Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data.

ABSTRACT: With the recent increase in study sample sizes in human genetics, there has been growing interest in inferring historical population demography from genomic variation data. Here, we present an efficient inference method that can scale up to very large samples, with tens or hundreds of thousands of individuals. Specifically, by utilizing analytic results on the expected frequency spectrum under the coalescent and by leveraging the technique of automatic differentiation, which allows us to compute gradients exactly, we develop a very efficient algorithm to infer piecewise-exponential models of the historical effective population size from the distribution of sample allele frequencies. Our method is orders of magnitude faster than previous demographic inference methods based on the frequency

SUBMITTER: Bhaskar A 

PROVIDER: S-EPMC4315300 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature