A Markov chain Monte Carlo method for estimating the relative effects of mi
gration and isolation on genetic diversity in a pair of populations from DN
A sequence data is developed and tested using simulations. The two populati
ons are assumed to be descended from a panmictic ancestral population at so
me time in the past and may (or may not) after that be connected by migrati
on. The use of a Markov chain Monte Carlo method allows the joint estimatio
n of multiple demographic parameters in either a Bayesian or a likelihood f
ramework. The parameters estimated include the migration rate for each popu
lation, the time since the two populations diverged from a common ancestral
population, and the relative size of each of the two current populations a
nd of the common ancestral population. The results show that even a single
nonrecombining genetic locus can provide substantial power to test the hypo
thesis of no ongoing migration and/or to test models of symmetric migration
between the mio populations. The use of the method is illustrated in an ap
plication to mitochondrial DNA sequence data from a fish species: the three
spine stickleback (Gasterosteus aculeatus).