"Using the archive of available video and photographic records from the Hawaiʻi Undersea Research Laboratory (HURL) and the Pacific Islands Fisheries Science Center (PIFSC), we developed a model to predict the occurrence of two dominant mesophotic coral genera, Leptoseris and Montipora, across the main Hawaiian Islands. The overall prediction success (73.6% and 74.3%, respectively) was relatively high, and these predictions were translated to spatially independent habitat suitability maps of the main Hawaiian Islands at 25 m2 resolution. Montipora presence peaks in the middle mesophotic zone (50 - 80 m) in areas sheltered from high intensity winter swells, whereas Leptoseris tends to colonize steep, rugose, well-flushed areas in the lower mesophotic zone (> 80 m)"--Executive Summary.

Despite decades of research, factors that drive population patterns and connectivity in the ocean are hotly debated and largely unknown. With a changing climate and an ever increasing anthropogenic strain, protecting our oceans for future generations is vital. Coral reefs are some of the most productive ecosystems on earth, and in order to protect them we need to gain a deeper understanding of the biological and physical dynamics that govern species distributions and survival. This dissertation aims to explore larval dispersal and population connectivity in the Hawaiian Archipelago. To effectively manage coral reef ecosystems, it is imperative to understand where the new generation comes from. To gain insight into the drivers behind observed larval distribution patterns I ground-truthed a biophysical model with in situ larval distributions obtained during midwater trawling off the coast of West Hawai'i Island. I was able to show that a connectivity model explained observed larval abundances and distributions of the yellow tang, Zebrasoma flavescens, to a significant degree. The dispersal model also showed that successful larvae most likely inhabit the deeper waters around 100 m for optimum settlement success and that larvae can travel from one end of the Main Hawaiian Islands to the other in 45 days. The groundtruthed model allowed me to explore modeled potential connectivity in the Hawaiian Archipelago and generate a comprehensive estimate of connectivity of passive particles for the region. Genetic population connectivity has been studied extensively in the Hawaiian Archipelago, but to date no study has looked at large scale modeled larval connectivity patterns. By comparing genetic population connectivity patterns with modeled larval connectivity patterns driven by the physical environment we can begin to understand drivers of population connectivity. I found that modeled self-recruitment was high throughout the archipelago. This is important because being able to provide your own young makes a population less reliant on outside sources of genes and larvae. Results from the biophysical model indicate that connectivity in the NWHI is predominantly driven by physical factors e.g. ocean currents. Connectivity patterns in the Main Hawaiian Islands are not explained by the physical oceanographic environment, rather, biological and anthropogenic factors are likely important for dispersal. The biophysical model identified distinct breaks in the archipelago where larval exchange is limited, and I was able to describe the directionality and relative size of dispersal between the MHI and the NWHI. Understanding larval exchange between the MHI and NWHI is important because the MHI are heavily fished while the NWHI are protected as part of one of the largest marine protected areas in the world, Papahānaumokuākea Marine National Monument. In the final part of this work I investigate how El Nino Southern Oscillation (ENSO) change connectivity patterns in the Hawaiian Archipelago. Having a deeper understanding of changes in connectivity during relatively extreme events such as ENSO allows us to better plan for management in a changing climate. The study showed that unique connectivity pathways open up between the Hawaiian Archipelago and Johnston Atoll during El Niño events providing a pathway for larval exchange between the Hawaiian Archipelago and other islands in the Pacific Ocean. During La Niña years Johnston Atoll acts as an outpost, with modeled connectivity pathways opening up from Hawai'i towards Johnston Atoll. El Niño years had longer mean dispersal distances, and more larvae that traveled further, compared with normal and La Niña years. These periodic long distance dispersal events may contribute to the exchange of genes between distant populations, and allowing greater genetic diversity and potentially building resilience towards changing environments.

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.

Published by the American Geophysical Union as part of the Coastal and Estuarine Studies, Volume 61. The effects of increased atmospheric carbon dioxide and related climate change on shallow coral reefs are gaining considerable attention for scientific and economic reasons worldwide. Although increased scientific research has improved our understanding of the response of coral reefs to climate change, we still lack key information that can help guide reef management. Research and monitoring of coral reef ecosystems over the past few decades have documented two major threats related to increasing concentrations of atmospheric CO2: (1) increased sea surface temperatures and (2) increased seawater acidity (lower pH). Higher atmospheric CO2 levels have resulted in rising sea surface temperatures and proven to be an acute threat to corals and other reef-dwelling organisms. Short periods (days) of elevated sea surface temperatures by as little as 1–2°C above the normal maximum temperature has led to more frequent and more widespread episodes of coral bleaching-the expulsion of symbiotic algae. A more chronic consequence of increasing atmospheric CO2 is the lowering of pH of surface waters, which affects the rate at which corals and other reef organisms secrete and build their calcium carbonate skeletons. Average pH of the surface ocean has already decreased by an estimated 0.1 unit since preindustrial times, and will continue to decline in concert with rising atmospheric CO2. These climate-related Stressors combined with other direct anthropogenic assaults, such as overfishing and pollution, weaken reef organisms and increase their susceptibility to disease.

"The primary objective of this study was to predict the distribution of mesophotic hard corals in the Auʻau Channel in the Main Hawaiian Islands (MHI). Mesophotic hard corals are light-dependent corals adapted to the low light conditions at approximately 30 to 150 m in depth. Several physical factors potentially influence their spatial distribution, including aragonite saturation, alkalinity, pH, currents, water temperature, hard substrate availability and the availability of light at depth. Mesophotic corals and mesophotic coral ecosystems (MCEs) have increasingly been the subject of scientific study because they are being threatened by a growing number of anthropogenic stressors. They are the focus of this spatial modeling effort because the Hawaiian Islands Humpback Whale National Marine Sanctuary (HIHWNMS) is exploring the expansion of its scope--beyond the protection of the North Pacific Humpback Whale (Megaptera novaeangliae)--to include the conservation and management of these ecosystem components. The present study helps to address this need by examining the distribution of mesophotic corals in the Auʻau Channel region. This area is located between the islands of Maui, Lanai, Molokai and Kahoolawe, and includes parts of the Kealaikahiki, Alalākeiki and Kalohi Channels. It is unique, not only in terms of its geology, but also in terms of its physical oceanography and local weather patterns. Several physical conditions make it an ideal place for mesophotic hard corals, including consistently good water quality and clarity because it is flushed by tidal currents semi-diurnally; it has low amounts of rainfall and sediment run-off from the nearby land; and it is largely protected from seasonally strong wind and wave energy. Combined, these oceanographic and weather conditions create patches of comparatively warm, calm, clear waters that remain relatively stable through time"--Executive summary.

Tropical coral reefs, one of the world's oldest ecosystems which support some of the highest levels of biodiversity on the planet, are currently facing an unprecedented ecological crisis during this massive human-activity-induced period of extinction. Hence, tropical reefs symbolically stand for the destructive effects of human activities on nature [4], [5]. Artificial reefs are excellent examples of how architectural design can be combined with ecosystem regeneration [6], [7], [8]. However, to work at the interface between the artificial and the complex and temporal nature of natural systems presents a challenge, i.a. in respect to the B-rep modelling legacy of computational modelling. The presented doctorate investigates strategies on how to apply digital practice to realise what is an essential bulwark to retain reefs in impossibly challenging times. Beyond the main question of integrating computational modelling and high precision monitoring strategies in artificial coral reef design, this doctorate explores techniques, methods, and linking frameworks to support future research and practice in ecology led design contexts. Considering the many existing approaches for artificial coral reefs design, one finds they often fall short in precisely understanding the relationships between architectural and ecological aspects (e.g. how a surface design and material composition can foster coral larvae settlement, or structural three-dimensionality enhance biodiversity) and lack an integrated underwater (UW) monitoring process. Such a process is necessary in order to gather knowledge about the ecosystem and make it available for design, and to learn whether artificial structures contribute to reef regeneration or rather harm the coral reef ecosystem. For the research, empirical experimental methods were applied: Algorithmic coral reef design, high precision UW monitoring, computational modelling and simulation, and validated through parallel real-world physical experimentation - two Artificial Reef Prototypes (ARPs) in Gili Trawangan, Indonesia (2012-today). Multiple discrete methods and sub techniques were developed in seventeen computational experiments and applied in a way in which many are cross valid and integrated in an overall framework that is offered as a significant contribution to the field. Other main contributions include the Ecosystem-aware design approach, Key Performance Indicators (KPIs) for coral reef design, algorithmic design and fabrication of Biorock cathodes, new high precision UW monitoring strategies, long-term real-world constructed experiments, new digital analysis methods and two new front-end web-based tools for reef design and monitoring reefs. The methodological framework is a finding of the research that has many technical components that were tested and combined in this way for the very first time. In summary, the thesis responds to the urgency and relevance in preserving marine species in tropical reefs during this massive extinction period by offering a differentiated approach towards artificial coral reefs - demonstrating the feasibility of digitally designing such 'living architecture' according to multiple context and performance parameters. It also provides an in-depth critical discussion of computational design and architecture in the context of ecosystem regeneration and Planetary Thinking. In that respect, the thesis functions as both theoretical and practical background for computational design, ecology and marine conservation - not only to foster the design of artificial coral reefs technically but also to provide essential criteria and techniques for conceiving them.

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.