The algorithm described above computes the MPs for a particular mutation rate μ.
After testing for the mutation rate, the comparison of topologies assuming a particular mutation rate distribution allows us to check for which topology presents a higher posterior probability.
Most adaptation is performed by adjusting parameters at the population level; for example, if a particular crossover (mutation) rate is used over the entire population, this crossover (mutation) rate is a candidate to undergo adaptation.
RNA viruses in particular have high mutation rates, can evolve rapidly, and may exhibit adaptation to specific hosts and/or tissues.
These estimates are used in most theoretical studies, and should be viewed as conservative estimates (in particular, per zygote mutation rates are likely to be higher in most species of conservation concern than in Drosophila species, [ 51, 54]).
In particular, loci presenting high mutation rates are more prone to confound the estimations, which makes sense considering that an excessive polymorphism is expected to mask the haplotype structures that have evolved over time, making it difficult to analyze the presence or absence of recombination (Awadalla 2003).
In these systems, the evolution of particular genomic properties (high mutation rates at loci involved in sex determination), mate recognition, and dispersal abilities (Ode et al. 1995; Metzger et al. 2010; Ruf et al. 2011) are convincing illustrations of how natural selection could shape the Allee effect.
Our data suggest different mutation rates during particular stages of an H. pylori infection, which we attempted to analyse in more detail.
There is substantial evidence for the evolution of elevated mutation rates at particular loci or traits in response to fluctuating environments (Jansen and Stumpf 2005).
Environmental stress (e.g. starvation, osmotic or temperature stress) could directly affect mutation rates of particular traits by inducing stress-directed mutagenesis (Wright 2004; Heidenreich 2007).
