Dynamics of gene duplication and transposons in microbial genomes following a sudden environmental change

References

• Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nat Rev Genet 2009; 10:551 - 564; http://dx.doi.org/10.1038/nrg2593;:19597530
   PubMed Web of Science ®Google Scholar
• Bergthorsson U, Andersson DI, Roth JR. Ohno's dilemma: Evolution of new genes under continuous selection. Proc Natl Acad Sci USA 2007; 104:17004 - 17009; http://dx.doi.org/10.1073/pnas.0707158104;PMID:17942681
   PubMed Web of Science ®Google Scholar
• Ohno S. Evolution by gene duplication 1970; London George Alien & Unwin Ltd Berlin, Heidelberg and New York: Springer-Verlag
   Google Scholar
• Chen FC, Chen CJ, Li WH, Chuang TJ. Gene family size conservation is a good indicator of evolutionary rates. Mol Biol Evol 2010; 27:1750; PMID: 20194423; http://dx.doi.org/10.1093/molbev/msq055
   PubMed Web of Science ®Google Scholar
• DeLuna A, Vetsigian K, Shoresh N, Hegreness M, Colón-González M, Chao S, et al. Exposing the fitness contribution of duplicated genes. Nat Genet 2008; 40:676 - 681; PMID: 18408719; http://dx.doi.org/10.1038/ng.123
   PubMed Web of Science ®Google Scholar
• Chia N, Goldenfeld N. Dynamics of gene duplication and transposons in microbial genomes following a sudden environmental change. Phys Rev E Stat Nonlin Soft Matter Phys 2011; 83:21906; PMID: 21405862; http://dx.doi.org/10.1103/PhysRevE.83.021906
   PubMed Web of Science ®Google Scholar
• Moran NA, Plague GR. Genomic changes following host restriction in bacteria. Curr Opin Genet Dev 2004; 14:627 - 633; PMID: 15531157; http://dx.doi.org/10.1016/j.gde.2004.09.003
   PubMed Web of Science ®Google Scholar
• Plague GR, Dunbar HE, Tran PL, Moran NA. Extensive proliferation of transposable elements in heritable bacterial symbionts. J Bacteriol 2007; 1:1082 - 1087; PMID: 17981967; http://dx.doi.org/10.1128/JB.01082-07
   PubMed Web of Science ®Google Scholar
• Chia N, Goldenfeld N. Statistical mechanics of horizontal gene transfer in evolutionary ecology. J Stat Phys 2010; 1 - 15
   Google Scholar
• Reams AB, Kofoid E, Savageau M, Roth JR. Duplication frequency in a population of Salmonella enterica rapidly approaches steady state with or without recombination. Genetics 2010; 184:1077; PMID: 20083614; http://dx.doi.org/10.1534/genetics.109.111963
   PubMed Web of Science ®Google Scholar
• Parkhill J, Sebaihia M, Preston A, Murphy LD, Thomson N, Harris DE, et al. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat Genet 2003; 35:32 - 40; PMID: 12910271; http://dx.doi.org/10.1038/ng1227
   PubMed Web of Science ®Google Scholar
• Aminov RI, Mackie RI. Evolution and ecology of antibiotic resistance genes. FEMS Microbiol Lett 2007; 271:147 - 161; PMID: 17490428; http://dx.doi.org/10.1111/j.1574-6968.2007.00757.x
   PubMed Web of Science ®Google Scholar
• Shibata D. Mutation and epigenetic molecular clocks in cancer. Carcinogenesis 2011; 32:123; PMID: 21076057; http://dx.doi.org/10.1093/carcin/bgq239
   PubMed Web of Science ®Google Scholar
• Lambert G, Estévez-Salmeron L, Oh S, Liao D, Emerson BM, Tlsty TD, et al. An analogy between the evolution of drug resistance in bacterial communities and malignant tissues. Nat Rev Cancer 2011; 11:375 - 382; PMID: 21508974; http://dx.doi.org/10.1038/nrc3039
   PubMed Web of Science ®Google Scholar
• Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, et al. Tumour evolution inferred by single-cell sequencing. Nature 2011; 472:90 - 94; PMID: 21399628; http://dx.doi.org/10.1038/nature09807
   PubMed Web of Science ®Google Scholar
• Sandegren L, Andersson DI. Bacterial gene amplification: implications for the evolution of antibiotic resistance. Nat Rev Microbiol 2009; 7:578 - 588; PMID: 19609259; http://dx.doi.org/10.1038/nrmicro2174
   PubMed Web of Science ®Google Scholar
• Novick RP, Christie GE, PenadÊs JR. The phage-related chromosomal islands of Gram-positive bacteria. Nat Rev Microbiol 2010; 8:541 - 551; PMID: 20634809; http://dx.doi.org/10.1038/nrmicro2393
   PubMed Web of Science ®Google Scholar
• Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, et al. Mapping copy number variation by population-scale genome sequencing. Nature 2011; 470:59 - 65; PMID: 21293372; http://dx.doi.org/10.1038/nature09708
   PubMed Web of Science ®Google Scholar
• Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, Burleigh A, et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 2009; 461:809 - 813; PMID: 19812674; http://dx.doi.org/10.1038/nature08489
   PubMed Web of Science ®Google Scholar
• Eigen M. Molecular self-organization and the early stages of evolution. Q Rev Biophys 1971; 4:149 - 212; PMID: 5134461; http://dx.doi.org/10.1017/S0033583500000627
   PubMedGoogle Scholar
• Drake JW. A constant rate of spontaneous mutation in DNA-based microbes. Proc Natl Acad Sci USA 1991; 88:7160; PMID: 1831267; http://dx.doi.org/10.1073/pnas.88.16.7160
   PubMed Web of Science ®Google Scholar
• Lynch M. Evolution of the mutation rate. Trends Genet 2010; 26:345 - 352; PMID: 20594608; http://dx.doi.org/10.1016/j.tig.2010.05.003
   PubMed Web of Science ®Google Scholar
• Rosenberg SM. Evolving responsively: adaptive mutation. Nat Rev Genet 2001; 2:504 - 515; PMID: 11433357; http://dx.doi.org/10.1038/35080556
   PubMed Web of Science ®Google Scholar
• Earl DJ, Deem MW. Evolvability is a selectable trait. Proc Natl Acad Sci USA 2004; 101:11531; PMID: 15289608; http://dx.doi.org/10.1073/pnas.0404656101
   PubMed Web of Science ®Google Scholar
• Perry GH, Tchinda J, McGrath SD, Zhang J, Picker SR, Cáceres AM, et al. Hotspots for copy number variation in chimpanzees and humans. Proc Natl Acad Sci USA 2006; 103:8006 - 8011; PMID: 16702545; http://dx.doi.org/10.1073/pnas.0602318103
   PubMed Web of Science ®Google Scholar
• Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature 2001; 409:860 - 921; PMID: 11237011; http://dx.doi.org/10.1038/35057062
   PubMed Web of Science ®Google Scholar
• McCarroll SA, Altshuler DM. Copy-number variation and association studies of human disease. Nat Genet 2007; 39:37 - 42; PMID: 17597780; http://dx.doi.org/10.1038/ng2080
   PubMed Web of Science ®Google Scholar
• Zhang F, Gu W, Hurles ME, Lupski JR. Copy number variation in human health, disease and evolution. Annu Rev Genomics Hum Genet 2009; 10:451 - 481; PMID: 19715442; http://dx.doi.org/10.1146/annurev.genom.9.081307.164217
   PubMed Web of Science ®Google Scholar
• Pollack JR, Sørlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, et al. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA 2002; 99:12963; PMID: 12297621; http://dx.doi.org/10.1073/pnas.162471999
   PubMed Web of Science ®Google Scholar
• Dumas L, Kim YH, Karimpour-Fard A, Cox M, Hopkins J, Pollack JR, et al. Gene copy number variation spanning 60 million years of human and primate evolution. Genome Res 2007; 17:1266; PMID: 17666543; http://dx.doi.org/10.1101/gr.6557307
   PubMed Web of Science ®Google Scholar