Preservation of duplicate genes by complementary, degenerative mutations

Genetics

Volumn 151, Issue 4, 1999, Pages 1531-1545

  Force, Allan ^a   Lynch, Michael ^a   Pickett, F Bryan ^b   Amores, Angel ^a   Yan, Yi Lin ^a   Postlethwait, John ^a  

^a UNIVERSITY OF OREGON   (United States)

^b LOYOLA UNIVERSITY CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN;

ANIMAL MODEL; ARTICLE; BINDING SITE; EMBRYO; EVOLUTION; GENE DUPLICATION; GENE MUTATION; GENETIC TRANSCRIPTION; GENOME; MOUSE; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL;

ANIMALS; BASE SEQUENCE; DNA PRIMERS; EVOLUTION; GENE DUPLICATION; GENES, REGULATOR; GENETIC COMPLEMENTATION TEST; HUMANS; MODELS, GENETIC; MUTATION; PHYLOGENY;

ANIMALIA; DANIO RERIO; EUKARYOTA;

EID: 0032893932     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (95)

1. AHN, S., and S. D. TANKSLEY, 1993 Comparative linkage maps of the rice and maize genomes. Proc. Natl. Acad. Sci. USA 90: 7980-7984.
2. ALLENDORF, F. W., F. M. UTTER and B. P. MAY, 1975 Gene duplication within the family Salmonidae: II. Detection and determination of the genetic control of duplicate loci through inheritance studies and the examination of populations, pp. 415-432 in Isozymes, edited hy C. L. MARKERT. Academic Press, New York.
3. AMORES, A., A. FORCE, Y.-L. YAN, L. JOLY, C. AMEMIYA et al., 1998 Zebrafish hox clusters and vertebrate genome evolution. Science 282: 1711-1714.
4. ARNONE, M. I., and E. H. DAVIDSON, 1997 The hardwiring of development: organization and function of genomic regulatory systems. Development 124: 1851-1864.
5. BAILEY, G. S., R. T. M. POULTER and P. A. STOCKWELL, 1978 Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci. Proc. Natl. Acad. Sci. USA 75: 5575-5579.
6. BENDER, W., M. AKAM, F. KARCH, P. A. BEACHY, M. PEIFER et al., 1983 Molecular genetics of the Bithorax complex in Drosophila melanogaster. Science 221: 23-29.
7. BISBEE, C. A., M. A. BAKER, A. C. WILSON, H. A. IRANDOKHT and M. FISCHBERG, 1977 Albumin phylogeny for clawed frogs (Xenopus). Science 195: 785-787.
8. BRADLEY, D., R. CARPENTER, H. SOMMER, N. HARTLEY and E. COEN, 1993 Complementary floral homeotic phenotypes result from opposite orientations of a transposon at the plena locus of Antirrhinum. Cell 72: 85-95.
9. CARR, J. L., C. S. SHASHIKANT, W. J. BAILEY and F. H. RUDDLE, 1998 Molecular evolution of Hox gene regulation: cloning and transgenic analysis of the lamprey HoxQ8 gene. J. Exp. Zool. 280: 73-85.
10. CHEN, J., and H. E. RULEY, 1998 An enhancer element in the EphA2 (Eck) gene sufficient for rhombomere-specific expression is activated by HOXA1 and HOXB1 homeobox proteins. J. Biol. Chem. 273: 24670-24675.
11. CLARK, A. G., 1994 Invasion and maintenance of a gene duplication. Proc. Natl. Acad. Sci. USA 91: 2950-2954.
12. COEN, E. S., and E. M. MEYEROWITZ, 1991 War of the whorls: genetic interactions controlling flower development. Nature 353: 31-37.
13. COOKE, J. M. A., M. A. NOWAK, M. BOERLIJST and J. MAYNARD SMITH, 1997 Evolutionary origins and maintenance of redundant gene expression during metazoan development. Trends Genet. 13: 360-364.
14. DAVIS, C. A., D. P. HOMYARD, K. J. MILLEN and A. L. JOYNER, 1991 Examining pattern formation in mouse, chicken and frog embryos with an En-specific antiserum. Development 2: 287-298.
15. DUBOULE, D., and P. DOLLÉ, 1989 The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. EMBO J. 8: 1497-1505.
16. DUPÉ, V., M. DAVENNE, J. BROCARD, P. DOLLÉ, M. MARK et al., 1997 In vivo functional analysis of the Hoxa-1 3′ retinoic acid response element (3′RARE). Development 124: 399-410.
17. EKKER, M., J. WEGNER, M.-A. AKIMENKO and M. WESTERFIELD, 1992 Coordinate expression of three zebrafish engrailed genes. Development 116: 1001-1010.
18. EKKER, S. C., A. R. UNGAR, P. GREENSTEIN, D. P. VONKESSLER, J. A. PORTER et al., 1995 Patterning activities of vertebrate hedgehog proteins in the developing eye and brain. Curr. Biol. 5: 944-955.
19. EKKER, M., M. AKIMENKO, M. ALLENDE, R. SMITH, G. DROUIN et al., 1997 Relationships among msx gene structure and function in zebrafish and other vertebrates. Mol. Biol. Evol. 14: 1008-1022.
20. ELLIES, D., D. STOCK, G. HATCH, G. GIROUX, K. WEISS et al., 1997 Relationship between the genomic organization and the overlapping embryonic expression patterns of the zebrafish dlx genes. Genomics 45: 580-590.
21. FERRIS, S. D., and G. S. WHITT, 1977 Loss of duplicate gene expression after polyploidization. Nature 265: 258-260.
22. FERRIS, S. D., and G. S. WHITT, 1979 Evolution of the differential regulation of duplicate genes after polyploidization. J. Mol. Evol. 12: 267-317.
23. GARDNER, C. A., and K. F. BARALD, 1992 Expression patterns of engrailed-like proteins in the chick embryo. Dev. Dyn. 193: 370-388.
24. GAUT, B. S., and J. F. DOEBLEY, 1997 DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. USA 94: 6809-6814.
25. GAVAIAS, A., M. STUDER, A. LUMSDEN, F. RIJLI, R. KRUMLAUF et al., 1998 Hoxa1 and Hoxb1 synergize in patterning the hindbrain, cranial nerves and second pharyngeal arch. Development 125: 1123-1136.
26. GERHART, J., and M. KIRSCHNER, 1997 Cells, Embryos, and Evolution. Blackwell Science, Malden, MA.
27. GOODMAN, M. M., C. W. STUBER, K. NEWTON and H. H. WEISSINGER, 1980 Linkage relationships of 19 enzyme loci in maize. Genetics 96: 697-710.
28. GRAF, J. D., and H. R. KOBEL, 1991 Xenopus laevis: practical uses in cell and molecular biology, pp. 19-34 in Methods in Cell Biology, edited by B. K. KAY and H. B. PENG. Academic Press, New York.
29. GRENIER, J. K., T. L. GARBER, R. WARREN, P. M. WHITINGTON and S. CARROLL, 1997 Evolution of the entire arthropod Hox gene set predated the origin and radiation of the onychophoran/ arthropod clade. Curr. Biol. 7: 547-553.
30. HALDANE, J. B. S., 1933 The part played by recurrent mutation in evolution. Am. Nat. 67: 5-9.
31. HELENTJARIS, T., D. WEBER and S. WRIGHT, 1988 Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. Genetics 118: 353-363.
32. HOLLAND, L. Z., M. KENE, N. A. WILLIAMS and N. D. HOLLAND, 1997 Sequence and embryonic expression of the amphioxus engrailed gene (AmphiEn): the metameric pattern of transcription resembles that of its segment-polarity homolog in Drosophila. Development 124: 1723-1732.
33. HOLLAND, P. W., and J. GARCIA-FERNANDEZ, 1996 Hox genes and chordate evolution. Dev. Biol. 173: 382-395.
34. HOLLAND, P. W. H., J. GARCIA-FERNANDEZ, N. A. WILLIAMS and A. SIDOW, 1994 Gene duplications and the origins of vertebrate development. Development (Suppl.), 125-133.
35. HUGHES, A. L., 1994 The evolution of functionally novel proteins after gene duplication. Proc. R. Soc. Lond. Ser. B Biol. Sci. 256: 119-124.
36. HUGHES, M. K., and A. L. HUGHES, 1993 Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol. Biol. Evol. 10: 1360-1369.
37. JACK, J., and Y. DELOTTO, 1995 Structure and regulation of a complex locus: the cut gene of Drosophila. Genetics 139: 1689-1700.
38. JACK, J. W., 1985 Molecular organization of the cut locus of Drosophila melanogaster. Cell 42: 869-876.
39. JOWETT, T., M. MANCERA, A. AMORES and Y.-L. YAN, 1995 In situ hybridization to embryo whole mounts and tissue sections: mRNA detection and application to developmental studies, pp. 91-121 in In situ Hybridization, edited by M. CLARK. Chapman & Hall, Weinheim, Germany.
40. JOYNER, A. L., and G. R. MARTIN, 1987 En-1 and En-2, two mouse genes with sequence homology to the Drosophila engrailed gene: expression during embryogenesis. Genes Dev. 1: 29-38.
41. KAPPEN, C., and F. RUDDLE, 1993 Evolution of a regulatory gene family: HOM/HOX genes. Curr. Opin. Genet. Dev. 3: 931-938.
42. KIDWELL, M. G., and D. LISCH, 1997 Transposable elements as sources of variation in animals. Proc. Natl. Acad. Sci. USA 94: 7704-7711.
43. KIMURA, M., 1983 The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK.
44. KIRCHHAMER, C. V., C.-H. YUH and E. H. DAVIDSON, 1996 Modular cis-regulatory organization of developmentally expressed genes: two genes transcribed territorially in the sea urchin embryo, and additional examples. Proc. Natl. Acad. Sci. USA 93: 9322-9328.
45. KRUMLAUF, R., 1994 Hox genes in vertebrate development. Cell 78: 191-201.
46. LANGSTON, A. W., J. R. THOMPSON and L. J. GUDAS, 1997 Retinoic acid-responsive enhancers located 3′ of the Hox A and Hox B homeobox gene clusters. Functional analysis. J. Biol. Chem. 272: 2167-2175.
47. LEE, K. H., Q. H. XU and R. E. BREITBART, 1996 A new tinman-related gene, nkx2.7, anticipates the expression of nkx2.5 and nkx2.3 in zebrafish heart and pharyngeal endoderm. Dev. Biol. 180: 722-731.
48. LEWIS, E. B., 1978 A gene complex controlling segmentation in Drosophila. Nature 276: 565-570.
49. LEWIS, W. H., 1979 Polyploidy: Biological Relevance. Plenum, New York.
50. LI, W.-H., 1980 Rate of gene silencing at duplicate loci: a theoretical study and interpretation of data from tetraploid fishes. Genetics 95: 237-258.
51. LI, X., and M. NOLL, 1994 Evolution of distinct developmental functions of three Drosophila genes by acquisition of different cis-regulatory regions. Nature 367: 83-87.
52. LIU, S., E. MCLEOD and J. JACK, 1991 Four distinct regulatory regions of the cut locus and their effect on cell type specification in Drosophila. Genetics 127: 151-159.
53. LOGAN, C., H. F. WILLARD, J. M. ROMMENS and A. L. JOYNER, 1989 Chromosomal localization of the human homeobox-containing genes, EN1 and EN2. Genomics 4: 206-209.
54. LUNDIN, L. G., 1993 Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse. Genomics 16: 1-19.
55. LYNCH, M., and J. B. WALSH, 1998 Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, MA.
56. MACONOCHIE, M. K., S. NONCHEV, M. STUDER, S. K. CHAN, H. PÖPPERL et al., 1997 Cross-regulation in the mouse HoxB complex: the expression of Hoxb2 in rhombomere 4 is regulated by Hoxb1. Genes Dev. 11: 1885-1895.
57. MENA, M., B. A. AMBROSE, R. B. MEELEY, S. P. BRIGGS, M. F. YANOFSKY et al., 1996 Diversification of C-function activity in maize flower development. Science 274: 1537-1540.
58. MORIZOT, D. C., S. A. SLAUGENHAUPT, K. D. KALLMAN and A. CHAKRAVARTI, 1991 Genetic linkage map of fishes of the genus Xiphophorus (Teleostei: Poeciliidae). Genetics 127: 399-410.
59. NADEAU, J. H., and D. SANKOFF, 1997 Comparable rates of gene loss and functional divergence after genome duplications early in vertebrate evolution. Genetics 147: 1259-1266.
60. NEI, M., and A. K. ROYCHOUDHURY, 1973 Probability of fixation of nonfunctional genes at duplicate loci. Am. Nat. 107: 362-372.
61. NOWAK, M. H., M. C. BOERLIJST, J. COOKE and J. MAYNARD SMITH, 1997 Evolution of genetic redundancy. Nature 388: 167-171.
62. OHNO, S., 1970 Evolution by Gene Duplication. Springer-Verlag, Heidelberg, Germany.
63. OZCELIK, T., M. H. PORTEUS, J. L. R. RUBENSTEIN and U. FRANCKE, 1992 DLX2 (TES1), a homeobox gene of the Distal-less family, assigned to conserved regions on human and mouse chromosomes 2. Genomics 13: 1157-1161.
64. PALOPOLI, M. F., and N. H. PATEL, 1998 Evolution of the interaction between Hox genes and a downstream target. Curr. Biol. 8: 587-590.
65. PÉBUSQUE, M.-J., F. COULIER, D. BIRNBAUM and P. PONTAROTTI, 1998 Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. Mol. Biol. Evol. 15: 1145-1159.
66. PENDLETON, J. W., B. K. NAGAI, M. T. MURTHA and F. H. RUDDLE, 1993 Expansion of the Hox gene family and the evolution of chordates. Proc. Natl. Acad. Sci. USA 90: 6300-6304.
67. PIATGORSKY, J., and G. WISTOW, 1991 The recruitment of crystallins: new functions precede gene duplication. Science 252: 1078-1079.
68. PICKETT, F. B., and D. R. MEEKS-WAGNER, 1995 Seeing double: appreciating genetic redundancy. Plant Cell 7: 1347-1356.
69. PÖPPERL, H., M. BIENZ, M. STUDER, S. CHAN, S. APARICIO et al., 1995 Segmental expression of Hoxb-1 is controlled by a highly conserved autoregulatory loop dependent upon exd/pbx. Cell 81: 1031-1042.
70. POSTLETHWAIT, J., Y. YAN, M. GATES, S. HORNE, A. AMORES et al., 1998 Vertebrate genome evolution and the zebrafish gene map [see comments]. Nat. Genet. 18: 345-349.
71. RAFF, R. A., 1996 The Shape of Life. University of Chicago Press, Chicago, IL.
72. SAITOU, N., and M. NEI, 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
73. SEOIGHE, C., and K. H. WOLFE, 1998 Extent of genomic rearrangement after genome duplication in yeast. Proc. Natl. Acad. Sci. USA 95: 4447-4452.
74. SHUBIN, N., C. TABIN and S. CARROLL, 1997 Fossils, genes and the evolution of animal limbs. Nature 388: 639-648.
75. SIDOW, A., 1996 Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6: 715-722.
76. SLUSARSKI, D. C., C. K. MOTSNY and R. HOLMGREN, 1995 Mutations that alter the timing and pattern of cubitus interruptus gene expression in Drosophila melanogaster. Genetics 139: 229-240.
77. STOCK, D. W., D. L. ELLIES, Z. Y. ZHAO, M. EKKER, F. H. RUDDLE et al., 1996 The evolution of the vertebrate Dlx gene family. Proc. Natl. Acad. Sci. USA 93: 10858-10863.
78. STUDER, M., H. PÖPPERL, H. MARSHALL, A. KUROIWA and R. KRUMLAUF, 1994 Role of conserved retinoic acid response element in rhombomere restriction of Hoxb-1. Science 265: 1728-1732.
79. STUDER, M., A. LUMSDEN, L. ARIZA-MCNAUGHTON, A. BRADLEY and R. KRUMLAUF, 1996 Altered segmental identity and abnormal migration of motor neurons in mice lacking Hoxb-1. Nature 384: 630-634.
80. STUDER, M., A. GAVALAS, H. MARSHALL, L. ARIZA-MCNAUGHTON, F. M. RIJLI et al., 1998 Genetic interactions between Hoxa1 and Hoxb1 reveal new roles in regulation of early patterning. Development 125: 1025-1036.
81. TAKAHATA, N., and T. MARUYAMA, 1979 Polymorphism and loss of duplicate gene expression: a theoretical study with application to tetraploid fish. Proc. Natl. Acad. Sci. USA 76: 4521-4525.
82. THISSE, C., B. THISSE, T. F. SCHILLING and J. H. POSTLETHWAIT, 1993 Structure of the zebrafish snail1 gene and its expression in wild-type, spadetail and no tail mutant embryos. Development 119: 1203-1215.
83. THOMPSON, J. R., S. W. CHEN, L. HO, A. W. LANGSTON and L. J. GUDAS, 1998 An evolutionary conserved element is essential for somite and adjacent mesenchymal expression of the Hoxa1 gene. Dev. Dyn. 211: 97-108.
84. WALSH, J. B., 1995 How often do duplicated genes evolve new functions? Genetics 139: 421-428.
85. WATTERSON, G. A., 1983 On the time for gene silencing at duplicate loci. Genetics 105: 745-766.
86. WENDEL, J. F., C. W. STUBER, M. D. EDWARDS and M. M. GOODMAN, 1986 Duplicated chromosome segments in Zea mays L.: further evidence from hexokinase isozymes. Theor. Appl. Genet. 72: 178-185.
87. WESSLER, S. R., T. E. BUREAU and S. E. WHITE, 1995 LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5: 814-821.
88. WHITE, S., and J. DOEBLEY, 1998 Of genes and genomes and the origin of maize. Trends Genet. 14: 327-332.
89. WHITE, S. E., L. F. HABERA and S. R. WESSLER, 1994 Retrotransposons in the flanking regions of normal plant genes: a role for copia-like elements in the evolution of gene structure and function. Proc. Natl. Acad. Sci. USA 91: 11792-11796.
90. WHITKUS, R., J. DOEBLEY and M. LEE, 1992 Comparative genome mapping of Sorghum and maize. Genetics 132: 1119-1130.
91. WOLFE, K. H., and D. C. SHIELDS, 1997 Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387: 708-713.
92. YANOFSKY, M. F., H. MA, J. L. BOWMAN, G. N. DREWS, K. A. FELMANN et al., 1990 The protein encoded by the Arabidopsis homeotic gene Agamous resembles transcription factors. Nature 346: 35-39.
93. ZARDOYA, R., E. ABOUHEIF and A. MEYER, 1996 Evolutionary analyses of hedgehog and Hoxd-10 genes in fish species closely related to the zebrafish. Proc. Natl. Acad. Sci. USA 93: 13036-13041.
94. ZHANG, J., and M. NEI, 1996 Evolution of Antennapedia-class homeobox genes. Genetics 142: 295-303.
95. ZHOU, Y. H., and W. H. LI, 1996 Gene conversion and natural selection in the evolution of X-linked color vision genes in higher primates. Mol. Biol. Evol. 13: 780-783.