Perfect Simulation From Nonneutral Population Genetic Models: Variable Population Size and Population Subdivision

Perfect simulation from nonneutral population genetic models: variable population size and population subdivision.

We show how the idea of monotone coupling from the past can produce simple algorithms for simulating samples at a nonneutral locus under a range of demographic models. We specifically consider a biallelic locus and either a general variable population size mode or a general migration model for population subdivision. We investigate the effect of demography on the efficacy of selection and the e...

Population Genetic Applications Using a Coalescent Simulation including Selection, Recombination, and Variable Population Size

Effective population size and population subdivision in demographically structured populations.

A fast-timescale approximation is applied to the coalescent process in a single population, which is demographically structured by sex and/or age. This provides a general expression for the probability that a pair of alleles sampled from the population coalesce in the previous time interval. The effective population size is defined as the reciprocal of twice the product of generation time and t...

Kinship and Population Subdivision

The coefficient of kinship between two diploid organisms describes their overall genetic similarity to each other relative to some base population. For example, kinship between parent and offspring of 1/4 describes gene sharing in excess of random sharing in a random mating population. In a subdivided population the statistic Fst describes gene sharing within subdivisions in the same way. Since...

Likelihoods and simulation methods for a class of nonneutral population genetics models.

Methods for simulating samples and sample statistics, under mutation-selection-drift equilibrium for a class of nonneutral population genetics models, and for evaluating the likelihood surface, in selection and mutation parameters, are developed and applied for observed data. The methods apply to large populations in settings in which selection is weak, in the sense that selection intensities, ...