Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics

Systematic Biology

Volumn 58, Issue 4, 2009, Pages 381-394

  Sheffield, Nathan C ^a,b   Song, Hojun ^a   Cameron, Stephen L ^c   Whiting, Michael F ^a  

^a BRIGHAM YOUNG UNIVERSITY   (United States)

^b DUKE UNIVERSITY   (United States)

^c CSIRO   (Australia)

Author keywords

Base compositional heterogeneity; Coleoptera; Logdet; Model of evolution; Nonstationary evolution; Nucleotide composition; Phylogeny

Indexed keywords

ANIMAL; ARTICLE; BEETLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; DNA BASE COMPOSITION; GENETICS; MITOCHONDRIAL GENOME; PHYLOGENY; TIME;

ANIMALS; BASE COMPOSITION; BEETLES; GENOME, MITOCHONDRIAL; MODELS, GENETIC; PHYLOGENY; TIME FACTORS;

COLEOPTERA; HEXAPODA;

EID: 70349434888     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syp037     Document Type: Article

References (82)

1. Arnoldi F.G.C., Ogoh K., Ohmiya Y., Viviani V.R. 2007. Mitochondrial genome sequence of the Brazilian luminescent click beetle Pyrophorus divergens (Coleoptera: Elateridae): mitochondrial genes utility to investigate the evolutionary history of Coleoptera and its bioluminescence. Gene 405:1-9. (Pubitemid 350017861)
2. Bae J.S., Kim I., Sohn H.D., Jin B.R. 2004. The mitochondrial genome of the firefly, Pyrocoelia rufa: complete DNA sequence, genome organization, and phylogenetic analysis with other insects. Mol. Phylogenet. Evol. 32:978-985.
3. Barrowclough G.F., Groth J.G., Mertz L.A. 2006. The rag-1 exon in the avian order caprimulgiformes: phytogeny, heterozygosity, and base composition. Mol. Phylogenet. Evol. 41:238-248.
4. Beard C.B., Hamm D.M., Collins F.H. 1993. The mitochondrial genome of the mosquito Anopheles gambiae. DNA sequence, genome organization, and comparisons with mitochondrial sequences of other insects. Insect Mol. Biol. 2:103-124.
5. Bergsten J. 2005. A review of long-branch attraction. Cladistics 21: 163-193.
6. Beutel R.G., Ge S., Hornschemeyer T. 2008. On the head morphology of Tetraphalerus, the phytogeny of Archostemata and the basal branching events in Coleoptera. Cladistics 24:270-298.
7. Beutel R.G., Haas F 2000. Phylogenetic relationships of the suborders of Coleoptera (Insecta). Cladistics 16:103-141. (Pubitemid 32152112)
8. Bevan R.B., Bryant D., Lang B.F. 2007. Accounting for gene rate heterogeneity in phylogenetic inference. Syst. Biol. 56:194-205.
9. Blanquart S., Lartillot N. 2006. A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution. Mol. Biol. Evol. 23:2058.
10. Bocakova M., Bocak L., Hunt T., Teravainen M., Vogler A.P. 2007. Molecular phylogenetics of Elateriformia (Coleoptera): evolution of bioluminescence and neoteny. Cladistics 23:477-496. (Pubitemid 47512280)
11. Boussau B., Gouy M. 2006. Efficient likelihood computations with nonreversible models of evolution. Syst. Biol. 55:756-768.
12. Brown W.M., Prager E.M., Wang A., Wilson A.C. 1982. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J. Mol. Evol. 18:225-239.
13. Cameron S.L., Barker S.C., Whiting M.F. 2006. Mitochondrial genomics and the relationships and validity of the new insect order Mantophasmatodea. Mol. Phylogenet. Evol. 38:274-279.
14. Cameron S.L., Lambkin CL., Barker S.C., Whiting M.F. 2007. A mitochondrial genome phytogeny of Diptera: whole genome sequence data accurately resolve relationships over broad timescales with high precision. Syst. Entomol. 32:40-59.
15. Cameron S.L., Miller K.B., D'Haese C.A., Whiting M.F., Barker S.C. 2004. Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Athropoda). Cladistics 20:534-557.
16. Campbell D.L., Brower A.V.Z., Pierce N.E. 2000. Molecular evolution of the wingless gene and its implications for the phylogenetic placement of the butterfly family Riodinidae (Lepidoptera: Papilionoidea). Mol. Biol. Evol. 17:684-696.
17. Caveney S. 1986. The phylogenetic significance of ommatidium structure in the compound eyes of polyphagan beetles. Can. J. Zool. 64:1787-1819.
18. Chang B.S.W., Campbell D.L. 2000. Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences. Mol. Biol. Evol. 17:1220-1231.
19. Clary D.O., Wolstenholme D.R. 1985. The mitochondrial DNA molecule of Drosophila yakuba: Nucleotide sequence, gene organization, and genetic code. J. Mol. Evol. 22:252-271.
20. Coates B.S., Sumerford D.V., Hellmich R.L., Lewis L.C. 2005. Partial mitochondrial genome sequences of Ostrinia nubilalis and Ostrinia furnicalis. Int. J. Biol. Sci. 1:13.
21. Collins T.M., Fedrigo O., Naylor G.J.P. 2005. Choosing the best genes for the job: the case for stationary genes in genome-scale phytogenies. Syst. Biol. 54:493-500.
22. Collins T.M., Wimberger P.H., Naylor G.J.P. 1994. Compositional bias, character-state bias, and character-state reconstruction using parsimony. Syst. Biol. 43:482-496.
23. Conant G.C., Lewis P.O. 2001. Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference. Mol. Biol. Evol. 18:1024-1033.
24. Cox C.J., Foster P.G., Hirt R.P., Harris S.R., Embley TM. 2008. The archaebacterial origin of eukaryotes. Proc. Natl. Acad. Sci. U.S.A. 105: 20356-20361
25. Crowson R.A. 1960. The phytogeny of Coleoptera. Annu. Rev. Entomol. 5:111-134.
26. Delsuc F., Philips M.J., Penny D. 2003. Comment on "Hexapod origins: monophyletic or paraphyletic?" Science 301:1482e.
27. Edgar R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792.
28. Erixon P., Svennblad B., Britton T., Oxelman B. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol. 52:665-673.
29. Eyre-Walker A. 1998. Problems with parsimony in sequences of biased base composition. J. Mol. Evol. 47:686-690.
30. Felsenstein J. (1978). Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
31. Fenn J.D., Song H., Cameron S.L., Whiting M.F. 2008. A mitochondrial genome phytogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data. Mol. Phylogenet. Evol. 49:59-68.
32. Foster P.G. 2004. Modeling compositional heterogeneity. Syst. Biol. 53:485-495.
33. Foster P.G., Hickey D.A. 1999. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J. Mol. Evol. 48:284-290
34. Friedrich M., Muqim N. 2003. Sequence and phylogenetic analysis of the complete mitochondrial genome of the flour beetle Tribolium castanaeum. Mol. Phylogenet. Evol. 26:502-512.
35. Galtier N., Gouy M. 1995. Inferring phytogenies from DNA sequences of unequal base compositions. Proc. Natl. Acad. Sci. U.S.A. 92:11317-11321.
36. Galtier N., Gouy M. 1998. Inferring pattern and process: maximumlikelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15:871-879.
37. Gibson A., Gowri-Shankar V, Higgs P.G., Rattray M. 2005. A comprehensive analysis of mammalian mitochondrial genome base composition and improved phylogenetic methods. Mol. Biol. Evol. 22:251-264.
38. Gowri-Shankar V., Rattray M. 2007. A reversible jump method for Bayesian phylogenetic inference with a nonhomogeneous substitution model. Mol. Biol. Evol. 24:1286-1299.
39. Gruber K.F., Voss R.S., Jansa S.A. 2007. Base-compositional heterogeneity in the RAGl locus among didelphid marsupials: implications for phylogenetic inference and the evolution of GC content. Syst. Biol. 56:83-96.
40. Herbeck J.T., Degnan PH., Wernegreen J.J. 2005. Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gammaProteobacteria). Mol. Biol. Evol. 22:520-532.
41. Ho S.Y., Jermiin L. 2004. Tracing the decay of the historical signal in biological sequence data. Syst. Biol. 53:623-637.
42. Hrdy I., Hirt R.P., Dolezal P., Bardonova L., Foster P.G., Tachezy J., Embley T.M. 2004. Trichomonas hydrogenosomes contain the nadh dehydrogenase module of mitochondrial complex I. Nature 432:618-622. (Pubitemid 39626267)
43. Hughes J., Longhorn S.J., Papadopoulou A., Theodorides K., de Riva A., Mejia-Chang M., Foster P.G., Vogler A.P. 2006. Dense taxonomie EST sampling and its applications for molecular systematics of the Coleoptera (beetles). Mol. Biol. Evol. 23:268-278.
44. Hunt T., Bergsten J., Levkanicova Z., Papadopoulou A., John O.S., Wild R., Hammond P.M., Ahrens D., Balke M., Caterino M.S. 2007. A comprehensive phytogeny of beetles reveals the evolutionary origins of a superradiation. Science 318:1913.
45. Jermiin L., Ho S.Y., Ababneh F., Robinson J., Larkum A.W. 2004. The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Syst. Biol. 53:638-643.
46. Kolaczkowski B., Thornton J.W. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984. (Pubitemid 39434418)
47. Kumar S., Gadagkar S.R. 2001. Disparity index: a simple statistic to measure and test the homogeneity of substitution patterns between molecular sequences. Genetics 158:1321-1327. (Pubitemid 32667114)
48. Lake J.A. 1994. Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc. Natl. Acad. Sci. U.S.A. 91:1455-1459.
49. Lawrence J.F. 1988. Rhinorrhipidae, a new beetle family from Australia, with comments on the phytogeny of the Elateriformia. Invertebr. Taxon. 2:1-53.
50. Lawrence J.F., Newton A.F. Jr. 1982. Evolution and classification of beetles. Annu. Rev Ecol. Syst. 13:261-290.
51. Li X., Ogoh K., Ohba N., Liang X., Ohmiya Y. 2007. Mitochondrial genomes of two luminous beetles, Rhagophthalmus lufengensis and R. ohbai (Arthropoda, Insecta, Coleóptera). Gene 392: 196-205.
52. Lockhart P.J., Steel M.A., Hendy M.D., Penny D. 1994. Recovering evolutionary trees under a more realistic model of sequence evolution. Mol. Biol. Evol. 11:605.
53. Loomis W.F., Smith D.W. 1990. Molecular phytogeny of Dictyostelium discodeum by protein sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 87:9093-9097.
54. Nardi F., Carapelli A., Fanciulli 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.
55. Nishiyama T., Kato M. 1999. Molecular phylogenetic analysis among bryophytes and tracheophytes based on combined data of plastid coded genes and the 18s rrna gene. Mol. Biol. Evol. 16: 1027-1036.
56. Nylander J.A.A. 2004. MrModeltest. Version 2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.
57. Nylander J.A.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. 2008. AWTY (are we there yet?): a system for graphical exploration of mcmc convergence in Bayesian phylogenetics. Bioinformatics 24:581-583.
58. Philippe H., Zhou Y., Brinkmann H., Rodrigue N., Delsuc F. 2005. Heterotachy and long-branch attraction in phylogenetics. BMC Evol. Biol. 5:50.
59. Phillips M.J., Delsuc F., Penny D. 2004. Genome-scale phytogeny and the detection of systematic biases. Mol. Biol. Evol. 21:1455-1458.
60. Phillips M.J., Penny D. 2003. The root of the mammalian tree inferred from whole mitochondrial genomes. Mol. Phylogenet. Evol. 28: 171-185.
61. Poll M. 1932. Note sur la fonction des tubes de Malpighi des Coléoptères. Bull. Ann. Soc. Ent. Belg. 72:103-109.
62. Ponomarenko A.G. 1969. Historical development of the ColeopteraArchostemata. Trudy Paleontol. Inst. Akad. Nauk SSSR 125:1-240.
63. R Development Core Team. 2008. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing. Available from: URL http://www.R-project.org.
64. Rodriguez-Ezpeleta N., Brinkmann H., Roure B., Lartillot N., Lang B.F., Philippe H. 2007. Detecting and overcoming systematic errors in genome-scale phytogenies. Syst. Biol. 56:389-399.
65. Rodríguez -Trelles F., Tarrío R., Ayala F.J. 1999. Molecular evolution and phytogeny of the Drosophila saltans species group inferred from the Xdh gene. Mol. Phylogenet. Evol. 13:110-121.
66. Ronquist F., Huelsenbeck J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. (Pubitemid 37038874)
67. Ruano-Rubio V., Fares M.A. 2007. Artifactual phytogenies caused by correlated distribution of substitution rates among sites and lineages: the good, the bad, and the ugly. Syst. Biol. 56:68-82.
68. Rubinoff D., Holland B.S. 2005. Between two extremes: mitochondrial DNA is neither the panacea nor the nemesis of phylogenetic and taxonomie inference. Syst. Biol. 54:952-961.
69. Sheffield N.C., Song H., Cameron S.L., Whiting M.F. 2008. A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles. Mol. Biol. Evol. 25: 2499-2509.
70. Stammer H.J. 1934. Bau und bedeutung der malpighischen gefässe der coleopteren. Zoomorphology 29:196-217.
71. Steel M. 2005. Should phylogenetic models be trying to 'fit an elephant'? Trends Genet. 21:307-309.
72. Steel M., Huson D., Lockhart P.J. 2000. Invariable sites models and their use in phytogeny reconstruction. Syst. Biol. 49:225-232.
73. Stewart J.B., Beckenbach A.T. 2003. Phylogenetic and genomic analysis of the complete mitochondrial DNA sequence of the spotted asparagus beetle Crioceris duodecimpunctata. Mol. Phylogenet. Evol. 26:513-526.
74. Swofford D.L. 2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland (MA): Sinauer Assoicates.
75. Tamura K., Dudley J., Nei M., Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596.
76. Tarrlo R., Rodriguez-Trelles F., Ayala F.J. 2000. Tree rooting with outgroups when they differ in their nucleotide composition from the ingroup: the Drosophila saltans and willistoni groups, a case study. Mol.Phylogenet. Evol. 16:344-349.
77. Tarrlo R., Rodriguez-Trelles F. Ayala F.J. 2001. Shared nucleotide composition biases among species and their impact on phylogenetic reconstructions of the Drosophilidae. Mol. Biol. Evol. 18: 1464-1473.
78. van den Bussche R.A., Baker R.J., Huelsenbeck J.P, Hillis D.M. 1998. Base compositional bias and phylogenetic analyses: a test of the "flying DNA" hypothesis. Mol. Phylogenet. Evol. 10:408-416.
79. Wachmann E. 1977. Vergleichende analyse der feinstrukturellen organisation offener rhabdome in den augen der Cucujiformia (Insecta, Coleoptera), unter besonderer berücksichtigung der Chrysomelidae. Zoomorphology 88:95-131.
80. Waddell PJ., Okada N., Hasegawa M. 1999. Towards resolving the interordinal relationships of placental mammals. Syst. Biol. 48:1-5.
81. Yang Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends. Ecol. Evol. 11:367-372.
82. Yang Z., Roberts D. 1995. On the use of nucleic acid sequences to infer early branchings in the tree of life. Mol. Biol. Evol. 12:451-458.