Coral Decline and Reef Habitat Loss in the Caribbean: Modeling Abiotic Limitations on Coral Populations and Communities

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Viehman, T. Shay


Halpin, Patrick N
Hench, James L

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Coral reef habitats are well-known for biodiversity, yet are declining worldwide due to multiple stressors from local to global scales. Scleractinian corals, as foundation species, contribute to building the three-dimensional reef structure, yet this structure can be degraded through natural or anthropogenic disturbances. Conservation actions such as restoration depend on an understanding of the spatial distributions of potential habitat. In this dissertation, I address how abiotic environmental limitations shape coral species habitat niches and relate to recovery from disturbances. To accomplish this, I first describe local limitations on reef recovery after physical disturbances and then scale up to regional models of environmental niche constraints on coral species and communities.

First, I compare divergent recovery trajectories at two proximal reefs disturbed by ship groundings that created abrupt and clearly delineated areas of altered substrate. Despite similar initial physical disturbances, there were marked differences between the grounding sites with higher coral recruitment and survival on disturbed pavement than rubble bottom, reference reef, or restoration structures. I hypothesized that subsequent episodic disturbances from rubble mobilization could be a mechanism driving divergent recovery patterns. To estimate whether local hydrodynamic conditions were sufficient to mobilize rubble, I used a combination of long-term monitoring, hydrodynamic modeling, and rubble transport mechanics to hindcast the potential for substrate mobility. Long-term model simulations of hydrodynamic forcing at the study sites show multiple events where bottom-orbital velocities exceeded thresholds required to mobilize rubble via sliding or overturning. The data and analyses indicate that the wave energy mobilizes rubble substrate multiple times annually and suggests a physical limitation on survival of coral recruits relative to those on pavement substrate. The combination of multiple hydrodynamic disturbances and unstable substrate limits coral recovery and contributes to prolonged habitat loss.

I next scaled up to a seascape approach to model how environmental limitations on individual species impact the coral community response. I used a joint species distribution modeling approach with new and spatially extensive coral monitoring data from Puerto Rico and the U.S. Virgin Islands. Using a multivariate spatial modeling approach, I explained relationships between species and environments and predicted species abundances (and associated uncertainties) into new, unsurveyed geographic areas in the U.S. Caribbean region. Joint model results showed how coral populations and communities are structured by geomorphological and climate factors. Species abundances and sizes showed correlations between species niches relative to depth, slope, wave energy near the seafloor, and thermal stress. Using inverse prediction, I showed how a scenario of increased wave energy or increased temperature ranges may shift habitats for individual species and impact overall species richness.

I then focused specifically on four of the major reef-building coral species that are currently listed as Threatened under the Endangered Species Act: Acropora cervicornis, Orbicella annularis, O. faveolata, and O. franksi. I modeled environmental limitations on species distributions in terms of occurrence, abundance, and size in Puerto Rico and the U.S. Virgin Islands. I used Bayesian Generalized Linear Models to predict species occurrence and abundance. I then compared results to the generalized joint attribute models that included abundance and size. Specific model applications were dependent on data availability. All species responded in different ways to environmental predictors, yet all showed environmental limitations from depth, wave energy near the seafloor, and thermal regimes.

In summary, in this dissertation I modeled limitations on coral habitat by abiotic variables and, in particular, wave energy. I applied multiple spatial quantitative approaches from local scales to seascape scales. Information about disturbance frequency and wave energy constraints on habitat recovery are applicable to support habitat restoration efforts. Predicted spatial distributions from community and species modeling approaches will support species-based and site-based restoration, conservation, and management efforts.





Viehman, T. Shay (2017). Coral Decline and Reef Habitat Loss in the Caribbean: Modeling Abiotic Limitations on Coral Populations and Communities. Dissertation, Duke University. Retrieved from


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