Originally published as Genetics Published Articles Ahead of Print on August 24, 2007.

Genetics, Vol. 177, 1043-1057, October 2007, Copyright © 2007
doi:10.1534/genetics.107.078998

Joint Estimation of Migration Rate and Effective Population Size Using the Island Model

Garrick T. Skalski1

Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045

1 Corresponding author: 1637 Merion Pl., Lawrence, KS 66047.
E-mail: gt.skalski{at}gmail.com

Using the island model of population demography, I report that the demographic parameters migration rate and effective population size can be jointly estimated with equilibrium probabilities of identity in state calculated using a sample of genotypes collected at a single point in time from a single generation. The method, which uses moment-type estimators, applies to dioecious populations in which females and males have identical demography and monoecious populations with no selfing and requires that offspring genotypes are sampled following reproduction and prior to migration. I illustrate the estimation procedure using the infinite-island model with no mutation and the finite-island model with three kinds of mutation models. In the infinite-island model with no mutation, the estimators can be expressed as simple functions of estimates of the F-statistic parameters FIT and FST. In the finite-island model with mutation among k alleles, mutation rate, migration rate, and effective population size can be simultaneously estimated. The estimates of migration rate and effective population size are somewhat robust to violations in assumptions that may arise in empirical applications such as different kinds of mutation models and deviations from temporal equilibrium.