Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species

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.