Coral reef habitats in Hawai'i are common in shallow waters and extend into mesophotic depths (30-150 m). However, habitat monitoring efforts have been concentrated in depths constrained by safe dive limits of 0-30 m. Mesophotic coral ecosystems (MCEs), located in depths of 30-150 m, are important components of the coral reef ecosystem, but only a small number of surveys have been conducted in these depths. Data for these deep-water habitats are essential for evaluating and monitoring their health and resilience. Classifying benthic habitats in mesophotic depths is challenging due to dive safety limits and water penetration capabilities of remote sensing options, such as satellite imagery and Light Detection and Ranging (LiDAR). The results of this effort show that acoustic data can be used to provide detailed substrate and biological cover maps that include mesophotic coral ecosystems. Here we employ a combination of principal component analyses and unsupervised classification techniques to derive six substrate and five biological cover classes from multi-beam acoustic data, which are validated by optical seafloor imagery to create a complete benthic habitat map for the West Hawai'i Habitat Focus Area (WHHFA). Our results show that the overall accuracy of the benthic habitat maps is 59% for substrate classification and 61% for biological cover classification. Accuracy was higher for the following individual classes; 76% Complex Reef, 86% Sand, and 88% Coral. These habitat maps are the first within the WHHFA to incorporate mesophotic data and provide important information for evaluating and managing the coral reef ecosystem as a whole. [doi:10.7289/V5/TM-PIFSC-61 (https://doi.org/10.7289/V5/TM-PIFSC-61)]

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.

This book documents and examines the state of health of coral reefs in the eastern tropical Pacific region. It touches on the occurrence of coral reefs in the waters of surrounding countries, and it explores their biogeography, biodiversity and condition relative to the El Niño southern oscillation and human impacts. Additionally contained within is a field that presents information on many of the species presented in the preceding chapters.