Phylogenetic and genomic analysis of the complete mitochondrial DNA sequence of the spotted asparagus beetle Crioceris duodecimpunctata

Molecular Phylogenetics and Evolution

Volumn 26, Issue 3, 2003, Pages 513-526

  Stewart, James Bruce ^a   Beckenbach, Andrew T ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

Author keywords

Coleoptera; Complete mtDNA sequence; Crioceris; Insect molecular phylogenetics; Mitochondrial genome structure; Mitogenomic

Indexed keywords

ASPARAGUS; COLEOPTERA; CRIOCERIS; CRIOCERIS DUODECIMPUNCTATA; DIPTERA; ENDOPTERYGOTA; HEXAPODA; INSECTA; LEPIDOPTERA;

EID: 0037353318     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(02)00421-9     Document Type: Article

References (46)

1. Adachi, J., Hasegawa, H., 1996a. MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28, 1-50.
2. Adachi, J., Hasegawa, M., 1996b. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42, 459-468.
3. Arnason, U., Adegoke, J.A., Bodin, K.B., Born, E.W., Esa, Y.B., Gullberg, A., Nilsson, M., Short, R.V., Xu, X., Janke, A., 2002. Mammalian mitogenomic relationships and the root of the eitherian tree. Proc. Natl. Acad. Sci. USA 99, 8151-8156.
4. Arndt, A., Marquez, C., Lambert, P., Smith, M.J., 1996. Molecular phylogeny of eastern Pacific sea cucumbers (Echinodermata: Holothuroidea) based on mitochondrial DNA sequence. Mol. Phylogenet. Evol. 6, 425-437.
5. Ballard, J.W.O., 2000. Comparative genomics of mitochondrial DNA in members of the Drosophila melanogaster subgroup. J. Mol. Evol. 51, 48-63.
6. Beard, C.D., Hamm, D.M., Collins, F.H., 1993. The mitochondrial genome of the mosquito Anopheles gambiae: DNA sequence, genome organization, and comparisons with the mitochondrial sequences of other insects. Insect Mol. Biol. 2, 103-124.
7. Black IV, W.C., Roehrdanz, R.L., 1998. Mitochondrial gene order is not conserved in Arthropods: Prostriate and Metastriate tick mitochondrial genomes. Mol. Biol. Evol. 15, 1772-1785.
8. Carmean, D., Kimsey, L.S., Berbee, M.L., 1992. 18s rDNA sequences and the Holometabolous insects. Mol. Phylogenet. Evol. 1, 270-278.
9. Caterino, M.S., Soowon, C., Sperling, F.A.H, 2000. The current state of insect molecular phylogenetics: a thriving tower of Babel. Ann. Rev. Entomol. 45, 1-54.
10. Clary, D.O., Wolstenholme, D.R., 1985. The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organisation, and genetic code. J. Mol. Evol. 22, 252-271.
11. Clary, D.O., Wolstenholme, D.R., 1987. Drosophila mitochondrial DNA: conserved sequences in the A + T rich region and supporting evidence for a secondary structure model of the small ribosomal RNA. J. Mol. Evol. 25, 116-125.
12. Crease, T., 1999. The complete sequence of the mitochondrial genome of Daphnia pulex (Cladocerra: Crustacia). Gene 233, 89-99.
13. Crozier, R.H., Crozier, Y.C., 1993. The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization. Genetics 133, 97-117.
14. Dotson, E.M., Beard, C.D., 2001. Sequence and organization of the mitochondrial genome of the Chagas disease vector, Triatoma dimidiata. Insect Mol. Biol. 10, 205-215.
15. Flook, P.K., Rowell, C.H.F., Gellissen, G., 1995. The sequence, organization, and evolution of the Locusta migratoria mitochondrial genome. J. Mol. Evol. 41, 928-941.
16. Foster, P.G., Hickey, D.A., 1999. Compositional bias may affect both DNA and protein-based phylogenetic reconstruction. J. Mol. Evol. 48, 284-290.
17. Foster, P.G., Jermiin, L.S., Hickey, D.S., 1997. Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J. Mol. Evol. 44, 282-288.
18. Friedrich, M., Muqim, N., 2003. Sequence and phylogenetic analysis of the complete mitochondrial genome of the flour beetle Tribolium castanaeum. Mol. Phylogenet. Evol., in press.
19. Garesse, R., 1988. Drosophila melanogaster mitochondrial DNA: gene organization and evolutionary consideration. Genetics 118, 649-663.
20. Gaunt, M.W., Miles, M.A., 2002. An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks. Mol. Biol. Evol. 19, 746-761.
21. Hasegawa, M., Kishino, H., Yano, T., 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22, 160-174.
22. Hall, T.A., 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95-98.
23. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M., 2001. A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences. Mol. Phylogenet. Evol. 20, 275-285.
24. Kristensen, N.P., 1991. Phylogeny of extant hexapods. In: C.S.I.R. Organization (Ed.), The Insects of Australia, A Textbook for Students and Research Workers, second ed. Melbourne University Press, Victoria, pp. 125-142.
25. Lavrov, D.V., Brown, W.M., Boore, J.L., 2000. A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proc. Natl. Acad. Sci. USA 97, 13738-13742.
26. Lessinger, A.C., Junqueira, T.A., Lemos, T.A., Kemper, E.L., da Silva, F.R., Vettore, A.L., Arruda, P., Azeredo-Espin, A.M.L., 2000. The mitochondrial genome of the primary screwworm fly Cochliomyia hominivorax (Diptera: Calliphoridae). Insect Mol. Biol. 9, 521-529.
27. Liu, H., Beckenbach, A.T., 1992. Evolution of the mitochondrial cytochrome oxidase II gene among 10 orders of insects. Mol. Phylogenet. Evol. 1, 41-52.
28. Lowe, T.D., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964.
29. Mitchell, S.E., Cockburn, A.F., Seawright, J.A., 1993. The mitochondrial genome of Anopheles quadrimaculatus species A: complete nucleotide sequence and gene organisation. Genome 36, 1058-1073.
30. Miya, M., Kawaguchi, A., Nishida, M., 2001. Mitogenomic exploration of higher level teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol. Biol. Evol. 18, 1993-2009.
31. Miya, M., Nishida, M., 2000. Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol. Phylogenet. Evol. 17, 437-455.
32. Nardi, F., Carapelli, A., Faniulli, P.P., Dallai, R., Frati, F., 2001. The complete mitochondrial DNA sequence of the basal hexapod Tetrodontophora bielanensis: evidence for heteroplasmy and tRNA translocations. Mol. Biol. Evol. 18, 1293-1304.
33. Nei, M., Kumar, S., Takahashi, K., 1998. The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proc. Natl. Acad. Sci. USA 95, 12390-12397.
34. Ojala, D., Montoya, J., Attardi, G., 1981. tRNA punctuation model of RNA processing in the human mitochondria. Nature 290, 470-474.
35. Palumbi, S.R., Martin, A., Romano, S., McMilian, R.O., Stice, L., Grabowski, G., 1991. The Simple Fool's Guide to PCR, Version 2. University of Hawaii Zoology Department, Honolulu, Hawaii.
36. Pashley, D.P., McPheron, B.A., Zimmer, E.A., 1993. Systematics of holometabolous insect orders based on 18s ribosomal RNA. Mol. Phylogenet. Evol. 2, 132-142.
37. Shao, R., Campbell, N.J.H., Baker, S.C., 2001. Numerous gene rearrangements in the mitochondrial genome of the Wallaby Louse, Heterodoxus macropus (Phthriptera). Mol. Biol. Evol. 18, 858-865.
38. Simon, C., Frati, F., Beckenbach, A., Crespi, B., Lui, H., Flook, P., 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 87, 651-701.
39. Spanos, L., Koutroumbas, G., Kotsyfakis, M., Louis, C., 2000. The mitochondrial genome of the Mediterranean fruit fly, Ceratitis capitata. Insect Mol. Biol. 9, 139-144.
40. Steinberg, S., Cedergren, R., 1994. Structural compensation in atypical mitochondrial tRNAs. Struct. Biol. 1, 507-510.
41. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, MA.
42. Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties, and weight matrix choice. Nucleic Acids Res. 11, 4673-4680.
43. Whiting, M., Carpenter, J.C., Wheeler, Q.D., Wheeler, W.C., 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.
44. Wolstenholme, D.R., 1992. Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141, 173-216.
45. Yukuhiro, K., Sezutsu, H., Itoh, M., Shimizu, K., Banno, Y., 2002. Significant levels of sequence divergence and gene rearrangements have occurred between the mitochondrial genomes of the Wild Mulberry Silkmoth, Bombyx mandarina and its close relative, the Domesticated Silkmoth, Bombyx mori. Mol. Biol. Evol. 19, 1385-1389.
46. Zhang, D., Szymura, J.M., Hewitt, G.M., 1995. Evolution and structural conservation of the control region of insect mitochondrial DNA. J. Mol. Evol. 40, 382-391.