Graduation Year


Document Type




Degree Name

Master of Science (M.S.)

Degree Granting Department

Marine Science

Major Professor

Frank Muller-Karger, Ph.D.

Committee Member

Christopher Stallings, Ph.D.

Committee Member

Steve Gittings, Ph.D.


Species Richness, Biodiversity, Functional Diversity, Species traits


The biological diversity of reef-fish in the Florida Keys National Marine Sanctuary (FKNMS) from 1999 – 2016 was evaluated in terms of abundance, biomass, species richness, evenness, Shannon diversity, Simpson diversity, and functional diversity, using observations collected by multiple agencies and institutions under the Reef Visual Census (RVC) program. To compare the different diversity indices species richness, Shannon diversity, Simpson diversity, and functional diversity were converted into effective number of species. I examined the seven indices by no-take marine zones, in seven benthic habitat strata, and across the three-distinct geographic subregions in the Florida Keys domain (Upper, Middle, and Lower Keys). The objective was to describe changes in reef fish community responses through time and space in the Florida Keys, and to determine whether patterns in reef fish diversity indices were attributable to levels of protection, benthic habitat strata, or geographic subregion. The goal was to develop a framework for reef fish biodiversity assessments that can inform management and policy in the FKNMS, and support updates to the periodic Condition Reports generated by the Sanctuary.

Diversity indices (with the exception of evenness) were significantly higher in no-take marine zones compared to areas open to fishing. All indices were significantly different by strata type. High Relief Reef habitats had the highest abundance, biomass, richness, Simpson diversity, Shannon diversity, and functional diversity, but had moderate evenness values. The biodiversity metrics for the Upper Keys and Lower Keys were not significantly different, but both of these areas were significantly different from the Middle Keys for all indices except species richness, which did not vary by subregion. Generalized additive models revealed that the principal driver across indices was habitat structure (strata and depth). Time (year), space (latitude, longitude), and no-take marine zones (0, unprotected and 1, protected) explained roughly similar proportions of deviance across all indices.

Simpson diversity, Shannon diversity, and functional diversity showed similar trends in no-take marine zones, strata, and subregion through time. The Florida Keys is characterized as having relatively low functional diversity due to a few common traits shared by many individuals and many rare traits shared by a few individuals. This suggests that the Florida Keys reef fish are less vulnerable to functional loss due to high functional redundancy among species. However, functionally rare traits, those possessed by few individuals, are vulnerable to functional loss and will have a larger impact on ecosystem functioning than species that share similar traits. Low functional diversity also suggests lower adaptability to environmental perturbations. Given the minimal robustness of traits, the ecosystem is less likely to possess functions that can withstand disturbances.

The impacts of two types of perturbations were examined in a qualitative manner: hurricanes and cold-temperature events. Disturbance by hurricanes in 2004 and 2005 and the extreme cold event of January 2010 had a high impact on reef fish community composition. Between 2004 and 2006, following two consecutive years of hurricanes, abundance of reef fish declined 31%, biomass declined 53%, species richness declined 18%, Simpson diversity declined 12%, Shannon diversity declined 14%, and functional diversity declined 8%. Following a year without hurricanes in 2007 abundance of reef fish increased 11%, biomass increased 13%, richness increased 14%, Simpson and Shannon diversity increased 10%, and functional diversity increased 6%. After the January 2010 extreme cold event, reef fish abundance and biomass also declined 17%, richness declined 10%, Simpson diversity and Shannon diversity declined 5% and 6%, and functional diversity declined 2%. All matrices increased the following year, where abundance increased 13%, biomass increased 31%, richness increased 13%, Simpson diversity increased 7%, Shannon diversity increased 10%, and functional diversity increased 8%.

Based on my findings and literature review, to better preserve biodiversity and enhance ecosystem functioning, I recommend prioritizing conservation efforts in source habitats (e.g., High Relief Reefs) and habitats with varying complexity by implementing corridor reserves that facilitate the natural migration of organisms between different habitat types. I also recommend prioritizing preservation of species that possess functionally rare traits with few individuals (e.g., cleaner species) by preserving areas with greater functional diversity (e.g., Higher Relief Reefs and Forereef Deep Linear Reefs).