Demographic inference using spectral methods on SNP data, with an analysis of the human out-of-Africa expansion.

ABSTRACT: We present an implementation of a recently introduced method for estimating the allele-frequency spectrum under the diffusion approximation. For single-nucleotide polymorphism (SNP) frequency data from multiple populations, the method computes numerical solutions to the allele-frequency spectrum (AFS) under a complex model that includes population splitting events, migration, population expansion, and admixture. The solution to the diffusion partial differential equation (PDE) that mimics the evolutionary process is found by means of truncated polynomial expansions. In the absence of gene flow, our computation of frequency spectra yields exact results. The results are compared to those that use a finite-difference method and to forward diffusion simulations. In general, all the methods yie

SUBMITTER: Lukic S 

PROVIDER: S-EPMC3454885 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature