Forest fragments along the Atlantic coastland of Brazil have been highly impacted by extensive human activities for the last 400 years. Caesalpinia echinata (Leguminosae– Caesalpinioideae), brazilwood, was overexploited during this period due to its economical importance as a dye. As a result, the species has become endangered and today its total population size is very restricted. We have assessed the distribution of genetic variation between five natural populations of brazilwood by means of RAPD (random amplified polymorphic DNA) markers. Of the total genetic variability, 28.5% was attributable to differences between two geographical groups, 29.6% to population differences within groups and 42.0% to individual differences within populations. The high level of population differentiation observed is in contrast to that expected for a primarily outcrossed woody perennial plant, and suggests that there may be a degree of inbreeding. Our results are in agreement with previous studies which postulated that C. echinata has always occurred in clumps, being common in some places but rare in between. From a conservation point of view, different populations representing different regions should be protected and, yet, plants with different origins should not be synthesized into populations in a recovery process at the risk of loss and dilution of genetic information. This study demonstrates that RAPD markers were effective in establishing a clear correlation between genetic and geographical distance and in identifying areas of maximum diversity, and may be used as an initial approach to assess the partitioning of genetic variation in this endangered species.
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