Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences (original) (raw)

References

  1. Abele, L. G., Kim, W. & Felgenhauer, B. E. Molecular evidence for inclusion of the phylum Pentastomida in the Crustacea. Mol. Biol. Evol. 6, 685–691 (1989)
    Google Scholar
  2. Friedrich, M. & Tautz, D. Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods. Nature 376, 165–167 (1995)
    Article ADS CAS Google Scholar
  3. Regier, J. C. & Shultz, J. W. Molecular phylogeny of the major arthropod groups indicates polyphyly of crustaceans and a new hypothesis for the origin of hexapods. Mol. Biol. Evol. 14, 902–913 (1997)
    Article CAS Google Scholar
  4. Giribet, G., Edgecombe, G. D. & Wheeler, W. C. Arthropod phylogeny based on eight molecular loci and morphology. Nature 413, 157–161 (2001)
    Article ADS CAS Google Scholar
  5. Hwang, U. W., Friedrich, M., Tautz, D., Park, C. J. & Kim, W. Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature 413, 154–157 (2001)
    Article ADS CAS Google Scholar
  6. Mallatt, J. & 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, 772–794 (2006)
    Article CAS Google Scholar
  7. Budd, G. E. & Telford, M. J. The origin and evolution of arthropods. Nature 457, 812–817 (2009)
    Article ADS CAS Google Scholar
  8. Boore, J. L., Lavrov, D. V. & Brown, W. M. Gene translocation links insects and crustaceans. Nature 392, 667–668 (1998)
    Article ADS CAS Google Scholar
  9. Phillips, M. J., Delsuc, F. & Penny, D. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21, 1455–1458 (2004)
    Article CAS Google Scholar
  10. Rota-Stabelli, O. & Telford, M. J. A multi criterion approach for the selection of optimal outgroups in phylogeny: recovering some support for Mandibulata over Myriochelata using mitogenomics. Mol. Phylogenet. Evol. 48, 103–111 (2008)
    Article CAS Google Scholar
  11. Snodgrass, R. E. Evolution of the Annelida, Onychophora and Arthropoda (Smithsonian Inst. Press, 1938)
    Google Scholar
  12. Mallatt, J. M., Garey, J. R. & 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, 178–191 (2004)
    Article CAS Google Scholar
  13. Dunn, C. W. et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452, 745–749 (2008)
    Article ADS CAS Google Scholar
  14. Timmermans, M. J. T. N., Roelofs, D., Mariën, J. & Van Straalen, N. M. Revealing pancrustacean relationships: phylogenetic analysis of ribosomal protein genes places Collembola (springtails) in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers. BMC Evol. Biol. 8, 83 (2008)
    Article CAS Google Scholar
  15. Philippe, H. et al. Phylogenomics revives traditional views on deep animal relationships. Curr. Biol. 19, 706–712 (2009)
    Article CAS Google Scholar
  16. Regier, J. C. et al. Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Syst. Biol. 57, 920–938 (2008)
    Article CAS Google Scholar
  17. Holder, M. T., Zwickl, D. J. & Dessimoz, C. Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes. Phil. Trans. R. Soc. B 363, 4013–4021 (2008)
    Article CAS Google Scholar
  18. Seo, T. & Kishino, H. Statistical comparison of nucleotide, amino acid, and codon substitution models for evolutionary analysis of protein-coding sequences. Syst. Biol. 58, 199–210 (2009)
    Article CAS Google Scholar
  19. Podsiadlowski, L., Braband, A. & Mayer, G. The complete mitochondrial genome of the onychophoran Epiperipatus biolleyi reveals a unique transfer RNA set and provides further support for the Ecdysozoa hypothesis. Mol. Biol. Evol. 25, 42–51 (2008)
    Article CAS Google Scholar
  20. Shultz, J. W. A phylogenetic analysis of the arachnid orders based on morphological characters. Zool. J. Linn. Soc. 150, 221–265 (2007)
    Article Google Scholar
  21. Schram, F. R. ed. Crustacean Phylogeny (Balkema, 1983)
    Google Scholar
  22. Fanenbruck, M., Harzsch, S. & Wagele, J. The brain of the Remipedia (Crustacea) and an alternative hypothesis on their phylogenetic relationships. Proc. Natl Acad. Sci. USA 101, 3868–3873 (2004)
    Article ADS CAS Google Scholar
  23. Harzsch, S. Neurophylogeny: architecture of the nervous system and a fresh view on arthropod phyologeny. Integr. Comp. Biol. 46, 162–194 (2006)
    Article Google Scholar
  24. Boxshall, G. A. Crustacean classification: on-going controversies and unresolved problems. Zootaxa 1668, 313–325 (2007)
    Google Scholar
  25. 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. 7 (suppl. 2). S8 (2007)
    Article Google Scholar
  26. Hennig, W. Insect Phylogeny (Wiley, 1981)
    Google Scholar
  27. Zrzavy, J., Hypsa, V. & Vlaskova, M. in Arthropod Relationships (eds Fortey, R. A. & Thomas, R. H.) 97–107 (Chapman and Hall, 1997)
    Google Scholar
  28. Gai, Y.-H., Song, D., Sun, H. & Zhou, K. Myriapod monophyly and relationships among myriapod classes based on nearly complete 28S and 18S rDNA sequences. Zool. Sci. 23, 1101–1108 (2006)
    Article CAS Google Scholar
  29. Zwickl, D. J. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion. PhD thesis, Univ. Texas Austin (2006)
    Google Scholar
  30. Goldman, N., Thorne, J. L. & Jones, D. T. Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J. Mol. Biol. 263, 196–208 (1996)
    Article CAS Google Scholar
  31. Remm, M., Storm, C. E. & Sonnhammer, E. L. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314, 1041–1052 (2001)
    Article CAS Google Scholar
  32. Regier, J. C. & Shi, D. Increased yield of PCR product from degenerate primers with nondegenerate, nonhomologous 5′ tails. Biotechniques 38, 34–38 (2005)
    Article CAS Google Scholar
  33. Staden, R., Judge, D. & Bonfield, J. Sequence assembly and finishing methods. Methods Biochem. Anal. 43, 303–322 (2001)
    CAS PubMed Google Scholar
  34. Smith, S. W., Overbeck, R., Woese, C. R., Gilbert, W. & Gillevet, P. M. The genetic data environment and expandable GUI for multiple sequence analysis. Comp. Appl. Biosci. 10, 671–675 (1994)
    CAS PubMed Google Scholar
  35. Katoh, K., Kuma, K., Toh, H. & Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511–518 (2005)
    Article CAS Google Scholar
  36. PAUP*. v.4.0 (Sinauer Associates, Sunderland, Massachusetts, 2002)
  37. Huelsenbeck, J. P. & Ronquist, F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17, 754–755 (2001)
    Article CAS Google Scholar
  38. Ronquist, F. & Huelsenbeck, J. P. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574 (2003)
    Article CAS Google Scholar
  39. Altekar, G., Dwarkadas, S., Huelsenbeck, J. P. & Ronquist, F. Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20, 407–415 (2004)
    Article CAS Google Scholar
  40. MRMODELTEST. v.2 (Evolutionary Biology Centre, Uppsala University, 2004)
  41. Regier, J. C. & Shultz, J. W. Elongation factor-2: a useful gene for arthropod phylogenetics. Mol. Phylogenet. Evol. 20, 136–148 (2001)
    Article CAS Google Scholar
  42. Cummings, M. & Huskamp, J. Grid computing. EDUCAUSE Rev. 40, 116–117 (2005)
    Google Scholar
  43. Bazinet, A. L. & Cummings, M. C. in Distributed & Grid Computing–Science Made Transparent for Everyone. Principles, Applications and Supporting Communities (ed. Weber, M. H. W.) 2–13 (Tectum, 2009)
    Google Scholar

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