Tracking recent adaptive evolution in microbial species using TimeZone

Nature Protocols

Volumn 8, Issue 4, 2013, Pages 652-665

  Chattopadhyay, Sujay ^a   Paul, Sandip ^a   Dykhuizen, Daniel E ^b   Sokurenko, Evgeni V ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BACTERIAL GENOME; COMPUTER PROGRAM; ESCHERICHIA COLI; EVOLUTIONARY ADAPTATION; GENETIC ANALYSIS; GENETIC RECOMBINATION; GENETIC SELECTION; INTERNET; MICROBIAL GENETICS; NONHUMAN; ORTHOLOGY; POINT MUTATION; PREDICTION; PRIORITY JOURNAL;

ADAPTATION, BIOLOGICAL; BIOLOGICAL EVOLUTION; ESCHERICHIA COLI; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; PHYLOGENY; SELECTION, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; VIRULENCE;

ESCHERICHIA COLI;

EID: 84875515469     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2013.031     Document Type: Article

References (37)

1. Gomez-Duarte, O.G. et al. Genetic diversity of the gene cluster encoding longus, a type IV pilus of enterotoxigenic Escherichia coli. J. Bacteriol. 189, 9145-9149 (2007).
2. Korotkova, N. et al. Selection for functional diversity drives accumulation of point mutations in Dr adhesins of Escherichia coli. Mol. Microbiol. 64, 180-194 (2007).
3. Weissman, S.J. et al. Clonal analysis reveals high rate of structural mutations in fimbrial adhesins of extraintestinal pathogenic Escherichia coli. Mol. Microbiol. 59, 975-988 (2006).
4. Zhang, W. et al. Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms. Genome Res. 16, 757-767 (2006).
5. Golding, G.B. & Dean, A.M. The structural basis of molecular adaptation. Mol. Biol. Evol. 15, 355-369 (1998).
6. Pallen, M.J. & Wren, B.W. Bacterial pathogenomics. Nature 449, 835-842 (2007).
7. Yang, Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15, 568-573 (1998).
8. Yang, Z. & Nielsen, R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19, 908-917 (2002).
9. Chattopadhyay, S., Dykhuizen, D.E. & Sokurenko, E.V. ZPS: visualization of recent adaptive evolution of proteins. BMC Bioinformatics 8, 187 (2007).
10. Totsika, M., Beatson, S.A., Holden, N. & Gally, D.L. Regulatory interplay between pap operons in uropathogenic Escherichia coli. Mol. Microbiol. 67, 996-1011 (2008).
11. Weissman, S.J. et al. High-resolution two-locus clonal typing of extraintestinal pathogenic Escherichia coli. Appl. Environ. Microbiol. 78, 1353-1360 (2012).
12. Dennis, G. Jr. et al. DAVID: database for annotation, visualization, and integrated discovery. Genome Biol. 4, P3 (2003).
13. Sokurenko, E.V. et al. Selection footprint in the FimH adhesin shows pathoadaptive niche differentiation in Escherichia coli. Mol. Biol. Evol. 21, 1373-1383 (2004).
14. Chattopadhyay, S. et al. Haplotype diversity in 'source-sink' dynamics of Escherichia coli urovirulence. J. Mol. Evol. 64, 204-214 (2007).
15. Hughes, A.L. & Nei, M. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335, 167-170 (1988).
16. Christin, P.-A., Weinreich, D.M. & Besnard, G. Causes and evolutionary significance of genetic convergence. Trends Genet. 26, 400-405 (2010).
17. Tenaillon, O. et al. The molecular diversity of adaptive convergence. Science 335, 457-461 (2012).
18. Chattopadhyay, S. et al. Adaptive evolution of class 5 fimbrial genes in enterotoxigenic Escherichia coli and its functional consequences. J. Biol. Chem. 287, 6150-6158 (2012).
19. Kisiela, D.I. et al. Convergent evolution of invasive serovars of Salmonella enterica via point mutations in the type 1 fimbrial adhesion FimH. PLoS Pathog. 8, e1002733 (2012).
20. Smith, J.M. Analyzing the mosaic structure of genes. J. Mol. Evol. 34, 126-129 (1992).
21. Weiller, G.F. Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol. Biol. Evol. 15, 326-335 (1998).
22. Bush, R.M., Smith, C.B., Cox, N.J. & Fitch, W.M. Effects of passage history and sampling bias on phylogenetic reconstruction of human influenza A evolution. Proc. Natl Acad. Sci. USA 97, 6974-6980 (2000).
23. Fitch, W.M., Bush, R.M., Bender, C.A. & Cox, N.J. Long term trends in the evolution of H(3) HA1 human influenza type A. Proc. Natl Acad. Sci. USA 94, 7712-7718 (1997).
24. Nei, M. & Gojobori, T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418-426 (1986).
25. Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123, 585-595 (1989).
26. Fu, Y.X. & Li, W.H. Statistical tests of neutrality of mutations. Genetics 133, 693-709 (1993).
27. Chattopadhyay, S. et al. High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection. Proc. Natl Acad. Sci. USA 106, 12412-12417 (2009).
28. Chattopadhyay, S., Paul, S., Kisiela, D.I., Linardopoulou, E.V. & Sokurenko, E.V. Convergent molecular evolution of genomic cores in Salmonella enterica and Escherichia coli. J. Bacteriol. 194, 5002-5011 (2012).
29. Chattopadhyay, S., Paranjpye, R.N., Dykhuizen, D.E., Sokurenko, E.V. & Strom, M.S. Comparative evolutionary analysis of the major structural subunit of Vibrio vulnificus type IV pili. Mol. Biol. Evol. 26, 2185-2196 (2009).
30. Giacani, L. et al. Footprint of positive selection in Treponema pallidum subsp. pallidum genome sequences suggests adaptive microevolution of the syphilis pathogen. PLoS Negl. Trop. Dis. 6, e1698 (2012).
31. Paul, S. et al. Role of homologous recombination in adaptive diversification of extra-intestinal Escherichia coli. J. Bacteriol. 195, 231-242 (2013).
32. Thompson, J.D., Higgins, D.G. & Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 (1994).
33. Swofford, D.L. PAUP;: Phylogenetic Analysis Using Parsimony and Other Methods (software) (Sinauer Associates, 2000).
34. Morrison, D.A. Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences. Syst. Biol. 56, 988-1010 (2007).
35. Efron, B. Bootstrap methods: another look at the jackknife. Ann. Statist. 7, 1-26 (1979).
36. Graham, J., McNeney, B. & Seillier-Moiseiwitsch, F. Stepwise detection of recombination breakpoints in sequence alignments. Bioinformatics 21, 589-595 (2005).
37. Sokurenko, E.V., Gomulkiewicz, R. & Dykhuizen, D.E. Source-sink dynamics of virulence evolution. Nat. Rev. Microbiol. 4, 548-555 (2006).