Feldman RA, Eccersley AJ, Hardie JM. Epidemiology of Helicobacter pylori: acquisition, transmission, population prevalence and disease-to-infection ratio. Br Med Bull. 1998;54:39–53.
Article
CAS
Google Scholar
Algood HMS, Cover TL. Helicobacter pylori persistence: an overview of interactions between H. pylori and host immune defenses. Clin Microbiol Rev. 2006;19:597–613.
Article
CAS
Google Scholar
Israel DA, Peek RM. The role or persistence in Helicobacter pylori pathogenesis. Curr Opin Gastroenterol. 2006;22:3–7.
Article
Google Scholar
Kansau I, Raymond J, Bingen E, Courcoux P, Kalach N, Bergeret M, Braimi N, Dupont C, Labigne A. Genotyping of Helicobacter pylori isolates by sequencing of PCR products and comparison with the RAPD technique. Res Microbiol. 1996;147:661–9.
Article
CAS
Google Scholar
Suerbaum S, Smith JM, Bapumia K, Morelli G, Smith NH, Kunstmann E, Dyrek I, Achtman M. Free recombination within Helicobacter pylori. Proc Natl Acad Sci U S A. 1998;95:12619–24.
Article
CAS
Google Scholar
Achtman M, Azuma T, Berg DE, Ito Y, Morelli G, Pan ZJ, Suerbaum S, Thompson SA, van der Ende A, van Doorn LJ. Recombination and clonal groupings within Helicobacter pylori from different geographic regions. Mol Microbiol. 1999;32:459–70.
Article
CAS
Google Scholar
Surebaum S, Achtman M. Evolution of Helicobacter pylori: the role of recombination. Trends Microbiol. 1999;7:182–4.
Article
Google Scholar
Falush D, Kraft C, Taylor NS, Correa P, Fox JG, Achtman M, Suerbaum S. Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proc Natl Acad Sci U S A. 2001;98:15056–61.
Article
CAS
Google Scholar
Kraft C, Suerbaum S. Mutation and recombination in Helicobacter pylori: mechanisms and role in generating strain diversity. Int J Med Microbiol. 2005;295:299–305.
Article
CAS
Google Scholar
Kullick S, Moccia C, Didelot X, Falush D, Kraft C, Suerbaum S. Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori. PLoS One. 2008;3:e3797.
Article
Google Scholar
Lin EA, Zhang XS, Levine SM, Gill SR, Falush D, Blaser MJ. Natural transformation of Helicobacter pylori involves the integration of short DNA fragments interrupted by gaps of variable size. PLoS Pathog. 2009;5:e1000337.
Article
Google Scholar
Morelli G, Didelot X, Kusecek B, Schwarz S, Bahlawane C, Falush D, Suerbaum S, Achtman M. Microevolution of Helicobacter Pylori during prolonged infection of single hosts and within families. PLoS Genet. 2010;6:e1001036.
Article
Google Scholar
Dorer MS, Sessler TH, Salama NR. Recombination and DNA repair in Helicobacter pylori. Annu Rev Microbiol. 2011;65:329–48.
Article
CAS
Google Scholar
Yahara K, Kawai M, Furuta Y, Takahashi N, Handa N, Tsuru T, Oshima K, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I. Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species. Genome Biol Evol. 2012;4:628–40.
Article
Google Scholar
Hughes AL, Nei M. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature. 1988;335:167–70.
Article
CAS
Google Scholar
Castoe TA, de Koning AP, Pollock DD. Adaptive molecular convergence: molecular evolution versus molecular phylogenetics. Commun Integr Biol. 2010;3:67–9.
Article
Google Scholar
Christin P-A, Weinreich DM, Besnard G. Causes and evolutionary significance of genetic convergence. Trends Genet. 2010;26:400–5.
Article
CAS
Google Scholar
Tenaillon O, Rodríguez-Verdugo A, Gaut RL, McDonald P, Bennett AF, Long AD, Gaut BS. The molecular diversity of adaptive convergence. Science. 2012;335:457–61.
Article
CAS
Google Scholar
Chattopadhyay S, Weissman SJ, Minin VN, Russo TA, Sokurenko EV. High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection. Proc Natl Acad Sci U S A. 2009;106:12412–7.
Article
CAS
Google Scholar
Chattopadhyay S, Paul S, Kisiela DI, Linardopoulou EV, Sokurenko EV. Convergent molecular evolution of genomic cores in Salmonella enterica and Escherichia coli. J Bacteriol. 2012;194:5002–11.
Article
CAS
Google Scholar
Paul S, Minnick MF, Chattopadhyay S. Mutation-driven divergence and convergence indicate adaptive evolution of the intracellular human-restricted pathogen, Bartonella bacilliformis. PLoS Negl Trop Dis. 2016;10:e0004712.
Article
Google Scholar
Maynard Smith J, Smith NH. Detecting recombination from gene trees. Mol Biol Evol. 1998;15:590–9.
Article
CAS
Google Scholar
Funk DJ, Helbling L, Wernegreen JJ, Moran NA. Intraspecific phylogenetic congruence among multiple symbiont genomes. Proc Biol Sci. 2000;267:2517–21.
Article
CAS
Google Scholar
Meinersmann RJ, Romero-Gallo J, Blaser MJ. Rate heterogeneity in the evolution of Helicobacter pylori and the behavior of homoplastic sites. Infect Genet Evol. 2008;8:593–602.
Article
CAS
Google Scholar
Caballero A, Quesada H. Homoplasy and distribution of AFLP fragments: an analysis in silico of the genome of different species. Mol Biol Evol. 2010;27:1139–51.
Article
CAS
Google Scholar
Montano V, Didelot X, Foll M, Linz B, Reinhardt R, Suerbaum S, Moodley Y, Jensen JD. Worldwide population structure, long-term demography, and local adaptation of Helicobacter pylori. Genetics. 2015;200:947–63.
Article
Google Scholar
Israel DA, Salama N, Krishna U, Rieger UM, Atherton JC, Falkow S, Peek RM Jr. Helicobacter pylori genetic diversity within the gastric niche of a single human host. Proc Natl Acad Sci U S A. 2001;98:14625–30.
Article
CAS
Google Scholar
Patra R, Chattopadhyay S, De R, Ghosh P, Ganguly M, Chowdhury A, Ramamurthy T, Nair GB, Mukhopadhyay AK. Multiple infection and microdiversity among Helicobacter pylori isolates in a single host in India. PLoS One. 2012;7:e43370.
Article
CAS
Google Scholar
Bruen TC, Philippe H. Bryant D. a simple and robust statistical test for detecting the presence of recombination. Genetics. 2006;172:2665–81.
Article
CAS
Google Scholar
Schwarz S, Morelli G, Kusecek B, Manica A, Balloux F, Owen RJ, Graham DY, van der Merwe S, Achtman M, Suerbaum S. Horizontal versus familial transmission of Helicobacter pylori. PLoS Pathog. 2008;4:e1000180.
Article
Google Scholar
Chi PB, Chattopadhyay S, Lemey P, Sokurenko EV, Minin VN. Synonymous and nonsynonymous distances help untangle convergent evolution and recombination. Stat Appl Genet Mol Biol. 2015;14:375–89.
Article
CAS
Google Scholar
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B. 1995;57:289–300.
Google Scholar
Bowser FP. The African slave in colonial Peru, 1524–1650. Stanford, California: Stanford University Press; 1974.
Sokurenko EV, Feldgarden M, Trintchina E, Weissman SJ, Avagyan S, Chattopadhyay S, Johnson JR, Dykhuizen DE. Selection footprint in the FimH adhesin shows pathoadaptive niche differentiation in Escherichia coli. Mol Biol Evol. 2004;21:1373–83.
Article
CAS
Google Scholar
Korotkova N, Chattopadhyay S, Tabata TA, Beskhlebnaya V, Vigdorovich V, Kaiser BK, Strong RK, Dykhuizen DE, Sokurenko EV, Moseley SL. Selection for functional diversity drives accumulation of point mutations in Dr adhesins of Escherichia coli. Mol Microbiol. 2007;64:180–94.
Article
CAS
Google Scholar
Chattopadhyay S, Feldgarden M, Weissman SJ, Dykhuizen DE, van Belle G, Sokurenko EV. Haplotype diversity in "source-sink" dynamics of Escherichia coli urovirulence. J Mol Evol. 2007;64:204–14.
Article
CAS
Google Scholar
Weissman SJ, Beskhlebnaya V, Chesnokova V, Chattopadhyay S, Stamm WE, Hooton TM, Sokurenko EV. Differential stability and trade-off effects of pathoadaptive mutations in the Escherichia coli FimH adhesin. Infect Immun. 2007;75:3548–55.
Article
CAS
Google Scholar
Totsika M, Beatson SA, Holden N, Gally DL. Regulatory interplay between pap operons in uropathogenic Escherichia coli. Mol Microbiol. 2008;67:996–1011.
Article
CAS
Google Scholar
Chattopadhyay S, Tchesnokova V, McVeigh A, Kisiela DI, Dori K, Navarro A, Sokurenko EV, Savarino SJ. Adaptive evolution of class 5 fimbrial genes in enterotoxigenic Escherichia coli and its functional consequences. J Biol Chem. 2012;287:6150–8.
Article
CAS
Google Scholar
Kisiela DI, Chattopadhyay S, Libby SJ, Karlinsey JE, Fang FC, Tchesnokova V, Kramer JJ, Beskhlebnaya V, Samadpour M, Grzymajlo K, Ugorski M, Lankau EW, Mackie RI, Clegg S, Sokurenko EV. Convergent evolution of invasive serovars of Salmonella enterica via point mutations in the type 1 fimbrial adhesion FimH. PLoS Pathog. 2012;8:e1002733.
Article
CAS
Google Scholar
Cao Q, Didelot X, Wu Z, Li Z, He L, Li Y, Ni M, You Y, Lin X, Li Z, Gong Y, Zheng M, Zhang M, Liu J, Wang W, Bo X, Falush D, Wang S, Zhang J. Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis. Gut. 2015;64:554–61.
Article
CAS
Google Scholar
Schrag SJ, Perrot V, Levin BR. Adaptation to the fitness costs of antibiotic resistance in Escherichia coli. Proc Biol Sci. 1997;264:1287–91.
Article
CAS
Google Scholar
Björkholm B, Sjölund M, Falk PG, Berg OG, Engstrand L, Andersson DI. Mutation frequency and biological cost of antibiotic resistance in Helicobacter pylori. Proc Natl Acad Sci U S A. 2001;98:14607–12.
Article
Google Scholar
Kawai M, Furuta Y, Yahara K, Tsuru T, Oshima K, Handa N, Takahashi N, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I. Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori east Asian genomes. BMC Microbiol. 2011;11:104.
Article
CAS
Google Scholar
Yahara K, Furuta Y, Morimoto S, Kikutake C, Komukai S, Matelska D, Dunin-Horkawicz S, Bujnicki JM, Uchiyama I, Kobayashi I. Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori. DNA Res. 2016;23:135–43.
Article
CAS
Google Scholar
Hamilton HL, Dillard JP. Natural transformation of Neisseria gonorrhoeae: from DNA donation to homologous recombination. Mol Microbiol. 2006;59:376–85.
Article
CAS
Google Scholar
Carrolo M, Pinto FR, Melo-Cristino J, Ramirez M. Pherotype influences biofilm growth and recombination in Streptococcus pneumoniae. PLoS One. 2014;9:e92138.
Article
Google Scholar
Ogura M, Perez JC, Mittl PR, Lee HK, Dailide G, Tan S, Ito Y, Secka O, Dailidiene D, Putty K, Berg DE, Kalia A. Helicobacter pylori evolution: lineage- specific adaptations in homologs of eukaryotic Sel1-like genes. PLoS Comput Biol. 2007;3:e151.
Article
Google Scholar
Gehmert S, Velapatiño B, Herrera P, Balqui J, Santivañez L, Cok J, Vargas G, Combe J, Passaro DJ, Wen S, Meyer F, Berg DE, Gilman RH. Interleukin-1 beta single-nucleotide polymorphism's C allele is associated with elevated risk of gastric cancer in Helicobacter pylori-infected Peruvians. Am J Trop Med Hyg. 2009;81:804–10.
Article
CAS
Google Scholar
Atherton JC, Blaser MJ. Coadaptation of Helicobacter pylori and humans: ancient history, modern implications. J Clin Invest. 2009;119:2475–87.
Article
CAS
Google Scholar
Bugaytsova JA, Björnham O, Chernov YA, Gideonsson P, Henriksson S, Mendez M, Sjöström R, Mahdavi J, Shevtsova A, Ilver D, Moonens K, Quintana-Hayashi MP, Moskalenko R, Aisenbrey C, Bylund G, Schmidt A, Åberg A, Brännström K, Königer V, Vikström S, Rakhimova L, Hofer A, Ögren J, Liu H, Goldman MD, Whitmire JM, Ådén J, Younson J, Kelly CG, Gilman RH, Chowdhury A, Mukhopadhyay AK, Nair GB, Papadakos KS, Martinez-Gonzalez B, Sgouras DN, Engstrand L, Unemo M, Danielsson D, Suerbaum S, Oscarson S, Morozova-Roche LA, Olofsson A, Gröbner G, Holgersson J, Esberg A, Strömberg N, Landström M, Eldridge AM, Chromy BA, Hansen LM, Solnick JV, Lindén SK, Haas R, Dubois A, Merrell DS, Schedin S, Remaut H, Arnqvist A, Berg DE, Borén T. Helicobacter pylori adapts to chronic infection and gastric disease via pH-responsive BabA-mediated adherence. Cell Host Microbe. 2017;21:376–89.
Article
CAS
Google Scholar
Swofford DLPAUP. Phylogenetic analysis using parsimony and other methods. Version 4. Sunderland, MA: Sinauer Associates; 2000.
Chattopadhyay S, Paul S, Dykhuizen DE, Sokurenko EV. Tracking recent adaptive evolution in microbial species using TimeZone. Nat Protoc. 2013;8:652–65.
Article
CAS
Google Scholar
Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986;3:418–26.
CAS
PubMed
Google Scholar
Chan CX, Beiko RG, Ragan MA. A two-phase strategy for detecting recombination in nucleotide sequences. South African Comp J. 2007;38:20–7.
Google Scholar
Hall BG. Simulating DNA coding sequence evolution with EvolveAGene 3. Mol Biol Evol. 2008;25:688–95.
Article
CAS
Google Scholar
Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44–57.
Article
CAS
Google Scholar