title: Pervasive recombination and sympatric genome diversification driven by frequency-dependent selection in Borrelia burgdorferi, the Lyme disease bacterium.
abstract: How genomic diversity within bacterial populations originates and is maintained in the presence of frequent recombination is a central problem in understanding bacterial evolution. Natural populations of Borrelia burgdorferi, the bacterial agent of Lyme disease, consist of diverse genomic groups co-infecting single individual vertebrate hosts and tick vectors. To understand mechanisms of sympatric genome differentiation in B. burgdorferi, we sequenced and compared 23 genomes representing major genomic groups in North America and Europe. Linkage analysis of >13,500 single-nucleotide polymorphisms revealed pervasive horizontal DNA exchanges. Although three times more frequent than point mutation, recombination is localized and weakly affects genome-wide linkage disequilibrium. We show by computer simulations that, while enhancing population fitness, recombination constrains neutral and adaptive divergence among sympatric genomes through periodic selective sweeps. In contrast, simulations of frequency-dependent selection with recombination produced the observed pattern of a large number of sympatric genomic groups associated with major sequence variations at the selected locus. We conclude that negative frequency-dependent selection targeting a small number of surface-antigen loci (ospC in particular) sufficiently explains the maintenance of sympatric genome diversity in B. burgdorferi without adaptive divergence. We suggest that pervasive recombination makes it less likely for local B. burgdorferi genomic groups to achieve host specialization. B. burgdorferi genomic groups in the northeastern United States are thus best viewed as constituting a single bacterial species, whose generalist nature is a key to its rapid spread and human virulence.
authors: Department of Biology, The Graduate Center, City University of New York, New York, New York 10016, USA.
authors: James
authors: J
authors: Haven
authors: Levy C
authors: LC
authors: Vargas
authors: Emmanuel F
authors: EF
authors: Mongodin
authors: Vincent
authors: V
authors: Xue
authors: Yozen
authors: Y
authors: Hernandez
authors: Pedro
authors: P
authors: Pagan
authors: Claire M
authors: CM
authors: Fraser-Liggett
authors: Steven E
authors: SE
authors: Schutzer
authors: Benjamin J
authors: BJ
authors: Luft
authors: Sherwood R
authors: SR
authors: Casjens
authors: Wei-Gang
authors: WG
authors: Qiu
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D000818:Animals; D025065:Borrelia burgdorferi / Q000235:genetics* / Q000502:physiology; D017124:Conserved Sequence; D019143:Evolution, Molecular; D005785:Gene Conversion / Q000235:genetics; D049810:Genetic Speciation; D014644:Genetic Variation / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D008193:Lyme Disease / Q000382:microbiology*; D008957:Models, Genetic; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics*; D015203:Reproducibility of Results; D012641:Selection, Genetic; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D061350:Sympatry / Q000235:genetics*