Aligned 18S and insect phylogeny

Systematic Biology

Volumn 53, Issue 3, 2004, Pages 506-514

  Kjer, Karl M ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

18S; Alignment; Doublet model; Insecta; Paleoptera

Indexed keywords

RNA 18S;

ANIMAL; ARTICLE; BASE PAIRING; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; INSECT; PHYLOGENY; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

ANIMALS; BASE PAIRING; BAYES THEOREM; INSECTS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; RNA, RIBOSOMAL, 18S; SEQUENCE ALIGNMENT;

COLLEMBOLA; ENDOPTERYGOTA; EPHEMEROPTERA; HEXAPODA; INSECTA; NEOPTERA; NEXUS; ORTHOPTEROIDEA; PALAEOPTERA; PARANEOPTERA;

EID: 3242721251     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150490445922     Document Type: Article

References (82)

1. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Bechly, G. 1994. A cladistic study of the Odonata and a reconstruction of the wing venation in the ground plan of crown group Odonata. Petalura 1:1-24.
3. Bitsch, C., and J. Bitsch. 2000. The phylogenetic interrelationships of the higher taxa of apterygote hexapods. Zoologica Scripta 29:131-156.
4. Brauckmann, C., and W. Zessen. 1989. Neue Meganeuridae aus dem Namurium von Hagen-Vorhalle (BRD) und die Phylogenie der Meganisoptera (Insecta, Odonata) Deut. Entomol, Zeit. (N.F.) 36:177-215.
5. Buckley, T. R., and C. W. Cunningham. 2002. The effects of Nucleotide substitution model assumptions on estimates of nonparameteric bootstrap support. Mol. Biol. Evol. 19:394-405.
6. Carapelli, A., F. Frati, F. Nardi, R. Dallai, and C. Simon. 2000. Molecular phylogeny of the apterygotan insects based on nuclear and mitochondrial genes. Pedobiologia 44:361-373.
7. Carle, F. L. 1982a. Evolution of the odonate copulatory process. Odonatologica 11:271-286.
8. Carle, F. L. 1982b. Thoughts on the origin of insect flight. Ent. News 93:159-172.
9. Carle, F. L. 1982c. The wing vein homologies and phylogeny of the Odonata: A continuing debate. Soc. Int. Odonatol. Rapid Comm., 4:x + 66p.
10. Carle, F. L. 1995. Evolution, taxonomy and biogeography of ancient gondwanian Libelluloids, with comments on anisopteroid evolution and phylogenetics. Odonatologica 24:383-424.
11. Carmean D., L. S. Kimsey, and M. L. Berbee. 1992. 18S rDNA sequences and holometabolous insects. Mol. Phylogenet. Evol. 1:270-278.
12. Chalwatzis, N., J. Hauf, Y. van de Peer, R. Kinzelbach, and F. K. Zimmermann. 1996. 18S ribosomal RNA genes of insects: Primary structure of the genes and molecular phylogeny of Holometabola. Ann. Entomol. Soc. Amer. 89:775-787.
13. Cunningham, C. O., Aliesky, H., and C. M. Collins. 2000. Sequence and secondary structure variation in the Gyrodactylus (Platyhelminthes: Monogenea) ribosomal RNA gene array. J. Parasitol. 86:567-576.
14. Delsuc, F., M. J. Phillips, and D. Penny. Comment on "Hexapod Origins: Monophyletic or Paraphyletic." Science 301:1482d.
15. Eggleton, P. 2001. Termites and trees: A review of recent advances in termite phylogenetics. Insectes Soc. 48:187-193.
16. Flook, P. K., and C. H. F. Rowell. 1997. The effectiveness of mitochondrial rRNA sequences for the reconstruction of the phylogeny of an insect order (Orthoptera). Mol. Phylogenet. Evol. 8:177-192.
17. Gladstein, D. S., and W. C. Wheeler. 1997. "POY: The optimization of alignment characters." Program and documentation. New York. Available at ftp.amnh.org/pub/molecular.
18. Goertzen, L. R., Cannone, J. J., Gutell, R. R., and R. K. Jansen. 2003. ITS secondary structure derived from comparative analysis: Implications for sequence alignment and phylogeny of the Asteraceae. Mol. Phylogenet. Evol. 29:216-234.
19. Gonzalez, P., and 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.
20. Gu, X., Y.-X. Fu, and W.-H. Li. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12:546-557.
21. Gutell, R. R., N. Larsen, and C. R. Woese. 1994. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58:10-26.
22. Hickson, R. E., C. Simon, A. J. Cooper, G. Spicer, J. Sullivan, and D. Penny. 1996. Refinement of a secondary structure model for the third domain of animal 12S rRNA, with a comparison of alignment programs. Mol. Biol. Evol. 13:150-169.
23. Hickson, R. E., Simon, C., and S. W. 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.
24. Hovmöller, R., T. Pape, and M. Kallersjö. 2002. The Paleoptera problem: Basal Pterygote phylogeny inferred from 18S and 28S rDNA sequences. Cladistics 18:313-323.
25. Huelsenbeck, J. P. 1998. Systematic Bias in phylogenetic analysis: Is the Strepsiptera problem solved? Syst. Biol. 47:519-537.
26. Huelsenbeck, J. P, and R. Nielsen. 1999. Effect of nonindependent substitution on phylogenetic accuracy. Syst. Biol. 48:317-328.
27. Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
28. Huelsenbeck, J. P., and F. Ronquist. 2002. MrBayes 3: Bayesian analysis of phylogeny. Computer program distributed by the authors. Department of Ecology, Behavior and Evolution, University of California, San Diego.
29. Hwang, U. W., W. Kiim, D. Tautz, and M. Friedrich. 1998. Molecular phylogenetics at the Felsenstein zone: Approaching the Strepsipera problem using 5.8S and 28S rDNA sequences. Mol. Phylogenet. Evol. 9:470-480.
30. Johnson, K. P., and M. F. Whiting. 2002. Multiple genes and the monophyly of Ischnocera (Insecta: Phthiraptera). Mol. Phylogenet. Evol. 22:101-110.
31. Kjer, K. M. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from the frogs. Mol. Biol. Evol. 4:314-330.
32. Kjer, K. M. 1997. An alignment template for amphibian 12S rRNA, domain III: Conserved primary and secondary structural motifs. J. Herpetol. 31:599-604.
33. Kjer, K. M., G. D. Baldridge, and A. M. Fallon. 1994. Mosquito large subunit ribosomal RNA: Simultaneous alignment of primary and secondary structure. Biochim. Biophys. Acta 1217:147-155.
34. Kjer, K. M., R. J. Blahnik, and R. W. Holzenthal. 2001. Phylogeny of Trichoptera (Caddisflies): Characterization of signal and noise within multiple datasets. Syst. Biol. 50:781-816.
35. Kjer, K. M., R. J. Blahnik, and R. W. Holzenthal. 2002. Phylogeny of Caddisflies (Insecta, Trichoptera). Zoologica Scripta 31:83-91.
36. Kristensen, N. P. 1975. The phylogeny of hexapod "orders." A critical review of recent accounts. Z. Zool. Syst. Evollutionforsch. 13:1-44.
37. Kristensen, N. P. 1981. Phylogeny of insect orders. Annu. Rev. Entomol. 26:135-157.
38. Kristensen, N. P. 1991. Phylogeny of extant hexapods. Pages 125-140 in The insects of Australia, 2nd ed. (I. D. Nielsen, J. P. Spradberry, R. W. Taylor, M. J. Whitten, and M. J. Littlejohn, eds.). CSIRO, Melbourne University Press, Melbourne.
39. Kristensen, N. P. 1995. Forty years' insect phylogenetic systematics. Zool. Beitr. N. F. 36:83-124.
40. Kristensen, N. P. 1997. The ground plan and basal diversification of the hexapods. Pages 281-293 in Arthropod relationships (R. A. Fortey and R. H. Thomas, eds.). Chapman and Hall, London.
41. Liu, H., and A. T. Beckenbach. 1992. Evolution of the mitochondrial oxydase II gene among 10 orders of insects. Mol. Phylogenet. Evol. 1:41-52.
42. Lo, N., G. Tokuda, H. Watanabe, H. Rose, M. Slaytor, K. Maekawa, C. Bandi, and H. Noda. 2000. Evidence from multiple gene sequences indicates that termites evolved from wood-feeding cockroaches. Curr. Biol. 10:801-804.
43. Lutzoni F., P. Wagener, V. Reev, and S. Zoller. 2000. Integrating ambiguously aligned regions of DNA sequence in phylogenetic analyses without violating positional homology. Syst. Biol. 49:628-651.
44. Lyal, C. H. C. 1985. Phylogeny and classification of the Psocodea, with particular reference to the lice (Psocodea: Phthiraptera). Syst. Entomol. 10:145-165.
45. Lydeard, C., W. E. Holznagel, M. N. Schnare, and R. R. Gutell. 2000. Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures. Mol. Phylogenet. Evol. 15:83-102.
46. Maddison, D. R., and W. P. Maddison. 2000. MacClade 4. Computer program. Sinauer, Sunderland, MA.
47. Mallatt, J. M., J. R. Garey, and J. W. Schultz. 2004. Ecdysozoan phylogeny and Bayesian inference: First use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Mol. Phylogenet. Evol. 31:178-191.
48. Misof, B., A. M. Rickert, T. R. Buckley, G. Fleck, and K. P. Sauer. 2001. Phylogenetic signal and its decay in mitochondrial SSU and LSU rRNA gene fragments of Anisoptera. Mol. Biol. Evol. 18:27-37.
49. Morin, L. 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.
50. Morrison, D. A., and J. T. Ellis. 1997. Effects of nucleotide sequence alignment on phylogeny estimation: A case study of 18S rDNAs of Apicomplexa. Mol. Biol. Evol. 14:428.
51. Mugridge, N. B., D. A. Morrison, T. Jakel, A. R. Heckeroth, A. M. Tenter, and A. M. Johnson. 2000. Effects of sequence alignment and structural domains of ribosomal DNA on phylogeny reconstruction for the protozoan family Scacocystidae. Mol. Biol Evol. 17:1842.
52. Nardi, F., G. Spinsanti, J. Boore, A. Carapelli, R. Dallai, and F. Frati. 2003. Hexapod Origins: Monophyletic or paraphyletic. Science 299:1887-1889.
53. Notredame, C., E. A. O'Brien, and D. G. Higgins. 1997. RAGA: RNA sequence alignment by genetic algorithm. Nucleic Acids Res. 25:4570-4580.
54. Ogden, T. H., and M. F. Whiting. 2003. The problem with "the Paleoptera Problem" sense and sensitivity. Cladistics 19:432-442.
55. Pashley, D. P., B. A. McPheron, and E. A. Zimmer. 1993. Systematics of holometabolous insect orders based on 18S ribosomal RNA. Mol. Phylogenet. Evol. 2:132-142.
56. Posada, D., and K. A. Crandall. 1998. ModelTest: Testing the model of DNA substitution. Bioinformatics 14:817-818.
57. Rehn, A. C. 2003. Phylogenetic analysis of higher-level relationships of Odonata Syst. Entomol. 28:181-241.
58. Schmidt, E. 1915. Vergleichende morphologie des 2. und 3. abdominalegmentes bei mannlichen Libellen. Zool. Jb. (Abt. Anat.) 39:87-196.
59. Schöniger, M., and A. von Haeseler. 1994. A stochastic model and the evolution of autocorrelated DNA sequences. Mol. Phylogenet. Evol. 3:240-247.
60. Stys, P., and J. Zrzavy. 1994. Phylogeny and classification of extant Arthropoda: Review of hypotheses and nomenclature. Eur. J. Entomol. 91:257-275.
61. Stys, P., J. Zrzavy, and F. Weyda. 1993. Phylogeny of the hexapoda and ovarian metamerism. Biol. Rev. 68:365-379.
62. Tavare, S. 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lect. Math. Life Sci. 17:57-86, 368-376.
63. Titus, T., and D. R. Frost. 1996. Molecular homology assessment and phylogeny in the lizard family Opluridae (Squamata: Iguania). Mol. Phylogenet. Evol. 6:49-62.
64. Uchida, H., K. Kitae, K. I. Tomizawa, and A. Yokota. 1998. 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. 8:403-408.
65. Van de Peer, Y., J.-M. Neefs, P. De Rijk, and R. DeWacter. 1993. Reconstructing evolution om eukaryotic small-subunit RNA sequences: Calibration of the molecular clock. Mol. Evol. 37:221-232.
66. Wheeler, W. C. 1989. The systematics of insect ribosomal DNA. Pages 307-321 in The hierarchy of life. Molecules and morphology in phylogenetic analysis (B. Fernholm, K. Bremer, and H. Jörnvall, eds.). Elsevier, Amsterdam.
67. Wheeler, W. C. 1995. Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Syst. Biol. 44:321-331.
68. Wheeler, W. C. 1996. Optimization alignment: The end of multiple sequence alignment in phylogenetics. Cladistics 12:1-9.
69. Wheeler, W. C. 1999. Heuristic reconstruction of hypothetical-ancestral DNA sequences: Sequence alignment vs direct optimization. Pages 106-113 in Homology and Systematics: Coding characters for phylogenic analysis (R. W. Scotland, ed.). CRC Press.
70. Wheeler, W. C. 2001. Homology AND DNA sequence data. Pages 303-317 in The character concept in evolutionary biology (G. P. Wagner, ed.). Academic Press, San Diego, CA.
71. Wheeler, W. C. 2003. Implied alignment: A synapomorphy-based multiple-sequence alignment method and its use in cladogram search. Cladistics 19:261-268.
72. Wheeler, W. C., M. F. Whiting, Q. D. Wheeler, and J. M. Carpenter. 2001. The phylogeny of extant insect orders. Cladistics 17:113-169.
73. Whitfield, J. B. 1997. Molecular and morphological data suggest a single orignin of the polydnaviruses among brachonid wasps. Naturwissenschaften 84:502-507.
74. Whitfield, J. B. and S. A. Cameron. 1998. Hierarchical analysis of variation in the mitochondrial 16S rRNA gene among Hymenoptera. Mol. Biol. Evol. 15:1728-1743.
75. Whiting, M. F., J. C. Carpenter, Q. D. Wheeler, and W. C. Wheeler. 1997. The Strepsiptera problem: Phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology. Syst. Biol. 46:1-68.
76. Whiting, M. F. 2002. Mecoptera is paraphyletic: Multiple genes and phylogeny of Mecoptera and Siphonaptera. Zoologica Scripta 31:93-104.
77. Xia, X. 2000. Phylogenetic relationship among horseshoe crab species: The effect of substitution models on phylogenetic analyses. Syst. Biol. 49:87-100.
78. Xia, X., Z. Xie, and K. M. Kjer. 2003. 18S ribosomal RNA and tetrapod phylogeny. Syst. Biol. 52:283-295.
79. Yang, Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
80. Yang, Z. 1994a. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:105-111.
81. Yang, Z. 1994b. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. Syst. Biol. 44:384-399.
82. Yang, Z. 1996. Among-site rate variation and its impact on phylogenetic analysis. TREE 11:367-372.