RT Journal Article
SR Electronic
T1 Understanding Admixture Fractions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 008078
DO 10.1101/008078
A1 Mason Liang
A1 Rasmus Nielsen
YR 2014
UL http://biorxiv.org/content/early/2014/08/16/008078.abstract
AB Estimation of admixture fractions has become one of the most commonly used computational tools in population genomics. How ever, there is remarkably little population genetic theory on their statistical properties. We develop theoretical results that can accurately predict means and variances of admixture proportions within a population using models with recombination and genetic drift. Based on established theory on measures of multilocus disequilibrium, we show that there is a set of recurrence relations that can be used to derive expectations for higher moments of the admixture fraction distribution. We obtain closed form solutions for some special cases. Using these results, we develop a method for estimating admixture parameters from estimated admixture proportion obtained from programs such as Structure or Admixture. We apply this method to HapMap data and find that the population history of African Americans, as expected, is not best explained by a single admixture event between people of European and African ancestry. A model of constant gene flow for the past 11 generations until 2 generations ago gives a better fit.