title: A model for the effect of homologous recombination on microbial diversification.
abstract: The effect of homologous recombination (HR) on the evolution of microbial genomes remains contentious as competing hypotheses seek to explain the evolutionary dynamics of microbial species. Evidence for HR between microbial genomes is widespread, and this process has been proposed to act as a cohesive force that can constrain the diversification of microbial lineages. We seek to characterize the evolutionary dynamics of sympatric populations to explore the impact of HR on microbial speciation. We describe a simple equation for quantifying the cohesive effect of HR on microbial populations as a function of their nucleotide divergence, μ/ρ=πg10(-20 πg). The model was verified using a forward-time microbial population simulator that can explore the evolutionary dynamics of sympatric populations in nonoverlapping niche space. The model was also evaluated using multilocus sequence data from a range of microbial species, providing criteria for dividing them into either cohesively recombining or clonally diverging lineages. We conclude that models of microbial diversification that appear contradictory can be explained in a unified manner as the natural and predictable consequence of variation in a small number of population parameters.
authors.affiliation: Department of Microbiology, Cornell University, Ithaca, New York, USA.
authors.forename: James R
authors.initials: JR
authors.lastname: Doroghazi
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Buckley
mesh_terms: D001419:Bacteria / Q000235:genetics*; D003198:Computer Simulation; D022761:Gene Transfer, Horizontal; D049810:Genetic Speciation; D059765:Homologous Recombination; D008954:Models, Biological; D058885:Multilocus Sequence Typing; D009154:Mutation
references.citation: ISME J. 2009 Feb;3(2):199-208
references.pmid: 18830278
references.citation: J Bacteriol. 2009 Sep;191(18):5824-31
references.pmid: 19617370
references.citation: Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):1975-84
references.pmid: 17062415
references.citation: Science. 2007 Jan 26;315(5811):476-80
references.pmid: 17255503
references.citation: Genetics. 1986 Mar;112(3):441-57
references.pmid: 3007275
references.citation: Int J Syst Evol Microbiol. 2002 May;52(Pt 3):1043-1047
references.pmid: 12054223
references.citation: Curr Biol. 2007 May 15;17(10):R373-86
references.pmid: 17502094
references.citation: Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):15056-61
references.pmid: 11742075
references.citation: Proc Natl Acad Sci U S A. 1992 Jul 15;89(14):6492-6
references.pmid: 1631148
references.citation: Res Microbiol. 2000 Jul-Aug;151(6):465-9
references.pmid: 10961460
references.citation: Science. 2008 Apr 11;320(5873):237-9
references.pmid: 18403712
references.citation: mBio. 2011 Apr 12;2(2):
references.pmid: 21486909
references.citation: Genome Biol Evol. 2010;2:646-55
references.pmid: 20688752
references.citation: Nature. 1968 Feb 17;217(5129):624-6
references.pmid: 5637732
references.citation: Science. 2007 Aug 24;317(5841):1093-6
references.pmid: 17717188
references.citation: Proc Natl Acad Sci U S A. 1997 Sep 2;94(18):9763-7
references.pmid: 9275198
references.citation: Genetics. 2006 Feb;172(2):759-69
references.pmid: 16322518
references.citation: Annu Rev Microbiol. 2002;56:457-87
references.pmid: 12142474
references.citation: Trends Microbiol. 2009 May;17(5):196-204
references.pmid: 19375326
references.citation: Genetics. 1995 Jul;140(3):917-32
references.pmid: 7672591
references.citation: Philos Trans R Soc Lond B Biol Sci. 1995 Jan 30;347(1319):5-12
references.pmid: 7746854
references.citation: Science. 2009 Feb 6;323(5915):741-6
references.pmid: 19197054
references.citation: J Bacteriol. 2000 Feb;182(4):1016-23
references.pmid: 10648528
references.citation: Nat Rev Microbiol. 2008 Jun;6(6):431-40
references.pmid: 18461076
references.citation: Bioinformatics. 2002 Feb;18(2):337-8
references.pmid: 11847089
references.citation: Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):2045-53
references.pmid: 17062419
references.citation: Genetics. 1999 Aug;152(4):1459-74
references.pmid: 10430576
references.citation: J Clin Microbiol. 2005 Jan;43(1):340-7
references.pmid: 15634992
references.citation: PLoS Genet. 2009 Aug;5(8):e1000601
references.pmid: 19680442
references.citation: Proc Natl Acad Sci U S A. 2005 May 17;102(20):7332-7
references.pmid: 15878987
references.citation: Science. 2009 Jun 12;324(5933):1454-7
references.pmid: 19520963
references.citation: Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):1929-40
references.pmid: 17062412
references.citation: Genetics. 1999 Dec;153(4):1525-33
references.pmid: 10581263
references.citation: Genetics. 2007 Sep;177(1):407-16
references.pmid: 17603112
references.citation: Appl Environ Microbiol. 2010 Mar;76(6):1913-25
references.pmid: 20097815
references.citation: Nat Rev Microbiol. 2005 Sep;3(9):733-9
references.pmid: 16138101
references.citation: Genetics. 2008 Apr;178(4):2417-27
references.pmid: 18430959
references.citation: Biochemistry. 1995 Aug 15;34(32):10194-204
references.pmid: 7640274