Dataset: Multilocus microsatellite genotypes of Acropora palmata from the Caribbean and North-West Atlantic from 2015-2016 (Coral Hybridization project)

Final no updates expectedDOI: 10.26008/1912/bco-dmo.666350.1Version 1 (2016-11-30)Dataset Type:Other Field Results

Principal Investigator: Iliana B. Baums (Pennsylvania State University)

BCO-DMO Data Manager: Nancy Copley (Woods Hole Oceanographic Institution)


Project: Collaborative research: Is hybridization among threatened Caribbean coral species the key to their survival or the harbinger of their extinction? (Coral Hybridization)


Abstract

Genotypes for the coral, Acropora palmata collected throughout the Caribbean from five microsatellite loci . A. palmata is a diploid species, however, somatic mutations in the form of third and fourth alleles per locus are occasionally detected. Data are in columns of region, database_id, genet_id, mutant_id, locus, allele, and size_bp. These data were deposited in DRYAD: http://dx.doi.org/10.5061/dryad.f6600 and published in the paper Devlin-Durante et al, Mol Ecol. (2016).

Adult Acropora palmata colonies were sampled (1 cm2) with hammer and chisel and tissues were preserved in 96% non-denature Ethanol. DNA was extracted using the DNEasy tissue kit (Qiagen) following manufacturer’s instructions.  Two multiplex Polymerase Chain Reactions (PCR) were performed per sample using fluorescently labeled primers to assay five loci containing AAT repeats. These five microsatellite loci have previously been demonstrated to be mendelian and coral-specific using controlled crosses (Baums et al., 2005). PCR products were visualized with an automated sequencer (ABI 3730). An internal size standard (Gene Scan 500-Liz, Applied Biosystems CA) ensured accurate sizing. Electropherograms were analyzed with GeneMapper Software 3.0 (Applied Biosystems, CA). Alleles were scored as PCR product size.

References:

Baums IB, Devlin-Durante MK, LaJeunesse TC (2014) New insights into the dynamics between reef corals and their associated dinoflagellate endosymbionts from population genetic studies. Molecular Ecology 23, 4203-4215.

Baums IB, Hughes CR, Hellberg MH (2005) Mendelian microsatellite loci for the Caribbean coral Acropora palmata. Marine Ecology - Progress Series 288, 115-127 for details on PCR amplification.

Devlin-Durante MK, Miller MW, Caribbean Acropora Research G, Precht WF, Baums IB. How old are you? Genet age estimates in a clonal animal. Mol Ecol. 2016. doi: 10.1111/mec.13865 for details on how mutations were scored.


Related Datasets

Different Version

Dataset: https://doi.org/10.5061/dryad.f6600
Devlin-Durante, M. K., Miller, M. W., Caribbean Acropora Research Group, Precht, W. F., and Baums, I. B. (2017). Data from: How old are you? Genet age estimates in a clonal animal (Version 2) [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.f6600
IsRelatedTo

Dataset: Acropora palmata mutations
Baums, I. B. (2021) Mutations at microsatellite loci of Acropora palmata in the Caribbean and North-West Atlantic from 2015-2016 (Coral Hybridization project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2017-10-19 doi:10.26008/1912/bco-dmo.666321.2

Related Publications

Results

Devlin-Durante, M. K., Miller, M. W., Precht, W. F., & Baums, I. B. (2016). How old are you? Genet age estimates in a clonal animal. Molecular Ecology, 25(22), 5628–5646. doi:10.1111/mec.13865
General

Baums, I. B., Devlin-Durante, M. K., & LaJeunesse, T. C. (2014). New insights into the dynamics between reef corals and their associated dinoflagellate endosymbionts from population genetic studies. Molecular Ecology, 23(17), 4203–4215. doi:10.1111/mec.12788
Methods

Baums, I., Hughes, C., & Hellberg, M. (2005). Mendelian microsatellite loci for the Caribbean coral Acropora palmata. Marine Ecology Progress Series, 288, 115–127. doi:10.3354/meps288115