Defense Date

12-2-2025

Document Type

Thesis

Degree Type

Master of Science

Degree Name

Marine Science

First Advisor

Jose V. Lopez, Ph.D.

Second Advisor

Steven L. Miller, Ph.D., smiller52@gmail.com

Third Advisor

Karen Neely, Ph.D.

Keywords

environmental DNA, critically endangered species, functionally extinct species, Acropora cervicornis, species-specific detection

Abstract

Historically, Acropora cervicornis was a dominant coral on Caribbean reef systems, but an outbreak of white band disease in the late 1970s marked the beginning of devastating, multi-decadal population declines that led to the coral being listed as “critically endangered” on the IUCN Red List in 2022. Today, after a record-setting marine heat wave in 2023 triggered a mass bleaching event on Florida’s Coral Reef (FCR), A. cervicornis is considered functionally extinct on the FCR. While individuals of A. cervicornis do remain on the FCR, the small population size of the coral makes in situ surveys difficult. However, surveys using environmental DNA (eDNA) are proving very useful in ecological studies of low-density species, as eDNA is capable of detecting organisms that may be missed by traditional visual methods. Although eDNA surveys are very popular, most studies using them are designed for the detection of mobile animals, with very few studies using targeted eDNA techniques to detect sessile marine invertebrates. This study designed an eDNA protocol for the targeted, species-specific detection of the critically endangered Caribbean staghorn coral, A. cervicornis. Beyond establishing eDNA collection and extraction techniques, this protocol presents three universal and two targeted primers that are capable of amplifying A. cervicornis DNA in tissue and aquaria (i.e. tank water) samples. Unfortunately, only one primer was capable of amplifying A. cervicornis eDNA from a field sample. However, this field sample was collected directly above a tree of A. cervicornis fragments, suggesting that water samples ought to be collected above living corals to have a higher chance of containing detectable coral eDNA. This protocol requires further optimization to consistently detect A. cervicornis eDNA in field samples, but it is a first step in exploring the potential for eDNA techniques to complement traditional ones for monitoring low density coral species.

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