We can design an equivalent for sequence data: for each sequence, apply some random number of possible mutations under a chosen model, then estimate all pairwise distances under the same model, and finally subtract from that estimate the number of mutations applied in the perturbation step to each of the two sequences a method we denote BP.
Then, TMRCA was obtained assuming the HKY85 mutation model (excluding indels, and hotspot mutations such as 16182C, 16183C and 16519C), and used the gamma-distributed rates (approximated by a discrete distribution with 32 categories) and three partitions: Hypervariable region I (HVS-I: positions 16051 16400), Hypervariable region II (HVS-II: positions 68 263), and the coding region.
The model then is used to predict the distribution of mutations, with good correspondence to data.
Assuming an infinite alleles mutation model and a time interval of length T generations, if mutations are Poisson distributed, then homozygosity, or the probability that no mutation occurs on an interval of length T, is e 2μ T, where μ is the per-generation mutation rate (Wakeley 2009, p. 107).
Then, the phylogeny of Tibetan highlanders was used to examine the assumption of a molecular clock under the HKY + G mutation model.
Bottleneck effects on average heterozygosity and genetic distance with the stepwise mutation model.
We had hypothesized that CCM lesion genesis occurs due to second-site somatic mutations, following a "two-hit" mutation model.
There is no useful mutation model, but the TOE is built up on useful effects of mutations".
SMM: stepwise mutation model.
As one approach, Springman et al. (2010) developed a model that partitioned lethals separately from other deleterious mutations and then parameterized the model so that the predicted fitness drop was restricted to the nonlethal component.
