A Coalescent Model of Ancestry for a Rare Allele

Corresponding author: Elizabeth A. Thompson, Department of Statistics, University of Washington, Box 354322, Seattle, WA 98195., thompson{at}stat.washington.edu (E-mail)

Communicating editor: S. TAVARÉ

In disequilibrium mapping from data on a rare allele, interest may focus on the ancestry of a random sample of current descendants of a mutation. The mutation is assumed to have been introduced into the population as a single copy a known time ago and to have reached a given copy number within the population. Theory has been developed to describe the ancestral distribution under arbitrary patterns of population expansion. Further results permit convenient realization of the ancestry for a random sample of copies of a rare allele within populations of constant size or within populations growing or shrinking at constant exponential rate. In this article, we present an efficient approximate method for realizing coalescence times under more general patterns of population growth. We also apply diagnostics, checking the age of the mutation. In the course of the derivation, some additional insight is gained into the dynamics of the descendants of the mutation.