[1] Didelot X, Maiden MCJ. Impact of recombination on bacterial evolution. Trends Microbiol , 2010, 18(7): 315-322.
[2] Thomas CM, Nielsen KM. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol , 2005, 3(9): 711-721.
[3] Feavers IM, Heath AB, Bygraves JA, Maiden MCJ. Role of horizontal genetic exchange in the antigenic variation of the class 1 outer membrane protein of Neisseria meningitidis . Mol Microbiol , 1992, 6(4): 489-495.
[4] Spratt BG, Bowler LD, Zhang QY, Zhou J, Smith JM. Role of interspecies transfer of chromosomal genes in the evolution of penicillin resistance in pathogenic and commensal Neisseria species. J Mol Evol , 1992, 34(2): 115-125.
[5] Vos M. Why do bacteria engage in homologous recombination? Trends Microbiol , 2009, 17(6): 226-232.
[6] Hacker J, Carniel E. Ecological fitness, genomic islands and bacterial pathogenicity: a darwinian view of the evolution of microbes. EMBO Rep , 2001, 2(5): 376-381.
[7] Arnold ML, Sapir Y, Martin NH. Genetic exchange and the origin of adaptations: prokaryotes to primates. Philos Trans R Soc Lond B Biol Sci , 2008, 363(1505): 2813-2820.
[8] Achtman M. Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annu Rev Microbiol , 2008, 62: 53-70.
[9] Cui YJ, Yu C, Yan YF, Li DF, Li YJ, Jombart T, Weinert LA, Wang ZY, Guo ZB, Xu LZ, Zhang YJ, Zheng HC, Qin N, Xiao X, Wu MS, Wang XY, Zhou DS, Qi ZZ, Du ZM, Wu HL, Yang XW, Cao HZ, Wang H, Wang J, Yao SS, Rakin A, Li YR, Falush D, Balloux F, Achtman M, Song YJ, Wang J, Yang RF. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis . Proc Natl Acad Sci USA , 2013, 110(2): 577-582.
[10] Zhou ZM, McCann A, Weill FX, Blin C, Nair S, Wain J, Dougan G, Achtman M. Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever. Proc Natl Acad Sci USA , 2014, 111(33): 12199-12204.
[11] Cui YJ, Yang XW, Didelot X, Guo CY, Li DF, Yan YF, Zhang YQ, Yuan YT, Yang HM, Wang J, Wang J, Song YJ, Zhou DS, Falush D, Yang RF. Epidemic clones, oceanic gene pools, and Eco-LD in the free living marine pathogen Vibrio parahaemolyticus . Mol Biol Evol , 2015, 32(6): 1396-1410.
[12] Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol , 2006, 23(2): 254-267.
[13] Bandelt H-J, Dress AWM. A canonical decomposition theory for metrics on a finite set. Adv Math , 1992, 92(1): 47-105.
[14] Bryant D, Moulton V. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol , 2004, 21(2): 255-265.
[15] Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Dunning Hotopp JC, Hu FZ, Riley DR, Covacci A, Mitchell TJ, Bentley SD, Kilian M, Ehrlich GD, Rappuoli R, Moxon ER, Masignani V. Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol , 2010, 11(10): R107.
[16] Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics , 2005, 21(2): 263-265.
[17] McVean G, Auton A. LDhat 2.1: a package for the population genetic analysis of recombination. Department of Statistics, Oxford, OX1 3TG, UK , 2007.
[18] Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics , 2003, 19(18): 2496-2497.
[19] Hudson RR. Two-locus sampling distributions and their application. Genetics , 2001, 159(4): 1805-1817.
[20] McVean G, Awadalla P, Fearnhead P. A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics , 2002, 160(3): 1231-1241.
[21] Jolley KA, Wilson DJ, Kriz P, McVean G, Maiden MC. The influence of mutation, recombination, population history, and selection on patterns
