Coral reefs are increasingly under threat, necessitating an emphasis to identify coral reefs with reduced susceptibilities to local and/or global anthropogenic impacts. Mesophotic coral reefs (MCEs; >30m) are proposed as potential refugia and/or propagule sources, yet little information is known about deep reefs' abilities to harbor, replenish, or conserve shallow species. In this dissertation, I examine the plausibility of MCEs to act as refugia for shallow reef fishes in the Hawaiian Islands. Chapter One explores reef fish community structure and habitat composition along a 3-50m gradient in West Hawai'i. Reef fish communities change gradually with depth, with >78% of species observed at mesophotic depths (>30m) found at shallow depths. Changes in community structure are linked closely with feeding behavior, with shallow reefs dominated by herbivores, while mesophotic reefs are dominated by invertivore and planktivore trophic assemblages. Changes in fish assemblages are tied to indirect effects of depth and available coral habitat, as deeper reefs contain more patchily-distributed habitat. Chapter Two examines mechanisms underlying herbivorous fish distributions using a suite of observational and experimental field and laboratory techniques. Herbivorous fishes are not limited by food resources at MCE depths, as MCE algae had similar nutritional content, species assemblages, and appears to be highly palatable from algal choice experiments. Instead, changes with depth are likely the result of top-down, non-consumptive predation effects and behavioral choices. Chapter Three undertakes a critical analysis of the deep refugia hypothesis for coral reef fishes across the Main Hawaiian Islands. Upper MCEs (30-60m) may act as refugia for shallow reef fishes, as we found they are more thermally stable and >70% of reef fishes encountered were shallow species. Conversely, MCEs contain reduced densities of reef fishes and communities are comprised almost solely of invertivore and planktivore trophic groups. The near-absence of herbivorous fishes below 30m indicate MCEs will have a limited capacity to re-seed shallow reefs with species of ecological or economic importance. Overall, MCEs may act as refugia for biodiversity conservation but their ability to restock shallow reef fish communities will result in fundamentally different community compositions that shift towards smaller-bodied and less economically/ecologically valuable species.

Mesophotic coral ecosystems (MCE) are defined as phototrophic coral habitats found deeper than 30 m. Despite being aware of these ecosystems for over 200 years, surprisingly little information is available on their ecology and biology. Recently, MCE have received renewed interest, as it appears that depth and distance from shore have the potential to buffer coral organisms from the detrimental effects of coastal development and climate change. The "deep reef refugia hypothesis" (DRRH) is an umbrella term for a collection of hypotheses concerning the role of MCE in the uncertain future of coral reefs, yet our predictions are limited by shortcomings in our understanding of some very basic effects of depth on corals and associated communities. In order to investigate the effects of depth on coral reproductive biology, sampling of Montastraea faveolata and Porites astreoides coral tissues was conducted along a depth gradient from 5 to 40 m during coral reproductive seasons in the Northern United States Virgin Islands (USVI), and observations of coral spawning and planulation were made. Samples were histologically analyzed for gamete development, reproductive activity and fecundity. Mesophotic populations of both M. faveolata and P. astreoides were reproductively active in MCE with similar gametogenic cycles to nearby shallow coral populations. There was evidence of M. faveolata split spawning in August and September at all depths, and oocyte development was delayed but more rapid in mesophotic corals. M. faveolata fecundities were significantly higher in MCE (35-40 m) than in shallow (5-10 m) sites, but the differences were not significant between mid-depth (15-22 m) and either shallow or mesophotic sites. There was no difference found in P. astreoides fecundity between mesophotic, mid-depth and shallow sites, however planulation appeared to be delayed in mesophotic colonies by 1-2 weeks. Differences in fecundity per area and coral cover between depths determine the number of propagules a unit reef will produce at different depths. In the case of M. faveolata, ova production is likely an order of magnitude greater at 35 m than at 10 m. The Connectivity Modeling System, an individual-based stochastic biophysical model of larval dispersal, parameterized with depth-specific productivity estimates and species-specific reproductive seasons and larval traits, was used to evaluate the vertical connectivity of M. faveolata and P. astreoides larvae between MCE and shallow coral habitats in the Northern USVI. Sensitivity analyses were performed to test the sensitivity of mesophotic larval subsidy into shallow habitats to depth-specific productivity, pelagic larval mortality, depth-specific fertilization rates and depth-specific post-settlement survivorship. Simulated mesophotic subsidies to shallow recruitment were found to be considerably robust, and mesophotic subsidy to shallow recruitment accounted for a greater proportion of total recruitment as shallow productivity was reduced. Even when modeled mesophotic fertilization rates and larval post-settlement survivorship were dramatically reduced, the model predicted what would likely be demographically significant mesophotic larval subsidy into shallow habitat. Mesophotic M. faveolata skeletal density, extension and calcification were estimated using micro-computed tomography. Results suggest that rates of linear extension of M. faveolata in USVI MCE may be quite fast compared to other Caribbean MCE, and that total calcification in MCE may rival shallow coral calcification. Lastly, consistencies and inconsistencies in the population connectivity of two coral and three fish constituent species in Caribbean coral reef assemblages were investigated using a nested biophysical model. Connectivity networks of coral species were more fragmented than fish, and the networks of corals and fish showed different patterns of betweenness centrality. This suggests that populations of corals and fish will likely be affected by habitat fragmentation in different ways, and that they require specific management consideration. This dissertation suggests that MCE are integral to the population connectivity of corals in the USVI and likely to wider Caribbean metapopulation connectivity as well. Further study of these highly productive ecosystems is necessary to better understand the DRRH and the role of MCE in the past, present and future of coral reefs.

The structural complexity and geomorphic diversity of coral reefs are vital foundational characteristics responsible for the many ecological and economic benefits these ecosystems provide. Shallow-water coral reef geomorphology and structural sustainability is mostly determined by varying reef sedimentary components including: (1) sediment production (matrix) and deposition, (2) framework production and secondary carbonate accretion; (3) bioerosion; and (4) cementation. However, little is known regarding the variability and influence of these sedimentary processes in mesophotic coral ecosystems (MCEs), deep reef communities 30-150 m below sea-level. Despite recent increases in biological and ecological MCE studies, many crucial sedimentological research questions remain unaddressed. These unaddressed questions impede a greater understanding of mesophotic reef structural sustainability and potentially related habitat heterogeneity, carbonate reef shelf development and variability in mesophotic depths, and the general origins of modern coral reef biodiversity. Critical gaps in knowledge of mesophotic coral reef geomorphology and structural sustainability were addressed in this dissertation by conducting one of the first extensive sedimentological analyses of a mesophotic coral reef ecosystem. Beyond a general exploration of MCEs, the overall research goal was to identify basic sedimentary processes integral to the development, modification, and sustainability of mesophotic coral reef structure. The goal was also to determine the variability of the identified processes at different mesophotic reef habitats and investigate how these processes and potential variability impact shelf-wide habitat heterogeneity and long-term accretion. To address these goals, sedimentary analyses and ecological surveys were conducted at mesophotic coral reef habitats with distinct structurally characteristics, and neighboring shallow-water reef counterparts in the northern U.S. Virgin Islands (USVI). Analyses at all reefs were designed to address four specific aims: (1) categorization and comparison of various mesophotic reef sediment and cement attributes; (2) determination of exposed consolidated substrate reef bioerosion rates, and the distribution and variability of bioeroding groups; (3) quantification and determination of primary coral mesophotic reef framework builder linear growth and calcification rate variability, and comparison to live mesophotic framework bioerosion and secondary accretion rates; and (4) application of study results for carbonate budget analysis and assessment of geomorphic carbonate production status. Sediment and cement analysis (first aim) indicated that distinct MCE habitats produce subfacies. The interpreted hydrodynamic and biological interactions controlling mesophotic USVI subfacies have implications towards paleoenvironmental interpretations of ancient mesophotic reef deposits with similar sediment and cement characteristics. Significant differences in exposed consolidated substrate bioerosional processes were discovered between the analyzed habitats. These differences were found to primarily result from variation in parrotfish biomass and related controls on substrate exposure time and location in macroboring succession. Results also broadly confirm pervious hypothesizes that bioerosion decreases with depth along a carbonate shelf and have implications leaning toward rejection of traditional reef accretion theories. Analysis of coral growth identified statistically significant differences in mesophotic coral reef calcification rates, implying another potential long-term mechanism for enhancing mesophotic reef structural heterogeneity. However, on a larger scale, linear extension rates were found to fit within previously proposed models of decreasing coral growth rate with increasing depth. Mesophotic coral reef sedimentary analyses were compared in a newly developed carbonate budget model to analyze structural sustainability and consider implications of these analyses on mesophotic reef habitat heterogeneity and Holocene carbonate shelf accretion. All USVI mesophotic habitats examined were identified with net positive carbonate production despite significant variability in geomorphic production states. Additionally, comparisons with earlier benthic surveys suggest higher net USVI mesophotic reef carbonate production in the recent past, potentially implying these deeper reefs are not fully immune to modern global stressors impacting shallow-water reefs. Results indicated that mesophotic reef accretion was not the main driver of shelf-scale topographic relief. However, mesophotic carbonate production variability substantially contributes to habitat-scale structural relief and complexity and relatedly to overall ecosystem diversity. Specific mesophotic reef sedimentology research methods and the need for similar studies at other mesophotic reef habitats were suggested. Comprehensive sedimentology analysis of mesophotic coral reefs in the USVI provide new insight into reef structural sustainability, geomorphic status, and potential impacts from global stressors, and should be considered when developing specific reef sustainability models and management strategies.

"Mesophotic coral ecosystems (MCEs) are light-dependent communities of corals, algae, sponges, and other organisms that exist at depths between approximately 30 m to 150 m. Little known until recently and understudied relative to shallower reefs, MCEs may contain significant coral reef ecosystem resources, including both luxuriant coral reefs and diverse fish communities. Research in the Pacific Islands Region over the last few years has produced data to facilitate a better awareness of the distribution and potential significance of MCEs, but they are still relatively unknown and remain absent from most coral reef ecosystem monitoring programs and management considerations. We synthesize results of research to map the distribution of benthic habitats and communities at mesophotic depths within the region and discuss them within the context of requirement to identify and manage essential fish habitat for managed species mandated by the Magnuson-Stevens Fishery Conservation and Management Act"--Abstract.

As shallow reefs continue to decline, scientists are searching for the key to their persistence; as it turns out, they may just need to look deeper. Below many shallow tropical reefs, there exist healthy and more stable mesophotic coral reef communities. The ability of these reefs to act as a refuge for declining shallow populations has garnered significant interest among the scientific community; however, the reproductive and larval aspects necessary for this to occur are unknown. This study assesses the ability of deep reefs to act as a reproductive refuge for shallow counterparts by examining gametic compatibility, viability and larval settlement preferences. Gametes from Orbicella franksi inhabiting the shallow (14-20m) and the upper mesophotic (27-32m) were introduced in a series of inter- and intra-depth crosses and found to be compatible. Larval settlement experiments found no natal depth preference, with deep larvae significantly preferring to settle on shallow conditioned substrate. Our findings support the plausibility of healthy mesophotic reefs acting as a refuge for depauperate shallow populations by (1) providing gametes to mix with limited shallow gametes resulting in increased fertilization and (2) providing larvae that recruit and repopulate shallow reefs. This is the first study to comprehensively evaluate the Deep Reef Refugia Hypothesis from a reproductive and larval settlement standpoint. Our results suggest a close coupling between shallow and mesophotic reefs through gamete and larval export and illustrate the current and future importance of these mesophotic reefs.