The mitochondrial genome of Bacillus stick insects (Phasmatodea) and the phylogeny of orthopteroid insects

Molecular Phylogenetics and Evolution

Volumn 58, Issue 2, 2011, Pages 304-316

  Plazzi, Federico ^a   Ricci, Andrea ^a   Passamonti, Marco ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

Bacillus; MtDNA; Phasmatodea; Phylogenetic informativeness; Phylogeny

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE GENOMIC HYBRIDIZATION; DNA SEQUENCE; GENETICS; GENOME; INSECT; MITOCHONDRIAL GENOME; MOLECULAR EVOLUTION; PHYLOGENY; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; COMPARATIVE GENOMIC HYBRIDIZATION; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENOME, INSECT; GENOME, MITOCHONDRIAL; INSECTS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

BACILLUS (STICK INSECT); DICTYOPTERA; HEXAPODA; MANTOPHASMATODEA; MYA; ORTHOPTERA; ORTHOPTEROIDEA; PHASMATODEA;

EID: 79951578321     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.12.005     Document Type: Article

References (114)

1. Akaike H. Information theory and an extension of the maximum likelihood principle. Second International Symposium on Information Theory 1973, 267. Akademiai Kiado, Budapest. B.N. Petrox, F. Caski (Eds.).
2. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
3. Bae J.S., Kim H.D., Sohn B.R. The mitochondrial genome of the firefly Pyrocoelia rufa: complete genome sequence, genome organisation and phylogenetic analysis with other insects. Mol. Phylogenet. Evol. 2004, 32:978-985.
4. Beutel R.G., Gorb S.N. Ultrastructure of attachment specializations of hexapods (Arthropoda): evolutionary patterns inferred from a revised ordinal phylogeny. J. Zool. Syst. Evol. Res. 2001, 39:177-207.
5. Beutel R.G., Gorb S.N. A revised interpretation of the evolution of attachment structures in Hexapoda with special emphasis on Mantophasmatodea. Arthropod Syst. Evol. 2006, 64:3-25.
6. Boore J.L. Animal mitochondrial genomes. Nucleic Acids Res. 1999, 27:1767-1780.
7. Boore J.L., Lavrov D.V., Brown W.M. Gene translocation links insects and crustaceans. Nature 1998, 392:667-668.
8. Boudreaux H.B. Arthropod Phylogeny with Special Reference to Insects 1987, John Wiley, New York.
9. Bradler, S., 2003. Phasmatodea, Gespentschrecken. In: Dathe, H.H. (Ed.), Lehrbuch der speziellen Zoologie. I. Wirbellose Tiere. 5. Insecta. Spektrum. Heidelberg, Berlin, pp. 251-260.
10. Bradler, S., 2009. Die Phylogenie der Stab-und Gespenstschrecken (Insecta: Phasmatodea). S P E, vol. 2.1. Universitätsverlag Göttingen, Göttingen.
11. Brandley M.C., Schmitz A., Reeder T.W. Partitioned Bayesian analysis, partition choice, and the phylogenetic relationships of scincid lizards. Syst. Biol. 2005, 54:373-390.
12. Brusca R.C., Brusca G.J. Invertebrates 2003, Sinauer Associates, Sunderland. second ed.
13. Buckley T.R., Attanayake D., Bradler S. Extreme convergence in stick insect evolution: phylogenetic placement of the Lord Howe Island tree lobster. Proc. Biol. Sci. 2009, 22:1055-1062.
14. Cameron S.L., Whiting M.F. Mitochondrial genomic comparisons of the subterranean termites from the Genus Reticulitermes (Insecta: Isoptera: Rhinotermitidae). Genome 2007, 50:188-202.
15. Cameron S.L., Whiting M.F. The complete mitochondrial genome of the tobacco hornworm, Manduca sexta, (Insecta: Lepidoptera: Sphingidae), and an examination of mitochondrial gene variability within butterflies and moths. Gene 2008, 408:112-123.
16. Cameron S.L., Miller K.B., D'Haese C.A., Whiting M.F., Barker S.C. Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda). Cladistics 2004, 20:534-557.
17. Cameron S.L., Barker S.C., Whiting M.F. Mitochondrial genomics and the new insect order Mantophasmatodea. Mol. Phylogenet. Evol. 2006, 38:274-279.
18. Cameron S.L., Beckenbach A.T., Dowton M., Whiting M.F. Evidence from mitochondrial genomics on interordinal relationships in insects. Arthropod Syst. Phylogenet. 2006, 64:27-34.
19. Cameron S.L., Lambkin C.L., Barker S.C., Whiting M.F. A mitochondrial genome phylogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision. Syst. Entomol. 2007, 32:40-59.
20. Cameron S.L., Sullivan J., Song H., Miller K.B., Whiting M.F. A mitochondrial genome phylogeny of the Neuropterida (lace-wings, alderflies and snakeflies) and their relationship to the other holometabolous insect orders. Zool. Scr. 2009, 38:575-590.
21. Carapelli A., Liò P., Nardi F., Van der Wath E., Frati F. Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea. BMC Evol. Biol. 2007, 7:S8.
22. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 2000, 17:540-552.
23. Castro L.R., Dowton M. The position of the Hymenoptera within the Holometabola as inferred from the mitochondrial genome of Perga condei (Hymenoptera: Symphyta: Pergidae). Mol. Phylogenet. Evol. 2005, 34:469-479.
24. Castro L.R., Dowton M. Mitochondrial genomes in the Hymenoptera and their utility as phylogenetic markers. Syst. Entomol. 2007, 32:60-69.
25. Conant G.C., Wolfe K.H. GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics 2008, 24:861-862.
26. Delsuc F., Phillips M.J., Penny D. Comment on " Hexapod origins: Monophyletic or Paraphyletic?" Science 2003, 301:1482.
27. Dowton M., Cameron S.L., Austin A.D., Whiting M.F. Phylogenetic approaches for the analysis of mitochondrial genome sequence data in the Hymenoptera - a lineage with both rapidly and slowly evolving mitochondrial genomes. Mol. Phylogenet. Evol. 2009, 52:512-519.
28. Engel M.S., Grimaldi D.A. A winged Zorotypus in Miocene amber from the Dominican Republic (Zoraptera: Zorotypidae), with the discussion on relationships of and within the order. Acta Geologica Hispanica 2000, 35:149-164.
29. Engel M.S., Grimaldi D.A. New light shed on the oldest insect. Nature 2004, 427:627-630.
30. Engel M.S., Grimaldi D.A., Krishna K. Termites (Isoptera): their phylogeny, classification, and rise to ecological dominance. Am. Mus. Novit. 2009, 3650:1-27.
31. Eriksson, T., 2007. The r8s Bootstrap Kit (Distributed by the Author).
32. Felsenstein, J., 1993. PHYLIP: Phylogenetic Inference Package (Distributed by the Author).
33. Feng X., Liu D.-F., Wang N.-X., Zhu C.-D., Jiang G.-F. The mitochondrial genome of the butterfly Papilio xuthus (Lepidoptera: Papilionidae) and related phylogenetic analyses. Mol. Biol. Rep. 2010, 37:3877-3888.
34. Fenn J.D., Cameron S.L., Whiting M.F. The complete mitochondrial genome sequence of the Mormon cricket (Anabrus simplex: Tettigoniidae: Orthoptera) and an analysis of control region variability. Insect Mol. Biol. 2007, 16:239-252.
35. Fenn J.D., Song H., Cameron S.L., Whiting M.F. A preliminary mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data. Mol. Phylogenet. Evol. 2008, 49:59-68.
36. Flook P.K., Rowell C.H.F. Inferences about orthopteroid phylogeny and molecular evolution from small subunit nuclear ribosomal DNA sequences. Insect Mol. Biol. 1998, 7:163-178.
37. Flook P.K., Rowell C.H.F., Gellissen G. The sequence, organization, and evolution of the Locusta migratoria mitochondrial genome. J. Mol. Evol. 1995, 41:928-941.
38. Gelman A., Rubin D.B. Inference from iterative simulation using multiple sequences. Stat. Sci. 1992, 7:457-511.
39. A Geologic Time Scale 2004 2004, Cambridge University Press, Cambridge. F.M. Gradstein, J.G. Ogg, A.G. Smith (Eds.).
40. Grimaldi D.A. 400million years on six legs: on the origin and early evolution of Hexapoda. Arthropod Struct. Dev. 2010, 39:191-203.
41. Grimaldi D.A., Engel M.S. Evolution of the Insects 2005, Cambridge University Press, Cambridge.
42. Gullan, P.J., Cranston, P.S., 2005. The Insects. An Outline of Entomology, Auflage, vol. 3. Blackwell Publishing, Berlin.
43. Haas F., Kukalová-Peck J. Dermaptera hindwing structure and folding: new evidence for familial, ordinal and superordinal relationships within Neoptera (Insecta). Eur. J. Entomol. 2001, 98:445-509.
44. Hennig, W., 1969. Die Stammesgechichte der Insekten. Kramer, Frankfurt am Main.
45. Hennig, W., 1981. Insect Phylogeny. John Wiley and Sons, New York (Translated and Edited by Pont, A.C. and revisionary notes by Schlee, D.).
46. Hennig W. Wirbellose II. Gliedertiere. 5 AuX. (Nachdruck) 1994, Gustav Fischer, Jena.
47. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 2001, 17:754-755.
48. Huelsenbeck J.P., Larget B., Alfaro M.E. Bayesian phylogenetic model selection using reversible jump markov chain Monte Carlo. Mol. Biol. Evol. 2004, 21:1123-1133.
49. Huson D.H., Richter D.C., Rausch C., Dezulian T., Franz M., Rupp R. Dendroscope - an interactive viewer for large phylogenetic trees. BMC Bioinf. 2007, 8:460.
50. Ishiwata, K., Sasaki, G., Ogawa, J., Miyata, T., Su, Z.-H., 2010. Phylogenetic relationships among insect orders based on three nuclear protein-coding gene sequences. Mol. Phylogenet. Evol. doi:10.1016/j.ympev.2010.11.001.
51. Jamieson B.G.M. The Ultrastructure and Phylogeny of Insect Spermatozoa 1987, Cambridge Univ. Press, Cambridge.
52. Jordan G.E., Piel W.H. PhyloWidget: Web-based visualizations for the tree of life. Bioinformatics 2008, 15:1641-1642.
53. Kambhampati S. A phylogeny of cockroaches and related insects based on DNA sequence of mitochondrial ribosomal RNA genes. Proc. Natl. Acad. Sci. USA 1995, 92:2017-2020.
54. Kass R.E., Raftery A.E. Bayes factors. J. Am. Stat. Assoc. 1995, 90:773-795.
55. Katoh K., Toh H. Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. BMC Bioinf. 2008, 25:212.
56. Katoh K., Misawa K., Kuma K.I., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002, 30:3059-3066.
57. Kim I., Cha S.Y., Yoon M.H., Hwang J.S., Lee S.M., Sohn H.D., Jin B.R. The complete nucleotide sequence and gene organization of the mitochondrial genome of the oriental mole cricket, Gryllotalpa orientalis (Orthoptera: Gryllotalpidae). Gene 2005, 353:155-168.
58. Kjer K.M. Aligned 18S and insect phylogeny. Syst. Biol. 2004, 53:506-514.
59. Kjer K.M., Honeycutt R.L. Site specific rates of mitochondrial genome and phylogeny of eutheria. BMC Evol. Biol. 2007, 7:8.
60. Kjer K.M., Carle F.L., Litman J., Ware J. A molecular phylogeny of Insecta. Arthropod Syst. Phylogenet. 2006, 64:35-44.
61. Klass K.-D., Zompro O., Kristensen N.P., Adis J. Mantophasmatodea: a new insect order with extant members in the afrotropics. Science 2002, 296:1456-1459.
62. Klass K.-D., Picker M.D., Damgaard J., Van Noort S., Tojo K. The taxonomy, genitalic morphology and phylogenetic relationships of southern African Mantophasmatodea (Insecta). Entomol. Abhandl. 2003, 61:3-67.
63. Klug R., Bradler S. The pregenital abdominal musculature in phasmids and its implications for the basal phylogeny of Phasmatodea (Insecta: Polyneoptera). Org. Divers. Evol. 2006, 6:171-184.
64. Komoto N., Yukuhiro K., Ueda K., Tomita S. Exploring the molecular phylogeny of phasmids with the whole mitochondrial genome sequences. Mol. Phylogenet. Evol. 2011, 58:43-52.
65. Korb J. Termites. Curr. Biol. 2007, 17:R995-R999.
66. Kristensen N.P. Phylogeny of insect orders. Annu. Rev. Entomol. 1981, 26:135-157.
67. Kristensen N.P. Forty years' insect phylogenetic systematics. Zool. Beitr. NF 1995, 36:83-124.
68. Kukalová-Peck, J., 1991. Fossil history and the evolution of hexapod structures. In: CSIRO (Eds.), The Insects of Australia, second ed. Melbourne University Press, Carlton, pp. 141-179.
69. Kukalová-Peck J., Peck S.B. Zoraptera wing structures: evidence for new genera and relationship with the blattoid orders (Insecta: Blattoneoptera). Syst. Entomol. 1993, 18:333-350.
70. Labandeira, C.C., 1994. A compendium of fossil insect families. In: Watkins, R. (Ed.), Contributions in Biology and Geology, vol. 88. Milwaukee Public Museum, Wisconsin, pp. 15-71.
71. Laslett D., Canbäck B. ARWEN, a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics 2008, 24:172-175.
72. Lowe T.M., Eddy S.R. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25:955-964.
73. Maekawa K., Kitade O., Matsumoto T. Molecular phylogeny of orthopteroid insects based on the mitochondrial cytochrome oxidase II gene. Zool. Sci. 1999, 16:175-184.
74. Mantovani B., Passamonti M., Scali V. The mitochondrial cytochrome oxidase II gene in Bacillus stick insects: ancestry of hybrids, androgenesis, and phylogenetic relationships. Mol. Phylogenet. Evol. 2001, 19:157-163.
75. Martynov A.B. Über zwei Grundtypen der Flügel bei den Insecten und ihre evolution. Zeitschrift zur Morphologie und Ökologie der Tiere 1925, 4:465-501.
76. Nardi F., Carapelli A., Fanciulli P.P., Dallai R., Frati F. The complete mitochondrial DNA sequence of the basal hexapod Tetrodontophora bielanensis: evidence for heteroplasmy and tRNA translocations. Mol. Biol. Evol. 2001, 18:1293-1304.
77. Nardi F., Spinsanti G., Boore J.L., Carapelli A., Dallai R., Frati F. Hexapod origins: monophyletic or paraphyletic?. Science 2003, 299:1887-1889.
78. Nuin, P., 2008. MrMTgui: cross-platform interface for ModelTest and MrModeltest. http://www.genedrift.org/mtgui.php.
79. Ogg J.G., Ogg G., Gradstein F.M. The Concise Geologic Time Scale 2008, Cambridge University Press, Cambridge.
80. Posada D., Buckley T.R. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio test. Syst. Biol. 2004, 53:793-808.
81. Posada D., Crandall K.A. ModelTest: testing the best-Wt model of nucleotide substitution. Bioinformatics 1998, 14:817-818.
82. Rähle W. Untersuchungen an Kopf und Prothorax von Embia ramburi Rimsky-Korsakoff 1906 (Embioptera, Embiidae). Zoologischer Jahrbücher, Abteilung für Anatomie und Ontogenie der Tiere 1970, 87:248-330.
83. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
84. Sanderson M.J. R8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 2003, 19:301-302.
85. Sheffield N.C., Song H., Cameron S.L., Whiting M.F. A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles. Mol. Biol. Evol. 2008, 25:2499-2509.
86. Shimodaira H., Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 1999, 16:1114-1116.
87. Simmons M.P., Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 2000, 49:369-381.
88. Simon C., Frati F., Beckenbach A., Crespi B., Liu H., Flook P. Evolution, weighting and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 1994, 87:651-701.
89. Simon C., Buckley T.R., Frati F., Stewart J.B., Beckenbach A.T. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Ann. Rev. Ecol. Evol. Syst. 2006, 37:545-579.
90. Stewart J.B., Beckenbach A.T. Phylogenetic and genomic analysis of the complete mitochondrial DNA sequence of the spotted asparagus beetle Crioceris duodecimpunctata. Mol. Phylogenet. Evol. 2003, 26:513-526.
91. Strugnell J., Norman M., Jackson J., Drummond A.J., Cooper A. Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework. Mol. Phylogenet. Evol. 2005, 37:426-441.
92. *and other methods) 1999, Sinauer Associates, Sunderland.
93. Taanman J.-W. The mitochondrial genome: structure, transcription, translation and replication. Biochim. Biophys. Acta 1999, 1410:103-123.
94. Talavera G., Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 2007, 56:564-577.
95. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
96. Terry M.D., Whiting M.F. Mantophasmatodea and phylogeny of the lower neopterous insects. Cladistics 2005, 21:240-257.
97. Thomas M.A., Walsh K.A., Wolf M.R., McPheron B.A., Marden J.H. Molecular phylogenetic analysis of evolutionary trends in stonefly wing structure and locomotor behavior. Proc. Natl. Acad. Sci. USA 2000, 97:13178-13183.
98. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
99. Thorne B.L., Carpenter J.M. Phylogeny of the dictyoptera. Syst. Entomol. 1992, 17:253-268.
100. Tilgner E.H., Kiselyova T.G., McHugh J.V. A morphological study of Timema cristinae Vickery with implications for the phylogenetics of Phasmida. Dtsche. Entomol. Z. 1999, 46:149-162.
101. Townsend J.P. Profiling phylogenetic informativeness. Syst. Biol. 2007, 56:222-231.
102. Wedmann S., Bradler S., Rust J. The first fossil leaf insect: 47million years of specialized cryptic morphology and behavior. Proc. Natl. Acad. Sci. USA 2007, 104:565-569.
103. Wheeler W.C., Whiting M.F., Wheeler Q.D., Carpenter J.M. The phylogeny of the extant hexapod orders. Cladistics 2001, 17:113-169.
104. Whitfield J.B., Kjer K.M. Ancient rapid radiations of insects: challenges for phylogenetic analysis. Annu. Rev. Entomol. 2008, 53:449-472.
105. Whiting M.F. Mecoptera is paraphyletic: multiple genes and phylogeny of Mecoptera and Siphonaptera. Zool. Scr. 2002, 31:93-104.
106. Whiting M.F., Bradler S., Maxwell T. Loss and recovery of wings in stick insects. Nature 2003, 421:264-267.
107. Willmann R. Die phylogenetischen Beziehungen der Insecta: offene Fragen und Probleme. Verhandlungen Westdeutscher Entomologentag 2003, 2001:1-64.
108. Willmann R. Phylogenetic relationships and evolution of insects. Assembling the Tree of Life 2004, 330-344. Oxford University Press, Oxford. J. Cracraft, M.J. Donoghue (Eds.).
109. Xia X., Xie Z. DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 2001, 92:371-373.
110. Xia X., Xie Z., Salemi M., Chen L., Wang Y. An index of substitution saturation and its application. Mol. Phylogenet. Evol. 2003, 26:1-7.
111. Yamauchi M.M., Miya M.U., Nishida M. Use of a PCR-based approach for sequencing whole mitochondrial of insects: two examples (cockroach and dragonfly) based on method developed for decapod crustaceans. Insect Mol. Biol. 2004, 13:435-442.
112. Young N.D., Healy J. GapCoder automates the use of indel characters in phylogenetic analysis. BMC Bioinf. 2003, 4:6.
113. Zhang J., Zhou C., Gai Y., Song D., Zhou K. The complete mitochondrial genome of Parafronurus youi (Insecta: Ephemeroptera) and phylogenetic position of the Ephemeroptera. Gene 2008, 424:18-24.
114. Zompro O. The Phasmatodea and Raptophasma n. gen., Orthoptera incertae sedis, in Baltic amber (Insecta: Orthoptera). Mitteilungen Geol. Paläontol. Inst. Hamburg 2001, 85:229-261.