Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Theor Popul Biol. 2011 Jun;79(4):203-19. doi: 10.1016/j.tpb.2011.02.003. Epub 2011 Mar 2.

Non-equilibrium allele frequency spectra via spectral methods.

Author information

  • 1Department of Genetics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854, USA.

Abstract

A major challenge in the analysis of population genomics data consists of isolating signatures of natural selection from background noise caused by random drift and gene flow. Analyses of massive amounts of data from many related populations require high-performance algorithms to determine the likelihood of different demographic scenarios that could have shaped the observed neutral single nucleotide polymorphism (SNP) allele frequency spectrum. In many areas of applied mathematics, Fourier Transforms and Spectral Methods are firmly established tools to analyze spectra of signals and model their dynamics as solutions of certain Partial Differential Equations (PDEs). When spectral methods are applicable, they have excellent error properties and are the fastest possible in high dimension; see Press et al. (2007). In this paper we present an explicit numerical solution, using spectral methods, to the forward Kolmogorov equations for a Wright-Fisher process with migration of K populations, influx of mutations, and multiple population splitting events.

Copyright © 2011 Elsevier Inc. All rights reserved.

PMID:
21376069
[PubMed - indexed for MEDLINE]
PMCID:
PMC3410934
Free PMC Article

Images from this publication.See all images (8)Free text

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Icon for Elsevier Science Icon for PubMed Central
    Loading ...
    Write to the Help Desk