Exploring Population Size Changes Using SNP Frequency Spectra

Nat Genet. 2015 May;47(5):555-9. doi: 10.1038/ng.3254. Epub 2015 Apr 6.

Abstract

Inferring demographic history is an important task in population genetics. Many existing inference methods are based on predefined simplified population models, which are more suitable for hypothesis testing than exploratory analysis. We developed a novel model-flexible method called stairway plot, which infers changes in population size over time using SNP frequency spectra. This method is applicable for whole-genome sequences of hundreds of individuals. Using extensive simulation, we demonstrate the usefulness of the method for inferring demographic history, especially recent changes in population size. We apply the method to the whole-genome sequence data of 9 populations from the 1000 Genomes Project and show a pattern of fluctuations in human populations from 10,000 to 200,000 years ago.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Gene Frequency
  • Genome, Human
  • Haplotypes
  • Humans
  • Models, Genetic*
  • Polymorphism, Single Nucleotide*
  • Population Dynamics*