Graduation Year


Document Type




Degree Name

Doctor of Philosophy (Ph.D.)

Degree Granting Department

Marine Science

Major Professor

Pamela Hallock Muller, Ph.D.

Committee Member

Kendra Daly, Ph.D.

Committee Member

Ilsa Kuffner, Ph.D.

Committee Member

Brad Rosenheim, Ph.D.

Committee Member

Armando Hoare, Ph.D.

Committee Member

Walt Jaap, B.S.


bioindicator, gorgonian, isotope, PERMANOVA, photogrammetry, SfM


One consequence of dramatic stony-coral loss has been recognition that gorgonian octocorals (Anthozoa: Octocorallia) have emerged among the dominant reef fauna. However, gorgonians are notoriously difficult to field-identify and consequently have been underrepresented in most monitoring efforts resulting in a lack of long-term data. The rich diversity of habitats, close proximity to the urban center of Miami, and connectivity to other areas of Florida have made Biscayne National Park an active location for reef research since its establishment in 1968. As such, a plethora of data (e.g., museum specimen and species abundance data) has been collected and stored in archives over time. This dissertation examines strategies to document and quantify changes in gorgonian assemblages using both archival and newly-collected data sources, and proposes methods that can be applied more widely to document the responses of gorgonians to ongoing environmental changes associated with both local and global processes.

To begin, I compiled widely scattered taxonomical, biological, and ecological research on shallow-water symbiotic gorgonians in the wider-Caribbean to identify data gaps and provide a comprehensive resource document to inform and promote future work. Then I used multivariate techniques to compare an archived octocoral assemblage dataset collected annually from 1977–81 in Biscayne National Park (BNP), with data collected at the same sites in 2016. The data revealed an overall decline in abundance of gorgonians since the 1970s, with a substantial increase in the relative abundance of stress-tolerant species such as Antillogorgia spp. Long-term comparative studies such as this are essential to understanding shifts in community structure and to provide a permanent record by which future change, can be assessed and managed.

Because field identification is time-consuming and often requires microscopic verification by taxonomic experts, I developed a method to identify gorgonians to genus level using high-resolution orthomosaic imagery, based on morphologic characters that are visible in images taken from a top-down perspective. This first attempt at developing criteria for macroscopically identifying gorgonians from landscape images yielded classification success of 92% for an observer familiar with gorgonian taxonomy and 88% for a novice observer. With refinement, this method has the potential to encourage more detailed evaluation of gorgonians in monitoring programs and to provide opportunities for filling research gaps using retrospective studies of archived photographic data.

Accurate classifications are heavily reliant on image quality; however, underwater images often exhibit a range of degradations caused by absorption and scattering of light. Image enhancements are a practical solution to counteract these degradations and provide added flexibility for acquisition. Therefore, in addition to classification methods I also evaluated the performance of nine accessible and automated image-enhancement techniques for use in shallow-water benthic surveys, as well as explored the effect of enhancement on orthomosaic alignment. The top performing enhancement techniques for shallow water to be Contrast Limited Adaptive Histogram Equalization on each color channel (CLAHE RGB) and three user-friendly Adobe® Photoshop® automated techniques.

More recently, gorgonians are being used in stable-isotopic studies as proxies for detecting anthropogenic nutrient inputs from heavily urbanized locations and offer a potential solution for filling data gaps. Using museum and freshly-collected specimens of three abundant gorgonian species, Antillogorgia acerosa, Eunicea flexuosa, and Pterogorgia anceps, I examined species, temporal, and spatial variations in δ15N and δ13C values from two sites in BNP: a north-central site at the mouth of Biscayne Bay and a south central site on the outer reef. Significant differences in δ15N were detected between sites, but not between species or years, while δ13C values were significantly different between species, sites, and years.

In summary, gorgonians are essential components of shallow-water coral reefs and other hard-bottom communities around the western Atlantic, Caribbean and Gulf of Mexico, yet have been under-represented in most monitoring efforts. This dissertation summarizes historical data and provides recommendations on strategies to more fully utilize previously collected samples and data, which then can be compared with results from recent or proposed field-sampling efforts. The results can provide resource management with more comprehensive information on long-term changes in these essential habitats.