Molecular phylogeny of the Gasterosteidae: The importance of using multiple genes

Molecular Phylogenetics and Evolution

Volumn 30, Issue 2, 2004, Pages 366-377

  Mattern, Michelle Y ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

12S rRNA; 16S rRNA; Apeltes; ATPase 6; Control region; Culaea; Cytochrome b; Gasterosteidae; Gasterosteus; Mitochondrial DNA; Molecular; Phylogeny; Pungitius; Spinachia; Stickleback

Indexed keywords

APELTES; CULAEA; GASTEROSTEIDAE; GASTEROSTEUS; PUNGITIUS; SPINACHIA;

EID: 0842331064     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(03)00190-8     Document Type: Article

References (76)

1. Attardi, G., 1985. Animal mitochondrial DNA: an extreme example of genetic economy. Int. Rev. Cytol. 93, 93-145.
2. Baker, R.H., DeSalle, R., 1997. Multiple sources of character information and the phylogeny of Hawaiian Drosophilids. Syst. Biol. 46, 654-673.
3. Bakker, T.C.M., Milinski, M., 1991. Sequential female choice and the previous male effect in sticklebacks. Beh. Ecol. Sociobiol. 29, 205-210.
4. Bell, M.A., 1994. Palaeobiology and evolution of threespine stickleback. In: Bell, M.A., Foster, S.A. (Eds.), The Evolutionary Biology of the Threespine Stickleback. Oxford Science, Oxford, pp. 438-471.
5. Bowne, P.S., 1985. The systematic position of gasterosteiformes. Ph.D. Dissertation, University of Alberta, Edmonton, AB.
6. Bremer, K., 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42, 795-803.
7. Brooks, D.R., McLennan, D.A., 2002. The Nature of Diversity: An Evolutionary Voyage of Discovery. University of Chicago Press, Chicago, IL.
8. Brown, G.G., 1985. Structural conservation and variation in the D-loop-containing region of vertebrate mitochondrial DNA. J. Mol. Biol. 192, 503-511.
9. Echelle, A.A., Echelle, A.F., 1993. Allozyme perspective on mitochondrial-DNA variation and evolution of the Death-Valley pupfishes (Cyprinodontidae, Cyprinodon). Copeia 1993, 275-287.
10. Farris, J.S., Källersjö, M., Kluge, A.G., Bult, C., 1995. Testing significance of incongruence. Cladistics 10, 315-319.
11. Fu, J., 1999. Phylogeny of Lacertid lizards (Squamata: Lacertidae) and the evolution of unisexuality. Ph.D. dissertation, Zoology, University of Toronto, Toronto.
12. Fu, J., 2000. Toward the phylogeny of the family Lacertidae: why 4708 base pairs of mtDNA sequences cannot draw the picture. Biol. J. Linn. Soc. 71, 203-217.
13. Gach, M.H., 1996. Geographic variation in mitochondrial DNA and biogeography of Culaea inconstant. Copeia 1996, 563-575.
14. Graur, D., Li, W.-H., 2000. Fundamentals of Molecular Evolution. Sinauer Associates, Sunderland, MA.
15. Greenfield, D.W., Greenfield, T., 1972. Introgressive hybridization between Gila orcutti and Hesperoleucus symmetricus (Pisces, Cyprinidae) in Cuyama river basin, California. 1. Meristics, morphometrics and breeding. Copeia 1972, 849-859.
16. Haglund, T.R., Buth, D.G., Lawson, R., 1992a. Allozyme variation and phylogenetic relationships of Asian, North American, and European populations of the ninespine stickleback, Pungitius pungitius. In: Mayden, R.L. (Ed.), Systematics, Historical Ecology, and North American Freshwater Fishes. Stanford University Press, Stanford, CA, pp. 438-452.
17. Haglund, T.R., Buth, D.G., Lawson, R., 1992b. Allozyme variation and phylogenetic relationships of Asian, North American, and European populations of the threespine stickleback, Gasterosteus aculeatus. Copeia 1992, 432-443.
18. Hassanin, A., Lecointre, G., Tillier, S., 1998. The 'evolutionary signal' of homoplasy in protein-coding gene sequences and its consequences for a priori weighting in phylogeny. C. R. Acad. Sci. Paris, Sciences de la vie 321, 611-620.
19. Huelsenbeck, J.P., 2000. MrBayes: Bayesian inference of phylogeny. Department of Biology, University of Rochester, Rochester, NY (Distributed by the author).
20. Huelsenbeck, J.P., Crandall, K.A., 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Ann. Rev. Ecol. Syst. 28, 437-466.
21. Huelsenbeck, J.P., Rannala, B., 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276, 227-232.
22. Huelsenbeck, J.P., Ronquist, F., 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
23. Irwin, D.M., Kocher, T.D., Wilson, A.C., 1991. Evolution of cytochrome b gene of mammals. J. Mol. Evol. 32, 128-144.
24. Keivany, Y., Nelson, J.S., 2000. Taxonomic review of the genus Pungitius, ninespine sticklebacks (Gasterosteidae). Cybium 24, 107-122.
25. Keivany, Y., Nelson, J.S., Economidis, P.S., 1997. Validity of Pungitius hellenicus Stephanidis, 1971 (Teleostei, Gasterosteidae), a stickleback fish from Greece. Copeia 1997, 558-564.
26. Kimura, M., 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
27. 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.
28. Kluge, A.J., 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38, 7-25.
29. Kluge, A.J., 1998. Total evidence or taxonomic congruence: cladistics or consensus classification. Cladistics 14, 151-158.
30. Kocher, T.D., Thomas, W.K., Meyer, A., Edwards, S.V., Paabo, S., Villablanca, F.X., Wilson, A.C., 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 86, 6196-6200.
31. Lee, W.J., Conroy, J., Howell, W.H., Kocher, T.D., 1995. Structure and evolution of teleost mitochondrial control regions. J. Mol. Evol. 41, 54-66.
32. Maddison, W.P., Maddison, D.R., 2000. MacClade: Interactive Analysis of Phylogeny and Character Evolution, Version 4. Sinauer Associates, Sunderland, MA.
33. 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.
34. Martin, A.P., Naylor, G.J.P., Palumbi, S.R., 1992. Rates of mitochondrial DNA evolution in sharks are slow compared with mammals. Nature 357, 153-155.
35. McLennan, D.A., 1991. Integrating phylogeny and experimental ethology: from pattern to process. Evolution 45, 1773-1789.
36. McLennan, D.A., 1993. Phylogenetic relationships in the Gasterosteidae: an updated tree based on behavioral characters with a discussion of homoplasy. Copeia 1993, 318-326.
37. McLennan, D.A., 1996. Integrating phylogenetic and experimental analyses: the evolution of male and female nuptial coloration in the Gasterosteidae. Syst. Biol. 45, 261-277.
38. McLennan, D.A., Mattern, M.Y., 2001. The phylogeny of the Gasterosteidae: combining behavioral and morphological data sets. Cladistics 17, 11-27.
39. McLennan, D.A., McPhail, J.D., 1989. Experimental investigations of the evolutionary significance of sexually dimorphic nuptial colouration in Gasterosteus aculeatus (L.): temporal changes in the structure of the male mosaic signal. Can. J. Zool. 67, 1767-1777.
40. McLennan, D.A., McPhail, J.D., 1990. Experimental investigations of the evolutionary significance of sexually dimorphic nuptial colouration in Gasterosteus aculeatus (L.): the relationship between male colour and female behaviour. Can. J. Zool. 68, 482-492.
41. McLennan, D.A., Brooks, D.R., McPhail, J.D., 1988. The benefits of communication between comparative ethology and phylogenetic systematics: a case study using gasterosteid fishes. Can. J. Zool. 66, 2177-2190.
42. McPhail, J.D., 1984. Ecology and evolutions of sympatric sticklebacks (Gasterosteus): morphological and genetic evidence for a species pair in Enos Lake, British Columbia. Can. J. Zool. 62, 1402-1408.
43. McPhail, J.D., 1992. Ecology and evolution of sympatric sticklebacks (Gasterosteus): evidence foe a species pair in Paxton lake, Texada island, British Columbia. Can. J. Zool. 70, 361-369.
44. McPhail, J.D., 1994. Speciation and the evolution of reproductive isolation in sticklebacks (Gasterosteus) of southwest British Columbia. In: Bell, M.A., Foster, S.A. (Eds.), The Evolutionary Biology of the Threespine Stickleback. Oxford Science, Oxford, pp. 28-60.
45. Meyer, A., 1993. Evolution of mitochondrial DNA in fishes. In: Hochachka, P.W., Mommsen, T.P. (Eds.), Biochemistry and Molecular Biology of Fishes, vol. 2. Elsevier, Amsterdam, pp. 1-38.
46. Milinski, M., Bakker, T.C.M., 1990. Female sticklebacks use male coloration in mate choice and hence avoid parasitized males. Nature 344, 331-333.
47. Ortí, G., Bell, M.A., Reimchen, T.E., Meyer, A., 1994. Global survey of mitochondrial DNA sequences in the threespine stickleback: evidence for recent migrations. Evolution 48, 608-622.
48. Ortí, G., 1996. Radiation of characiform fishes: evidence from mitochondrial and nuclear DNA sequences. In: Kocher, T.D., Stepien, C.A. (Eds.), Molecular Systematics of fishes. Academic Press, London, pp. 219-244.
49. Paepke, H.J., 1983. Die Stichlinge. Die Neue Brehm-Bücherei Number 10, A. Ziemsen Verlag, Wittenberg, Lutherstadt.
50. Paepke, H.J., 1996. Die Stichlinge. Die Neue Brehm-Bücherei Number10, second ed. Westarp Wissenschaften, Magdeburg.
51. Page, R.D.M., Holmes, E.C., 1998. Molecular Evolution: A Phylogenetic Approach. Blackwell, Oxford.
52. Palumbi, S.R., 1996. Nucleic acids II: the polymerase chain reaction. In: Hillis, D.M., Moritz, C., Mable, B.K. (Eds.), Molecular Systematics, second ed. Sinauer Associates, Sunderland, MA, pp. 205-248.
53. Parker, A., 1996. Combining molecular and morphological data in fish systematics: examples from the Cyprinodontiformes. In: Kocher, T.D., Stepien, C.A. (Eds.), Molecular Systematics of Fishes. Academic Press, London, pp. 163-188.
54. Pelkwijk, J.J., ter, Tinbergen, N., 1937. Eine reizbiologische analyse einiger Verhaltensweisen von Gasterosteus aculeatus L. Z. Tierpsychol. 1, 193-200.
55. Posada, D., Crandall, K.A., 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818.
56. Prager, E.M., Wilson, A.C., 1988. Ancient origin of lactalbumin from lysozyme - analysis of DNA and amino-acid sequences. J. Mol. Evol. 27, 326-335.
57. Rannala, B., Yang, Z., 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43, 304-311.
58. Rodriguez, F.J., Oliver, J.L., Marin, A., Medina, J.R., 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142, 485-501.
59. Saccone, C., Attimonelli, M., Sbisà, E., 1987. Structural elements highly preserved during the evolution of the D-loop-containing region in vertebrate mitochondrial DNA. J. Mol. Evol. 26, 205-211.
60. Saiki, R.K., Gelfand, D.H., Stoeffel, S., Scharf, S.J., Higuchi, R., Horn, G.T., Mullis, K.B., Erlich, H.A., 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239, 487-491.
61. Schluter, D., 1993. Adaptive radiation in sticklebacks: size, shape, and habitat use efficiency. Ecology 74, 699-709.
62. Schluter, D., 1994. Experimental evidence that competition promotes divergence in adaptive radiation. Science 266, 798-801.
63. Schueler, F.W., Rising, J.D., 1976. Phenetic evidence of natural hybridization. Syst. Zool. 25, 283-289.
64. Shimodaira, H., Hasegawa, M., 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116.
65. Simon, C., Pääbo, S., Kocher, T.D., Wilson, A.C., 1990. Evolution of mitochondrial ribosomal RNA in insects as shown by the polymerase chain reaction. In: Clegg, M., O'Brien, S.J. (Eds.), Molecular Evolution. UCLA Symposium on Molecular and Cellular Biology, New Series, vol. 122. Wiley-Liss, New York, pp. 235-244.
66. Sorenson, M.D., 1999. TreeRot, Version 2. Boston University, Boston, MA.
67. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods), Version 4. Sinauer Associates, Sunderland, MA.
68. Takahashi, K., Goto, A., 2001. Evolution of East Asian ninespine stickleback as shown by mitochondrial DNA control region sequences. Mol. Phylogenet. Evol. 21, 135-155.
69. Templeton, A.R., 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37, 221-244.
70. Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
71. Trepanier, T.L., 2002. Conserving genetic diversity in fringe-toed lizards: a phylogenetic approach. Ph.D. Dissertation, Zoology, University of Toronto, Toronto.
72. Wang, H.-Y., Lee, S.-C., 2002. Secondary structure of mitochondrial 12S rRNA among fish and its phylogenetic applications. Mol. Biol. Evol. 19, 138-148.
73. Wilson, A.B., Vincent, A., Ahnesjö, I., Meyer, A., 2001. Male pregnancy in seahorses and pipefishes (family Syngnathidae): rapid diversification of paternal brood pouch morphology inferred from a molecular phylogeny. J. Hered. 92, 159-166.
74. Wootton, R.J., 1976. The Biology of the Sticklebacks. Academic Press, London.
75. Wootton, R.J., 1984. The Biology of the Sticklebacks, second ed. Academic Press, London.
76. Yamada, M., Higuchi, M., Goto, A., 2001. Extensive introgression of mitochondrial DNA found between two genetically divergent forms of threespine stickleback, Gasterosteus aculeatus, around Japan. Environ. Biol. Fishes 61, 269-284.