Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic variants within and between populations. For candidate models we numerically compute the expected spectrum using a diffusion approximation to the one-locus, two-allele Wright-Fisher process, involving up to three simultaneous populations. Our approach is a composite likelihood scheme, since linkage between neutral loci alters the variance but not the expectation of the frequency spectrum. We thus use bootstraps incorporating linkage to estimate uncertainties for parameters…

• NS
  National Science Foundation

  Awards: DE-AC52-06NA25396, PHY05-51164
• UD
  U.S. Department of Energy

  Awards: DE-AC52-06NA25396, AC52-06NA25396, contract DE-AC52-06NA25396
• NI
  National Institutes of Health

  Award: DE-AC52-06NA25396
• NI
  National Institute of Environmental Health Sciences