Term of Award

Summer 2017

Degree Name

Master of Science in Biology (M.S.)

Document Type and Release Option

Thesis (open access)

Copyright Statement / License for Reuse

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.


Department of Biology

Committee Chair

Daniel Gleason

Committee Member 1

John Harrison

Committee Member 2

Marc Frischer


As coral cover has declined throughout the Caribbean, interest in the role that recruitment processes play in reef recovery has increased. Studies investigating these processes have been hampered by the inability to identify many species of coral larvae or recently settled recruits using morphology. In this study, the utility of targeting the non-coding internal transcribed spacer (ITS) regions with a multiplex PCR assay to identify common Caribbean coral species was explored. To design this assay, a database of ITS sequences was developed for 17 Caribbean scleractinian coral species that are important reef builders and/or common in the Florida Keys. It was predicted that the ITS region would contain enough genetic variation to allow for separation of these corals to the species level, and that this variation could be targeted using a single-step nested multiplex PCR technique. Analyzing the ITS region, sufficient genetic variation was detected that would allow for nine of the seventeen Caribbean coral species targeted to be categorized to the genus level, and the remaining eight to the species level. Subsequently, three genus-specific primers and six species-specific primers were designed for use in a SSNM-PCR protocol that facilitates coral identification. While still under development, this genetic assay showed significant promise as an efficient method of identifying planula larvae and recently settled coral recruits to the genus or species level. The increased accuracy and abbreviated timeframe offered by this technique for identifying coral larvae and recruits justifies its use as a tool for evaluating Caribbean reef recovery moving forward.

Research Data and Supplementary Material


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