Varying signals of the effects of natural selection during teleost growth hormone gene evolution

Genome

Volumn 49, Issue 1, 2006, Pages 42-53

  Ryynänen, Heikki J ^a   Primmer, Craig R ^a,b  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF TURKU   (Finland)

Author keywords

Growth hormone; Molecular evolution; Non synonymous substitution; Positive selection; Synonymous substitution; Teleost fish

Indexed keywords

GROWTH HORMONE;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CLASSIFICATION; FISH; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY;

AMINO ACID SEQUENCE; ANIMALS; EVOLUTION, MOLECULAR; FISHES; GROWTH HORMONE; MOLECULAR SEQUENCE DATA; PHYLOGENY;

MAMMALIA; SALMONIFORMES; TELEOSTEI; VERTEBRATA;

EID: 33644954174     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/g05-079     Document Type: Article

References (68)

1. Bargelloni, L., Marcato, S., and Patarnello, T. 1998. Antarctic fish hemoglobins: evidence for adaptive evolution at subzero temperature. Proc. Natl. Acad. Sci. U.S.A. 95: 8670-8675.
2. Bendtsen, D.J., Nielsen, H., von Heijne, G., and Brunak, S. 2004. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340: 783-795.
3. Bernardi, G., D'Onofrio, G., Caccio, S., and Bernardi, G. 1993. Molecular phylogeny of bony fishes, based on the amino acid sequence of the growth hormone. J. Mol. Evol. 37: 644-649.
4. Berra, T.M. 2001. Freshwater fish distribution. Academic Press, San Diego, Calif.
5. Bielawski, J.P., and Yang, Z. 2001. Positive and negative selection in the DAZ gene family. Mol. Biol. Evol. 18: 523-529.
6. Bielawski, J.P., and Yang, Z. 2003. Maximum likelihood methods for detecting adaptive evolution after gene duplication. J. Struct. Funct. Genomics 3: 201-212.
7. Bishop, J.G., Dean, A.M., and Mitchell-Olds, T. 2000. Rapid evolution in plant chitinases: Molecular targets of selection in plant-pathogen coevolution. Proc. Natl. Acad. Sci. U.S.A. 97: 5322-5327.
8. Björnsson, B.T., Johansson, V., Benedet, S., Einarsdottir, I.E., Hildahl, J., Ágústsson, T., and Jönsson, E. 2004. Growth hormone endocrinology of salmonids: regulatory mechanisms and mode of action. Fish Physiol. Biochem. 27: 227-242.
9. Blanc, G., and Wolfe, K.H. 2004. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell, 16: 1679-1691.
10. Bugiotti, L., and Primmer, C.R. 2006. Molecular evolution of the avian growth hormone gene and comparison with its mammalian counterpart. J. Evol. Biol. In press. doi: 10.1111/j.1420-9101. 2005.01042.x.
11. Chen, T.T., Marsh, A., Shamblott, M., Chan, K.-M., Tang, Y.-L., Chen, C.M., and Yang, B.-Y. 1994. Structure and evolution of fish growth hormone and insulinlike growth factor genes. In Fish physiology. Edited by N.M. Sherwood and C.L. Hew. Academic Press, San Diego, Calif. pp. 179-224.
12. Christoffels, A., Koh, E.G.L., Chia, J.-M., Brenner, S., Aparicio, S., and Venkatesh, B. 2004. Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol. Biol. Evol. 21: 1146-1151.
13. Conant, G.C., and Wagner, A. 2003. Asymmetric sequence divergence of duplicate genes. Genome Res. 13: 2052-2058.
14. Davidson, M.B. 1987. Effect of growth hormone on carbohydrate and lipid metabolism. Endocr. Rev. 8: 115-131.
15. Endo, T., Ikeo, K., and Gojobori, T. 1996. Large-scale search for genes on which positive selection may operate. Mol. Biol. Evol. 13: 685-690.
16. Fares, M.A. 2004. SWAPSC: sliding window analysis procedure to detect selective constraints. Bioinformatics, 20: 2867-2868.
17. Fares, M.A., Elena, S.F., Ortiz, J., Moya, A., and Barrio, E. 2002. A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses. J. Mol. Evol. 55: 509-521.
18. Ford, M.J. 2001. Molecular evolution of transferrin: evidence for positive selection in salmonids. Mol. Biol. Evol. 18: 639-647.
19. Forsyth, I.A., and Wallis, M. 2002. Growth hormone and prolactin - molecular and functional evolution. J. Mamm. Gland Biol. Neoplasia, 7: 291-312.
20. Goldman, N., and Yang, Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11: 725-736.
21. Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41: 95-98.
22. Harvey, S., Scanes, C.G., and Daughaday, W.H. 1995. Growth Hormone. CRC Press, Boca Raton, Fla.
23. Hughes, A.L., Green, J.A., Garbayo, J.M., and Roberts, R.M. 2000. Adaptive diversification within a large family of recently duplicated, placentally expressed genes. Proc. Natl. Acad. Sci. U.S.A. 97: 3319-3323.
24. Huttley, G.A., Easteal, S., Southey, M.C., Tesoriero, A., Giles, G.G., McCredie, M.R., Hopper, J.L., and Venter, D.J. 2000. Adaptive evolution of the tumour suppressor BRCA1 in humans and chimpanzees. Nat. Genet. 25: 410-413.
25. Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, New York, N.Y.
26. Korber, B. 2000. HIV signature and sequence variation analysis. In Computational analysis of HIV molecular sequences. Edited by A.G. Rodrigo and G.H. Learn. Kluwer Academic Publishers, Dordrecht, Netherlands. pp. 55-72.
27. Kumar, S., Tamura, K., and Nei, M. 2004. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5: 150-163.
28. Li, W.-H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36: 96-99.
29. Li, W.-H. 1997. Molecular evolution. Sinauer Associates, Sunderland, Mass.
30. Lioupis, A., Wallis, O.C., and Wallis, M. 1997. Cloning and characterisation of the gene encoding red deer (Cervus elaphus) growth hormone: implications for the molecular evolution of growth hormone in artiodactyls. J. Mol. Endocrinol. 19: 259-266.
31. Liu, J.C., Makova, K.D., Adkins, R.M., Gibson, S., and Li, W.-H. 2001. Episodic evolution of growth hormone in primates and emergence of the species specificity of human growth hormone receptor. Mol. Biol. Evol. 18: 945-953.
32. Lynch, M., and Conery, J.S. 2000. The evolutionary fate and consequences of duplicate genes. Science (Washington, D.C.), 290: 1151-1155.
33. Maisey, J.G. 1996. Discovering fossil fishes. Henry Holt and Company, New York, N.Y.
34. McKay, S.J., Trautner, J., Smith, M.J., Koop, B.F., and Devlin, R.H. 2004. Evolution of duplicated growth hormone genes in autotetraploid salmonid fishes. Genome, 47: 714-723.
35. Merritt, T.J.S., and Quattro, J.M. 2001. Evidence for a period of directional selection following gene duplication in a neurally expressed locus of triosephosphate isomerase. Genetics, 159: 689-697.
36. Messier, W., and Stewart, C.-B. 1997. Episodic adaptive evolution of primate lysozymes. Nature (London), 385: 151-154.
37. Nei, M., and Gojobori, T. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3: 418-426.
38. Nielsen, R., and Yang, Z. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148: 929-936.
39. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, Heidelberg, Germany.
40. Ohta, T. 1993. Pattern of nucleotide substitutions in growth hormone-prolactin gene family: a paradigm for evolution by gene duplication. Genetics, 134: 1271-1276.
41. Perez-Sanchez, J. 2000. The involvement of growth hormone in growth regulation, energy homeostasis and immune function in the gilthead sea bream (Sparus aurata): a short review. Fish Physiol. Biochem. 22: 135-144.
42. Reinecke, M., Bjornsson, B.T., Dickhoff, W.W., McCormick, S.D., Navarro, I., Power, D.M., and Gutierrez, J. 2005. Growth hormone and insulin-like growth factors in fish: where we are and where to go. Gen. Comp. Endocrinol. 142: 20-24.
43. Rubin, D.A., and Dores, R.M. 1995. Obtaining a more resolute teleost growth hormone phylogeny by the introduction of gaps in sequence alignment. Mol. Phylogenet. Evol. 4: 129-138.
44. Sorhannus, U. 2003. The effect of positive selection on a sexual reproduction gene in Thalassiosira weissflogii (Bacillariophyta): results obtained from maximum-likelihood and parsimony-based methods. Mol. Biol. Evol. 20: 1326-1328.
45. Suzuki, Y., and Gojobori, T. 1999. A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16: 1315-1328.
46. Suzuki, Y., and Nei, M. 2001. Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 18: 2179-2185.
47. Suzuki, Y., and Nei, M. 2004. False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus. Mol. Biol. Evol. 21: 914-921.
48. Swanson, W.J., Yang, Z., Wolfner, M.F., and Aquadro, C.F. 2001. Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. Proc. Natl. Acad. Sci. U.S.A. 98: 2509-2514.
49. Swofford, D.L. 1998. PAUP* 4.0 - phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, Mass.
50. Thompson, J., Higgins, D., and Gibson, T. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
51. Thorne, J.L., and Kishino, H. 2002. Divergence time and evolutionary rate estimation with multilocus data. Syst. Biol. 51: 689-702.
52. Wallis, M. 1994. Variable evolutionary rates in the molecular evolution of mammalian growth hormones. J. Mol. Evol. 38: 619-627.
53. Wallis, M. 1996. The molecular evolution of vertebrate growth hormones: a pattern of near-stasis interrupted by sustained bursts of rapid change. J. Mol. Evol. 43: 93-100.
54. Wallis, C.O., and Wallis, M. 2001. Molecular evolution of growth hormone (GH) in Cetartiodactyla: cloning and characterization of the gene encoding GH from a primitive ruminant, the Chevrotain (Tragulus javanicus). Gen. Comp. Endocrinol. 123: 62-72.
55. Wallis, C.O., Zhang, Y.-P., and Wallis, M. 2001. Molecular evolution of GH in primates: characterisation of the GH genes from slow loris and marmoset defines an episode of rapid evolutionary change. J. Mol. Endocrinol. 26: 249-258.
56. Willett, C.S. 2000. Evidence for directional selection acting on pheromone-binding proteins in the genus Choristoneura. Mol. Biol. Evol. 17: 553-562.
57. Williams, E.J.B., Pal, C., and Hurst, L.D. 2000. The molecular evolution of signal peptides. Gene, 253: 313-322.
58. Yang, Z. 1997. PAML: a package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
59. Yang, Z. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15: 568-573.
60. Yang, Z. 2002. Inference of selection from multiple species alignments. Curr. Opin.Genet. Dev. 12: 688-694.
61. Yang, Z., and Bielawski, J.P. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15: 496-503.
62. Yang, L., and Gui, J.-F. 2004. Positive selection on multiple antique allelic lineages of transferrin in the polyploid Carassius auratus. Mol. Biol. Evol. 21: 1264-1277.
63. Yang, Z., and Nielsen, R. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19: 908-917.
64. Yang, Z., Nielsen, R., and Hasegawa, M. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15: 1600-1611.
65. Yang, Z., Nielsen, R., Goldman, N., and Pedersen, A.-M.K. 2000a. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics, 155: 431-449.
66. Yang, Z., Swanson, W.J., and Vacquier, V.D. 2000b. Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites. Mol. Biol. Evol. 17: 1446-1455.
67. Zanotto, P.M.d.A., Kallas, E.G., de Souza, R.F., and Holmes, E.C. 1999. Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics, 153: 1077-1089.
68. Zhang, J., Rosenberg, H.F., and Nei, M. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. U.S.A. 95: 3708-3713.