Ecdysozoan phylogeny and Bayesian inference: First use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin

Molecular Phylogenetics and Evolution

Volumn 31, Issue 1, 2004, Pages 178-191

  Mallatt, Jon M ^a   Garey, James R ^b   Shultz, Jeffrey W ^c  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b UNIVERSITY OF SOUTH FLORIDA   (United States)

^c Bldg 142   (United States)

Author keywords

28S rRNA; Arthropod; Ecdysozoa; Large subunit ribosomal RNA; Phylogeny; Protostome; Small subunit ribosomal RNA

Indexed keywords

ANIMALIA; ARANEAE; ARTHROPODA; CHELICERATA; CHILOPODA; CRUSTACEA; DECAPODA (CRUSTACEA); DIPLOPODA; ECDYSOZOA; HEXAPODA; MANDIBULATA; MAXILLOPODA; MEROSTOMATA; MYRIAPODA; NEMATODA; NEMATOMORPHA; ONYCHOPHORA; PANARTHROPODA; PANCRUSTACEA; PYCNOGONIDA; SCORPIONES; TARDIGRADA; UNIRAMIA;

EID: 0347457283     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2003.07.013     Document Type: Article

References (109)

1. Aguinaldo, A.M.A., Turbeville, J.M., Linford, L.S., Rivera, M.C., Garey, J.R., Raff, R.A., Lake, J.A., 1997. Evidence for a clade of nematodes, arthropods, and other moulting animals. Nature 387, 489-492.
2. Alfaro, M.E., Zoller, S., Lutzoni, F., 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov Chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20, 255-266.
3. Antezana, M., 2003. When being "most likely" is not enough: examining the performance of three uses of parametric bootstrapping in phylogenetics. J. Mol. Evol. 56, 198-222.
4. Blaxter, M., 2001. Sum of the arthropod parts. Nature 413, 121-122.
5. Blaxter, M.L., De Ley, P., Garey, J.R., Liu, L.X., Scheldeman, P., Vierstraete, A., Vanfleteren, J.R., Mackey, L.Y., Dorris, M., Frisse, L.M., Vida, J.T., Thomas, W.K., 1998. A molecular evolutionary framework for the phylum Nematoda. Nature 392, 71-75.
6. Bleidorn, C., Schmidt-Rhaesa, A., Garey, J.R., 2002. Systematic relationships of nematomorpha based on molecular and morphological data. Invert. Biol. 121, 357-364.
7. Bollback, J.P., 2002. Bayesian model adequacy and choice in phylogenetics. Mol. Biol. Evol. 19, 1171-1180.
8. Brown, J.R., Douady, C.J., Italia, M.J., Marshall, W.E., Stanhope, M.J., 2001. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28, 281-295.
9. Brusca, R.C., Brusca, G.J., 1990. Invertebrates. Sinauer, Sunderland, MA.
10. Brusca, R.C., Brusca, G.J., Burness, T.J., 2003. Invertebrates, second ed. Sinauer, Sunderland, MA.
11. Campbell, B.C., Steffen-Campbell, J.D., Sorensen, J.T., Gill, R.J., 1995. Paraphyly of Homoptera and Auchenorrhyncha inferred from 18S rDNA nucleotide sequences. Syst. Entom. 20, 175-194.
12. Chalwatzis, N., 1995. Unpublished submission to GenBank, Accession number X89492.
13. Cisne, J.L., 1974. Trilobites and the origin of arthropods. Science 186, 13-18.
14. Colgan, D.J., McLauchlan, A., Wilson, G.D.F., Livingston, S.P., Edgecombe, G.D., Macaranas, J., Cassis, G., Gray, M.R., 1998. Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Austr. J. Zool. 46, 419-437.
15. Cook, C.E., Smith, M.L., Telford, M.J., Bastianello, A., Akam, M., 2001. Hox genes and the phylogeny of the arthropods. Curr. Biol. 11, 759-763.
16. Dietrich, C.H., Rakitov, R.A., Holmes, J.L., Black, W.C., 2001. Phylogeny of the major lineages of Membracoidea (Insecta: Hemiptera: Cicadomorpha) based on 28S rDNA sequences. Mol. Phylogenet. Evol. 18, 293-305.
17. de Rosa, R., Grenier, J.K., Andreeva, T., Cook, C.E., Adoutte, A., Akam, M., Carroll, S.B., Balavoine, G., 1999. Hox genes in brachiopods and priapulids and protostome evolution. Nature 399, 772-776.
18. Dewel, R.A., Dewel, W.C., 1997. The place of tardigrades in arthropod evolution. In: Fortey, R.A., Thomas, R.H. (Eds.), Arthropod Relationships. Chapman & Hall, London, pp. 109-123.
19. Dohle, W., 2001. Are the insects terrestrial crustraceans? A discussion of some new facts and arguments and the proposal of the proper name 'Tetraconata' for the monophyletic unit Crustacea + Hexapoda. Ann. Soc. Entomol. Fr. (N.S.) 37, 85-103.
20. Douady, C.J., Delsuc, F., Boucher, Y., Doolittle, W.F., Douzery, E.J.P., 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20, 248-254.
21. Edgecombe, G.D., Giribet, G., 2002. Myriapod phylogeny and the relationships of Chilopoda. In: Bousquets, J.E., Morrone, J.J., Ponce Ulloa, H. (Eds.), Biodiversidad, taxonomia y biogeografia de artrópodos de México: hacia una sintesis de su conocimeinto. Prensas de Ciencias. Universidad Nacional Autónomade México, México D.F, pp. 143-168.
22. Efron, B., 1985. Bootstrap confidence intervals for a class of parametric problems. Biometrika 72, 45-58.
23. Ehlers, U., Alrichs, W., Lemburg, C., Schmidt-Rhaesa, A., 1996. Phylogenetic systematization of the Nemathelminthes (Aschelminthes). Verh. Dtsch. Zool. Ges. 89.1, 8.
24. Eriksson, B.J., Tait, N.N., Budd, G.E., 2003. Head development in the onychophoran Euperipatoides kanangrensis with particular reference to the central nervous system. J. Morph. 255, 1-23.
25. Felsenstein, J., 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27, 401-410.
26. Friedrich, M., Tautz, D., 1995. Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods. Nature 376, 165-167.
27. Friedrich, M., Tautz, D., 2001. Arthropod rDNA phylogeny revisited: a consistency analysis using Monte Carlo simulation. Ann. Soc. Entomol. Fr. (N.S.) 37, 21-40.
28. Garey, J.R., 2001. Ecdysozoa: the relationship between Cycloneuralia and Panarthropoda. Zool. Anz. 240, 321-330.
29. 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, 748-761.
30. Giribet, G., 2002. Current advances in the phylogenetic reconstruction of metazoan evolution, A new paradigm for the Cambrian explosion? Mol. Phy. Evol. 24, 345-357.
31. Giribet, G., Carrunza, S., Baguñà, J., Riutort, M., Ribera, C., 1996. First molecular evidence for the existence of a Tardigrada + Arthropoda clade. Mol. Biol. Evol. 13, 76-84.
32. Giribet, G., Distel, D.L., Polz, M., Sterrer, W., Wheeler, W.C., 2000. Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathelminthes, and Chaetognatha: A combined approach of 18S rDNA sequences and morphology. Syst. Biol. 49, 539-562.
33. Giribet, G., Edgecombe, G.D., Wheeler, W.C., 2001. Arthropod phylogeny based on eight molecular loci and morphology. Nature 413, 157-161.
34. Giribet, G., Ribera, C., 2000. A review of arthropod phylogeny: new data based on ribosomal DNA sequences and direct character optimization. Cladistics 16, 204-231.
35. Giribet, G., Wheeler, W.C., 2001. Some unusual small-subunit ribosomal RNA sequences of metazoans. Am. Mus. Novit. 3337, 14.
36. Goldman, N., Anderson, J.P., Rodrigo, A.G., 2000. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49, 652-670.
37. Gutell, R.R., 1994. Collection of small subunit (16S- and 16S-like) ribosomal RNA structures. Nucl. Acids Res. 22, 3502-3507.
38. Haas, F., Waloszek, D., Hartenberger, R., 2003. Devonohexapodus bocksbergensis, a new marine hexapod from the Lower Devonian Hunsrück Slates, and the origin of Atelocerata and Hexapoda. Org. Divers. Evol. 3, 39-54.
39. Hall, B.G., 2001. Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists. Sinauer Associates Inc, Sunderland, MA.
40. Hassouna, N., Michot, B., Bachellerie, J.-P., 1984. The complete nucleotide sequence of mouse 28S rRNA gene: implications for the process of size increase of the large subunit rRNA in higher eukaryotes. Nucl. Acids Res. 12, 3563-3583.
41. Hausdorf, B., 2000. Early evolution of the Bilateria. Syst. Biol. 49, 130-142.
42. Hillis, D.M., Bull, J.J., 1993. An empirical test of bootstrapping as a method for addressing confidence in phylogenetic analysis. Syst. Biol. 42, 182-192.
43. Hillis, D.M., Dixon, M.T., 1991. Ribosomal DNA: molecular evolution and phylogenetic inference. Q. Rev. Biol. 66, 411-453.
44. Huelsenbeck, J.P., Hillis, D.M., Jones, R., 1996. Parametric bootstrapping in molecular phylogenetics: applications and performance. In: Ferraris, J.E., Palumbi, S.R. (Eds.), Molecular Zoology: Advances, Strategies, and Protocols. Wiley-Liss, New York, pp. 19-45.
45. Huelsenbeck, J.P., Ronquist, F., 2001. MrBayes: Bayesian inference of phylogeny. Version 2.01. Distributed by the author. Department of Biology, University of Rochester.
46. Huelsenbeck, J.P., Ronquist, F., Hall, B., 2001a. MrBayes: A program for the Bayesian inference of phylogeny. Instruction Manual for Version 2.01, 17 p.
47. Huelsenbeck, J.P., Ronquist, F., Nielsen, R., Bollback, J.P., 2001b. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310-2314.
48. Huelsenbeck, J.P., Larget, B., Miller, R.E., Ronquist, F., 2002. Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol. 51, 673-688.
49. Hwang, U.W., Friedrich, M., Tautz, D., Park, C.J., Kim, W., 2001. Mitochondrial protein phylogeny joins myriapods with chelicerates. Nature 413, 154-157.
50. Koepf, H., Hankeln, T., Schmidt, E.R., 1996. Organization and evolution of the rDNA genes in Chironomus. Unpublished submission to GenBank, Accession number X99212.
51. Kraus, O., 2001. "Myriapoda" and the ancestry of the Hexapoda. Ann. Soc. Entomol. Fr. (N.S.) 37, 105-127.
52. Lake, J.A., 1994. Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc. Natl. Acad. Sci. USA 91, 1455-1459.
53. Lake, J.A., 1998. Optimally recovering rate variation information from genomes and sequences: pattern filtering. Mol. Biol. Evol. 15, 1224-1231.
54. Larget, B., Simon, D., 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16, 750-759.
55. Lewis, P.O., 2001. A likelihood approach to estimating phylogeny from discrete morphological character data. Syst. Biol. 50, 913-925.
56. Leache, A.D., Reeder, T.W., 2002. Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches. Syst. Biol. 51, 44-68.
57. 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, 605-612.
58. Mallatt, J., Sullivan, J., 1998. 28S and 18S rDNA sequences support the monophyly of lampreys and hagfishes. Mol. Biol. Evol. 15, 1706-1718.
59. Mallatt, J., Sullivan, J., Winchell, C.J., 2001. The relationships of lampreys to hagfishes: a spectral analysis of ribosomal DNA sequences. In: Ahlberg, P. (Ed.), Major Events in Early Vertebrate Evolution: Palaeontology, Phylogeny, and Development. Taylor and Francis, London, pp. 106-118.
60. Mallatt, J., Winchell, C.J., 2002. Testing the new animal phylogeny: first use of combined large-subunit and small-subunit rRNA gene sequences to classify the protostomes. Mol. Biol. Evol. 19, 289-301.
61. Manuel, M., Kruse, M., Muller, W.E.G., Le Parco, Y., 2000. The comparison of beta-thymosin homologues among metazoa supports an arthropod-nematode link. J. Mol. Evol. 51, 378-381.
62. Medina, M., Collins, A.G., Silberman, J.D., Sogin, M.L., 2001. Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA. Proc. Natl. Acad. Sci. USA 98, 9707-9712.
63. Mittmann, B., 2002. Early neurogenesis in the horseshoe crab Limulus polyphemus and its implication for arthropod relationships. Biol. Bull. 203, 221-222.
64. Murphy, W.J., Eizirik, E., O'Brien, S.J., Madsen, O., Scally, M., Douady, C.J., Teeling, E., Ryder, O.A., Stanhope, M.J., de Jong, W.W., Springer, M.S., 2001. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294, 2348-2351.
65. Nardi, F., Spinsanti, G., Boore, J.L., Carapelli, A., Dallai, R., Frati, F., 2003. Hexapod origins: monophyletic or paraphyletic? Science 299, 1887-1889.
66. Nielsen, C., 1995. Animal Evolution, Interrelationships of the Living Phyla. Oxford University Press, Oxford, England.
67. Nielsen, C., 2001. Animal Evolution, Interrelationships of the Living Phyla, second ed. Oxford University Press, Oxford, England.
68. Ohnishi, H., 2000. Unpublished submission to GenBank, Accession number AB052895.
69. Omilian, A.R., Taylor, D.J., 2001. Rate acceleration and long-branch attraction in a conserved gene of cryptic daphniid (crustacea) species. Mol. Biol. Evol. 18, 2201-2212.
70. Peterson, K.J., Eernisse, D.J., 2001. Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences. Evol. Develop. 3, 170-205.
71. Rambaut, A., Grassly, N.C., 2001. Seq-Gen Sequence Generator: An application for the Monte-Carlo simulation of DNA sequence evolution along phylogenetic trees. Version 1.2.3.
72. Ramsköld, L., Chen, J.-Y., 1998. Cambrian lobopodians: morphology and phylogeny. In: Edgecombe, G.D. (Ed.), Arthropod Fossils and Phylogeny. Columbia University Press, New York, pp. 107-150.
73. Regier, J.C., Shultz, J.W., 1997. Molecular phylogeny of major arthropod groups indicates polyphyly of crustaceans and a new hypothesis for the origin of hexapods. Mol. Biol. Evol. 14, 902-913.
74. Regier, J.C., Shultz, J.W., 2001. Elongation factor-2: a useful gene for arthropod phylogenetics. Mol. Phy. Evol. 20, 136-148.
75. Richter, S., 2002. The Tetraconata concept: hexapod-crustacean relationships and the phylogeny of Crustacea. Organ. Diver. Evolut. 2, 217-237.
76. Sanderson, M.J., Driskell, A.C., Ree, R.H., Eulenstein, O., Langley, S., 2003. Obtaining maximal concatenated phylogenetic data sets from large sequence databases. Mol. Biol. Evol. 20, 1036-1042.
77. Schmidt-Rhaesa, A., 1998. Phylogenetic relationships of the nematomorpha - a discussion of current hypotheses. Zool. Anz. 236, 203-216.
78. Schmidt-Rhaesa, A., 2002. Are the genera of Nematomorpha monophyletic taxa? Zool. Scr. 31, 185-200.
79. Schmidt-Rhaesa, A., Bartolomaeus, T., Lemburg, C., Ehlers, U., Garey, J.R., 1998. The position of the arthropoda in the phylogenetic system. J. Morphol. 238, 263-285.
80. Schnare, M.N., Damberger, S.H., Gray, M.W., Gutell, R., 1996. Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23S-like) ribosomal RNA. J. Mol. Biol. 256, 701-719.
81. Scholtz, G., 2002. The Articulata hypothesis - or what is a segment? Organ. Diver. Evolut. 2, 197-215.
82. Schram, F.R., Jenner, R.A., 2001. The origin of hexapoda: a crustacean perspective. Ann. Soc. Entomol. Fr. (N.S.) 37, 243-264.
83. Shear, W.A., 1997. The fossil record and evolution of the myriapoda. In: Fortey, R.A., Thomas, R.H. (Eds.), Arthropod Relationships. Chapman & Hall, London, pp. 211-219.
84. Shimodaira, H., Hasegawa, M., 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116.
85. Shultz, J.W., Regier, J.C., 2000. Phylogenetic analysis of arthropods using two nuclear protein-encoding genes supports a crustacean + hexapod clade. Proc. R. Soc. London B 267, 1011-1019.
86. Smith, S., Overbeek, W.R., Woese, C.R., Gilbert, W., Gillevet, P.M., 1994. The genetic data environment: an expandable GUI for multiple sequence analysis. CABIOS 10, 671-675.
87. Snodgrass, R.E., 1938. Evolution of the Annelida, Onychophora and Arthropoda. Smithson. Misc. Collect. 97, 1-159.
88. Spears, T., Abele, L.G., 1997. Crustacean phylogeny inferred from 18S rDNA. In: Fortey, R.A., Thomas, R.H. (Eds.), Arthropod Relationships. Chapman & Hall, London, pp. 169-187.
89. Sullivan, J., Markert, J.A., Kilpatrick, C.W., 1997. Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood. Syst. Biol. 46, 426-440.
90. Sullivan, J., Swofford, D.L., 2001. Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst. Biol. 50, 723-729.
91. Suzuki, Y., Glazko, G.V., Nei, M., 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99, 16138-16143.
92. Swofford, D.L., 2001. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4.0 beta 10. Sinauer Associates, Sunderland, MA.
93. Swofford, D.L., Olsen, G.J., Waddell, P.J., Hillis, D.M., 1996. Phylogenetic inference. In: Hillis, D.M., Moritz, C., Mable, B.K. (Eds.), Molecular Systematics, second ed. Sinauer, Sunderland, MA, pp. 407-514.
94. Swofford, D.L., Waddell, P.J., Huelsenbeck, J.P., Foster, P.G., Lewis, P.O., Rogers, J.S., 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50, 525-539.
95. Takezaki, N., Figueroa, F., Zaleska-Rutczynska, Z., Klein, J., 2003. Molecular phylogeny of early vertebrates: monopyly of the agnathans as revealed by sequences of 35 genes. Mol. Biol. Evol. 29, 287-292.
96. Turbeville, J.M., Pfeifer, D.M., Field, K.G., Raff, R.A., 1991. The phylogenetic status of arthropods, as inferred from 18S rRNA sequences. Mol. Biol. Evol. 8, 669-686.
97. Wägele, J.W., Misof, B., 2001. On quality of evidence in phylogeny reconstruction: a reply to Zrzavy's defence of the 'Ecdysozoa' hypothesis. J. Zool. Syst. Evol. Res. 39, 165-176.
98. Walossek, D., Müller, K.J., 1998. Early arthropod phylogeny in light of the Cambrian "Orsten" fossils. In: Edgecombe, G.D. (Ed.), Arthropod Fossils and Phylogeny. Columbia University Press, New York, pp. 185-232.
99. Waloszek, D., Dunlop, J.A., 2002. A larval sea spider (Arthropoda: Pycnogonida) from the Upper Cambrian 'Orsten' of Sweden, and the phylogenetic position of pycnogonids. Palaeontology 45, 421-446.
100. Wang, S., Zhao, M., Li, T., 2003. Complete sequence of the 10.3 kb silkworm Attacus ricini rDNA repeat, determination of the transcriptional initiation site and functional analysis of the intergenic spacer. DNA Seq. 14, 95-101.
101. Wheeler, W.C., 1997. Sampling, groundplans, total evidence and the systematics of arthropods. In: Fortey, R.A., Thomas, R.H. (Eds.), Arthropod Relationships. Chapman & Hall, London, pp. 87-96.
102. Wheeler, W.C., Whiting, M., Wheeler, Q.D., Carpenter, J.M., 2001. The phylogeny of extant hexapod orders. Cladistics 17, 113-169.
103. Wilcox, T.P., Zwickl, D.J., Heath, T.A., Hillis, D.M., 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phy. Evol. 25, 361-371.
104. Wills, M.A., Briggs, D.E.G., Fortey, R.A., 1997. Evolutionary correlates of arthropod tagmosis: scrambled legs. In: Fortey, R.A., Thomas, R.H. (Eds.), Arthropod Relationships. Chapman & Hall, London, pp. 57-66.
105. Wills, M.A., Briggs, D.E.G., Fortey, R.A., Wilkinson, M., Sneath, P.H.A., 1998. An arthropod phylogeny based on fossil and recent taxa. In: Edgecombe, G.D. (Ed.), Arthropod Fossils and Phylogeny. Columbia University Press, New York, pp. 33-106.
106. Wilson, K., Cahill, V., Ballment, E., Benzie, J., 2000. The complete sequence of the mitochondrial genome of the crustacean Penaeus monodon: are malacostracan crustaceans more closely related to insects than to branchiopods? Mol. Biol. Evol. 17, 863-874.
107. Winchell, C.J., 2001. Combining large-and small-subunit ribosomal RNA genes for phylogenetic comparison: robust results for the deuterostome animals and the elasmobranch fishes. M.S. thesis. Washington State University, Pullman.
108. Winchell, C.J., Sullivan, J., Cameron, C.B., Swalla, B.J., Mallatt, J., 2002. Evaluating hypotheses of deuterostome phylogeny and chordate evolution with new LSU and SSU ribosomal DNA data. Mol. Biol. Evol. 19, 762-776.
109. Zrzavy, J., Stys, P., 1997. The basic body plan of arthropods: Insights from evolutionary morphology and developmental biology. J. Evol. Biol. 10, 353-367.