Gene copy-number polymorphism in nature

Proceedings of the Royal Society B: Biological Sciences

Volumn 277, Issue 1698, 2010, Pages 3213-3221

  Schrider, Daniel R ^a   Hahn, Matthew W ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

Copy number variation; Drosophila; Duplication; Humans; Natural selection; Paralogue

Indexed keywords

ADAPTATION; FLY; GENE EXPRESSION; GENETIC ANALYSIS; HOMINID; HOMOLOGY; MOLECULAR ANALYSIS; NATURAL SELECTION; PHENOTYPIC PLASTICITY; POLYMORPHISM; PROTEIN;

EID: 77958130354     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2010.1180     Document Type: Review

References (57)

1. Bailey, J. A., Gu, Z. P., Clark, R. A., Reinert, K., Samonte, R. V., Schwartz, S., Adams, M. D., Myers, E. W., Li, P. W. & Eichler, E. E. 2002 Recent segmental duplications in the human genome. Science 297, 1003-1007. (doi:10.1126/science.1072047)
2. Begun, D. J. et al. 2007 Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol. 5, e310. (doi:10.1371/journal.pbio.0050310)
3. Burbano, H. A. et al. 2010 Targeted investigation of the Neandertal genome by array-based sequence capture. Science 328, 723-725. (doi:10.1126/science.1188046)
4. Cardoso-Moreira, M. M. & Long, M. 2010 Mutational bias shaping fly copy number variation: implications for genome evolution. Trends Genet. 26, 243-247. (doi:10.1016/j.tig.2010.03.002)
5. Carreto, L., Eiriz, M. F., Gomes, A. C., Pereira, P. M., Schuller, D. & Santos, M. A. S. 2008 Comparative geno-mics of wild type yeast strains unveils important genome diversity. BMC Genomics 9, 17.
6. Chen, W. K., Swartz, J. D., Rush, L. J. & Alvarez, C. E. 2009 Mapping DNA structural variation in dogs. Genome Res. 19, 500-509. (doi:10.1101/gr. 083741.108)
7. Conrad, D. F., Andrews, T. D., Carter, N. P., Hurles, M. E. & Pritchard, J. K. 2006 A high-resolution survey of deletion polymorphism in the human genome. Nat. Genet. 38, 75-81. (doi:10.1038/ng1697)
8. Conrad, D. F. et al. 2010 Origins and functional impact of copy number variation in the human genome. Nature 464, 704-712. (doi:10.1038/nature08516)
9. Demuth, J. P., De Bie, T., Stajich, J. E., Cristianini, N. & Hahn, M. W. 2006 The evolution of mammalian gene families. PLoS ONE 1, e85. (doi:10.1371/journal.pone. 0000085)
10. Dopman, E. B. & Hartl, D. L. 2007 A portrait of copy-number polymorphism in Drosophila melanogaster. Proc. Natl Acad. Sci. USA 104, 19 920-19 925. (doi:10.1073/pnas.0709888104)
11. Eichler, E. E. 2001 Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends Genet. 17, 661-669. (doi:10.1016/S0168- 9525(01)02492-1)
12. Emerson, J. J., Cardoso-Moreira, M., Borevitz, J. O. & Long, M. 2008 Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster. Science 320, 1629-1631. (doi:10.1126/science.1158078)
13. Eyre-Walker, A. & Keightley, P. D. 2007 The distribution of fitness effects of new mutations. Nat. Rev. Genet. 8, 610-618. (doi:10.1038/nrg2146)
14. Graubert, T. A. et al. 2007 A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet. 3, e3. (doi:10.1371/journal. pgen.0030003)
15. Griffin, D. et al. 2008 Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution. BMC Genomics 9, 168. (doi:10. 1186/1471-2164-9-168)
16. Gu, Z. L., Cavalcanti, A., Chen, F. C., Bouman, P. & Li, W. H. 2002 Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol. Biol. Evol. 19, 256-262.
17. Hahn, M. W. 2009 Distinguishing among evolutionary models for the maintenance of gene duplicates. J. Hered. 100, 605-617. (doi:10.1093/jhered/ esp047)
18. Hahn, M. W., Demuth, J. P. & Han, S. G. 2007a Accelerated rate of gene gain and loss in primates. Genetics 177, 1941-1949. (doi:10.1534/genetics. 107.080077)
19. Hahn, M. W., Han, M. V. & Han, S. G. 2007b Gene family evolution across 12 Drosophila genomes. PLoS Genet. 3, e197. (doi:10.1371/journal.pgen. 0030197)
20. Hastings, P. J., Lupski, J. R., Rosenberg, S. M. & Ira, G. 2009 Mechanisms of change in gene copy number. Nat. Rev. Genet. 10, 551-564. (doi:10.1038/nrg2593)
21. Hudson, R. R., Kreitman, M. & Aguade, M. 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153-159.
22. Itsara, A. et al. 2009 Population analysis of large copy number variants and hotspots of human genetic disease. Am. J. Hum. Genet. 84, 148-161. (doi:10.1016/j.ajhg.2008.12.014)
23. Kidd, J. M. et al. 2008 Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56-64. (doi:10.1038/nature06862)
24. Korbel, J. O. et al. 2007 Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420-426. (doi:10.1126/science. 1149504)
25. Lee, A. S., Gutierrez-Arcelus, M., Perry, G. H., Vallender, E. J., Johnson, W. E., Miller, G. M., Korbel, J. O. & Lee, C. 2008 Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies. Hum. Mol. Genet. 17, 1127-1136. (doi:10.1093/hmg/ddn002)
26. Liu, G. E. et al. 2010 Analysis of copy number variations among diverse cattle breeds. Genome Res. 20, 693-703. (doi:10.1101/gr.105403.110)
27. Locke, D. P. 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. (doi:10.1086/505653)
28. Lynch, M. & Conery, J. S. 2000 The evolutionary fate and consequences of duplicate genes. Science 290, 1151-1155. (doi:10.1126/science.290.5494.1151)
29. Maydan, J. S., Lorch, A., Edgley, M. L., Flibotte, S. & Moerman, D. G. 2010 Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans. BMC Genomics 11, 12.
30. McCarroll, S. A. et al. 2006 Common deletion polymorphisms in the human genome. Nat. Genet. 38, 86-92. (doi:10.1038/ng1696)
31. McCarroll, S. A. et al. 2008 Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet. 40, 1166-1174. (doi:10.1038/ng. 238)
32. McDonald, J. H. & Kreitman, M. 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351, 652-654. (doi:10.1038/351652a0)
33. McGrath, C. L., Casola, C. & Hahn, M. W. 2009 Minimal effect of ectopic gene conversion among recent duplicates in four mammalian genomes. Genetics 182, 615-622. (doi:10.1534/genetics.109.101428)
34. Meisel, R. P., Han, M. V. & Hahn, M. W. 2009 A complex suite of forces drives gene traffic from Drosophila X chromosomes. Genome Biol. Evol. 2009, 176-188.
35. Menashe, I., Man, O., Lancet, D. & Gilad, Y. 2003 Different noses for different people. Nat. Genet. 34, 143-144. (doi:10.1038/ng1160)
36. Mikkelsen, T. S., Hillier, L. W., Eichler, E. E., Zody, M. C., Jaffe, D. B., Yang, S. P. et al. 2005 Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69-87. (doi:10.1038/nature04072)
37. Newman, T. L., Tuzun, E., Morrison, V. A., Hayden, K. E., Ventura, M., McGrath, S. D., Rocchi, M. & Eichler, E. E. 2005 A genome-wide survey of structural variation between human and chimpanzee. Genome Res. 15, 1344-1356. (doi:10.1101/gr.4338005)
38. Nicholas, T. J., Cheng, Z., Ventura, M., Mealey, K., Eichler, E. E. & Akey, J. M. 2009 The genomic architecture of segmental duplications and associated copy number variants in dogs. Genome Res. 19, 491-499. (doi:10. 1101/gr.084715.108)
39. Ossowski, S., Schneeberger, K., Clark, R. M., Lanz, C., Warthmann, N. & Weigel, D. 2008 Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res. 18, 2024-2033. (doi:10.1101/gr.080200.108)
40. Perry, G. H. et al. 2006 Hotspots for copy number variation in chimpanzees and humans. Proc. Natl Acad. Sci. USA 103, 8006-8011. (doi:10.1073/pnas.0602318103)
41. Perry, G. H. et al. 2007 Diet and the evolution of human amylase gene copy number variation. Nat. Genet. 39, 1256-1260. (doi:10.1038/ng2123)
42. Perry, G. H. et al. 2008 Copy number variation and evolution in humans and chimpanzees. Genome Res. 18, 1698-1710. (doi:10.1101/gr.082016.108)
43. Redon, R. et al. 2006 Global variation in copy number in the human genome. Nature 444, 444-454. (doi:10.1038/nature05329)
44. Sabeti, P. C. et al. 2002 Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832-837. (doi:10.1038/ nature01140)
45. Schrider, D. R. & Hahn, M. W. 2010 Lower linkage disequilibrium at CNVs is due to both recurrent mutation and transposing duplications. Mol. Biol. Evol. 27, 103-111. (doi:10.1093/molbev/msp210)
46. Schuster-Bockler, B., Conrad, D. & Bateman, A. 2010 Dosage sensitivity shapes the evolution of copy-number varied regions. PLoS ONE 5, e9474. (doi:10.1371/journal.pone.0009474)
47. Sebat, J. et al. 2004 Large-scale copy number polymorphism in the human genome. Science 305, 525-528. (doi:10. 1126/science.1098918)
48. She, X. W., Cheng, Z., Zollner, S., Church, D. M. & Eichler, E. E. 2008 Mouse segmental duplication and copy number variation. Nat. Genet. 40, 909-914. (doi:10. 1038/ng.172)
49. Springer, N. M. et al. 2009 Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet. 5, e1000734. (doi:10.1371/journal.pgen.1000734)
50. Stajich, J. E. & Hahn, M. W. 2005 Disentangling the effects of demography and selection in human history. Mol. Biol. Evol. 22, 63-73. (doi:10.1093/molbev/msh252)
51. Stranger, B. E. et al. 2007 Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315, 848-853. (doi:10.1126/science.1136678)
52. Turner, D. J., Miretti, M., Rajan, D., Fiegler, H., Carter, N. P., Blayney, M. L., Beck, S. & Hurles, M. E. 2008a Germline rates of de novo meiotic deletions and duplications causing several genomic disorders. Nat. Genet. 40, 90-95. (doi:10.1038/ng.2007.40)
53. Turner, T. L., Levine, M. T., Eckert, M. L. & Begun, D. J. 2008b Genomic analysis of adaptive differentiation in Drosophila melanogaster. Genetics 179, 455-473. (doi:10. 1534/genetics.107.083659)
54. Tuzun, E. et al. 2005 Fine-scale structural variation of the human genome. Nat. Genet. 37, 727-732. (doi:10.1038/ng1562)
55. Voight, B. F., Kudaravalli, S., Wen, X. Q. & Pritchard, J. K. 2006 A map of recent positive selection in the human genome. PLoS Biol. 4, e72. (doi:10.1371/journal.pbio. 0040072)
56. Xue, Y. L. et al. 2008 Adaptive evolution of UGT2B17 copy-number variation. Am. J. Hum. Genet. 83, 337-346. (doi:10.1016/j.ajhg.2008.08.004)
57. Zhang, J. 2007 The drifting human genome. Proc. Natl Acad. Sci. USA 104, 20147-20148. (doi:10.1073/pnas. 0710524105)