Studies of gene flow and population structure in natural populations are no longer limited by the paucity of polymorphic genetic markers. Recently, simple sequence repeats (SSRs or microsatellites) and other DNA markers have increased the accuracy of previous estimates and broadened the resolution of studies. For several tropical tree species, we developed SSRs with up to 28 alleles at a single locus. We used these markers to assign paternity for up to 97% of the mating events; to characterize variation in outcrossing rates of individual trees; to estimate the average (142 m) and maximum (350 m) distance between mates within a population; and to estimate the percent of mating events that involved a male parent from outside the population. Further, our data indicate that deforestation has reduced gene flow and increased differentiation among isolated fragments. By combining the information obtained from nuclear SSRs and new maternally inherited organelle markers, we are now dissecting gene flow into pollen and seed flow components. The current assessment shows that these plastid markers also exhibit profound levels of polymorphism among congeners. We discuss these results in the context of landscape changes in the tropics and the overall strategies for conservation of biodiversity.

Key words: Carapa guianensis, chloroplast, microsatellites, Pithecellobium elegans, population structure, reduced geneflow