The neutral coalescent process for recent gene duplications and copy-number variants

Genetics

Volumn 177, Issue 2, 2007, Pages 987-1000

  Thornton, Kevin R ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; DNA POLYMORPHISM; GENE CONVERSION; GENE DUPLICATION; GENE MUTATION; GENETIC DRIFT; MATHEMATICAL MODEL; PRIORITY JOURNAL;

CROSSING OVER, GENETIC; GENE DOSAGE; GENE DUPLICATION; GENETIC DRIFT; MODELS, GENETIC; POLYMORPHISM, GENETIC; VARIATION (GENETICS);

EID: 35548940653     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.074948     Document Type: Article

References (74)

1. ANDOLFATTO, P., 2005 Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.
2. ARGUELLO, J. R., Y. CHEN, S. YANG, W. WANG and M. LONG, 2006 Origination of an X-linked testes chimeric gene by illegitimate recombination in Drosophila. PLoS Genet. 2: e77.
3. BAILEY, J. A., Z. GU, R. A. CLARK, K. REINERT, R. V. SAMONTE et al., 2002 Recent segmental duplications in the human genome. Science 297: 1003-1007.
4. BAILEY, J. A., D. M. CHURCH, M. VENTURA, M. ROCCHIAND E. E. EICHLER, 2004 Analysis of segmental duplications and genome assembly in the mouse. Genome Res. 14: 789-801.
5. BETRAN, E., and M. LONG, 2003 Dntf-2r, a young Drosophila retroposed gene with specificmale expression under positive Darwinian selection. Genetics 164: 977-988.
6. BETRAN, E., K. THORNTON and M. LONG, 2002 Retroposed new genes out of the X in Drosophila. Genome Res. 12: 1854-1859.
7. BRAVERMAN, J. M., R. R. HUDSON, N. L. KAPLAN, C. H. LANGLEY and W. STEPHAN, 1995 The hitchhiking effect on the site frequency-spectrum of DNA polymorphisms. Genetics 140: 783-796.
8. CHEUNG, J., X. ESTIVILL, R. KHAJA, J. R. MACDONALD, K. LAU et al., 2003 Genome-wide detection of segmental duplications and potential m assembly errors in the human genome sequence. Genome Biol. 4: R25.
9. CONRAD, D. F., T. D. ANDREWS, N. P. CARTER, M. E. HURLES and J. K. PRITCHARD, 2006 A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet. 38: 75-81.
10. COOP, G., and R. C. GRIFFITHS, 2004 Ancestral inference on gene trees under selection. Theor. Popul. Biol. 66: 219-232.
11. EWENS, W., 2004 Mathematical Population Genetics I. Theoretical Introduction, Ed. 2. Springer-Verlag, Berlin/Heidelberg, Germany/New York.
12. FAN, C., and M. LONG, 2007 A new retroposed gene in Drosophila heterochromatin detected by microarray-based genomic hybridization. J. Mol. Evol. 64: 272-283.
13. FAY, J., and C.-I. WU, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
14. FORCE, A., M. LYNCH, F. B. PICKETT, A. AMORES, Y. L. YAN et al., 1999 Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
15. FU, Y. X., and W. H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
16. GAO, L. Z., and H. INNAN, 2004 Very low gene duplication rate in the yeast genome. Science 306: 1367-1370.
17. GELMAN, A., J. B. CARLIN, H. S. STERN and D. B. RUBIN, 2003 Bayesian Data Analysis, Ed. 2. Chapman & Hall/CRC, London/New York.
18. GRAUBERT, T. A., P. CEHAN, D. EDWIN, R. R. SELZER, T. A. RICHMOND et al., 2007 A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet. 3: e3.
19. GRIFFITHS, R. C., 2003 The frequency spectrum of a mutation, and its age, in a general diffusion model. Theor. Popul. Biol. 64: 241-251.
20. GU, Z., D. NICOLAE, H. LU and W. LI, 2002a Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 18: 609-613.
21. GU, Z. L., A. CAVALCANTI, F. C. CHEN, P. BOUMAN and W. H. LI, 2002b Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol. Biol. Evol. 19: 256-262.
22. GU, Z. L., L. M. STEINMETZ, X. GU, C. SCHARFE, R. W. DAVIS et al., 2003 Role of duplicate genes in genetic robustness against null mutations. Nature 421: 63-66.
23. HUDSON, R. R., 1983 Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23: 183-201.
24. HUDSON, R. R., 1990 Gene genealogies and the coalescent process, pp. 1-42 in Oxford Surveys in Evolutionary Biology, Vol. 7, edited by D. FUTUYAMA and J. ANTONOVICS. Oxford University Press, Oxford.
25. HUDSON, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
26. HUDSON, R. R., and N. L. KAPLAN, 1988 The coalescent process in models with selection and recombination. Genetics 120: 831-840.
27. HUDSON, R. R., M. KREITMAN and M. AGUADE, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
28. IAFRATE, A. J., L. FEUK, M. N. RIVERA, M. L. LISTEWNIK, P. K. DONAHOW et al., 2004 Detection of large-scale variation in the human genome. Nat. Genet. 36: 949-951.
29. INNAN, H., 2003a The coalescent and infinite-site model of a small multigene family. Genetics 163: 803-810.
30. INNAN, H., 2003b A two-locus gene conversion model with selection and its application to the human RHCE and RHD genes. Proc. Natl. Acad. Sci. USA 100: 8793-8798.
31. JONES, C. D., A. W. CUSTER and D. J. BEGUN, 2005 Origin and evolution of a chimeric fusion gene in Drosophila subobscura, D. madeirensis and D. guanche. Genetics 170: 207-219.
32. KAPLAN, N. L., T. DARDEN and R. R. HUDSON, 1988 The coalescent process in models with selection. Genetics 120: 819-829.
33. KONDRASHOV, F., I. ROGOZON, Y. WOLFAND E. KOONIN, 2002 Selection in the evolution of gene duplications. Genome Biol. 3: 0008.1-0008.9.
34. KONDRASHOV, F. A., and A. S. KONDRASHOV, 2006 Role of selection in fixation of gene duplications. J. Theor. Biol. 239: 141-151.
35. LANGE, B. W., C. H. LANGLEY and W. STEPHAN, 1990 Molecular evolution of Drosophila metallothionein genes. Genetics 126: 921-932.
36. LEVINE, M., C. D. JONES, A. D. KERN, H. A. LINDFORS and D. J. BEGUN, 2006 Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc. Natl. Acad. Sci. USA 103: 9935-9939.
37. LI, J., T. JIANG, J.-H. MAO, A. BALMAIN, L. PETERSON et al., 2004 Genomic segmental polymorphisms in inbred mouse strains. Nat. Genet. 36: 952-954.
38. LINDSAY, S. J., M. KHAJAVI, J. R. LUPSKI and M. E. HURLES, 2006 A chromosomal rearrangement hotspot can be identified from population genetic variation and is coincident with a hotspot for allelic recombination. Am. J. Hum. Genet. 79: 890-902.
39. LOCKE, D. P., A. J. SHARPE, S. A. MCCARROLL, S. D. MCGRATH, T. L. NEWMAN et al., 2006 Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am. J. Hum. Genet. 79: 275-290.
40. LONG, M., E. BETRAN, K. THORNTON and W. WANG, 2003 The origin of new genes: glimpses from the young and old. Nat. Rev. Genet. 4: 865-875.
41. LONG, M. Y., and C. H. LANGLEY, 1993 Natural-selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science 260: 91-95.
42. LOOTENS, S., J. BURNETT and T. B. FRIEDMAN, 1993 An intraspecific gene duplication polymorphism of the urate oxidase gene of Drosophila virilis: a genetic and molecular analysis. Mol. Biol. Evol. 10: 635-646.
43. LOPPIN, B., D. LEPETIT, S. DORUS, P. COUBLE and T. L. KARR, 2005 Origin and neofunctionalization of a Drosophila paternal effect gene essential for zygote viability. Curr. Biol. 15: 87-93.
44. LYNCH, M., and J. S. CONERY, 2000 The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
45. MCDONALD, J., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
46. MCVEAN, G., and C. A. SPENCER, 2006 Scanning the human genome for signals of selection. Curr. Opin. Genet. Dev. 16: 624-629.
47. MOORE, R. C., and M. D. PURUGGANAN, 2003 The early stages of duplicate gene evolution. Proc. Natl. Acad. Sci. USA 100: 15,682-15,687.
48. NORDBORG, M., 2000 Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization. Genetics 154: 923-929.
49. PERRY, G. H., J. TCHINDA, S. D. MCG RATH, J. ZHANG, S. R. PICKER et al., 2006 Hotspots for copy number variation in chimpanzees and humans. Proc. Natl. Acad. Sci. USA 103: 8006-8011.
50. PRZEWORSKI, M., G. COOP and J. D. WALL, 2005 Signature of positive selection on standing variation. Evolution 59: 2312-2323.
51. RAEDT, T. D., M. STEPHENS, I. HEYNS, H. BREMS, D. THIJS et al., 2006 Conservation of hotspots for recombination in low-copy repeats associated with the NF1 microdeletion. Nat. Genet. 38: 1419-1423.
52. RAND, D. M., and L. M. KANN, 1996 Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice and humans. Mol. Biol. Evol. 13: 735-748.
53. REDON, R., S. ISHIKAWA, K. R. FITCH, L. FEUK, G. H. PERRY et al., 2006 Global variation in copy number in the human genome. Nature 444: 444-453.
54. ROBERTS, P. A., and D. J. BRODERICK, 1982 Properties and evolutionary potential of newly induced tandem duplications in Drosophila melanogaster. Genetics 102: 75-89.
55. RUBIN, G. M., M. D. YANDELL, J. R. WORTMAN, G. L. G. MIKLOS, C. R. NELSON et al., 2000 Comparative genomics of the eukaryotes. Science 287: 2204-2215.
56. SEBAT, J., B. LAKSHMI, J. TROGE, J. ALEXANDER, J. YOUNG et al., 2004 Large-scale copy number polymorphism in the human genome. Science 305: 525-528.
57. SEBAT, J., B. LAKSMI, D. MALHOTRA, J. TROGE, C. LESE-MARTIN et al., 2007 Strong association of de novo copy number mutations with autism. Science 316: 445-449.
58. SHARP, A. J., D. P. LOCKE, S. D. MCGRATH, J. A. BAILEY, R. U. VALLENTE et al., 2005 Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet. 77: 78-88.
59. SHARP, A. J., S. HANSEN, R. R. SELZER, Z. CHENG, R. REGAN et al., 2006 Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat. Genet. 38: 1038-1042.
60. TAJIMA, F., 1983 Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460.
61. TAJIMA, F., 1989 Statistical-method for testing the neutral mutation hypothesis by dna polymorphism. Genetics 123: 585-595.
62. TAJIMA, F., 1990 Relationship between DNA polymorphism and fixation time. Genetics 125: 447-454.
63. TAKANO, T., S. KUSAKABE, A. KOGAAND T. MUKAI, 1989 Polymorphism for the number of tandemly multiplicated glycerol-3-phosphate dehydrogenase genes in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 86: 5000-5004.
64. TESHIMA, K. M., and H. INNAN, 2004 The effect of gene conversion on the divergence between duplicated genes. Genetics 166: 1553-1560.
65. TESHIMA, K. M., and M. PRZEWORSKI, 2006 Directional positive selection on an allele of arbitrary dominance. Genetics 172: 713-718.
66. TESHIMA, K. M., G. COOP and M. PRZEWORSKI, 2006 How reliable are empirical genome scans for selective sweeps? Genome Res. 16: 702-712.
67. ++ class library for evolutionary genetic analysis. Bioinformatics 19: 2325-2327.
68. THORNTON, K., and M. LONG, 2002 Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome. Mol. Biol. Evolution, 19:918-925.
69. THORNTON, K., and M. LONG, 2005 Excess of amino acid substitutions relative to polymorphism between X-linked duplications in Drosophila melanogaster. Mol. Biol. Evol. 22: 273-284.
70. WANG, W., J. M. ZHANG, C. ALVAREZ, A. LLOPART and M. LONG, 2000 The origin of the jingwei gene and the complex modular structure of its parental gene, yellow emperor, in Drosophila melanogaster. Mol. Biol. Evol. 17: 1294-1301.
71. WANG, W., F. G. BRUNET, E. NEVO and M. LONG, 2002 Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 99: 4448-4453.
72. WANG, W., H. YU and M. LONG, 2004 Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species. Nat. Genet. 5: 523-537.
73. WATTERSON, G. A., 1975 On the number of segregating sites in genetic models without recombination. Theor. Popul. Biol. 7: 256-276.
74. WIUF, C., and J. HEIN, 2000 The coalescent with gene conversion. Genetics 155: 451-462.