Quantifying genetic variation across multiple populations

Supervisor: David Balding

Available for: MSc only

Location: Melbourne Integrative Genomics, University of Melbourne

Project title: Quantifying genetic variation across multiple populations

Description: The genetic distance between two populations has traditionally been measured by a parameter called F_ST (S is for subpopulation, T is for total population).  There has long been disagreement over its precise definition and the best way to estimate it.  These disagreements became important with the advent of genome-wide genotype data, with estimates of inter-continental human genetic distances differing almost by a factor of  two due to different definitions with different sensitivities to rare variants. The problem has now largely been resolved for pairs of populations, but there remains the problem of defining and estimating F_ST for multiple populations.  A recent academic visitor to Melbourne, Dr Tristan Mary-Huard from AgroParisTech, France, made considerable progress in clarifying the definition and developing fast and efficient method-of-moments estimators of F_ST for multiple populations.  He also developed a fast and simple procedure for building population trees in which the branch lengths correspond to F_ST. In this project we will develop this work further, in collaboration with Dr Mary-Huard, to construct more general graphical structures representing the genetic variation across a set of populations that may have had historical episodes of admixture, in particular the human populations of the Americas.