Arachnid relationships based on mitochondrial genomes: Asymmetric nucleotide and amino acid bias affects phylogenetic analyses

Molecular Phylogenetics and Evolution

Volumn 50, Issue 1, 2009, Pages 117-128

  Masta, Susan E ^a   Longhorn, Stuart J ^a   Boore, Jeffrey L ^b,c,d  

^a PORTLAND STATE UNIVERSITY   (United States)

^b DOE JOINT GENOME INSTITUTE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d Genome Project Solutions   (United States)

Author keywords

Arachnida; Chelicerata; Mutational bias; Phylogeny reconstruction; Strand bias

Indexed keywords

AMINO ACID; INSECT PROTEIN; MITOCHONDRIAL DNA; NUCLEOTIDE;

ANIMAL; ARACHNID; ARTICLE; CHEMISTRY; CLASSIFICATION; GENETICS; MITOCHONDRIAL GENOME; PHYLOGENY;

AMINO ACIDS; ANIMALS; ARACHNIDA; DNA, MITOCHONDRIAL; GENOME, MITOCHONDRIAL; INSECT PROTEINS; NUCLEOTIDES; PHYLOGENY;

ARACHNIDA; ARANEAE; ARTHROPODA; CHELICERATA; SCORPIONES;

EID: 57649183569     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.10.010     Document Type: Article

References (78)

1. Abascal F., Zardoya R., and Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21 (2005) 2104-2105
2. Adachi J., and Hasegawa M. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42 (1996) 459-468
3. Bernini F., Carnevale G., Bagnoli G., and Stouge S. An early Ordovician oribatid mite (Acari: Oribatida) from the island of Öland, Sweden. In: Bernini F., Nannelli R., Nuzzaci G., and de Lillo E. (Eds). Acarid Phylogeny and Evolution: Adaptations in Mites and Ticks (2002), Kluwer, The Hague 45-48
4. Black IV W.C., and Roehrdanz R.L. Mitochondrial gene order is not conserved in arthropods: prostriate and metastriate tick mitochondrial genomes. Mol. Biol. Evol. 15 (1998) 1772-1785
5. Boore J.L., Lavrov D.V., and Brown W.M. Gene translocation links insects and crustaceans. Nature 392 (1998) 667-668
6. Boore J.L., Medina M., and Rosenberg L.A. Complete Sequences of the Highly Rearranged Molluscan Mitochondrial Genomes of the Scaphopod Graptacme eborea and the Bivalve Mytilus edulis. Mol. Biol. Evol. 21 (2004) 1492-1503
7. Carapelli A., Lio P., Nardi F., van der Wath E., and Frati F. Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea. BMC Evolutionary Biology 7 (2007)
8. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17 (2000) 540-552
9. Cook C.E., Yue Q., and Akam M. Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. Proc. R. Soc. Lond. B Biol. Sci. 272 (2005) 1295-1304
10. Dávila S., Pinero D., Bustos P., Cevallos M.A., and Davila G. The mitochondrial genome sequence of the scorpion Centruroides limpidus (Karsch 1879) (Chelicerata; Arachnida). Gene 360 (2005) 92-102
11. Dayhoff M.O., Schwartz R.M., and Orcutt B.C. A model of evolutionary change in proteins. In: Dayhoff M.O. (Ed). Atlas of Protein Sequence and Structure (1978), National Biomedical Research Foundation, Washington, DC 345-352
12. Delsuc F., Phillips M.J., and Penny D. Comment on "Hexapod origins: monophyletic or paraphyletic?". Science 301 (2003)
13. Dunlop J.A., and Alberti G. The affinities of mites and ticks: a review. Journal of Zoological Systematics and Evolutionary Research 46 (2008) 1-18
14. Dunn C.W., Hejnol A., Matus D.Q., Pang K., Browne W.E., Smith S.A., Seaver E., Rouse G.W., Obst M., Edgecombe G.D., Sorensen M.V., Haddock S.H.D., Schmidt-Rhaesa A., Okusu A., Kristensen R.M., Wheeler W.C., Martindale M.Q., and Giribet G. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452 (2008) 745-749
15. Erixon P., Svennblad B., Britton T., and Oxelman B. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol. 52 (2003) 665-673
16. Fahrein K., Talarico G., Braband A., and Podsiadlowski L. The complete mitochondrial genome of Pseudocellus pearsei (Chelicerata: Ricinulei) and a comparison of mitochondrial gene rearrangements in Arachnida. BMC Genomics 8 (2007)
17. Foster P.G., Jermiin L.S., and Hickey D.A. Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. J. Mol. Evol. 44 (1997) 282-288
18. George D.G., Hunt L.T., and Barker W.C. Current methods in sequence comparison and analysis. In: Schlesinger D.H. (Ed). Macromolecular Sequencing and Synthesis (1988), Alan R. Liss, New York, N.Y 127-149
19. Giribet G., Edgecombe G.D., and Wheeler W.C. Arthropod phylogeny based on eight molecular loci and morphology. Nature 413 (2001) 157-161
20. Giribet G., Edgecombe G.D., Wheeler W.C., and Babbitt C. Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data. Cladistics 18 (2002) 5-70
21. Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
22. 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. 38 (2006) 100-116
23. Hassanin A., Leger N., and Deutsch J. Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences. Syst. Biol. 54 (2005) 277-298
24. Helfenbein K.G., Brown W.M., and Boore J.L. The complete mitochondrial genome of the articulate brachiopod Terebratalia transversa. Mol. Biol. Evol. 18 (2001) 1734-1744
25. Henikoff S., and Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89 (1992) 10915-10919
26. Huelsenbeck J.P., and Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
27. Hwang U.W., Friedrich M., Tautz D., Park C.J., and Kim W. Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature 413 (2001) 154-157
28. Jeffroy O., Brinkmann H., Delsuc F., and Philippe H. Phylogenomics: the beginning of incongruence?. Trends in Genetics 22 (2006) 225-231
29. Jones M., Gantenbein B., Fet V., and Blaxter M. The effect of model choice on phylogenetic inference using mitochondrial sequence data: lessons from the scorpions. Mol. Phylogenet. Evol. 43 (2007) 583-595
30. Klompen H., Lekveishvili M., and Black IV W.C. Phylogeny of parasitiform mites (Acari) based on rRNA. Mol. Phylogenet. Evol. 43 (2007) 936-951
31. Kolaczkowski B., and Thornton J.W. Effects of branch length uncertainty on Bayesian posterior probabilities for phylogenetic hypotheses. Mol. Biol. Evol. 24 (2007) 2108-2118
32. Lavrov D.V., Boore J.L., and Brown W.M. The complete mitochondrial DNA sequence of the horseshoe crab Limulus polyphemus. Mol. Biol. Evol. 17 (2000) 813-824
33. Lavrov D.V., Boore J.L., and Brown W.M. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss. Mol. Biol. Evol. 19 (2002) 163-169
34. Maddison D.R., and Maddison W.P. MacClade 4: Analysis of Phylogeny and Character Evolution (2000), Sinauer Associates, Inc., Sunderland, Massachusetts, USA
35. Mallatt J., and Giribet G. Further use of nearly complete, 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch. Mol. Phylogenet. Evol. 40 (2006) 772-794
36. Mallatt J.M., Garey J.R., and Shultz J.W. 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 (2004) 178-191
37. Masta S.E., and Boore J.L. The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs. Mol. Biol. Evol. 21 (2004) 893-902
38. Masta S.E., and Boore J.L. Parallel evolution of truncated transfer RNA genes in arachnid mitochondrial genomes. Mol. Biol. Evol. 25 (2008) 949-959
39. Masta S.E., Klann A.E., and Podsiadlowski L. A comparison of the mitochondrial genomes from two families of Solifugae (Arthropoda: Chelicerata): Eremobatidae and Ammotrechidae. Gene 417 (2008) 35-42
40. McDonald J.H., Grasso A.M., and Rejto L.K. Patterns of temperature adaptation in proteins from Methanococcus and Bacillus. Mol. Biol. Evol. 16 (1999) 1785-1790
41. McInerney J.O. GCUA: general codon usage analysis. Bioinformatics 14 (1998) 372-373
42. Min X.J., and Hickey D.A. DNA asymmetric strand bias affects the amino acid composition of mitochondrial proteins. DNA Research 14 (2007) 201-206
43. Miyata T., Miyazawa S., and Yasunaga T. Two types of amino acid substitutions in protein evolution. J. Mol. Evol. 12 (1979) 219-236
44. Navajas M., Le Conte Y., Solignac M., Cros-Arteil S., and Cornuet J.M. The complete sequence of the mitochondrial genome of the honeybee ectoparasite mite Varroa destructor (Acari: Mesostigmata). Mol. Biol. Evol. 19 (2002) 2313-2317
45. Naylor G.J.P., and Brown W.M. Structural biology and phylogenetic estimation. Nature 388 (1997) 527-528
46. Naylor G.J.P., Collins T.M., and Brown W.W. Hydrophobicity and phylogeny. Nature 373 (1995) 565-566
47. Negrisolo E., Minelli A., and Valle G. The mitochondrial genome of the house centipede Scutigera and the monophyly versus paraphyly of myriapods. Mol. Biol. Evol. 21 (2004) 770-780
48. Nylander J.A.A., Ronquist F., Huelsenbeck J.P., and Nieves-Aldrey J.L. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53 (2004) 47-67
49. Peden J.F. Analysis of Codon Usage (1999), University of Nottingham, UK
50. Perna N.T., and Kocher T.D. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J. Mol. Evol. 41 (1995) 353-358
51. Phillips M.J., Delsuc F., and Penny D. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21 (2004) 1455-1458
52. Phillips M.J., and Penny D. The root of the mammalian tree inferred from whole mitochondrial genomes. Mol. Phylogenet. Evol. 28 (2003) 171-185
53. Pisani D., Poling L., Lyons-Weiler M., and Hedges S. The colonization of land by animals: molecular phylogeny and divergence times among arthropods. BMC Biology 2 (2004) 1
54. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
55. Qiu Y., Song D., Zhou K., and Sun H. The mitochondrial sequences of Heptethela hangzhouensis and Ornithoctonus huwena reveal unique gene arrangements and atypical tRNAs. J. Mol. Evol. 60 (2005) 57-71
56. Regier J.C., Shultz J.W., and Kambic R.E. Pancrustacean phylogeny: hexapods are terrestrial crustaceans and maxillopods are not monophyletic. Proc. R. Sec. Lond. B. Biol. Sci. 272 (2005) 395-401
57. Reyes A., Gissi C., Pesole G., and Saccone C. Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol. Biol. Evol. 15 (1998) 957-966
58. Saccone C., De Giorgi C., Gissi C., Graziano P., and Reyes A. Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene 238 (1999) 195-209
59. Scouras A., and Smith M.J. The complete mitochondrial genomes of the sea lily Gymnocrinus richeri and the feather star Phanogenia gracilis: signature nucleotide bias and unique nad4L gene rearrangement within crinoids. Mol. Phylogenet. Evol. 39 (2006) 323-334
60. Selden P.A., Anderson J.M., Anderson H.M., and Fraser N.C. Fossil araneomorph spiders from the Triassic of South Africa and Virginia. J. Arachnol. 27 (1999) 401-414
61. Selden P.A., and Gall J.C. A Triassic mygalomorph spider from the northern Vosges, France. Palaeontology 35 (1992) 211-235
62. Shao R., Aoki Y., Mitani H., Tabuchi N., Barker S.C., and Fukunaga M. The mitochondrial genomes of soft ticks have an arrangement of genes that has remained unchanged for over 400 million years. Insect Mol. Biol. 13 (2004) 219-224
63. Shultz J.W. Evolutionary morphology and phylogeny of arachnida. Cladistics 6 (1990) 1-38
64. Shultz J.W. A phylogenetic analysis of the arachnid orders based on morphological characters. Zoological Journal of the Linnean Society 150 (2007) 221-265
65. Shultz J.W., and Regier J.C. Phylogenetic analysis of arthropods using two nuclear protein-encoding genes supports a crustacean + hexapod clade. Proc. R. Soc. Lond. B Biol. Sci. 267 (2000) 1011-1019
66. Simmons M.P., Pickett K.M., and Miya M. How meaningful are Bayesian support values?. Mol. Biol. Evol. 21 (2004) 188-199
67. Sullivan J., Abdo Z., Joyce P., and Swofford D.L. Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Mol. Biol. Evol. 22 (2005) 1386-1392
68. Suzuki Y., Glazko G.V., and Nei M. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99 (2002) 16138-16143
69. Swofford, D.L., 2000. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
70. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
71. van der Hammen L. Functional morphology and affinities of extant Chelicerata in evolutionary perspective. Transactions of the Royal Society of Edinburgh 76 (1985) 137-146
72. van der Hammen L. An introduction to comparative arachnology (1989), SPB Acad. Publ, The Hague
73. Wang H.-c., Singer G.A.C., and Hickey D.A. Mutational Bias Affects Protein Evolution in Flowering Plants. Mol. Biol. Evol. 21 (2004) 90-96
74. Wang X.Z., Wang J., He S.P., and Mayden R.L. The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cyprinifonnes) and an alternative pattern of mitogenomic evolution in vertebrate. Gene 399 (2007) 11-19
75. Weygoldt P. Evolution and systematics of the Chelicerata. Exp. Appl. Acarol. 22 (1998) 63-79
76. Weygoldt P., and Paulus H.F. Unteruschungen zur morphologie, taxonomie und phylogenie der Chelicerata. II. Cladogramme und die enfaltung der Chelicerata. Z. Zool. Syst. Evol. 17 (1979) 117-200
77. Wheeler W.C., and Hayashi C.Y. The phylogeny of the extant chelicerate orders. Cladistics 14 (1998) 173-192
78. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39 (1994) 306-414