Browsing by Author "Hench, James"

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.

Ocean circulation is integral to reef ecosystem health and resilience; waves and currents replenish nutrients, transport coral and fish larvae between populations, and moderate temperatures. On many reefs, wave-driven or tidal flow through reef passes is the dominant mechanism of exchange with the open ocean. The fate of the jet as it flows onto the forereef slope, however, is understudied. In this study, numerical simulations of wave-driven flow on an idealized coral island with periodically spaced reef passes were conducted and examined across a range of planetary rotation and bottom friction conditions. For higher latitude, lower friction cases, adjacent jets interacted due to the deflection of the jet by planetary rotation and weak attenuation by friction - a previously undescribed phenomenon. The physics of reef pass jet deflection were then examined using a novel reformulation of the barotropic vorticity balance in terms of flow curvature. The resultant curvature gradient equation was used to interpret a series of idealized numerical modeling experiments of a barotropic outflow jet onto a slope in shallow water using a depth-averaged circulation model (ROMS). The trajectory of the jet was explained by the curvature dynamics along its center streamline, with topography, planetary rotation, and bottom friction strongly influencing the course. Articulating the key processes of nearfield jet deflection in terms of curvature distilled the complex 2D phenomenon into a tractable 1D initial value problem, exhibiting predictive skill and clarifying the poorly understood dynamics of a nonlinear feature. A third element of this work examined population dynamics on reefs. Larval flux, as determined by demography and hydrodynamics, is integral to the recovery of a subpopulation after a disturbance, but few studies have connected annual time-scale coral population dynamics to larval recruitment.Here, a model for coral population growth was developed that synthesized metapopulation theory with classical population dynamics. It was validated against a case study of remarkable coral recovery after near extirpation. Model simulations suggest that a combination of steady background larvae source and favorable local growth conditions explain the recovery of coral on this reef, implying that the succeeding coral colonies are likely endogenic.

In shallow water systems like coral reefs, bottom friction is often a significant part of the overall momentum balance. The frictional effects of the bottom on the flow are in part determined by the structure of the topography, which varies over orders of magnitude in spatial scale. Predicting spatial and temporal patterns of water motion depends on adequately capturing the relevant properties of the topography. However, representing and quantifying the complex, heterogeneous structure of coral reefs using measures of roughness or geometry remains a challenge.

Many roughness metrics have been proposed to relate seafloor structure to biological and physical processes. In Chapter 1, we assess the properties captured by one-dimensional roughness metrics previously proposed for the seafloor, as well as metrics developed to characterize other types of rough surfaces. We consider three classes of metrics: properties of the bottom elevation distribution (e.g., standard deviation), length scale ratios (e.g., rugosity), and metrics that describe how topography varies with spatial scale (e.g., Hölder exponents). We evaluate these metrics using idealized topography and natural seafloor topography of a reef lagoon system from airborne lidar measurements. The analyses illustrate that common metrics of bathymetric roughness (e.g., rugosity) can have the same value for topographies that are geometrically very different, thus limiting their utility. Application of the wavelet leaders technique to the reef dataset demonstrates that the topography has a power law scaling behavior, but it is multifractal so a distribution of Hölder exponents is needed to describe its scaling behavior. Using principal component analysis, we identify three dominant modes of topographic variability, or ways metrics covary, among and within reef zones. While individual roughness metrics that capture specific topography properties relevant to a given process may be suitable for some studies, for many applications, adequately parameterizing bathymetric roughness will require a set of metrics.

For reefs where the roughness layer takes up a large fraction of the water column, parameterizations of bottom friction require a representation of three-dimensional canopy geometry. In Chapter 2, we assess the implications of using obstacle- and surface-based representations to estimate geometric properties of coral colonies needed to parameterize drag. We collected high-resolution topography data using a scanning multi-beam sonar that resolved individual coral colonies within a set of 100 m2 reef patches primarily composed of mounding Porites corals. The topography measurements yielded 1-cm resolution gridded surfaces consisting of a single elevation value for each position in a regular horizontal grid. These surfaces were analyzed by (1) defining discrete obstacles and quantifying their properties (dimensions, shapes), and (2) computing properties of the elevation field (rms elevations, rms slopes, spectra). We then computed the roughness density (i.e., frontal area per unit plan area) using both analysis approaches. The obstacle and surface-based estimates of roughness density did not agree, largely because small-scale topographic variations contributed significantly to total frontal area. These results challenge the common conceptualization of shallow-water canopies as obstacle arrays, which may not capture significant contributions of high-wavenumber roughness to total frontal area. In contrast, the full range of roughness length scales present in natural reefs is captured by the continuous surface representation. Parameterizations of drag could potentially be improved by considering the distribution of frontal area across length scales.

Collectively, the results presented in Chapters 1 and 2 show that coral reef topography is both multiscale and multifractal. However, there is a limited understanding of the effects of the structural complexity on water motion around individual and groups of corals. In Chapter 3, we present detailed hydrodynamic measurements from the same shallow reef sites for which we quantified reef geometry (Chapter 2). Using these measurements, we compare spatial and temporal variations in flow patterns across three sites: (1) a high relief site with waves; (2) a low relief site with waves; and (3) a high relief site without waves. Our observations suggest that the flow is likely unidirectional and current dominated over much of the backreef. These measurements also show that flow variations at different frequencies have different spatial patterns. At low frequencies, flow variations follow the spatial pattern of wakes. The lack of coherent structure in wave band variations can be explained by the distribution of orbital excursion length to colony diameter (Keulegan-Carpenter number), which is typically less than 2π, thus wakes do not form behind elements. Variations at high frequencies were up to two times larger in the canopy than upstream. In the future, these observations could be compared to computational models of flow at the sites, which would allow us to better understand mechanisms controlling frequency-dependent spatial patterns, as well as the importance of colony and patch-scale processes for reef and regional scale circulation.