Big-leaf mahogany (Swietenia macrophylla) is one of the most valuable and overharvested timber trees of tropical America. A description of the organization of genetic variation across its broad range would be useful for management of genetic diversity and for understanding its demographic history. Here we report on a phylogeographic analysis of mahogany based on six polymorphic cpDNA simple sequence repeat loci (cpSSRs) genotyped in 16 populations distributed across the Brazilian Amazon and Mesoamerica (N = 245 individuals). Of the 31 cpDNA haplotypes identified, 15 occurred in Amazonia and 16 in Mesoamerica with no single haplotype shared between the two regions. The populations from Central America showed moderate differentiation (FST = 0.36) while within population genetic diversity was generally high (mean Nei's HE = 0.639). In contrast, the Amazonian populations were strongly differentiated (FST = 0.95) and contained low haplotype diversity (mean HE = 0.176), with the exception of the highly diverse Marajoara population from the Eastern Amazon (HE = 0.925). SAMOVA identified a single Mesoamerican phylogroup and four Amazonian phylogroups, indicating stronger phylogeographic structure within Amazonia. The results demonstrate high levels of cpDNA variation and differentiation of regional S. macrophylla populations, and provide the first evidence of a major phylogeographic break between Mesoamerican and South American mahogany populations
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