Z Shang Y Du MJ Serra 2000 A story: Unpaired adenosine bases in ribosomal RNAs J Mol Biol 304 335 354
47. RR Gutell JC Lee JJ Cannone 2002 The accuracy of ribosomal RNA comparative structure models Curr Opin Struct Biol 12 301 310
48. K Han H-J Kim 1993 Prediction of common folding structures of homologous RNAs Nucleic Acids Res 21 1251 1257
49. JM Hancock GA Dover 1988 Molecular coevolution among cryptically simple expansion segments of eukaryotic 26S/28S rRNAs Mol Biol Evol 5 377 392
50. JM Hancock AP Vogler 2000 How slippage-derived sequences are incorporated into rRNA variable-region secondary structure: Implications for phylogeny reconstruction Mol Phylogenet Evol 14 366 374
51. RE Hickson C Simon A Cooper GS Spicer J Sullivan D Penny 1996 Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA Mol Biol Evol 13 150 169
52. RE Hickson C Simon SW Perrey 2000 The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence Mol Biol Evol 17 530 539
53. DM Hillis MT Dixon 1991 Ribosomal DNA: Molecular evolution and phylogenetic inference Q Rev Biol 66 411 453
54. IL Hofacker PF Stadler 1999 Automatic detection of conserved base-pairing patterns in RNA virus genomes Comp Chem 23 401 414
55. IL Hofacker M Fekete C Flamm MA Huynen S Rauscher PE Stolorz PF Stadler 1998 Automatic detection of conserved RNA structure elements in complete RNA virus genomes Nucleic Acids Res 26 3825 3836
56. CV Hudelot V Gowri-shankar H Jow M Rattray PG Higgs 2003 RNA-based phylogenetic methods: Application to mammalian mitochondrial RNA sequences Mol Phylogenet Evol 28 241 252
57. JP Huelsenbeck FR Ronquist 2001 MrBayes: Bayesian inference of phylogeny Bioinformatics 17 754 755
58. JP Huelsenbeck B Larget RE Miller F Ronquist 2002 Potential applications and pitfalls of Bayesian inference of phylogeny Syst Biol 51 673 688
59. SK Hwang JG Kim 2000 Secondary structure and phylogenetic implications of nuclear large subunit ribosomal RNA in the ectomycorrhizal fungus Tricholoma matsutake Curr Microbiol 40 250 256
60. UI Hwang W Kim D Tautz M Friedrich 1998 Molecular phylogenetics at the Felsenstein zone: Approaching the Strepsiptera problem using 5.8S and 28S rDNA sequences Mol Phylogenet Evol 9 470 480
61. H Ishikawa RW Newburgh 1972 Studies of thermal conversion of 28S RNA of Galleria mellonella (L) to an 18S product J Mol Biol 64 135 144
62. H Ishikawa 1977 Evolution of ribosomal RNA Comp Biochem Physiol B 58 1 7
63. H Jow C Hudelot M Rattay PG Higgs 2002 Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution Mol Biol Evol 19 1591 1601
64. V Juan C Wilson 1999 RNA secondary structure prediction based on free energy and phylogenetic analysis J Mol Biol 289 935 947
65. TH Jukes CR Cantor 1969 Evolution of protein molecules NH Munro Mammalian protein metabolism Academic New York 21 132
66. KM Kjer 1995 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 4 314 330
67. KM Kjer 1997 An alignment template for amphibian 12S rRNA, domain III: Conserved primary and secondary structural motifs J Herpetol 31 599 604
68. KM Kjer 2004 Aligned 18S and insect phylogeny Syst Biol 53 506 514
69. KM Kjer GD Baldridge AM Fallon 1994 Mosquito large subunit ribosomal RNA; Simultaneous alignment of primary and secondary structure Biochim Biophys Acta 1217 147 155
70. KM Kjer RJ Blahnik RW Holzenthal 2001 Phylogeny of Trichoptera (Caddisflies): Characterization of signal and noise within multiple datasets Syst Biol 50 781 816
71. KM Kjer RJ Blahnik RW Holzenthal 2002 Phylogeny of caddisflies (Insecta: Trichoptera) Zool Scripta 31 83 91
72. DJ Klein TM Schmeing PB Moore TA Steitz 2001 The kink-turn: A new RNA secondary structure motif EMBO J 20 4214 4221
73. DAM Konings RR Gutell 1995 A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs RNA 1 559 574
74. F Kraus L Jarecki M Miyamoto S Tanhauser P Laipis 1992 Mispairing and compensational changes during the evolution of mitochondrial ribosomal RNA Mol Biol Evol 9 770 774
75. S-Y Le M Zuker 1991 Predicting common foldings of homologous RNAs J Biomol Struct Dyn 8 1027 1044
76. G Levinson GA Gutman 1987 Slipped-strand mispairing: A major mechanism for DNA sequence evolution Mol Biol Evol 4 203 221
77. R Lück G Steger D Riesner 1996 Thermodynamic prediction of conserved secondary structure: Application to the RRE element of HIV, the tRNA-like element of CMV, and the mRNA of prion protein J Mol Biol 258 813 826
78. R Lück S Gräf G Steger 1999 Construct: A tool for thermodynamic controlled prediction of conserved secondary structure Nucleic Acids Res 27 4208 4217
79. F Lutzoni P Wagner V Reeb 2000 Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses using unequivocal coding and optimal character-state weighting Syst Biol 49 628 651
80. C Lydeard WE Holznagel MN Schnare RR Gutell 2000 Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures Mol Phylogenet Evol 15 83 102
81. M Manuel C Borchiellini E Alivon Y Le Parco J Vacelet N Boury-Esnault 2003 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 52 311 333
82. DH Mathews J Sabina M Zuker DH Turner 1999 Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J Mol Biol 288 911 940
83. B Michot N Hassouna J-P Bachellerie 1984 Secondary structure of mouse 28S rRNA and general model for the folding of the large rRNA in eukaryotes Nucleic Acids Res 12 4259 4279
84. RE Miller A McDonald PS Manos 2004 Systematics of Ipomoea subgenus Quamoclit (Convovulaceae) based on its sequence data and a Bayesian phylogenetic analysis Am J Bot 91 1208 1218
85. B Misof G Fleck 2003 Comparative analysis of mt LSU rRNA secondary structures of odonates: Structural variability and phylogenetic signal Insect Mol Biol 12 535 547
86. L Morin 2000 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 47 167 177
87. DA Morrison JT Ellis 1997 Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of Apicomplexa Mol Biol Evol 14 428 441
88. NB Mugridge DA Morrison AM Johnson K Luton J Dubey J Votypka AM Tenter 1999 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 29 957 972
89. W Musters VJ Venema G Van der Linden H van Heerikhuizen J Klootwijk RJ Planta 1989 A system for the analysis of yeast ribosomal DNA mutations Mol Cell Biol 9 551 559
90. W Musters PM Goncalves K Boon HA Raue H van Heerikhuizen RJ Planta 1991 The conserved GTPase center and variable region V9 from Saccharomyces cerevisiae 26 rRNA can be replaced by their equivalents from other prokaryotes or eukaryotes without detectable loss of ribosomal function Proc Natl Acad Sci USA 88 1469 1473
91. MA Nedbal MW Allard RL Honeycutt 1994 Molecular systematics of hystricognath rodents: Evidence from the mitochondrial 12S rRNA gene Mol Phylogenet Evol 3 206 220
92. P Nissen JA Ippolito N Ban PB Moore TA Steitz 2001 RNA tertiary interactions in the large ribosomal subunit: The A-minor motif Proc Natl Acad Sci USA 98 4899 4903
93. HP Noller J Kop V Wheaton J Brosius RR Gutell AM Kopylov F Dohme W Herr DA Stahl R Gupta CR Woese 1981 Secondary structure model for 23S ribosomal RNA Nucleic Acids Res 9 6167 6189
94. HF Noller BJ Van Stolk D Moazed S Douthwaite RR Gutell 1985 Studies on the structure and function of 16S ribosomal RNA using structure-specific chemical probes Proc Int Symp Biomol Struct Interact Suppl J Biosci 8 747 755
95. C Notredame EA O'Brien DG Higgins 1997 RAGA: RNA sequence alignment by genetic algorithm Nucleic Acids Res 25 4570 4580
96. K Ogino H Edafujiwara H Fujiwara H Ishikawa 1990 What causes the aphid 28S ribosomal RNA to lack the hidden break? J Mol Evol 30 509 513
97. G Ortí P Petry JIR Porto M Jégu A Meyer 1996 Patterns of nucleotide change in mitochondrial ribosomal RNA genes and the phylogeny of piranhas J Mol Evol 42 169 182
98. RDM Page 2000 Comparative analysis of insect mitochondrial small subunit ribosomal RNA using maximum weighted matching Nucleic Acids Res 28 3839 3845
99. Y-J Park AM Fallon 1990 Mosquito ribosomal RNA genes: Characterization of gene structure and evidence for changes in copy number during development Insect Biochem 20 1 11
100. G Petersen O Seberg L Aagesen S Frederiksen 2004 An empirical test of the treatment of indels during optimization alignment based on the phylogeny of the genus Secale (Poaceae) Mol Phylogenet Evol 30 733 742
101. D Posada K Crandall 1998 MODELTEST: Testing the model of DNA substitution Bioinformatics 14 817 818
102. Rambaut A, Drummond AJ (2004) Tracer v1,1. Available at: http://evolve,zoo.ox,ac.uk/
103. OJ Rimoldi B Raghu MK Mag GL Eliceiri 1993 Three new small nucleolar RNAs that are psoralen cross-linked in vivo to unique regions of pre-rRNA Mol Cell Biol 13 4382 4390
104. F Ronquist JP Huelsenbeck 2003 MRBAYES 3: Bayesian phylogenetic inference under mixed models Bioinformatics 19 1572 1574
105. F Rousset M Pelandakis M Solignac 1991 Evolution of compensatory substitutions through GU intermediate state in Drosophila rRNA Proc Natl Acad Sci USA 88 10032 10036
106. MN Schnare SH Damberger MW Gray RR Gutell 1996 Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23S-like) ribosomal RNA J Mol Biol 256 701 719
107. EA Schultes PT Hraber TH LaBean 1999 Estimating the contributions of selection and organization in RNA secondary structure J Mol Evol 49 76 83
108. MR Shaw T Huddleston 1991 Classification and biology of braconid wasps (Hymenoptera: Braconidae), Handbk Identif British Insects J Mol Biol 75 57 72
109. J Shine L Dalgarno 1973 Occurrence of heat-dissociable ribosomal RNA in insects: Presence of 3 polynucleotide chains in 26S RNA from cultured Aedes aegypti cells J Mol Biol 75 57 72
110. M Simmons 2004 Independence of alignment and tree search Mol Phylogenet Evol 31 874 879
111. MS Springer E Douzery 1996 Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules J Mol Evol 43 357 373
112. MS Springer LJ Hollar A Burk 1995 Compensatory substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals Mol Biol Evol 12 1138 1150
113. R Sweeney M-C Yao 1989 Identifying functional regions of rRNA by insertion mutagenesis and complete gene replacement in Tetrahymena thermophila EMBO J 8 933 938
114. R Sweeney L Chen M-C Yao 1994 An rRNA variable region has an evolutionary conserved essential role despite sequence divergence Mol Cell Biol 14 4203 4215
115. DL Swofford 1999 PAUP*; Phylogenetic analysis using parsimony (*and other methods), version 4 Sinauer Sunderland, MA
116. DJ Tauz JM Hancock DA Webb C Tautz GA Dover 1988 Complete sequences of the rRNA genes of Drosophila melanogaster Mol Biol Evol 5 366 376
117. TA Titus DR Frost 1996 Molecular homology assessment and phylogeny in the lizard family Opluridae (Squamata: Iguania) Mol Phylogenet Evol 6 49 62
118. H Uchida K Kitae KI Tomizawa A Yokota 1998 Comparison of the nucleotide sequence and secondary structure of the 5.8S ribosomal RNA gene of Chlamydomonas tetrasama with those of green algae DNA Seq 8 403 408
119. Y Van de Peer J Jansen P De Rijk R De Wachter 1997 Database on the structure of small ribosomal subunit RNA Nucleic Acids Res 5 111 116
120. Y Van de Peer E Robbrecht S de Hoog A Caers P De Rijk 1999 Database on the structure of small subunit ribosomal RNA Nucleic Acids Res 27 l79 183
121. L Vawter WM Brown 1993 Rates and patterns of base change in the small subunit ribosomal RNA gene Genetics 134 597 608
122. GM Veldman J Klootwijk VCFH De Regt RJ Planta C Branlant A Krol J-P Ebel 1981 The primary and secondary structure of yeast 26S rRNA Nucleic Acids Res 9 6935 6952
123. VC Ware R Renkawitz SA Gerbi 1985 rRNA processing: removal of only nineteen bases at the gap between 28S alpha and 28S beta rRNAs in Sciara coprophila Nucleic Acids Res 13 3581 3597
124. RA Wharton 2000 Can braconid classification be reconstructed to facilitate portrayal of relationships? AD Austin M Dowton Hymenoptera evolution, biodiversity and biological control CSIRO Collingwood 143 153
125. WC Wheeler 1996 Optimization alignment: The end of multiple sequence alignment in phylogenetics? Cladistics 12 1 9
126. WC Wheeler 1999 Fixed character states and the optimization of molecular sequence data Cladistics 15 379 385
127. WC Wheeler RL Honeycutt 1988 Paired sequence difference in ribosomal RNAs: Evolutionary and phylogenetic implications Mol Biol Evol 5 90 96
128. BM Wiegmann SC Tsaur DW Webb DK Yeates BK Cassel 2000 Monophyly and relationships of the Tabanomorpha (Diptera: Brachycera) based on 28S ribosomal gene sequences Ann Entomol Soc Am 93 1031 1038
129. CR Woese LJ Magrum R Gupta RB Siegel DA Stahl J Kop N Crawford J Brosius R Gutell JJ Hogan HF Noller 1980 Secondary structure model for bacterial 16S ribosomal RNA: Phylogenetic, enzymatic and chemical evidence Nucleic Acids Res 8 2275 2293
130. CR Woese R Gutell R Gupta HF Noller 1983 Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids Microbiol Rev 47 621 669
131. IG Wool 1986 Studies of the structure of eukaryotic (mammalian) ribosomes J Hardesty G Kramer Structure, function and genetics of ribosomes Springer-Verlag New York 391 411
132. J Wuyts P De Rijk Y Van de Peer G Pison P Rousseeuw R De Wachter 2000 Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA Nucleic Acids Res 28 4698 4708
133. X Xia 2000 Phylogenetic relationship among horseshoe crab species: The effect of substitution models on phylogenetic analyses Syst Biol 49 87 100
134. X Xia Z Xie KM Kjer 2003 18S ribosomal RNA and tetrapod phylogeny Syst Biol 52 283 295
135. DS Yu K Horstmann 1997 A catalogue of World Ichneumonidae (Hymenoptera). Part 1. Subfamilies Acaenitinae to Ophioninae Mem Am Ent Inst 58 1 763
136. M Zuker JA Jaeger DH Turner 1991 A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison Nucleic Acids Res 19 2707 2714
137. M Zuker DH Mathews DH Turner 1999 Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide J Barciszewski BFC Clark RNA biochemistry and biotechnology NATO ASI Series, Kluwer Academic Boston, MA 11 43