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We postprocessed the outputs using Seq-Gen (Rambaut and Grassly 1997) and the mutation transition matrix for D. pseudoobscura.
The program was run individually for each chromosome of each species using default parameters, with the exception that we individually estimated theta from each of our data sets (θpse = 0.01, θmir = 0.0058) using θ = S/a, where a = ∑ i = 1 n − 1 1 i, and created our own mutation transition matrices.
To obtain a fuller understanding of the dynamics of mutation rate evolution, the preceding formulations might be applied in a transition matrix approach for the various mutation rate classes, although in the absence of explicit information on the rates of origin of mutator/antimutator alleles, the issue is not pursued here.
In small populations that are in the sequential fixation regime, we simply add additional transient transition matrix elements representing different mutations, with the uphill mutations transitioning to the uphill absorbing state, and similarly for the valley-crossing mutations.
Two matrices mainly influence the model: a Transition matrix TM, and an Emission Matrix EM.
the state transition matrix.
F State transition matrix.
F Target trajectory transition matrix.
In the transition matrix Eqs.
A is the state transition matrix.
