| Summary: | <p>Abstract</p> <p>Background</p> <p>Mangroves are ecologically important and highly threatened forest communities. Observational and genetic evidence has confirmed the long distance dispersal capacity of water-dispersed mangrove seeds, but less is known about the relative importance of pollen vs. seed gene flow in connecting populations. We analyzed 980 <it>Avicennia germinans</it> for 11 microsatellite loci and 940 <it>Rhizophora mangle</it> for six microsatellite loci and subsampled two non-coding cpDNA regions in order to understand population structure, and gene flow within and among four major estuaries on the Caribbean and Pacific coasts of Panama.</p> <p>Results</p> <p>Both species showed similar rates of outcrossing (t= 0.7 in <it>A. germinans</it> and 0.8 in <it>R. mangle</it>) and strong patterns of spatial genetic structure within estuaries, although <it>A. germinans</it> had greater genetic structure in nuclear and cpDNA markers (7 demes > 4 demes and <it>Sp</it>= 0.02 > 0.002), and much greater cpDNA diversity (<it>H</it><sub><it>d</it></sub>= 0.8 > 0.2) than <it>R. mangle</it>. The Central American Isthmus serves as an exceptionally strong barrier to gene flow, with high levels nuclear (<it>F</it><sub><it>ST</it></sub>= 0.3-0.5) and plastid (<it>F</it><sub><it>ST</it></sub>= 0.5-0.8) genetic differentiation observed within each species between coasts and no shared cpDNA haplotypes between species on each coast. Finally, evidence of low ratios of pollen to seed dispersal (r = −0.6 in <it>A. germinans</it> and 7.7 in <it>R. mangle</it>), coupled with the strong observed structure in nuclear and plastid DNA among most estuaries, suggests low levels of gene flow in these mangrove species.</p> <p>Conclusions</p> <p>We conclude that gene dispersal in mangroves is usually limited within estuaries and that coastal geomorphology and rare long distance dispersal events could also influence levels of structure.</p>
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