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Maximum likelihood methods for detecting adaptive evolution after gene duplication

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Genome Evolution

Abstract

The rapid accumulation of genomic sequences in public databases will finally allow large scale studies of gene family evolution, including evaluation of the role of positive Darwinian selection following a duplication event. This will be possible because recent statistical methods of comparing synonymous and nonsynonymous substitution rates permit reliable detection of positive selection at individual amino acid sites and along evolutionary lineages. Here, we summarize maximum-likelihood based methods, and present a framework for their application to analysis of gene families. Using these methods, we investigated the role of positive Darwinian selection in the ECP-EDN gene family of primates and the Troponin C gene family of vertebrates. We also comment on the limitations of these methods and discuss directions for further improvements.

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References

  • Agulnik, A.I., Zharkikh, A., Boettger-Tong, H., Bourgeron, T., McElreavey, K. and Bishop, C.E. (1998) Evolution of the DAZ gene family suggests that Y-linked DAZ plays little, or a limited, role in spermatogenesis but underlines a recent African origin for human populations. Hum. Mol. Genet. 7, 1371–1377.

    Article  PubMed  CAS  Google Scholar 

  • Anisimova, M., Bielawski, J.P. and Yang, Z. (2001) Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol. Evol. 18, 1585–1592.

    Article  PubMed  CAS  Google Scholar 

  • Anisimova, M., Bielawski, J.P. and Yang, Z. (2002) Accuracy and power of Bayesian prediction of amino acid sites under positive selection. Mol Biol Evol. 19, 950–958.

    Article  PubMed  CAS  Google Scholar 

  • Bielawski, J.P. and Yang, Z. (2000) Positive and negative selection in the DAZ gene family. Mol Biol. Evol. 18, 523–528.

    Article  Google Scholar 

  • Bishop, J.G., Dean, A.M. and Mitchell-Olds, T. (2000) Rapid evolution of plant chitinases: molecular targets of selection in plant-pathogen coevolution. Proc. Natl Acad. Sci. USA 97, 5322–5327.

    Article  PubMed  CAS  Google Scholar 

  • Crandall, K.A., Kelsey, CR., Imanichi, H., Lane, H.C. and Salz-man, N.P. (1999) Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol. Biol Evol. 16, 372–382.

    Article  PubMed  CAS  Google Scholar 

  • Domachowske, J.B., Bonville, C.A., Dyer, K.D. and Rosenberg, H.F. (1998) Evolution of antiviral activity in the ribonuclease A gene superfamily: evidence for a specific interaction between eosinophil-derived neurotoxin (EDN/RNase 2) and respiratory syncytial virus. Nucleic Acids Res. 26, 5327–5332.

    Article  PubMed  CAS  Google Scholar 

  • Duda, T.F. and Palumbi, S.R. (1999) Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus. Proc. Natl. Acad. Sci. USA 96, 6820–6823.

    Article  PubMed  CAS  Google Scholar 

  • Dykhuizen, D. and Hartl, D.L. (1980) Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background. Genetics 96, 801–817.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Farah, CS. and Reinach, F.C. (1995) The troponin complex and regulation of muscle contraction. FASEB J. 9, 755–767.

    PubMed  CAS  Google Scholar 

  • Galtier, N. (2001) Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol. Biol. Evol. 18, 866–873.

    Article  PubMed  CAS  Google Scholar 

  • Golding, G.B. and Dean, A.M. (1998) The structural basis of molecular adaptation. Mol. Biol. Evol. 15, 355–369.

    Article  PubMed  CAS  Google Scholar 

  • Goldman, N. and Yang, Z. (1994) A codon based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11, 725–736.

    PubMed  CAS  Google Scholar 

  • Gu, X. (1999) Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 16, 1664–1674.

    Article  PubMed  CAS  Google Scholar 

  • Gu, X. (2001) Maximum-likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol. 18, 453–464.

    Article  PubMed  CAS  Google Scholar 

  • Haydon, D.T., Bastos, A.D., Knowles, N.J. and Samuel, A.R. (2001) Evidence for positive selection in foot-and-mouth-disease virus genes from field isolates. Genetics 157, 151–154.

    Google Scholar 

  • Hughes, A.L. (1999) Adaptive Evolution of Genes and Genomes, Oxford University Press, Oxford, UK.

    Google Scholar 

  • Hughes, A.L. and Nei, M. (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals over-dominant selection. Nature 335, 167–170.

    Article  PubMed  CAS  Google Scholar 

  • Kimura, M. (1983) The Neutral Theory of Molecular Evolution, Cambridge University Press, Cambridge, UK.

    Book  Google Scholar 

  • Leigh Brown, A.J. (1997) Analysis of HIV-1 env gene reveals evidence for a low effective number in the viral population. Proc. Natl. Acad. Sci. USA 94, 1862–1865.

    Article  Google Scholar 

  • Li, W.-H. (1985) Accelerated evolution following gene duplication and its implications for the neutralist-selectionist controversy. In Population Genetics and Molecular Evolution (Eds., Otha, T. and Aoki, K.), Japan Scientific Press, Tokyo, pp. 333–352.

    Google Scholar 

  • Lynch, M. and Conery, J.S. (2000) The evolutionary fate and consequences of duplicate genes. Science 290, 1151–1155.

    Article  PubMed  CAS  Google Scholar 

  • Muse, S.V. and Gaut, B.S. (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with applications to the chloroplast genome. Mol. Biol. Evol. 11,715–725.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Ohno, S. (1970) Evolution by Gene Duplication, Springer-Verlag, Berlin.

    Google Scholar 

  • Ohta, T. (1988a) Further simulation studies on evolution by gene duplication. Evolution 42, 375–386.

    Article  Google Scholar 

  • Ohta, T. (1988b) Multigene and supergene families. Oxf Surv. Evol. Biol. 5, 41–65.

    Google Scholar 

  • Ohta, T. (1993) Pattern of nucleotide substitution in growth hor-mone-prolactin gene family: a paradigm for evolution by gene duplication. Genetics 134:1271–1276.

    PubMed  CAS  Google Scholar 

  • Ohta, T. (1994) Further examples of evolution by gene duplication revealed through DNA sequence comparisons. Genetics 138, 1331–1337.

    PubMed  CAS  Google Scholar 

  • Plikat, U., Nieselt-Struwe, K. and Meyerhans, A. (1997) Genetic drift can dominate short-term human immunodeficiency virus type 1 nef quasispecies evolution in vivo. J. Virol. 71, 4233–4240.

    PubMed  CAS  Google Scholar 

  • Rooney, A.P. and Zhang, J. (1999) Rapid evolution of primate sperm protein: relaxation of functional constraint or positive Darwinian selection? Mol. Biol. Evol. 16, 706–710.

    Article  PubMed  CAS  Google Scholar 

  • Rosenberg, H.F. and Domachowske, J.B. (1999) Eosinophils, riob-nucleases and host defence: solving the puzzle. Immunol. Res. 20, 261–274.

    Article  PubMed  CAS  Google Scholar 

  • Rosenberg, H.F., Dyer, K.D., Tiffany, H.L. and Gonzalez, M. (1995) Rapid evolution of a unique family of primate ribonu-clease genes. Nature Genet. 10, 219–223.

    Article  PubMed  CAS  Google Scholar 

  • Schmidt, T.R., Goodman, M. and Grossman, L.I. (1999) Molecular evolution of the COX7A gene family in primates. Mol. Biol. Evol. 16, 619–626.

    Article  PubMed  CAS  Google Scholar 

  • Sharp, P.M. (1997) In search of molecular Darwinism. Nature 385, 401–404.

    Article  Google Scholar 

  • Swanson, W.J., Yang, Z., Wolfner, M.F. and Aquadro, C.F. (2001) Positive Darwinian selection in the evolution of mammalian female reproductive proteins. Proc. Natl. Acad. Sci. USA 98, 2509–2514.

    Article  PubMed  CAS  Google Scholar 

  • Ward, T.J., Honeycutt, R.L. and Derr, J.N. (1997) Nucleotide sequence evolution at the kappa-casein locus: evidence for positive selection within the family Bovidae. Genetics 147, 1863–1872.

    PubMed  CAS  Google Scholar 

  • Yang, Z. (1997) PAML: a program package for phylogenetic analyses by maximum likelihood. Cabios 13, 555–556.

    PubMed  CAS  Google Scholar 

  • Yang, Z. (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15, 568–573.

    Article  PubMed  CAS  Google Scholar 

  • Yang, Z. (2001) Adaptive molecular evolution. In Handbook of Statistical Genetics (Eds., Balding, D.J., Bishop, M. and Cannings, C), Wiley & Sons, New York, NY, pp. 327–350.

    Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Yang, Z. and Swanson, W.J. (2002) Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol., 19, 49–57.

    Article  PubMed  Google Scholar 

  • Yang, Z., Nielsen, R., Goldman, N. and A.-M.K. Pederson, W.J. (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155, 431–449.

    PubMed  CAS  Google Scholar 

  • Zanotto, P.M. de 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.

    PubMed  CAS  Google Scholar 

  • Zhang, J., Rosenburg, H.F. and Nei, M. (1998) Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. USA 95, 3708–3713.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Biology, University College London, Darwin Building, Gower Street, London, WCIE 6BT, UK

    Joseph P. Bielawski & Ziheng Yang

Authors
  1. Joseph P. Bielawski
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  2. Ziheng Yang
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Correspondence to Joseph P. Bielawski .

Editor information

Editors and Affiliations

  1. University of Konstanz, Germany

    Axel Meyer

  2. Ghent University, Belgium

    Yves Van de Peer

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© 2003 Springer Science+Business Media Dordrecht

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Bielawski, J.P., Yang, Z. (2003). Maximum likelihood methods for detecting adaptive evolution after gene duplication. In: Meyer, A., Van de Peer, Y. (eds) Genome Evolution. Springer, Dordrecht. https://doi.org/10.1007/978-94-010-0263-9_20

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  • DOI: https://doi.org/10.1007/978-94-010-0263-9_20

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-010-3957-4

  • Online ISBN: 978-94-010-0263-9

  • eBook Packages: Springer Book Archive

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