Why to account for finite sites in population genetic studies and how to do this with Jaatha 2.0.

ABSTRACT: With the advent of next-generation sequencing technologies, large data sets of several thousand loci from multiple conspecific individuals are available. Such data sets should make it possible to obtain accurate estimates of population genetic parameters, even for complex models of population history. In the analyses of large data sets, it is difficult to consider finite-sites mutation models (FSMs). Here, we use extensive simulations to demonstrate that the inclusion of FSMs is necessary to avoid severe biases in the estimation of the population mutation rate θ, population divergence times, and migration rates. We present a new version of Jaatha, an efficient composite-likelihood method for estimating demographic parameters from population genetic data and evaluate the usefulness of Jaath

SUBMITTER: Mathew LA 

PROVIDER: S-EPMC3810865 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature