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Open Access Highly Accessed Research article

Comparative genetic structure of two mangrove species in Caribbean and Pacific estuaries of Panama

Ivania Cerón-Souza12*, Eldredge Bermingham1, William Owen McMillan1 and Frank Andrew Jones13

Author Affiliations

1 Smithsonian Tropical Research Institute, Apartado, 0843-03092, Panama

2 University of Puerto Rico, Rio Piedras Campus, PO BOX 23360, San Juan, 00931-3360, Puerto Rico

3 Department of Botany and Plant Pathology, Oregon State University, 2070 Cordley Hall, Corvallis, OR, 97331, USA

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BMC Evolutionary Biology 2012, 12:205  doi:10.1186/1471-2148-12-205

Published: 18 October 2012

Additional files

Additional file 1:

Genetic diversity of nuclear (i.e. microsatellites) and chloroplast genomes for Avicennia germinans (black mangrove) and Rhizophora mangle (red mangrove) in Panama. The number of individuals analyzed per estuary, the number of alleles, observed heterocigosity (Ho), and the expected heterocigosity (He) of microsatellites calculated with GENALEX 6.0 is shown. In addition, the number of individuals analyzed per estuary, the number of haplotypes and the haplotype diversity found in chloroplast using DNASP 4.5 and NETWORK 4.5.1.0 (fluxus-engineering.com), and the GenBank accession number of each individual analyzed is indicated.

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Additional file 2:

Median joining network indicating and geographic distribution of cpDNA haplotypes found in Avicennia germinans (Black mangrove). Within the network, the haplotype name and the number of individuals per each haplotype is indicated. In addition, for each estuary, the geographic distribution of haplotypes and their frequency (i.e. pie) is indicated.

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Additional file 3:

Median joining network indicating and geographic distribution of cpDNA haplotypes found in Rhizophora mangle (Red mangrove). Within the network the haplotype name and the number of individuals per each haplotype is indicated. In addition, for each estuary the geographic distribution of haplotypes and their frequency (i.e. pie) is indicated.

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Additional file 4:

PCR conditions for 11 microsatellite loci for A. germinans (black mangrove) [[65,66]] and six microsatellite loci for R. mangle (red mangrove) [[67]] following established protocols [[13,65,66]] with modifications including three primers in the PCR thus: a dye tagged M13 universal forward primer (5’-CACGACGTTGTAAAACGAC-3’)[[68]], primer Forward (F) and primer Reverse (R) where either F or R primer (indicated with asterisk *) had a tail at the 5’ end that was identical to the M13 universal forward primer sequence. Amplified fragments from both mangrove species were electrophoretically separated on ABI 3130xl and analyzed using ABI PRISM® GeneMapper™ software version 3.7. For each estuary is indicated the frequency of null alleles calculated by the Brookfield method 1 in MICROCHECKER 2.2.3 [72].

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Open Data

Additional file 5:

Bayesian genetic assignment of Avicennia germinans (black mangrove) from two Caribbean (Bocas del Toro and Costa Arriba) and two Pacific (Montijo Gulf and San Miguel Gulf) estuaries in Panama based on STRUCTURE ver. 2.2 and GENELAND ver. 2.0.12. The true K for each procedure after simulations is indicated.

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Additional file 6:

Bayesian genetic assignment of Rhizophora mangle (Red mangrove) from two Caribbean (Bocas del Toro and Costa Arriba) and two Pacific (Montijo Gulf and San Miguel Gulf) estuaries in Panama based on STRUCTURE ver. 2.2, INSTRUCT and GENELAND. 2.0.12. The true K for each procedure after simulations is indicated. In addition, INSTRUCT was used to help to simultaneously infer the selfing rates of this mixed mating species and the demic structure on both sides of the Isthmus.

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