Academic journal article Genetics

Recombination-Driven Genome Evolution and Stability of Bacterial Species

Academic journal article Genetics

Recombination-Driven Genome Evolution and Stability of Bacterial Species

Article excerpt

(ProQuest: ... denotes formulae omitted.)

Bacterial genomes are extremely variable, comprising both a consensus "core" genome, which is present in the majority of strains in a population, and an "auxiliary" genome, comprising genes that are shared by some but not all strains (Medini et al. 2005; Tettelin et al. 2005; Hogg et al. 2007; Lapierre and Gogarten 2009; Touchon et al. 2009; Dixit et al. 2015; Marttinen et al. 2015).

Multiple factors shape the diversification of the core genome. For example, point mutations generate single-nucleotide polymorphisms (SNPs) within the population that are passed on from mother to daughter. At the same time, stochastic elimination of lineages leads to fixation of polymorphisms, which effectively reduces population diversity. The balance between point mutations and fixation determines the average number of genetic differences between pairs of individuals in a population, often denoted by 0.

During the last two decades, exchange ofgenetic fragments between closely related organisms has also been recognized as a significant factor in bacterial evolution (Guttman and Dykhuizen 1994; Milkman 1997; Falush et al. 2001; Thomas and Nielsen 2005; Studier etal. 2009; Touchon etal. 2009; Vos and Didelot 2009; Dixit et al. 2015). Transferred fragments are integrated into the recipient chromosome via homologous recombination. Notably, recombination between pairs of strains is limited by the divergence in transferred regions. The probability psuccess ~ e~s=STE of successful recombination of foreign DNA into a recipient genome decays exponentially with d, the local divergence between the donor DNA fragment and the corresponding DNA on the recipient chromosome (Vulic et al. 1997; Majewski 2001; Thomas and Nielsen 2005; Fraser et al. 2007; Polz et al 2013). Segments with divergence 8 greater than divergence 8TE have negligible probability of successful recombination. In this work, we refer to the divergence 8TE as the transfer efficiency. 8TE is shaped at least in part by the restriction modification (RM), the mismatch repair (MMR) systems, and the biophysical mechanisms of homologous recombination (Vulic et al. 1997; Majewski 2001). The transfer efficiency 8TE imposes an effective limit on the divergence among subpopulations that can successfully exchange genetic material with each other (Vulic et al. 1997; Majewski 2001).

In this work, we develop an evolutionary theoretical framework that allows us to study in broad detail the nature of competition between recombinations and point mutations across a range of evolutionary parameters. We identify two composite parameters that govern how genomes diverge from each other over time. Each of the two parameters corresponds to a competition between vertical inheritance of polymorphisms and their horizontal exchange via homologous recombination.

First is the competition between the recombination rate p and the mutation rate m. Within a coevolving population, consider a pair of strains diverging from each other. The average time between consecutive recombination events affecting any given small genomic region is 1/ (2pltr) where ltr is the average length of transferred regions. The total divergence accumulated in this region due to mutations in either of the two genomes is 8mut ~ 2p,/2pltr. If 8mut » 8TE, the pair of genomes is likely to become sexually isolated from each other in this region within the time that separates two successive recombination events. In contrast, if 8mut < 8TE, frequent recombination events would delay sexual isolation resulting in a more homogeneous population. Second is the competition between the population diversity 0 and 8TE. If 8TE C 0, one expects spontaneous fragmentation of the entire population into several transient sexually isolated subpopulations that rarely exchange genetic material between each other. …

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