Sentence examples for mutation rate prior from inspiring English sources

We assumed that the SSRs evolved according to the stepwise mutation model (SMM) with a uniform mutation rate prior bounded between 10−4 and 10−3 for all loci.

We used a coalescent constant size tree prior, and employed a strict clock (with uniform rates across branches) using a uniform prior distribution with a mutation rate prior of 1.4% sequence divergence per million years [ 55], but allowing for a range of 1.0%to2.4%4% sequence divergence per million years.

For the mutation rate prior distribution, we used a lognormal distribution with a mean rate of 1.4% sequence divergence per million years as estimated for Richardsonius, and specified a range of 1.0%to2.4%4% sequence divergence per million years to cover the range of mutation rates for cyt b for closely related genera [ 55] as well as reported mutation rates for CR in other cyprinids [ 77, 78].

The mutation rate priors for each locus were identical to those used for IMA.

To estimate the topology of the groups, the program was first used with relative mutation rate priors (meaning that the scale of the species tree will be in mutations rather than years).

Human influenza epidemics are caused by types A and B, with roughly 25% of human cases due to influenza B. Influenza B is a single-stranded RNA virus with a high mutation rate, and both prior immune history and vaccination put significant pressure on the virus to evolve.

To better understand the diversity present in the population, we repeated this analysis, but with a broader estimate of mutation rate (for the prior, the same mean as above, 5.5 x 10-10 mutations/butday, but with a larger standard deviation), resulting in a 5 to 55 fold increase in the estimated substitution rate, and a corresponding reduction in the likely TMRCA (Author response image 2B,C).

All microsatellite loci were simulated assuming a stepwise mutation model with mutation rate μ with a prior distribution N (0.0004, 0.0001) truncated at 0.0002 and 0.0006 [ 12, 65].

The admixture between the first and the second Norwegian populations occurred between 500 and 2,500 yr BP, before or after the sampling at t2. Mutation rates were treated as nuisance parameters, and we assumed a Kimura 2-parameter model [ 55] with prior mutation rate estimate range obtained from the BEAST analyses (see below).

We assumed a generalized stepwise mutation model [ 62] with a uniform prior distribution of mean mutation rate from 10-4 to 10-3, a prior distribution of individual locus mutation rates from 10-5 to 10-2 following a Gamma distribution with mean determined by the mean mutation rate across loci.

These priors returned posteriors of the mutation rate that were similar to the prior for mutation rate.