Recently many investigators have used microsatellite DNA loci for studying the evolutionary relationships of closely related populations or species, and some authors proposed new genetic distance measures for this purpose. However, the efficiencies of these distance measures in obtaining the correct tree topology remains unclear. We therefore investigated the probability of obtaining the correct topology (PC) for these new distances as well as traditional distance measures by using computer simulation. We used both the infinite-allele model (IAM) and the stepwise mutation model (SMM), which seem to be appropriate for classical markers and microsatellite loci, respectively. The results show that in both the IAM and SMM Cavalli-Sforza and Edwards' chord distance (Dc) and NEI et al.'s DA distance generally show higher PC values than other distance measures, whether the bottleneck effect exists or not. For estimating evolutionary times, however, NEI'S standard distance and Goldstein et al's (δμ) are more appropriate than other distances. Microsatellite DNA seems to be very useful for clarifying the evolutionary relationships of closely related populations.
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