  Chloroplast microsatellites have been widely used in population genetic
studies of conifers in recent years. However, their haplotype configurations
suggest that they could have high levels of homoplasy, thus limiting the power
of these molecular markers. A coalescent-based computer simulation was used to
explore the influence of homoplasy on measures of genetic diversity based on
chloroplast microsatellites. The conditions of the simulation were defined to
fit isolated populations originating from the colonization of one single
haplotype into an area left available after a glacial retreat. Simulated data
were compared with empirical data available from the literature for a species
of Pinus that has expanded north after the Last Glacial Maximum. In the
evaluation of genetic diversity, homoplasy was found to have little influence
on Nei's unbiased haplotype diversity (H(E)) while Goldstein's genetic distance
estimates (D2sh) were much more affected. The effect of the number of
chloroplast microsatellite loci for evaluation of genetic diversity is also
discussed.
