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For: Malcom CM, Wyckoff GJ, Lahn BT. Genic mutation rates in mammals: local similarity, chromosomal heterogeneity, and X-versus-autosome disparity. Mol Biol Evol 2003;20:1633-41. [PMID: 12885971 DOI: 10.1093/molbev/msg178] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Munasinghe M, Haller BC, Clark AG. Migration restores hybrid incompatibility driven by mitochondrial-nuclear sexual conflict. Proc Biol Sci 2022;289:20212561. [PMID: 35078356 PMCID: PMC8790342 DOI: 10.1098/rspb.2021.2561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
2
Krasovec M, Chester M, Ridout K, Filatov DA. The Mutation Rate and the Age of the Sex Chromosomes in Silene latifolia. Curr Biol 2018;28:1832-1838.e4. [PMID: 29804812 DOI: 10.1016/j.cub.2018.04.069] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/12/2018] [Accepted: 04/19/2018] [Indexed: 12/15/2022]
3
Link V, Aguilar-Gómez D, Ramírez-Suástegui C, Hurst LD, Cortez D. Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals. Genome Biol Evol 2018;9:2198-2210. [PMID: 28922870 PMCID: PMC5604096 DOI: 10.1093/gbe/evx155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 12/12/2022]  Open
4
Mendes FK, Hahn MW. Gene Tree Discordance Causes Apparent Substitution Rate Variation. Syst Biol 2016;65:711-21. [DOI: 10.1093/sysbio/syw018] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/23/2016] [Indexed: 01/01/2023]  Open
5
Zhu A, Guo W, Jain K, Mower JP. Unprecedented Heterogeneity in the Synonymous Substitution Rate within a Plant Genome. Mol Biol Evol 2014;31:1228-36. [DOI: 10.1093/molbev/msu079] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
6
Jäger N, Schlesner M, Jones DTW, Raffel S, Mallm JP, Junge KM, Weichenhan D, Bauer T, Ishaque N, Kool M, Northcott PA, Korshunov A, Drews RM, Koster J, Versteeg R, Richter J, Hummel M, Mack SC, Taylor MD, Witt H, Swartman B, Schulte-Bockholt D, Sultan M, Yaspo ML, Lehrach H, Hutter B, Brors B, Wolf S, Plass C, Siebert R, Trumpp A, Rippe K, Lehmann I, Lichter P, Pfister SM, Eils R. Hypermutation of the inactive X chromosome is a frequent event in cancer. Cell 2013;155:567-81. [PMID: 24139898 PMCID: PMC3898475 DOI: 10.1016/j.cell.2013.09.042] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 08/02/2013] [Accepted: 09/20/2013] [Indexed: 11/26/2022]
7
Johnson NA, Lachance J. The genetics of sex chromosomes: evolution and implications for hybrid incompatibility. Ann N Y Acad Sci 2012;1256:E1-22. [PMID: 23025408 PMCID: PMC3509754 DOI: 10.1111/j.1749-6632.2012.06748.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
8
Frenkel S, Kirzhner V, Korol A. Organizational heterogeneity of vertebrate genomes. PLoS One 2012;7:e32076. [PMID: 22384143 PMCID: PMC3288070 DOI: 10.1371/journal.pone.0032076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 01/23/2012] [Indexed: 01/06/2023]  Open
9
Variation in the mutation rate across mammalian genomes. Nat Rev Genet 2011;12:756-66. [PMID: 21969038 DOI: 10.1038/nrg3098] [Citation(s) in RCA: 303] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
10
Late replicating domains are highly recombining in females but have low male recombination rates: implications for isochore evolution. PLoS One 2011;6:e24480. [PMID: 21949720 PMCID: PMC3176772 DOI: 10.1371/journal.pone.0024480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 08/11/2011] [Indexed: 01/01/2023]  Open
11
Wilson Sayres MA, Venditti C, Pagel M, Makova KD. Do variations in substitution rates and male mutation bias correlate with life-history traits? A study of 32 mammalian genomes. Evolution 2011;65:2800-15. [PMID: 21967423 DOI: 10.1111/j.1558-5646.2011.01337.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
12
Mulugeta Achame E, Baarends WM, Gribnau J, Grootegoed JA. Evaluating the relationship between spermatogenic silencing of the X chromosome and evolution of the Y chromosome in chimpanzee and human. PLoS One 2010;5:e15598. [PMID: 21179482 PMCID: PMC3001880 DOI: 10.1371/journal.pone.0015598] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 11/12/2010] [Indexed: 02/06/2023]  Open
13
Cotton S, Wedekind C. Male mutation bias and possible long-term effects of human activities. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2010;24:1190-1197. [PMID: 20507353 DOI: 10.1111/j.1523-1739.2010.01524.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
14
Pink CJ, Hurst LD. Timing of replication is a determinant of neutral substitution rates but does not explain slow Y chromosome evolution in rodents. Mol Biol Evol 2009;27:1077-86. [PMID: 20026481 DOI: 10.1093/molbev/msp314] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
15
Pink CJ, Swaminathan SK, Dunham I, Rogers J, Ward A, Hurst LD. Evidence that replication-associated mutation alone does not explain between-chromosome differences in substitution rates. Genome Biol Evol 2009;1:13-22. [PMID: 20333173 PMCID: PMC2817397 DOI: 10.1093/gbe/evp001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2009] [Indexed: 12/12/2022]  Open
16
Fox AK, Tuch BB, Chuang JH. Measuring the prevalence of regional mutation rates: an analysis of silent substitutions in mammals, fungi, and insects. BMC Evol Biol 2008;8:186. [PMID: 18588686 PMCID: PMC2447844 DOI: 10.1186/1471-2148-8-186] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 06/27/2008] [Indexed: 12/22/2022]  Open
17
Walser JC, Ponger L, Furano AV. CpG dinucleotides and the mutation rate of non-CpG DNA. Genome Res 2008;18:1403-14. [PMID: 18550801 DOI: 10.1101/gr.076455.108] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
18
Tyekucheva S, Makova KD, Karro JE, Hardison RC, Miller W, Chiaromonte F. Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biol 2008;9:R76. [PMID: 18447906 PMCID: PMC2643947 DOI: 10.1186/gb-2008-9-4-r76] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 04/04/2008] [Accepted: 04/30/2008] [Indexed: 11/10/2022]  Open
19
Ellegren H. Characteristics, causes and evolutionary consequences of male-biased mutation. Proc Biol Sci 2007;274:1-10. [PMID: 17134994 PMCID: PMC1679872 DOI: 10.1098/rspb.2006.3720] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
20
Baines JF, Harr B. Reduced X-linked diversity in derived populations of house mice. Genetics 2007;175:1911-21. [PMID: 17287527 PMCID: PMC1855135 DOI: 10.1534/genetics.106.069419] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
21
Popesco MC, Maclaren EJ, Hopkins J, Dumas L, Cox M, Meltesen L, McGavran L, Wyckoff GJ, Sikela JM. Human lineage-specific amplification, selection, and neuronal expression of DUF1220 domains. Science 2006;313:1304-7. [PMID: 16946073 DOI: 10.1126/science.1127980] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
22
Vallender EJ, Paschall JE, Malcom CM, Lahn BT, Wyckoff GJ. SPEED: a molecular-evolution-based database of mammalian orthologous groups. Bioinformatics 2006;22:2835-7. [PMID: 16966361 DOI: 10.1093/bioinformatics/btl471] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
23
Vicoso B, Charlesworth B. Evolution on the X chromosome: unusual patterns and processes. Nat Rev Genet 2006;7:645-53. [PMID: 16847464 DOI: 10.1038/nrg1914] [Citation(s) in RCA: 358] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
24
Liao BY, Scott NM, Zhang J. Impacts of Gene Essentiality, Expression Pattern, and Gene Compactness on the Evolutionary Rate of Mammalian Proteins. Mol Biol Evol 2006;23:2072-80. [PMID: 16887903 DOI: 10.1093/molbev/msl076] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
25
Ohno M, Miura T, Furuichi M, Tominaga Y, Tsuchimoto D, Sakumi K, Nakabeppu Y. A genome-wide distribution of 8-oxoguanine correlates with the preferred regions for recombination and single nucleotide polymorphism in the human genome. Genome Res 2006;16:567-75. [PMID: 16651663 PMCID: PMC1457041 DOI: 10.1101/gr.4769606] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
26
Svensson O, Arvestad L, Lagergren J. Genome-wide survey for biologically functional pseudogenes. PLoS Comput Biol 2006;2:e46. [PMID: 16680195 PMCID: PMC1456316 DOI: 10.1371/journal.pcbi.0020046] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Accepted: 03/23/2006] [Indexed: 11/20/2022]  Open
27
Thornton K, Bachtrog D, Andolfatto P. X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution. Genes Dev 2006;16:498-504. [PMID: 16520459 PMCID: PMC1457026 DOI: 10.1101/gr.4447906] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 12/21/2005] [Indexed: 01/07/2023]
28
Li T, Chamberlin SG, Caraco MD, Liberles DA, Gaucher EA, Benner SA. Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics. BMC Evol Biol 2006;6:25. [PMID: 16545144 PMCID: PMC1435776 DOI: 10.1186/1471-2148-6-25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 03/20/2006] [Indexed: 11/10/2022]  Open
29
Berlin S, Brandström M, Backström N, Axelsson E, Smith NGC, Ellegren H. Substitution Rate Heterogeneity and the Male Mutation Bias. J Mol Evol 2006;62:226-33. [PMID: 16474985 DOI: 10.1007/s00239-005-0103-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Accepted: 10/18/2005] [Indexed: 10/25/2022]
30
Taylor J, Tyekucheva S, Zody M, Chiaromonte F, Makova KD. Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison. Mol Biol Evol 2005;23:565-73. [PMID: 16280537 DOI: 10.1093/molbev/msj060] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
31
Marques-Bonet T, Navarro A. Chromosomal rearrangements are associated with higher rates of molecular evolution in mammals. Gene 2005;353:147-54. [PMID: 15951139 DOI: 10.1016/j.gene.2005.05.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Revised: 04/25/2005] [Accepted: 05/10/2005] [Indexed: 10/25/2022]
32
Hellmann I, Prüfer K, Ji H, Zody MC, Pääbo S, Ptak SE. Why do human diversity levels vary at a megabase scale? Genome Res 2005;15:1222-31. [PMID: 16140990 PMCID: PMC1199536 DOI: 10.1101/gr.3461105] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Accepted: 02/26/2005] [Indexed: 01/14/2023]
33
Gaffney DJ, Keightley PD. The scale of mutational variation in the murid genome. Genome Res 2005;15:1086-94. [PMID: 16024822 PMCID: PMC1182221 DOI: 10.1101/gr.3895005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
34
Sandstedt SA, Tucker PK. Male-driven evolution in closely related species of the mouse genus Mus. J Mol Evol 2005;61:138-44. [PMID: 16007492 DOI: 10.1007/s00239-004-0279-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2004] [Accepted: 03/10/2005] [Indexed: 10/25/2022]
35
Wakefield MJ, Maxwell P, Huttley GA. Vestige: maximum likelihood phylogenetic footprinting. BMC Bioinformatics 2005;6:130. [PMID: 15921531 PMCID: PMC1156870 DOI: 10.1186/1471-2105-6-130] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2005] [Accepted: 05/29/2005] [Indexed: 11/24/2022]  Open
36
Sheldahl LA, Weinreich DM, Rand DM. Recombination, dominance and selection on amino acid polymorphism in the Drosophila genome: contrasting patterns on the X and fourth chromosomes. Genetics 2004;165:1195-208. [PMID: 14668375 PMCID: PMC1462837 DOI: 10.1093/genetics/165.3.1195] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
37
Vallender EJ, Lahn BT. Effects of chromosomal rearrangements on human-chimpanzee molecular evolution. Genomics 2004;84:757-61. [PMID: 15475253 DOI: 10.1016/j.ygeno.2004.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2004] [Accepted: 07/12/2004] [Indexed: 11/24/2022]
38
Lercher MJ, Chamary JV, Hurst LD. Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. Genome Res 2004;14:1002-13. [PMID: 15173108 PMCID: PMC419778 DOI: 10.1101/gr.1597404] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
39
Axelsson E, Smith NGC, Sundström H, Berlin S, Ellegren H. Male-biased mutation rate and divergence in autosomal, z-linked and w-linked introns of chicken and Turkey. Mol Biol Evol 2004;21:1538-47. [PMID: 15140948 DOI: 10.1093/molbev/msh157] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
40
Makova KD, Yang S, Chiaromonte F. Insertions and deletions are male biased too: a whole-genome analysis in rodents. Genome Res 2004;14:567-73. [PMID: 15059997 PMCID: PMC383300 DOI: 10.1101/gr.1971104] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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