, Volume 68, Issue 10, pp 749–753 | Cite as

Significance of positive selection and gene duplication in adaptive evolution: in memory of Austin L. Hughes

  • Ken WolfeEmail author
  • Colm Ó’hUigín
Mini Review


In this minireview, we highlight the contributions of the late Austin L. Hughes to two areas of molecular evolution: the role of positive (Darwinian) selection, and the impact of gene duplications during genome evolution.


Selection Duplication Evolution 


  1. Bjorkman PJ, Saper MA, Samraoui B, Bennett WS, Strominger JL, Wiley DC (1987a) The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens. Nature 329:512–518CrossRefPubMedGoogle Scholar
  2. Bjorkman PJ, Saper MA, Samraoui B, Bennett WS, Strominger JL, Wiley DC (1987b) Structure of the human class I histocompatibility antigen, HLA-A2. Nature 329:506–512CrossRefPubMedGoogle Scholar
  3. Clark AG, Kao TH (1991) Excess nonsynonymous substitution of shared polymorphic sites among self-incompatibility alleles of Solanaceae. Proc Natl Acad Sci U S A 88:9823–9827CrossRefPubMedPubMedCentralGoogle Scholar
  4. Dickerson RE (1971) The structures of cytochrome c and the rates of molecular evolution. J Mol Evol 1:26–45CrossRefPubMedGoogle Scholar
  5. Endo T, Ikeo K, Gojobori T (1996) Large-scale search for genes on which positive selection may operate. Mol Biol Evol 13:685–690CrossRefPubMedGoogle Scholar
  6. Flaherty L (1988) Major histocompatibility complex polymorphism: a nonimmune theory for selection. Hum Immunol 21:3–13CrossRefPubMedGoogle Scholar
  7. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531–1545PubMedPubMedCentralGoogle Scholar
  8. Friedman B, Hughes A (2016) Austin L. Hughes 1949–2015. Immunogenetics 68:1CrossRefPubMedGoogle Scholar
  9. Hill RE, Hastie ND (1987) Accelerated evolution in the reactive centre regions of serine protease inhibitors. Nature 326:96–99CrossRefPubMedGoogle Scholar
  10. Hittinger CT, Carroll SB (2007) Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449:677–681CrossRefPubMedGoogle Scholar
  11. Hughes AL (1991) Circumsporozoite protein genes of malaria parasites (Plasmodium spp.): evidence for positive selection on immunogenic regions. Genetics 127:345–353PubMedPubMedCentralGoogle Scholar
  12. Hughes AL (1994) The evolution of functionally novel proteins after gene duplication. Proc R Soc Lond B Biol Sci 256:119–124CrossRefGoogle Scholar
  13. Hughes AL (1999) Adaptive evolution of genes and genomes. Oxford University Press, New YorkGoogle Scholar
  14. Hughes AL (2007) Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level. Heredity (Edinb) 99:364–373CrossRefGoogle Scholar
  15. Hughes AL, Friedman R (2008) Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes. Immunogenetics 60:495–506CrossRefPubMedPubMedCentralGoogle Scholar
  16. Hughes AL, Nei M (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335:167–170CrossRefPubMedGoogle Scholar
  17. Kimura M (1977) Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267:275–276CrossRefPubMedGoogle Scholar
  18. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  19. Klein J (1986) Natural history of the major histocompatibility complex. Wiley, New YorkGoogle Scholar
  20. Klein J (1987) Origin of major histocompatibility complex polymorphism: the trans-species hypothesis. Hum Immunol 19:155–162CrossRefPubMedGoogle Scholar
  21. Lee J, Trowsdale J (1983) Molecular biology of the major histocompatibility complex. Nature 304:214–215CrossRefPubMedGoogle Scholar
  22. Li WH, Wu CI, Luo CC (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2:150–174PubMedGoogle Scholar
  23. Miyata T, Yasunaga T, Nishida T (1980) Nucleotide sequence divergence and functional constraint in mRNA evolution. Proc Natl Acad Sci U S A 77:7328–7332CrossRefPubMedPubMedCentralGoogle Scholar
  24. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426PubMedGoogle Scholar
  25. Ohno S (1970) Evolution by gene duplication. George Allen and Unwin, LondonCrossRefGoogle Scholar
  26. Ohno S (1973) Ancient linkage groups and frozen accidents. Nature 244:259–262CrossRefGoogle Scholar
  27. Robertson M (1982) The evolutionary past of the major histocompatibility complex and the future of cellular immunology. Nature 297:629–632CrossRefPubMedGoogle Scholar
  28. Swanson WJ, Vacquier VD (1995) Extraordinary divergence and positive Darwinian selection in a fusagenic protein coating the acrosomal process of abalone spermatozoa. Proc Natl Acad Sci U S A 92:4957–4961CrossRefPubMedPubMedCentralGoogle Scholar
  29. Trowsdale J (1987) Still more genes in the MHC. Immunol Today 8:35–36CrossRefPubMedGoogle Scholar
  30. Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.UCD Conway Institute and School of MedicineUniversity College DublinDublin 4Ireland
  2. 2.Cancer Inflammation Program, Laboratory of Experimental Immunology, Leidos-Frederick, IncorporatedFrederick National Laboratory for Cancer ResearchFrederickUSA

Personalised recommendations