recombination
Takuno S, Kado T, Sugino RP, Nakhleh L & Innan H 2012 Population genomics in bacteria: a case study of Staphylococcus aureus. Mol Biol Evol 29:797-809.
- for all three cases, the observed distributions significantly differ from the Poisson distribution
- the observed monotonically decreasing distributions have significantly large variances than predicted by the Poisson distribution or the strict clonal model
- this should be because the variance includes the stochastic variance of the time to MRCA due to the coalescent process
- in addition to the variance due to random placement of mutations
- this part of the variance corresponds to that explained by the Poisson process
- the expectation of r2 with free recombination is 1 / n in a panmictic population
- where n is the sample size
- in our analysis, the average r2 for long distance is 0.5
- which is much larger than 1 / n = 0.2
- indicating that the five strains are not a sample from a single panmictic population
- the result can be summarized that LD decays as increasing distance by recombination
- the genome-wide LD is elevated by population structure possibly due to geographic and/or physiological isolations between strains
- recombination rate and sequence similarity are negatively correlated
- homologous recombination should predominantly occur within species and recombination between different species should be relatively less frequent
- however, if it occurs, a number of nucleotide variations are introduced into the species
- this mechanism could play an important role in maintaining nucleotide variation within species
