Empirical tests of the reliability of phylogenetic trees constructed with microsatellite DNA

Microsatellite DNA loci or short tandem repeats (STRs) are abundant in eukaryotic genomes and are often used for constructing phylogenetic trees of closely related populations or species. These phylogenetic trees are usually constructed by using some genetic distance measure based on allele frequency data, and there are many distance measures that have been proposed for this purpose. In the past the efficiencies of these distance measures in constructing phylogenetic trees have been studied mathematically or by computer simulations. Recently, however, allele frequencies of 783 STR loci have been compiled from various human populations. We have therefore used these empirical data to investigate the relative efficiencies of different distance measures in constructing phylogenetic trees. The results showed that (1) the probability of obtaining the correct branching pattern of a tree (PC) is generally highest for DA distance; (2) FST*, standard genetic distance (DS), and FST/(1-FST) give similar PC-values, FST* being slightly better than the other two; and (3) (deltamu)2 shows PC-values much lower than the other distance measures. To have reasonably high PC-values for trees similar to ours, at least 30 loci with a minimum of 15 individuals are required when DA distance is used.