Searching factors causing implausible non-monophyly: Ssu rDNA phylogeny of Isopoda Asellota (Crustacea: Peracarida) and faster evolution in marine than in freshwater habitats

Molecular Phylogenetics and Evolution

Volumn 28, Issue 3, 2003, Pages 536-551

  Wägele, Johann Wolfgang ^a   Holland, Barbara ^a   Dreyer, Hermann ^b   Hackethal, Beate ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

^b UNIVERSITY OF VIENNA   (Austria)

Author keywords

Asellota; Covariotids; Crustacea; Deep sea; Isopoda; Long branch effects; Molecular systematics; Phylogenetic signal; Spectrum of supporting positions

Indexed keywords

ASELLOTA; CARPIAS; CRUSTACEA; ISOPODA; JAERA; MUNNOPSIDAE; PERACARIDA;

EID: 18144452601     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(03)00053-8     Document Type: Article

References (105)

1. Abouheif, E., Zardoya, R., Meyer, A., 1998. Limitations of metazoan 18S rRNA sequence data: implications for reconstructing a phylogeny of the animal kingdom and inferring the reality of the Cambrian explosion. J. Mol. Evol. 47, 394-405.
2. Adoutte, A., Philippe, H., 1993. The major lines of metazoan evolution: summary of traditional evidence and lessons from ribosomal RNA sequence analysis. In: Pichon, Y. (Ed.), Comparative Molecular Neurobiology. Birkhäuser, Basel, pp. 1-30.
3. Andreasen, K., Baldwin, B.G., 2001. Unequal evolutionary rates between annual and perennial lineages of checker mallows (Sidalcea, Malvaceae): evidence from 18S-26S rDNA internal and external transcribed spacers. Mol. Biol. Evol. 18, 936-944.
4. Banarescu, P., 1990. Zoogeography of Fresh Waters. Aula-Verlag, Wiesbaden.
5. Barnard, J.L., Menzies, R.J., Bacescu, M.C., 1962. Abyssal Crustacea. Columbia University Press, New York.
6. Bleiweiss, R., 1998. Slow rate of molecular evolution in high-elevation hummingbirds. Proc. Natl. Acad. Sci. USA 95, 612-616.
7. Bowman, T.E., Holmquist, C., 1975. Asellus (Asellus) alaskensis n.sp., the first Alaskan Asellus, with remarks on its Asian affinities (Crustacea: Isopoda: Asellidae). Proc. Biol. Soc. Wash. 88, 59-72.
8. Brandt, A., 2000. Hypotheses on Southern Ocean peracarid evolution and radiation (Crustacea, Malacostraca). Antarctic Sci. 12, 269-275.
9. Bromham, L., Rambaut, A., Harvey, P.H., 1996. Determinants of rate variation in mammalian DNA sequence evolution. J. Mol. Evol. 43, 610-621.
10. Brusca, R.C., Wilson, G.D.F., 1991. A phylogenetic analysis of the Isopoda with some classificatory recommendations. Mem. Queens. Mus. 31, 143-204.
11. Chang, B.S.W., Campbell, D.L., 2000. Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences. Mol. Biol. Evol. 17, 1220-1231.
12. Chappuis, P.A., 1965. Remarques générales sur le genre Asellus et description de quatre espèces nouvelles. Notes Biospéologiques 10, 163-182.
13. Chappuis, P.A., Delamare-Deboutteville, C., 1957. Un nouvel Asellide de L'Afrique du sud. Notes Biospéologiques 12, 29-36.
14. Coineau, N., 1968. Contribution à l'étude de la faune interstitielle Isopodes et Amphipodes. Mém. Mus. Natn. Hist. Nat. 55 (3), 147-216.
15. 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. Austral. J. Zool. 46, 419-437.
16. Collinge, W.E., 1944. On the freshwater isopod genus Caecidotea Packard. Ann. Mag. Nat. Hist. 11 (84), 815-817.
17. Crandall, K.A., Harris, D.J., Fetzner, J.W., 2001. The monophyletic origin of freshwater crayfish estimated from nuclear and mitochondrial DNA sequences. Proc. R. Soc. Lond. B Biol. 267, 1679-1686.
18. Dreyer, H., Wägele, J.-W., 2001. Parasites of crustaceans (Isopoda: Bopyridae) evolved from fish parasites: molecular and morphological evidence. Zoology 103, 157-178.
19. Dreyer, H., Wägele, J.W., 2002. The Scutocoxifera tax. nov. (Crustacea, Isopoda) and the information content of nuclear ssu rDNA sequences for reconstruction of isopod phylogeny (Peracarida: Isopoda). J. Crust. Biol. 22, 217-234.
20. Emerson, G.L., Kilpatrick, C.W., McNiff, B.E., Ottenwalder, J., Allard, M.W., 1999. Phylogenetic relationships of the order Insectivora based on complete 12SrRNA sequences from mitochondria. Cladistics 15, 221-230.
21. Felsenstein, J., 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool 27, 410-410.
22. Felsenstein, J., 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376.
23. Fitch, W.M., 1971. The nonidentity of invariable positions in the cytochrome c of different species. Biochem. Genet. 5, 231-241.
24. Fitch, W.M., Markowitz, E., 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4, 579-593.
25. 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.
26. Fuellen, G., Wägele, J.W., Giegerich, R., 2001a. Best systematist practice transferred to molecular data. Org. Divers. Evol. 1, 257-272.
27. Fuellen, G., Wägele, J.W., Giegerich, R., 2001b. Minimum conflict: a divide-and-conquer approach to phylogeny estimation. Bioinformatics 17, 1168-1178.
28. Galtier, N., 2001. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18, 866-873.
29. Germot, A., Philippe, H., 1999. Critical analysis of eukaryotic phylogeny: a case study based on the HSP70 family. J. Euk. Microbiol. 46, 116-124.
30. Goldman, N., Anderson, J.P., Rodrigo, A.G., 2000. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49, 652-670.
31. Hafner, M.S., Sudman, P.D., Villablanca, F.X., Spradling, T.A., Demastes, J.W., Nadler, S.A., 1994. Disparate rates of molecular evolution in cospeciating hosts and parasites. Science 265, 1087-1090.
32. Hendy, M.D., Penny, D., 1989. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38, 310-321.
33. Henry, J.P., Magniez, G., 1970. Contribution a la systematique des Asellides (Crustacea, Isopoda). Ann. Speleol. 25 (2), 335-367.
34. Henry, J.P., Lewis, J.J., Magniez, G., 1986. Isopoda: Asellota: Aselloidea, Gnathostenetroidoidea, Stenetrioidea. In: Botosaneanu, L. (Ed.), Stygofauna Mundi. E.J. Brill and Dr. W. Backhuys, Leiden.
35. Hessler, R.R., 1993. Swimming morphology in Eurycope cornuta (Isopoda: Asellota). J. Crust. Biol. 13, 667-674.
36. Hessler, R.R., Strömberg, J.O., 1989. Behavior of janiroidean isopods (Asellota), with special reference to deep-sea genera. Sarsia 74, 145-159.
37. Hessler, R.R., Wilson, G.D.F., Thistle, D., 1979. The deep-sea isopods: a biogeographic and phylogenetic overview. Sarsia 64, 67-75.
38. Hessler, R.R., Wilson, G.D.F., 1983. The origin and biogeography of malacostracan crustaceans in the deep sea. In: Sims, R.W., Price, J.H., Whalley, P.E.S. (Eds.), Evolution in Time and Space: The Emergence of the Biosphere. Academic Press, London and New York, pp. 227-254.
39. Huelsenbeck, J.P., 1997. Is the Felsenstein zone a fly trap. Syst. Biol. 46, 69-74.
40. Huelsenbeck, J.P., Bull, J.J., 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Syst. Bio.l 45, 92-98.
41. Huelsenbeck, J.P., Crandall, K.A., 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28, 437-466.
42. Jermiin, L.S., 1996. K2WuLi - Version 1.0: computer program for the relative rate test. The Australian National University.
43. Kishino, H., Hasegawa, M., 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29, 170-179.
44. Kobusch, W., 1999. The phylogeny of the Peracarida (Crustacea, Malacostraca). Cuvillier Verlag, Göttingen.
45. Kumar, S., Tamura, K., Nei, M., 1993. MEGA: Molecular Evolutionary Genetics Analysis, version 1.01. The Pennsylvania State University, University Park, PA 16802.
46. Kussakin, O.G., 1973. Peculiarities of the geographical and vertical distribution of marine isopods and the problem of deep sea fauna origin. Mar. Biol. 23, 19-34.
47. Kussakin. O.G., 1999. Marine and brackish-water Isopoda of the cold and temperate waters of the Northern Hemisphere. III. Suborder Asellota, Part 2, Akademia Nauk (Ed.), Petersburg.
48. Lake, J., 1994. Reconstructing evolutionary trees from DNA and protein sequences: Paralinear distances. Proc. Natl. Acad. Sci. USA 91, 1455-1459.
49. Lanave, C.G., Preparata, G., Saccone, C., Serio, G., 1984. A new method for calculating evolutionary substitution rates. J. Mol. Evol. 20, 86-93.
50. Littlewood, D.T.J., Olson, P.D., Telford, M.J., Herniou, E.A., Riutort, M., 2001. Elongation factor 1-alpha sequences alone do not assist in resolving the position of the Acoela within the Metazoa. Mol. Biol. Evol. 18, 437-442.
51. Lockhart, P.J., Larkum, A.W., Steel, M., Waddell, P.J., Penny, D., 1996. Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis. Proc. Natl. Acad. Sci. USA 93, 1930-1934.
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, 605-612.
53. Lockhart, P.J., Steel, M., Barbrook, A., Huson, D., Charleston, M.A., Howe, C.J., 1998. A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages. Mol. Biol. Evol. 15, 1183-1188.
54. Lyons-Weiler, J., Hoelzer, G.A., 1997. Escaping from the Felsenstein zone by detecting long branches in phylogenetic data. Mol. Phylog. Evol. 8, 375-384.
55. Magniez, G., 1983. Biogéographie et Paléobiogé ographie des Sténasellides (Crustacés Isopodes Asellotes des eaux souterraines continentales). Mém. Biospéol. 10, 187-191.
56. Magniez, G.J., 1997. État actuel des connaissances sur les Stenasellidae (Crustacea, Isopoda; Asellota des eaux souterraines continentales). Bull. Sci. Bourg. 49, 21-28.
57. Martin, A.P., Palumbi, S.R., 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl. Acad. Sci. USA 90, 4087-4091.
58. Menzies, R.J., 1963. The abyssal fauna of the sea floor of the Arctic Ocean. Proc. Arctic Basin Symp. 1963, 46-66.
59. Mitchell, A., Cho, S., Regier, J.C., Mitter, C., Poole, R.W., Matthews, M., 1997. Phylogenetic utility of elongation factor-1 alpha in Noctuoidea (Insecta: Lepidoptera:) The limits of synonymous substitution. Mol. Biol. Evol. 14, 381-390.
60. Miyamoto, M.M., Fitch, W.M., 1996. Constraints on protein evolution and the age of eubacteria/eukaryote split. Syst. Biol. 45, 568-575.
61. Nelles, L., Fang, B.L., Volckaert, G., Vandenberghe, A., Wachter, R., 1984. Nucleotide sequence of a crustacean 18S ribosomal RNA gene and secondary structure of eukaryotic small subunit ribosomal RNAs. Nucleic Acids Res. 12, 8749-8768.
62. Nicholas, K.B., Nicholas, H.B., Deerfield, D.W., 1997. GeneDoc: Analysis and Visualization of Genetic Variation. Embnews 4, 14 and http://www.cris.com/ ~Ketchup/genedoc.shtml.
63. Pawlowski, J., Bolivar, I., Fahrni, J.F., Vargas, C., Gouy, M., Zaninetti, L., 1997. Extreme differences in rates of molecular evolution of Foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record. Mol. Biol. Evol. 14, 498-505.
64. Philippe, H., Forterre, P., 1999. The rooting of the universal tree of life is not reliable. J. Mol. Evol. 49, 509-523.
65. Philippe, H., Laurent, J., 1998. How good are deep phylogenetic trees? Curr. Opin. Genet. Dev. 8, 616-623.
66. Pol, D., Siddall, M.E., 2001. Biases in maximum likelihood and parsimony: a simulation approach to a 10-taxon case. Cladistics 17, 266-281.
67. Posada, D., Crandall, K.A., 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics Appl. Note 14, 817-818.
68. Rambuat, A.E., Grassly, N.C., 1997. Seq-gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 1, 235-238.
69. Richter, S., 1999. The structure of the ommatidia of the Malacostraca (Crustacea) - a phylogenetic approach. Verh. naturwiss. Ver. Hamburg 38, 161-204.
70. Richter, S., Scholtz, G., 2001. Phylogenetic analysis of the Malacostraca (Crustacea). J. Zool. Syst. Evol. Res. 39, 113-136.
71. Saitou, N., Nei, M., 1987. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
72. Sars, G.O., 1909. Crustacea. Rep. Second Norwegian Arctic Exp. "Fram" 1989-1902 18, 1-47.
73. Schram, F.R., 1970. Isopod from the Pennsylvanian of Illinois. Science 169, 854-855.
74. Shoemaker, J.S., Fitch, W.B., 1989. Evidence from nuclear sequences that variable sites should be considered when sequence divergence is calculated. Mol. Biol. Evol. 6, 270-289.
75. Shultz, J.W., Regier, J.C., 1997. Progress toward a molecular phylogeny of the centipede orders (Chilopoda). Ent. Scand. Suppl. 51, 25-32.
76. Siddall, M.E., 1988. Success of parsimony in the four-taxon case: long-branch repulsion by likelihood in the Farris zone. Cladistics 14, 209-220.
77. Siebenaller, J.F., Hessler, R.R., 1981. The genera of the Nannoniscidae (Isopoda, Asellota). Trans. San Diego Soc. Nat. Hist. 19, 227-250.
78. Steiner, G., Müller, M., 1996. What can 18S rDNA do for bivalve phylogeny? J. Mol. Evol. 43, 58-70.
79. Steel, M.A., 1994. Recovery of a tree from the leaf coloration it generates under a Markov model. Appl. Math. Lett. 7, 19-23.
80. Steel, M.A., Lockhart, P.J., Penny, D., 1993. Confidence in evolutionary trees from biological sequence data. Nature 364, 440-442.
81. Steel, M.A., Huson, D., Lockhart, P.J., 2000. Invariable sites models and their use in phylogeny reconstruction. Syst. Biol. 49, 225-232.
82. Svavarsson, J., Strömberg, J.O., Brattegard, T., 1993. The deep-sea asellote (Isopoda, Crustacea) fauna of the Northern Seas: species composition, distributional patterns and origin. J. Biogeogr. 20, 537-555.
83. Swofford, D.L., 1998. PAUP*. Phylogenetic Analysis Using Parsimony (* and other methods). Version 4*. Sinauer Associates, Sunderland, MA.
84. Tavaré, S., 1986. Some probabilistic and statistical problems on the analysis of DNA sequences. Lec. Math. Life Sci. 17, 57-86.
85. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F.H., 1997. The ClustalX windows interface: flexible strategies for multiple sequece alignment aided by quality analysis tools. Nucleic Acids Res. 24, 4876-4882.
86. Lieshout, S.E.N., 1983. Calabozoidea, a new suborder of stygobiont Isopoda, discovered in Venezuela. Bijdr. Dierk. 53, 165-177.
87. Name, W.G., 1936. The American land and fresh-water isopod crustacea. Bull. Am. Mus. Nat. Hist. 71, 1-535.
88. Waddell, P.J., Penny, D., Moore, T., 1997. Hadamard conjugations and modeling sequence evolution with unequal rates across sites. Mol. Phylog. Evol. 8, 33-50.
89. Wägele, J.W., 1989. Evolution und phylogenetisches System der Isopoda. Stand der Forschung und neue Erkenntnisse. Zoologica 140, 1-262.
90. Wägele, J.W., Erikson, T., Lockhart, P., Misof, B., 1999. The Ecdysozoa: artifact or monophylum? J. Zool. Syst. Evol. Res. 37, 211-223.
91. Wägele, J.W., Misof, B., 2001. On quality of evidence in phylogeny recosntruction: a reply to Zrzavý's defence of the 'Ecdysozoa' hypothesis. Z. Zool. Syst. Evol. Res. 39, 165-176.
92. Wägele, J.W., Rödding, F., 1998a. A priori estimation of phylogenetic information conserved in aligned sequences. Mol. Phylog. Evol. 9, 358-365.
93. Wägele, J.W., Rödding, F., 1998b. Origin and phylogeny of metazoans as reconstructed with rDNA sequences. Prog. Mol. Subcell. Biol. 21, 45-70.
94. Wilson, G.D.F., 1987. The road to the Janiroidea: comparative morphology and evolution of the asellote isopod crustaceans. Z. f. Zool. Syst. Evolutionsforsch. 25, 257-280.
95. Wilson, G.D.F., 1994. A phylogenetic analysis of the isopod family Janiridae (Crustacea). Invertebr. Taxon 8, 749-766.
96. Wilson, G.D.F., 1998. Historical influences on deep-sea isopod diversity in the Atlantic Ocean. Deep-Sea Res. II 45, 279-301.
97. Wilson, G.D.F., 1999. Some of the deep-sea fauna is ancient. Crustaceana 72, 1019-1030.
98. Wilson, G.D.F., Ponder, W.F., 1992. Extraordinary new subterranean isopods (Peracarida: Crustacea) from the Kimberley Region, Western Australia. Rec. Austr. Mus. 44, 279-298.
99. Wolff, T., 1962. The systematics and biology of bathyal and abyssal Isopoda Aselllota. Galathea Rep. 6, 1-320.
100. Wu, C.-I., Li, W.-H., 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82, 1741-1745.
101. Yang, Z., 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11, 367-372.
102. Lopez, P., Forterre, P., Philippe, H., 1999. The root of the tree of life in the light of the covarion model. J. Mol. Evol. 49, 496-508.
103. Miyamoto, M.M., Fitch, W.M., 1995. Testing the covarion hypothesis of molecular evolution. Mol. Biol. Evol. 12, 503-513.
104. Sanders, H.L., 1968a. Marine benthic diversity; a comparative study. Amer. Nat. 102, 243-282.
105. Sanders, H.L., 1968b. Marine benthic diversity and the stability-time hypothesis. In: Woodwell, G.M., Smith, H.H. (Eds.), Diversity and Stability in Ecological Systems, Brookhaven Symposium on Biology, vol. 22. Brookhaven National Laboratory, pp. 71-81.