Evolution by gene duplication: An update

Trends in Ecology and Evolution

Volumn 18, Issue 6, 2003, Pages 292-298

  Zhang, Jianzhi ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTION; GENE; GENOME;

EID: 0037500141     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0169-5347(03)00033-8     Document Type: Review

References (78)

1. Bridges C.B. The Bar 'gene' a duplication. Science. 83:1936;210-211.
2. Stephens S.G. Possible significance of duplication in evolution. Adv. Genet. 4:1951;247-265.
3. Ohno S. Sex Chromosomes and Sex-Linked Genes. 1967;Springer.
4. Nei M. Gene duplication and nucleotide substitution in evolution. Nature. 221:1969;40-42.
5. Ohno S. Evolution by Gene Duplication. 1970;Springer.
6. Wolfe K. Yesterday's polyploids and the mystery of diploidization. Nat. Rev. Genet. 2:2001;333-341.
7. Friedman R., Hughes A.L. Pattern and timing of gene duplication in animal genomes. Genome Res. 11:2001;1842-1847.
8. Spring J. Genome duplication strikes back. Nat. Genet. 31:2002;128-129.
9. Lynch M., Conery J.S. The evolutionary fate and consequences of duplicate genes. Science. 290:2000;1151-1155.
10. Li W.H. Molecular Evolution. 1997;Sinauer.
11. Li W.H., et al. Evolutionary analyses of the human genome. Nature. 409:2001;847-849.
12. Gu Z., et al. Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol. Biol. Evol. 19:2002;256-262.
13. Lespinet O., et al. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 12:2002;1048-1059.
14. Mombaerts P. The human repertoire of odorant receptor genes and pseudogenes. Annu. Rev. Genomics Hum. Genet. 2:2001;493-510.
15. Zhang X., Firestein S. The olfactory receptor gene superfamily of the mouse. Nat. Neurosci. 5:2002;124-133.
16. Conant G.C., Wagner A. GenomeHistory: a software tool and its application to fully sequenced genomes. Nucleic Acids Res. 30:2002;3378-3386.
17. Long M. Evolution of novel genes. Curr. Opin. Genet. Dev. 11:2001;673-680.
18. Samonte R.V., Eichler E.E. Segmental duplications and the evolution of the primate genome. Nat. Rev. Genet. 3:2002;65-72.
19. Kimura M. The Neutral Theory of Molecular Evolution. 1983;Cambridge University Press.
20. Hughes A.L., Nei M. Evolution of the major histocompatibility complex: independent origin of nonclassical class I genes in different groups of mammals. Mol. Biol. Evol. 6:1989;559-579.
21. Nei M., et al. Purifying selection and birth-and-death evolution in the ubiquitin gene family. Proc. Natl. Acad. Sci. U. S. A. 97:2000;10866-10871.
22. Walsh J.B. How often do duplicated genes evolve new functions? Genetics. 139:1995;421-428.
23. Lynch M., et al. The probability of preservation of a newly arisen gene duplicate. Genetics. 159:2001;1789-1804.
24. Harisson P.M., et al. Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res. 12:2002;272-280.
25. Harrison P.M., et al. Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome. Nucleic Acids Res. 29:2001;818-830.
26. Rouquier S., et al. The olfactory receptor gene repertoire in primates and mouse: evidence for reduction of the functional fraction in primates. Proc. Natl. Acad. Sci. U. S. A. 97:2000;2870-2874.
27. Ota T., Nei M. Evolution of immunoglobulin VH pseudogenes in chickens. Mol. Biol. Evol. 12:1995;94-102.
28. Trabesinger-Ruef N., et al. Pseudogenes in ribonuclease evolution: a source of new biomacromolecular function? FEBS Lett. 382:1996;319-322.
29. Breukelman H.J., et al. Secretory ribonuclease genes and pseudogenes in true ruminants. Gene. 212:1998;259-268.
30. Kleineidam R.G., et al. Seminal-type ribonuclease genes in ruminants, sequence conservation without protein expression? Gene. 231:1999;147-153.
31. Piontkivska H., et al. Purifying selection and birth-and-death evolution in the histone H4 gene family. Mol. Biol. Evol. 19:2002;689-697.
32. Hurst L.D., Smith N.G.C. The evolution of concerted evolution. Proc. R. Soc. Lond. Ser. B. 265:1998;121-127.
33. Nowak M.A., et al. Evolution of genetic redundancy. Nature. 388:1997;167-171.
34. Jensen R.A. Enzyme recruitment in the evolution of new function. Annu. Rev. Microbiol. 30:1976;409-425.
35. Orgel L.E. Gene duplication and the origin of proteins with novel functions. J. Theor. Biol. 67:1977;773.
36. Hughes A.L. The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. Ser. B. 256:1994;119-124.
37. Force A., et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics. 151:1999;1531-1545.
38. Wagner A. Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate. Proc. Natl. Acad. Sci. U. S. A. 97:2000;6579-6584.
39. Gu Z., et al. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 18:2002;609-613.
40. Hughes A.L. Adaptive Evolution of Genes and Genomes. 1999;Oxford University Press.
41. Zhang J., et al. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat. Genet. 30:2002;411-415.
42. Zhang J., et al. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. U. S. A. 95:1998;3708-3713.
43. Rosenberg H.F. Recombinant human eosinophil cationic protein. Ribonuclease activity is not essential for cytotoxicity. J. Biol. Chem. 270:1995;7876-7881.
44. Yokoyama S., Yokoyama R. Molecular evolution of human visual pigment genes. Mol. Biol. Evol. 6:1989;186-197.
45. Asenjo A.B., et al. Molecular determinants of human red/green color discrimination. Neuron. 12:1994;1131-1138.
46. Dykhuizen D., Hartl D.L. Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background. Genetics. 96:1980;801-817.
47. Li W.H. Evolution of duplicate genes and pseudogenes. Nei M., Koehn R.K. Evolution of Genes and Proteins. 1983;14-37 Sinauer.
48. Ohta T. Further examples of evolution by gene duplication revealed through DNA sequence comparisons. Genetics. 138:1994;1331-1337.
49. Van de Peer Y., et al. The ghost of selection past: rates of evolution and functional divergence of anciently duplicated genes. J. Mol. Evol. 53:2001;436-446.
50. Tanaka T., Nei M. Positive darwinian selection observed at the variable-region genes of immunoglobulins. Mol. Biol. Evol. 6:1989;447-459.
51. Duda T.F. Jr, Palumbi S.R. Molecular genetics of ecological diversification: duplication and rapid evolution of toxin genes of the venomous gastropod Conus. Proc. Natl. Acad. Sci. U. S. A. 96:1999;6820-6823.
52. Zhang J., et al. Evolution of the rodent eosinophil-associated RNase gene family by rapid gene sorting and positive selection. Proc. Natl. Acad. Sci. U. S. A. 97:2000;4701-4706.
53. Hughes A.L., et al. Adaptive diversification within a large family of recently duplicated, placentally expressed genes. Proc. Natl. Acad. Sci. U. S. A. 97:2000;3319-3323.
54. Merritt T.J., Quattro J.M. Evidence for a period of directional selection following gene duplication in a neurally expressed locus of triosephosphate isomerase. Genetics. 159:2001;689-697.
55. Gu X. Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 16:1999;1664-1674.
56. Dermitzakis E.T., Clark A.G. Differential selection after duplication in mammalian developmental genes. Mol. Biol. Evol. 18:2001;557-562.
57. Knudsen B., Miyamoto M.M. A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proc. Natl. Acad. Sci. U. S. A. 98:2001;14512-14517.
58. Gaucher E.A., et al. Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem. Sci. 27:2002;315-321.
59. Wagner A. Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization. Proc. Natl. Acad. Sci. U. S. A. 91:1994;4387-4391.
60. Czerny T., et al. Twin of eyeless, a second Pax-6 gene of Drosophila, acts upstream of eyeless in the control of eye development. Mol. Cell. 3:1999;297-307.
61. Waterston R.H., et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420:2002;520-562.
62. Bailey J.A., et al. Recent segmental duplications in the human genome. Science. 297:2002;1003-1007.
63. Gagneux P., Varki A. Genetic differences between humans and great apes. Mol. Phylogenet. Evol. 18:2001;2-13.
64. Lynch M. Gene duplication and evolution. Science. 297:2002;945-947.
65. Himmelreich R., et al. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24:1996;4420-4449.
66. Tomb J.F., et al. The complete genome sequence of the gastric pathogen Helicobacterpylori. Nature. 388:1997;539-547.
67. Rubin G.M., et al. Comparative genomics of the eukaryotes. Science. 287:2000;2204-2215.
68. Klenk H.P., et al. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature. 390:1997;364-370.
69. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
70. Kay R.N.B., Davies A.G. Digestive physiology. Davies A.G., Oates J.F. Colobine Monkeys: Their Ecology Behaviour and Evolution. 1994;229-250 Cambridge University Press.
71. Barnard E.A. Biological function of pancreatic ribonuclease. Nature. 221:1969;340-344.
72. Beintema J.J. The primary structure of langur (Presbytis entellus) pancreatic ribonuclease adaptive features in digestive enzymes in mammals. Mol. Biol. Evol. 7:1990;470-477.
73. Gu X., Vander Velden K. DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics. 18:2002;500-501.
74. Wang Y., Gu X. Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction. Genetics. 158:2001;1311-1320.
75. Wagner A. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol. 18:2001;1283-1292.
76. Bhan C., et al. A duplication growth model of gene expression networks. Bioinformatics. 18:2002;1486-1493.
77. Kitami T., Nadeau J.H. Biochemical networking contributes more to genetic buffering in human and mouse metabolic pathways than does gene duplication. Nat. Genet. 32:2002;191-194.
78. Gu Z., et al. Role of duplicate genes in genetic robustness against null mutations. Nature. 421:2003;63-66.