Reconstructing intraordinal relationships in Lepidoptera using mitochondrial genome data with the description of two newly sequenced lycaenids, Spindasis takanonis and Protantigius superans (Lepidoptera: Lycaenidae)

Molecular Phylogenetics and Evolution

Volumn 61, Issue 2, 2011, Pages 436-445

  Kim, Min Jee ^a   Kang, Ah Rang ^a   Jeong, Heon Cheon ^b   Kim, Ki Gyoung ^c   Kim, Iksoo ^a  

^a Chonnam National University   (South Korea)

^b Insect Research Institute of Hampyeong   (South Korea)

^c National Institute of Biological Resources   (South Korea)

Author keywords

Complete mitogenome; Lepidopteran phylogeny; Macrolepidoptera; Mitochondrial DNA; Protantigius superans; Spindasis takanonis

Indexed keywords

MITOCHONDRIAL DNA; TRANSFER RNA;

ANIMAL; ARTICLE; BUTTERFLY; CLASSIFICATION; CONFORMATION; DNA SEQUENCE; GENETICS; GENOME; MITOCHONDRIAL GENOME; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ANIMALS; BASE SEQUENCE; BUTTERFLIES; DNA, MITOCHONDRIAL; GENOME, INSECT; GENOME, MITOCHONDRIAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA;

BOMBYCOIDEA; GEOMETROIDEA; HEXAPODA; LEPIDOPTERA; LYCAENIDAE; MACROLEPIDOPTERA; NOCTUOIDEA; NYMPHALIDAE; PAPILIONIDAE; PAPILIONOIDEA; PIERIDAE; PYRALOIDEA; TORTRICOIDEA;

EID: 80052709094     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2011.07.013     Document Type: Article

References (83)

1. Akaike H. A new look at the statistical model identification. IEEE Trans. Autom. Contr. 1974, 19:716-723.
2. Braband A., Cameron S.L., Podsiadlowski L., Daniels S.R., Mayer G. The mitochondrial genome of the onychophoran Opisthopatus cinctipes (Peripatopsidae) reflects the ancestral mitochondrial gene arrangement of Panarthropoda and Ecdysozoa. Mol. Phylogenet. Evol. 2010, 57:285-292.
3. Boore J.L., Lavrov D., Brown W.M. Gene translocation links insects and crustaceans. Nature 1998, 393:667-668.
4. Brown G.G., Gadaleta G., Pepe G., Saccone C., Sbisà E. Structural conservation and variation in the D loop-containing region of vertebrate mitochondrial DNA. J. Mol. Biol. 1986, 192:503-511.
5. Cameron S.L., Barker S.C., Whiting M.F. Mitochondrial genomics and the relationships and validity of the new insect order Mantophasmatodea. Mol. Phylogenet. Evol. 2006, 38:274-279.
6. Cameron S.L., D'Hearse C.A., Miller K.B., 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.
7. 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.
8. 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.
9. 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.
10. Cantatore P., Gadaleta M.N., Roberti M., Saccone C., Wilson A.C. Duplication and remodeling of tRNA genes during the evolutionary rearrangement of mitochondrial genomes. Nature 1987, 329:853-855.
11. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic tool. Curr. Opin. Genet. Dev. 2000, 8:668-674.
12. Caterino M.S., Sperling F.A.H. Papilio phylogeny based on mitochondrial cytochrome oxidase I and II genes. Mol. Phylogenet. Evol. 1999, 11:122-137.
13. Cha S.Y., Yoon H.J., Lee E.M., Yoon M.H., Hwang J.S., Jin B.R., Han Y.S., Kim I. The complete nucleotide sequence and gene organization of the mitochondrial genome of the bumblebee, Bombus ignitus (Hymenoptera: Apidae). Gene 2007, 392:206-220.
14. Clary D.O., Wolstenholme D.R. The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J. Mol. Evol. 1985, 22:252-271.
15. Coates B.S., Sumerford D.V., Hellmich R.L., Lewis L.C. Partial mitochondrial genome sequences of Ostrinia nubilalis and Ostrinia furnicalis. Int. J. Biol. Sci. 2005, 1:13-18.
16. 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.
17. Ehrlich P.R., Ehrlich A.H. The phenetic relationships of the butterflies. I. Adult taxonomy and the non-specificity hypothesis. Syst. Zool. 1967, 16:301-317.
18. Farris J.S. The retention index and the rescaled consistency index. Cladistics 1989, 5:417-419.
19. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 1981, 17:368-376.
20. 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 mitochondrial genome data. Mol. Phylogenet. Evol. 2008, 49:59-68.
21. Folmer O., Black M., Hoeh W., Lutz R., Vrijenhoek R. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 1994, 3:294-299.
22. Garey J.R., Wolstenholme D.R. Platyhelminth mitochondrial DNA: evidence for early evolutionary origin of a tRNA-ser(AGN) that contains a dihydrouridine arm replacement-loop, and of serine-specifying AGA and AGG codons. J. Mol. Evol. 1989, 28:374-387.
23. Gibson A., Gowri-Shankar V., Higgs P.G., Rattray M. A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods. Mol. Biol. Evol. 2005, 22:251-264.
24. Guindon S., Lethiec F., Duroux P., Gascuel O. PHYML online-a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 2005, 33:W557-W559.
25. Grimaldi D., Engel M.S. Evolution of the Insects 2005, Cambridge University Press, Cambridge, UK.
26. Hassanin A. Phylogeny of Arthropoda inferred from mitochondrial sequences: strategies for limiting the misleading effects of multiple changes in pattern and rates of substitution. Mol. Phylogenet. Evol. 2006, 38:100-116.
27. Hong M.Y., Lee E.M., Jo Y.H., Park H.C., Kim S.R., Hwang J.S., Jin B.R., Kang P.D., Kim K.-G., Han Y.S., Kim I. Complete nucleotide sequence and organization of the mitogenome of the silk moth Caligula boisduvalii (Lepidoptera: Saturniidae) and comparison with other lepidopteran insects. Gene 2008, 413:49-57.
28. Hong M.Y., Jeong H.C., Kim M.J., Jeong H.U., Lee S.H., Kim I. Complete mitogenome sequence of the jewel beetle, Chrysochroa fulgidissima (Coleoptera: Buprestidae). Mitochondrial DNA 2009, 20:46-60.
29. Hong G., Jiang S., Yu M., Yang Y., Li F., Xue F., Wei Z. The complete nucleotide sequence of the mitochondrial genome of the cabbage butterfly, Artogeia melete (Lepidoptera: Pieridae). Acta Biochim. Biophys. Sin. 2009, 41:446-455.
30. Hu J., Zhang D., Hao J., Huang D., Cameron S., Zhu C. The complete mitochondrial genome of the yellow coaster, Acraea issoria (Lepidoptera: Nymphalidae: Heliconiinae: Acraeini): sequence, gene organization and a unique tRNA translocation event. Mol. Biol. Rep. 2009, 37:3431-3438.
31. Huelsenbeck J.P., Ronquist F. MrBayes: Bayesian inference of phylogeny. Bioinformatics 2001, 17:754-755.
32. Jermiin L., Ho S.Y., Ababneh F., Robinson J., Larkum A.W. The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Syst. Biol. 2004, 53:638-643.
33. Jiang S.T., Hong G.Y., Yu M., Li N., Yang Y., Liu Y.Q., Wei Z.J. Characterization of the complete mitochondrial genome of the giant silkworm moth, Eriogyna pyretorum (Lepidoptera: Saturniidae). Int. J. Biol. Sci. 2009, 5:351-365.
34. Jobb G., von Haeseler A., Strimmer K. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 2004, 4:18.
35. Jones M., Gantenbein B., Fet V., Blaxter M. The effect of model choice on phylogenetic inference using mitochondrial sequence data: lessons from the scorpions. Mol. Phylogenet. Evol. 2007, 43:583-595.
36. Junqueira A.C., Lessinger A.C., Torres T.T., da Silva F.R., Vettore A.L., Arruda P., Azeredo Espin A.M. The mitochondrial genome of the blowfly Chrysomya chloropyga (Diptera: Calliphoridae). Gene 2004, 339:7-15.
37. Katoh K., Misawa K., Kuma K., Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002, 30:3059-3066.
38. Kim M.I., Baek J.Y., Kim M.J., Jeong H.C., Kim K.-G., Bae C.H., Han Y.S., Jin B.R., Kim I. Complete nucleotide sequence and organization of the mitogenome of the red-spotted apollo butterfly, Parnassius bremeri (Lepidoptera: Papilionidae) and comparison with other lepidopteran insects. Mol. Cells 2009, 28:347-363.
39. Kim S.R., Kim M.I., Hong M.Y., Kim K.Y., Kang P.D., Hwang J.S., Han Y.S., Jin B.R., Kim I. The complete mitogenome sequence of the Japanese oak silkmoth, Antheraea yamamai (Lepidoptera: Saturniidae). Mol. Biol. Rep. 2009, 36:1871-1880.
40. Kim I., Lee E.M., Seol K.Y., Yun E.Y., Lee Y.B., Hwang J.S., Jin B.R. The mitochondrial genome of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae). Insect Mol. Biol. 2006, 15:217-225.
41. Kim M.J., Wan X., Kim K.-G., Hwang J.S., Kim I. Complete nucleotide sequence and organization of the mitogenome of endangered Eumenis autonoe (Lepidoptera: Nymphalidae). Afr. J. Biotechnol. 2010, 9:735-754.
42. Kim M.I., Wan X., Kim M.J., Jeong H.C., Ahn N.-H., Kim K.-G., Han Y.S., Kim I. Phylogenetic relationships of true butterflies (Lepidoptera: Papilionoidea) inferred from COI, 16S rRNA and EF-1α sequences. Mol. Cells 2010, 30:409-425.
43. Kishino H., Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data and the branching order in Hominoidea. J. Mol. Evol. 1989, 29:170-179.
44. Kluge A., Farris J.S. Quantitative phyletics and the evolution of anurans. Syst. Zool. 1969, 18:1-32.
45. Kristensen N.P. Remarks on the family-level phylogeny of butterflies (Insecta Lepidoptera, Rhopalocera). Zeit. Zool. Syst. Evol. Forsch. 1976, 14:25-33.
46. Kristensen N.P., Scoble M.J., Karsholt O. Lepidoptera phylogeny and systematic: the state of inventorying moth and butterfly diversity. Zootaxa 2007, 1668:699-747.
47. Kristensen N.P., Skalski A.W. Phylogeny and palaeontology. Handbuch der Zoologie, vol. IV, Arthropoda: Insecta, Part 35, Lepidoptera, Moths and Butterflies, vol. 1: Evolution, Systematics, and Biogeography 1999, 7-25. Walter de Gruyter, Berlin & New York. N.P. Kristensen (Ed.).
48. Lee E.S., Shin K.S., Kim M.S., Park H., Cho S., Kim C.B. The mitochondrial genome of the smaller tea tortix Adoxophyes honmai (Lepidoptera: Tortricidae). Gene 2006, 373:52-57.
49. Liao F., Wang L., Wu S., Li Y.-P., Zhao L., Huang G.-M., Niu C.-J., Liu Y.-Q., Li M.-G. The complete mitochondrial genome of the fall webworm, Hyphantria cunea (Lepidoptera: Arctiidae). Int. J. Biol. Sci. 2010, 6:172-186.
50. Liu Y., Li Y., Pan M., Dai F., Zhu X., Lu C., Xiang Z. The complete mitochondrial genome of the Chinese oak silkmoth, Antheraea pernyi (Lepidoptera: Saturniidae). Acta Biochim. Biophys. Sin. 2008, 40:693-703.
51. 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.
52. Margam V.M., Coates B.S., Hellmich R.L., Agunbiade T., Seufferheld M.J., et al. Mitochondrial genome sequence and expression profiling for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae). PLoS One 2011, 6:e16444.
53. Massana R., Castresana J., Balagué V., Guillou L., Romari K., Groisillier A., Valentin K., Pedrós-Alió C. Phylogenetic and ecological analysis of novel marine stramenopiles. Appl. Environ. Microbiol. 2004, 70:3528-3534.
54. Minet J. Tentative reconstruction of the ditrysian phylogeny (Lepidoptera: Glossata). Entomol. Scand. 1991, 22:69-95.
55. Misawa K., Nei M. Reanalysis of Murphy et al'.s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees. J. Mol. Evol 2003, 57:S290-S296.
56. Mutanen M., Wahlberg N., Kaila L. Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies. Proc. Roy. Soc. B 2010, 277:2839-2848.
57. Nardi F., Caeapelli A., Dallai R., Frati F. The mitochondrial genome of the olive fly Bactrocera oleae: two haplotypes from distant geographic locations. Insect Mol. Biol. 2003, 12:605-611.
58. Nielsen E.S. Phylogeny of major lepidopteran groups. The Hierarchy of Life 1989, 281-294. Elsevier, Amsterdam. B. Fernholm, K. Bremer, H. Jörnvall (Eds.).
59. Ohtsuki T., Kawai G., Watanabe K. The minimal tRNA: unique structure of Ascaris suum mitochondrial tRNASer-UCU having a short T arm and lacking the entire D arm. FEBS Lett. 2002, 514:37-43.
60. Pons J., Ribera I., Bertranpetit J., Balke M. Nucleotide substitution rates for the full set of mitochondrial protein-coding genes in Coleoptera. Mol. Phylogenet. Evol. 2010, 56:796-807.
61. Posada D., Crandal K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
62. Regier J.C., Zwick A., Cummings M.P., Kawahara A.Y., Cho S., Weller S., Roe A., Baixeras J., Brown J.W., Parr C., Davis D.R., Epstein M., Hallwachs W., Hausmann A., Janzen D.H., Kitching I.J., Solis M.A., Yen S.-H., Bazinet A.L., Mitter C. Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study. BMC Evol. Biol. 2009, 9:280.
63. Rich A., RajBhandary U.L. Transfer RNA: molecular structure, sequence and properties. Annu. Rev. Biochem. 1976, 45:805-860.
64. Robbins R.K. Comparative morphology of the butterfly forleg coxa and trochanter (Lepidoptera) and its systematic implications. Proc. Entomol. Soc. Wash. 1988, 90:133-154.
65. Salvato P., Simonato M., Battisti A., Negrisolo E. The complete mitochondrial genome of the bag-shelter moth Ochrogaster lunifer (Lepidoptera, Notodontidae). BMC Genom. 2008, 9:331.
66. Scott J.A. The phylogeny of butterflies (Papilionoidea and Hesperioidea). J. Res. Lepid. 1985, 23:241-281.
67. Sheffield N.C., Song H., Cameron S.L., Whiting M.F. Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics. Syst. Biol. 2009, 58:381-394.
68. Shimodaira H., Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 1999, 16:1114-1116.
69. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 2002, 51:492-508.
70. Song H., Sheffield N.C., Cameron S.L., Miller K.B., Whiting M.F. When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics. Syst. Entomol. 2010, 35:429-448.
71. 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.
72. Strimmer K., Rambaut A. Inferring confidence sets of possibly misspecified gene trees. Proc. Biol. Sci. 2002, 269:137-142.
73. Swofford D.L. PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods). Ver. 4.10 2002, Sinauer Associates, Sunderland, MA.
74. Tamura K., Dudley J., Nei M., Kumar S. MEGA 4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
75. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL X windows interface. flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 24:173-216.
76. Wahlberg N., Braby M.F., Brower A.V.Z., de Jong R., Lee M.-M., Nylin S., Pierce N., Sperling F.A., Vila R., Warren A.D., Zakharov E. Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers. Proc. Roy. Soc. B 2005, 272:1577-1586.
77. Wei S.-J., Shi M., Chen X.-X., Sharkey M.J., van Achterberg C., Ye G.-Y., He J.-H. New views on strand asymmetry in insect mitochondrial genomes. PLoS One 2010, 5:e12708.
78. Weller S.J., Pashely D.P. In search of butterfly origins. Mol. Phylogenet. Evol. 1995, 4:235-246.
79. Weller S.J., Pashley D.P., Martin J.A. Reassessment of butterfly family relationships using independent genes and morphology. Ann. Entomol. Soc. Am. 1996, 89:184-192.
80. Wernersson R., Pedersen A.G. Multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res. 2003, 31:3537-3539.
81. Wilson K., Cahill V., Ballment E., Benzie J. The complete sequence of the mitochondrial genome of the crustacean Penaeus mondon: are malacostracan crustaceans more closely related to insects than to branchiopods?. Mol. Biol. Evol. 2000, 17:863-874.
82. Yang L., Wei Z.-J., Hong G.-Y., Jiang S.-T., Wen L.-P. The complete nucleotide sequence of the mitochondrial genome of Phthonandria atrilineata (Lepidoptera: Geometridae). Mol. Biol. Rep. 2009, 36:1441-1449.
83. Yukuhiro K., Sezutsu H., Itoh M., Shimizu K., Banno Y. Significant levels of sequence divergence and gene rearrangements have occurred between the mitochondrial genomes of the wild mulberry silk moth, Bombyx mandarina, and its close relative, the domesticated silk moth, Bombyx mori. Mol. Biol. Evol. 2002, 19:1385-1389.