When populations or species have recently separated they often share genetic variation.
However, it can be difficult to determine whether shared polymorphisms are the result of
gene flow, the result of the persistence of variation in both populations since the time
of common ancestry, or both of these factors. We have developed an empirical protocol
for using loci that include unique nuclear DNA sequence haplotypes together with linked
microsatellites or short tandem repeats (STRs). These 'HapSTRs' offer the potentially
high resolution associated with the high mutation rate of STRs, together with the
advantages of low homoplasy of unique sequence DNA. We also describe a new procedure for
estimating the likelihood of HapSTR data under an Isolation with Migration model. An
example using Cichlid fishes from Lake Malawi is described. The analysis suggests that
the species have been exchanging genes since the time they began to diverge.