Identifying concerted evolution and gene conversion in mammalian gene pairs lasting over 100 million years

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Carson, Andrew R ^a,b   Scherer, Stephen W ^a,b  

^a HOSPITAL FOR SICK CHILDREN   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BONE MORPHOGENETIC PROTEIN; BONE MORPHOGENETIC PROTEIN 8A; BONE MORPHOGENETIC PROTEIN 8B; RETINOIC ACID; RETINOIC ACID INDUCIBLE PROTEIN 19A; RETINOIC ACID INDUCIBLE PROTEIN 19B; TUBULIN; TUBULIN GAMMA; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; GENE CONVERSION; GENE DUPLICATION; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; ANIMAL; GENETIC ASSOCIATION; GENETIC SELECTION; GENETICS; HUMAN GENOME; INTRON; MAMMAL; MULTIGENE FAMILY;

EUTHERIA; MAMMALIA;

ANIMALS; EVOLUTION, MOLECULAR; GENE CONVERSION; GENE DUPLICATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INTRONS; MAMMALS; MULTIGENE FAMILY; PHYLOGENY; SELECTION (GENETICS);

EID: 68249104609     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-156     Document Type: Article

References (59)

1. Evolution by Gene Duplication. S Ohno, New York: Springer 1970
2. The Neutral Theory of Molecular Evolution. M Kimura, Cambridge, UK: Cambridge University Press 1983
3. Molecular Evolutionary Genetics. M Nei, New York: Columbia University Press 1987
4. Positive and negative selection on the human genome. JC Fay GJ Wyckoff CI Wu, Genetics 2001 158 3 1227 1234 11454770
5. Simulating Evolution by Gene Duplication. T Ohta, Genetics 1987 115 1 207 213 3557113
6. Preservation of Duplicate Genes by Complementary, Degenerative Mutations. A Force MF Lynch B Pickett A Amores Y-l Yan J Postlethwait, Genetics 1999 151 4 1531 1545 10101175
7. The Probability of Duplicate Gene Preservation by Subfunctionalization. M Lynch A Force, Genetics 2000 154 1 459 473 10629003
8. Evolution and Variation of Multigene Families. T Ohta, New York: Springer-Verlag 1980
9. Molecular Evolution. W-H Li, Sunderland, MA: Sinauer Assocs 1999
10. Population-genetic models of the fates of duplicate genes. B Walsh, Genetica 2003 118 2-3 279 294 10.1023/A:1024194802441 12868616 (Pubitemid 36821056)
11. Estimating the time to the whole-genome duplication and the duration of concerted evolution via gene conversion in yeast. RP Sugino H Innan, Genetics 2005 171 1 63 69 15972458 10.1534/genetics.105.043869 (Pubitemid 41437539)
12. Sequence-dependent gene conversion: can duplicated genes diverge fast enough to escape conversion? JB Walsh, Genetics 1987 117 3 543 557 3692140
13. Gene conversion may aid adaptive peak shifts. TF Hansen AJ Carter CH Chiu, J Theor Biol 2000 207 4 495 511 10.1006/jtbi.2000.2189 11093835
14. Role of diversifying selection and gene conversion in evolution of major histocompatibility complex loci. T Ohta, Proc Natl Acad Sci USA 1991 88 15 6716 6720 1862096 10.1073/pnas.88.15.6716
15. Reciprocal and nonreciprocal recombination at the glucocerebrosidase gene region: implications for complexity in Gaucher disease. N Tayebi BK Stubblefield JK Park E Orvisky JM Walker ME LaMarca E Sidransky, Am J Hum Genet 2003 72 3 519 534 12587096 10.1086/367850 (Pubitemid 36255951)
16. Mutations in SBDS are associated with Shwachman-Diamond syndrome. GR Boocock JA Morrison M Popovic N Richards L Ellis PR Durie JM Rommens, Nat Genet 2003 33 1 97 101 10.1038/ng1062 12496757 (Pubitemid 36068690)
17. Gene duplication and gene conversion in the Caenorhabditis elegans genome. C Semple KH Wolfe, J Mol Evol 1999 48 5 555 564 10.1007/PL00006498 10198121 (Pubitemid 29211430)
18. Characterization of the gene conversions between the multigene family members of the yeast genome. G Drouin, J Mol Evol 2002 55 1 14 23 10.1007/s00239-001-0085-y 12165839 (Pubitemid 34634356)
19. Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Genome-wide search of gene conversions in duplicated genes of mouse and rat. K Ezawa OO S N Saitou, Mol Biol Evol 2006 23 5 927 940 10.1093/molbev/msj093 16407460 (Pubitemid 43739266)
20. The effect of gene conversion on the divergence between duplicated genes. KM Teshima H Innan, Genetics 2004 166 3 1553 1560 15082568 10.1534/genetics. 166.3.1553 (Pubitemid 38507068)
21. Mosaic evolution of ruminant stomach lysozyme genes. Y Wen DM Irwin, Mol Phylogenet Evol 1999 13 3 474 482 10.1006/mpev.1999.0651 10620405 (Pubitemid 129499354)
22. Orthologs, paralogs and genome comparisons. JP Gogarten L Olendzenski, Curr Opin Genet Dev 1999 9 6 630 636 10.1016/S0959-437X(99)00029-5 10607614
23. Gene conversion drives GC content evolution in mammalian histones. N Galtier, Trends Genet 2003 19 2 65 68 10.1016/S0168-9525(02)00002-1 12547511 (Pubitemid 36120659)
24. Biased gene conversion: implications for genome and sex evolution. G Marais, Trends Genet 2003 19 6 330 338 10.1016/S0168-9525(03)00116-1 12801726 (Pubitemid 36694616)
25. GC-content evolution in mammalian genomes: the biased gene conversion hypothesis. N Galtier G Piganeau D Mouchiroud L Duret, Genetics 2001 159 2 907 911 11693127
26. Efficient repair of all types of single-base mismatches in recombination intermediates in Chinese hamster ovary cells. Competition between long-patch and G-T glycosylase-mediated repair of G-T mismatches. CA Bill WA Duran NR Miselis JA Nickoloff, Genetics 1998 149 4 1935 1943 9691048
27. Ectopic gene conversions in bacterial genomes. RT Morris G Drouin, Genome 2007 50 11 975 984 10.1139/G07-076 18059543
28. Gene conversion in the rice genome. S Xu T Clark H Zheng S Vang R Li GK Wong J Wang X Zheng, BMC Genomics 2008 9 93 18298833 10.1186/1471-2164-9-93
29. Duplication and gene conversion in the Drosophila melanogaster genome. N Osada H Innan, PLoS Genet 2008 4 12 e1000305 19079581 10.1371/journal.pgen. 1000305
30. Ectopic gene conversions in the human genome. D Benovoy G Drouin, Genomics 2009 93 1 27 32 10.1016/j.ygeno.2008.09.007 18848875
31. Gene conversion limits divergence of mammalian TLR1 and TLR6. EK Kruithof N Satta JW Liu S Dunoyer-Geindre RJ Fish, BMC Evol Biol 2007 7 148 17727694 10.1186/1471-2148-7-148 (Pubitemid 350119679)
32. An unusual mode of concerted evolution of the EGF-TM7 receptor chimera EMR2. MJ Kwakkenbos M Matmati O Madsen W Pouwels Y Wang RE Bontrop PJ Heidt RM Hoek J Hamann, Faseb J 2006 20 14 2582 2584 10.1096/fj.06-6500fje 17068111 (Pubitemid 44953787)
33. Gene conversion between mammalian CCR2 and CCR5 chemokine receptor genes: a potential mechanism for receptor dimerization. N Vazquez-Salat N Yuhki T Beck SJ O'Brien WJ Murphy, Genomics 2007 90 2 213 224 10.1016/j.ygeno.2007.04.009 17544254 (Pubitemid 47030810)
34. Gene structure and evolution of testicular haploid germ cell-specific genes, Oxct2a and Oxct2b. M Onishi T Yasunaga H Tanaka Y Nishimune M Nozaki, Genomics 2004 83 4 647 657 10.1016/j.ygeno.2003.09.018 15028287 (Pubitemid 38340806)
35. Signal transduction by bone morphogenetic proteins. M Kawabata T Imamura K Miyazono, Cytokine Growth Factor Rev 1998 9 1 49 61 10.1016/S1359-6101(97) 00036-1 9720756 (Pubitemid 28280536)
36. Bone morphogenetic proteins. D Chen M Zhao GR Mundy, Growth Factors 2004 22 4 233 241 10.1080/08977190412331279890 15621726 (Pubitemid 40136452)
37. Evidence that mouse Bmp8a (Op2) and Bmp8b are duplicated genes that play a role in spermatogenesis and placental development. GQ Zhao BL Hogan, Mech Dev 1996 57 2 159 168 10.1016/0925-4773(96)00543-6 8843393 (Pubitemid 26252550)
38. Bone morphogenetic protein 8A plays a role in the maintenance of spermatogenesis and the integrity of the epididymis. GQ Zhao L Liaw BL Hogan, Development 1998 125 6 1103 1112 9463357
39. Dead-box proteins: a family affair-active and passive players in RNP-remodeling. P Linder, Nucleic Acids Res 2006 34 15 4168 4180 16936318 10.1093/nar/gkl468 (Pubitemid 44542196)
40. The gamma-tubulin gene family in humans. DO Wise R Krahe BR Oakley, Genomics 2000 67 2 164 170 10.1006/geno.2000.6247 10903841 (Pubitemid 30614584)
41. Gene knockout analysis of two gamma-tubulin isoforms in mice. A Yuba-Kubo A Kubo M Hata S Tsukita, Dev Biol 2005 282 2 361 373 10.1016/j.ydbio.2005.03. 031 15893303 (Pubitemid 40799327)
42. BLAT-The BLAST-Like Alignment Tool. WJ Kent, Genome Res 2002 12 4 656 664 11932250
43. Basic local alignment search tool. SF Altshul WR Gish W Miller EW Myers DJ Lipman, J Mol Biol 1990 215 3 403 410 2231712
44. A molecular timescale for vertebrate evolution. S Kumar SB Hedges, Nature 1998 392 6679 917 920 10.1038/31927 9582070 (Pubitemid 28232061)
45. GENECONV: A computer package for the statistical detection of gene conversion. SA Sawyer, Distributed by the author, Department of Mathematics, Washington University in St Louis 1999 http://www.math.wustl.edu/∼sawyer/ geneconv/
46. Bone morphogenetic protein receptors. H Yamashita P Ten Dijke CH Heldin K Miyazono, Bone 1996 19 6 569 574 10.1016/S8756-3282(96)00259-1 8968021 (Pubitemid 27035834)
47. Bone morphogenetic proteins: multifunctional regulators of vertebrate development. BL Hogan, Genes Dev 1996 10 13 1580 1594 10.1101/gad.10.13.1580 8682290
48. Efficient expression of a heterodimer of bone morphogenetic protein subunits using a baculovirus expression system. M Hazama A Aono N Ueno Y Fujisawa, Biochem Biophys Res Commun 1995 209 3 859 866 10.1006/bbrc.1995.1578 7733977
49. NCBI's Entrez database. http://www.ncbi.nlm.nih.gov/Entrez
50. A greedy algorithm for aligning DNA sequences. Z Zhang S Schwartz L Wagner W Miller, J Comput Biol 2000 7 1-2 203 214 10.1089/10665270050081478 10890397 (Pubitemid 30412170)
51. UCSC genome browser. http://genome.ucsc.edu/
52. VISTA: visualizing global DNA sequence alignments of arbitrary length. C Mayor M Brudno JR Schwartz A Poliakov EM Rubin KA Frazer LS Pachter I Dubchak, Bioinformatics 2000 16 11 1046 1047 10.1093/bioinformatics/16.11.1046 11159318
53. VISTA: computational tools for comparative genomics. KA Frazer L Pachter A Poliakov EM Rubin I Dubchak, Nucleic Acids Res 2004 32 Web Server W273 279 15215394 10.1093/nar/gkh458 (Pubitemid 38997343)
54. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. S Kumar K Tamura M Nei, Brief Bioinform 2004 5 2 150 163 10.1093/bib/5.2.150 15260895
55. PAUP*:Phylogenetic Analysis Using Parsimony (*and other methods), Version 4.0b10. D Swofford, Sunderland, Massachusetts.: Sinauer Associates 2003 18428704
56. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucleic Acids Res 1994 22 22 4673 4680 7984417 10.1093/nar/22.22.4673
57. Inferring evolutionary trees with PAUP*. JC Wilgenbusch D Swofford, Curr Protoc Bioinformatics 2003 Chapter 6 Unit 6 4 18428704
58. MODELTEST: testing the model of DNA substitution. D Posada KA Crandall, Bioinformatics 1998 14 9 817 818 10.1093/bioinformatics/14.9.817 9918953
59. The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. M Brudno R Steinkamp B Morgenstern, Nucleic Acids Res 2004 32 Web Server W41 44 15215346 10.1093/nar/gkh361 (Pubitemid 38997296)