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Identification of newly settled Caribbean coral recruits by ITS-targeted single-step nested multiplex PCR

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Abstract

As coral cover has declined throughout the Caribbean, interest in determining the potential for reef recovery via natural recruitment processes has increased. Studies investigating recruitment have been hampered by the difficulty of identifying early stage corals that often lack distinguishing morphological characters. In this study, the utility of targeting the noncoding ribosomal internal transcribed spacer (ITS) regions with a single-step nested multiplex (SSNM) PCR assay to identify common Caribbean coral species was investigated. To design this assay, a database of ITS sequences for 17 common Caribbean coral species was developed. Phylogenies based on the ITS region were generally consistent with current published coral taxonomy and indicated that the ITS regions provided sufficient variability to be useful for distinguishing corals to at least the genus level. Ultimately, we developed ITS-targeted single-step nested multiplex PCR assays capable of differentiating six corals to the species level, two to the genus level, and a pair of coral species that were recently separated at the genus level. This assay was used to classify coral recruits previously identified based on morphological characters. Agreement between these two approaches was low and highlighted the ability of the SSNM-PCR assay to increase the certainty and accuracy of coral recruit identifications. The coral SSNM assay shows promise as an effective method of identifying early stage corals to the genus or species level, and as a valuable tool in studies investigating reef recovery.

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Acknowledgements

We would like to thank members of the Florida Fish and Wildlife Conservation Commission Coral and Collections Teams, including Leah Harper, Mike Colella, Lindsay Huebner, Vanessa Brinkhuis, Tiffany Boisvert, Ari Halperin, Ananda Ellis, Katy Cummings, Laura Wiggins, Paul Larson, Krista Austin, and Miguel Montaluo for assistance in the field. We would also like to thank the many laboratories and investigators who provided DNA samples: Andrew Baker (University of Miami), Mary Alice Coffroth (State University of New York at Buffalo), Daniel Brazeau (University of New England), and Stephanie Schopmeyer (University of Miami). This project was completed through a grant provided by the National Oceanic and Atmospheric Administration’s Coral Reef Conservation Program (Federal Award #MOA-2010-026/8081) via a sub-award with the Florida Fish and Wildlife Conservation Commission (FWC Agreement #14208). This study was supported in part by the US National Science Foundation Awards OCE 082599 and OCE 1459293 to MEF. This project was also funded in part by the PADI Foundation to EDO.

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Authors and Affiliations

  1. James H. Oliver, Jr., Institute for Coastal Plain Science, Georgia Southern University, P.O. Box 8042, Statesboro, GA, 30460, USA

    Elijah D. O’Cain & Daniel F. Gleason

  2. Skidaway Institute of Oceanography, University of Georgia, 10 Ocean Science Circle, Savannah, GA, 31411, USA

    Marc E. Frischer & Tina L. Walters

  3. Department of Biology, Georgia Southern University, P.O. Box 8042-1, Statesboro, GA, 30460, USA

    J. Scott Harrison

  4. Skidaway Institute of Oceanography, University of Georgia, Memorial Health University Medical Center, 4700 Waters Avenue, Savannah, GA, 31404, USA

    Megan E. Thompson

  5. Halmos College of Natural Science and Oceanography, Nova Southeastern University, 8000 N. Ocean Drive, Dania Beach, FL, 33004, USA

    Nicole D. Fogarty

  6. Corals Program, Florida Fish and Wildlife Conservation Commission, 100 8th Avenue Southeast, Saint Petersburg, FL, 33701, USA

    Rob Ruzicka

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  1. Elijah D. O’Cain
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  2. Marc E. Frischer
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Correspondence to Elijah D. O’Cain.

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O’Cain, E.D., Frischer, M.E., Harrison, J.S. et al. Identification of newly settled Caribbean coral recruits by ITS-targeted single-step nested multiplex PCR. Coral Reefs 38, 79–92 (2019). https://doi.org/10.1007/s00338-018-01763-8

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