The estimates of population mutation rate were computed for each locus in all rice species where genotypes are available.
For CpG sites within the same methylation level group, we estimated the mutation rate by computing the number of these SNPs (C/A, C/G, and C/T) over the total number of cytosine bases in the human genome.
For the fitness landscape with a peak mesa profile, the two-dimensional phase diagram in the mesa fitness and the mutation rate can be computed with minimal cost.
If a heterozygote cannot be fixed, there is no way the homozygote state can be fixed and the effective mutation rate used to compute the speed of the ratchet should be reduced accordingly to exclude such sites.
However, in the special case in which all loci have the same mutation rate, the computation simplifies dramatically, allowing us to compute MPs for 10 or more loci.
The nucleotide sequences of the rlrA islet were aligned, and the nucleotide diversity π and the Watterson estimator θ of the population mutation rate per site were computed using a sliding window of 100 bp along the sequences.
For each pair of transcripts, correlation between the population structure-adjusted mutation rate across strains was computed as a measure of coevolution of transcripts.
Given that we can compute p from the WGD pairs, we can compute the mutation rate r for each pair of WGD gene sequences as r = − l n (1 − p ) / (2 ∗ t ).
The number of segregating sites and levels of nucleotide diversity Pi, the average number of nucleotide differences per site between two sequences [ 32], and θ, an estimate of 4Neμ, where Ne is the effective population size and μ is the mutation rate per nucleotide [ 33], were computed in DnaSP (version 5.10.00).
Theta-estimates ('theta' θ = Neμ, where Ne is the effective population size in the case of a haploid locus and μ is the overall mutation rate at the haplotype level) were computed using ARLEQUIN v. 3.5 [ 55]: the expected level of diversity, θS, was derived from the observed number of segregating sites S and θπ from the observed mean number of pairwise nucleotide differences π.
