Recently, I reviewed several concepts about recombination and mutation in bacterial genomes when I was revising my manuscript of GeneMates. In this post, I summarise my understandings to two groups of terms and two measures (r/m and ρ/θ) that are relevant to these biological events, and tabulate values of these measures in six bacterial species.
Relatedness between bacterial isolates
Population structure or population stratification: systematic genetic variation between groups of individuals due to different ancestry [1–3]. The genetic variation arises from mutations and recombination occurred in bacterial evolutionary history . Notably, recombination is not accounted for by RAxML, PhyML or FastTree , resulting in biased tree estimates .
Phylogenetic signal or phylogenetic relatedness: the tendency for phylogenetically related organisms to resemble each other, and vice versa . These two concepts are similar to population structure for bacterial genomes.
Relative impacts of recombination and point mutations on genome divergence
r/m: relative substitution rate due to recombination versus mutations , or relative probability that a nucleotide substitution results from recombination relative to point mutations, which directly measures the relative impact of recombination on genetic variation [9, 10]. Symbols: r (rate of nucleotide substitutions resulting from recombination), m (rate of nucleotide substitutions resulting from point mutations). r/m can be calculated using LDhat, ClonalFrame and eBURST [8, 9].
ρ/θ = γ/μ: relative frequency at which recombination occurs relative to point mutations , which can be estimated using ClonalFrame [5, 11]. This measure ignores lengths and nucleotides of imported DNA fragments. Symbols: ρ (recombination parameter 4Neγ), θ (mutation parameter 4Neμ), where Ne is the effective population size, γ is the recombination rate and μ is the point mutation rate, per site per generation [4, 12]. The level of recombination can be considered moderate when ρ/θ = 0.5 .
Table: Overall or group specific r/m and ρ/θ estimates for six bacterial species and citations. MLST and genome-wide: sources of DNA sequences from which the ratios are estimated.
|Salmonella enterica||0.2 – 2.95 (genome-wide, lineage specific) ||0.37 (genome-wide) |
|Neisseria meningitidis||7.1 (MLST) ||0.08 – 2.66 (MLST) |
|Listeria monocytogenes||0.66 – 4.42 (MLST) ||0.13 – 0.71 (MLST) |
|Escherichia coli||0.91 – 12 (MLST, clone specific) ||0.33 – 5.55 (MLST, lineage specific) |
|Klebsiella pneumoniae||0.3 (MLST) ||0.42 (MLST) |
|Staphylococcus aureus||0.1 (MLST) , 0.83 (genome-wide) ||0.49 (MLST) |
In general, both r/m and ρ/θ vary extensively across species and lineages of the same species , and recombination drives genome innovation more efficiently than point mutations in E. coli , N. meningitidis , several lineages of S. enterica and L. monocytogenes [11, 14], and some E. coli clones . Therefore, the ability of a phylogenetic tree in capturing all genetic variation that results from the whole evolutionary history is limited when the effect of recombination is prominent.
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