Using a mutation and selection model, Knight et al. demonstrated that 'pairs of species with convergent GC content might also evolve convergent protein sequences, especially at functionally unconstrained positions'.
To replicate their procedure on simulated data, we randomly assigned mutation events to the tree under an infinite sites model using a mutation rate of 2.2E-8 per nucleotide per generation [ 23].
We implemented the GTR + I + G model of sequence evolution as determined by jModelTest [ 81] for the concatenated mtDNA sequences and applied a lognormal relaxed clock model using a mutation rate of 0.8%% per million years as described for cytochrome b in the salamander Taricha torosa [ 82].
The pipeline was applied to the randomly selected Cp1002 genome as a reference strain; the genomes of other strains were modelled using a mutation procedure, the sequences that present homology in both, i.e., the core genome, were already modelled in the reference strain Cp1002.
The probability (P) that the observed R mutations in the CDRs were chance occurrences was calculated by using a binomial mutation model: P=[ n!/ k!(n− k!)!] q k (1− q) n – k, where k is the number of observed R mutations in the CDRs and q is the probability that an R mutation will localise to CDRs (Zelenetz et al, 1992; Chang and Casali, 1994).
Hence, using a specific mutation model, the method tests for an heterozygosity excess in the real data set in comparison with an equivalent population in equilibrium conditions [4].
We evaluated multilocus estimates of RST, a measure of genetic differentiation using a stepwise mutation model of marker evolution.
We used a generalized mutation model in which the change in the number of repeat units forms a geometric random variable, with a variance of the geometric distribution fixed to 0.36, which is likely to be the most appropriate value for microsatellites [ 44].
We ran three replicates of MIGRATE using a Brownian motion mutation model with constant mutation rates and starting parameters based on FST calculations.
Using a plant model, mutations in animal pathogenic bacteria can easily be screened for putative virulence factors, a process which if done using existing animal infection models would be time-consuming and tedious.
