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Genetic diversity, population differentiation, and temporal variation in outcrossing rates were examined for Pithecellobium elegans, a Neotropical rain forest canopy tree. Several forest fragments and a large reserve (1500 ha) were compared for several population genetic parameters. For eight populations sampled on the Atlantic coastal plain of Costa Rica, allozyme heterozygosity (0.13), polymorphism (35%), and effective number of alleles (1.24) were similar to values reported for other tropical tree species that occur at similar densities of less than one individual per hectare. These measures of genetic variation were lowest in populations of the smallest size, farthest from the reserve, and more isolated from other populations. Differentiation among samples collected in small forest fragments and the reserve population accounted for 10% of the total genetic variation observed. There was a positive relationship between the level of differentiation of populations from the reserve population and their distance from the reserve. Though predominantly an annually flowering species, the number of trees in flower at any one time varied from 80% of observed trees to only 6%. Outcrossing rates did not differ for two episodes in which the proportions of flowering trees were 33% and 80%. But periods of low density of flowering adults resulted in poor seed crops or failure to set fruit for many individuals. Population size at many sites will be effectively decreased because of the variation in flowering. Fragmentation of what was once a large, continuous forested area is resulting in genetic erosion of small, isolated populations of Pithecellobium elegans.

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