Coral reefs have been part of the earth’s oceans since the Mesozoic Era, over 200 million years ago. In recent decades, however, reefs have been progressively suffering as a result of human activities. However, coral species vary in their response to ecological disturbance. The work described here examines aspects of the biology of two central Pacific species: Porites superfusa, a small encrusting coral, and Acropora cytherea, a dynamic, massive table coral. Both species are perforate corals, with skeletons permeated with an extensive canal system partially lined with living coral tissue. Thus far, the question of whether the perforate coral condition conveys functional advantages lacking in corals with imperforate (relatively dense) skeletons has been overlooked. The present work supported with field work and sample collections at Palmyra Atoll, Line Islands, USA, during approximately annual visits of several weeks each from 2012 to 2016. The reef is protected from fishing and local pollution but still exposed to wide-scale disturbances like climate change (especially evident in warm water bleachings in 2009, 2015, 2016). This dissertation explores the importance of coral regrowth, endoliths and adjacent epiliths to reef recovery dynamics. Long-term changes in coverage of Porites superfusa were followed in a time series of high-resolution photoquadrats that demonstrated new settlement as well as changes in existing colonies (growth, partial mortality, death, and “death” followed by resurrection). Partial mortality and survival was usually observed in larger individuals, whereas smaller individuals tended to grow progressively or apparently die out completely. However, quite often a new small individual would appear in the area where a colony had died previously in the time series. Although settlement of planula larvae from the water column could not be completely ruled out, the source of new growth could have been from a small amount of living tissue cryptically surviving in or on the “dead” colony. Further work would be required to see if new growth was seeded by small regions of viable tissue. For the other perforate coral in this dissertation, Acropora cytherea, the distribution of living tissues was studied in the canals permeating the skeleton in healthy and evidently dead (algae-covered) regions of the colony. Core samples were studied by scanning electron and light microscopy. In healthy regions, the living coral tissues lined only the intraskeletal canals to a depth of several millimeters from the surface of the colony. In healthy parts of the colony, the canals more than a few millimeters deep in the colony were bounded not by living coral tissues, but with calcareous skeleton. Although the coral skeleton was riddled with endoliths (algae, fungi and bacteria), they were relatively rarely observed in the canal space. In regions where the living part of the colony was covered over with turf algae and other invading organisms, these endoliths were detected, along with abundant sediment, packing the most superficial intracellular canals; surprisingly the canals deeper beneath the overgrown region were free of such extraneous material. In the light of these results, one can speculate that fluid (driven by flagella in the relatively superficial healthy part of the colony) might percolate throughout the intraskeletal canal system, even in regions underlying places overgrown with algae and other organisms. Such a flow could conceivably distribute nutrients or coral cells to regions where they might influence the repair of the locally overgrown parts of the colony overlying them. Light microscopic and molecular techniques (internal transcribed spacers, ITS and 18S cDNA) were combined to provide an overview of the overgrowing and endolithic organisms associated with A. cytherea. The sampled regions of the colony were living, recently dead (near living coral tissue) or long dead (far from living coral tissue). The data permitted mostly genus-level identification of macroalgae, endolithic and epilithic algae, and endolithic fungi. A comparison between living, recently dead, and long dead samples demonstrated a succession in community composition of the algae. Even so, there were notable similarities in the genera of endolithic fungi present in the skeleton of living and dead regions of the colony. The endolithic communities within the coral may be a link between live and dead coral in the calcium carbonate structures. This might reflect a uniformity and connectivity maintained by the deep circulation within the unobstructed lumens of the intraskeletal canal system throughout the colony, even beneath superficially overgrown areas. In sum, the results of the different parts of this dissertation point to the need for further studies of the recently neglected perforate skeleton character and connecting endoliths and their possible relationship to resilience of some perforate corals. Understanding partial survival and dead coral skeleton may hold additional hints at maintaining and protecting coral reef ecosystems.

List of fish taxa identified across surveys of the coral reef ecosystems of the U.S. Pacific islands. Taxa are organized alphabetically by family, and alphabetically within family by lowest identified level (typically species). Trophic classifications are provided in coarse groups based on major diet items integrated across the life stages of each species. The four groups are Primary Consumer (including herbivores and detritivores), Secondary Consumer (including invertivores, corallivores, and omnivores), Planktivores (primarily consuming zooplankton), and Piscivores (including species with fish as the dominant diet item).

A challenge in ecology is to understand how so many species are organized in their communities and which coexistence mechanisms act to maintain diversity. The methods of ecological theory can further challenge by incorporating implicit assumptions. The non-equilibrium approach is useful as it includes the fluctuating environments so prevalent in nature. A growing number of empirical works attempt to quantify coexistence mechanisms. Recent developments in Modern Coexistence Theory in combination with tools from Spatial Simulation can leverage long-term field observations as well as the experience of field ecologists to create spatial models for use as a hypotheses-testing platform. An individual-based model of community dynamics is presented using a framework of Pattern-Oriented Modeling to serve as validation.

Bleaching susceptibility of coral varies among species, environmental conditions, and spatial patterns on a reef. As bleaching events become more frequent and severe, understanding the factors that increase resiliency against thermal stress is critical. Here, we used large scale imagery collected at the remote atoll of Palmyra in the central Pacific during the 2015 thermal stress event to investigate the role of topographically produced shade in mitigating bleaching severity. Change in planar area over two years, bleaching severity, and estimated amount of shade provided by neighboring reef structures was measured for the common coral genus Pocillopora. Colonies that bleached more severely had higher rates of mortality than colonies with less severe bleaching. Further, those colonies with less severe bleaching had a higher proportion of colonies experiencing growth. Bleaching severity was correlated with the estimated irradiance, as more daily sunlight resulted in more severe bleaching than corals experiencing less daily sunlight. Structural complexity and variability in reef topography provide regions of shade where the compound impact of temperature and irradiance is alleviated, resulting in less-severe bleaching outcomes for an abundant and cosmopolitan coral genus. While some studies have considered artificially shading reefs during warm water events, we highlight the importance of existing structural complexity in providing shade, ultimately leading to increased reef resilience in the face of a changing climate.

Experimental fishing is a tool within adaptive management, but greater capacity exists to use experimentation to test alternative ideas to meet the national standards of the Magnuson-Stevens Act and promote sustainable fisheries. Few programs exist to allow for experimentation in federal waters, 3-200nm offshore, which is a crucial component of adaptive fisheries management. The exempted fishing permit (EFP) program, administered by the National Oceanic and Atmospheric Administration (NOAA), promotes collaboration between scientists, managers, and industry to develop creative solutions to evolving fisheries challenges by leveraging resources across fisheries sectors. To date, no synthesis of EFP implementation and efficacy has been conducted, leaving those who manage these fisheries in the dark as to their success more generally. Although regional managers discuss EFP projects on an individual basis, an analysis of the entire program provides useful guidance to management more broadly and describes trends in success to effectively translate experimentation to management. Here we developed the first standardized database of EFPs in the U.S. to summarize regional trends in applicant types, fisheries, gear types, goals, and exempted regulations. EFP documentation from 2008-2018 was compiled across seven broadly defined fisheries in four coastal regions in the U.S. We also evaluated factors that were associated with the degree to which EFPs were informative for fisheries management; ‘informative’ being defined as either informing regulatory change within a fishery or providing supporting data to fisheries reports (e.g. stock assessments, fishery management plans). We found strong differences between regions of the U.S. with the groundfish fishery strongly represented in the western regions and a mixed assortment of fisheries for the eastern regions. Western region projects had a greater focus on new gear and methods testing to reduce bycatch, whereas eastern regions had a mixture of goals, including projects that supplemented biological or ecological knowledge or contributed to stock assessments. We found strong coastal differences in the types of primary applicants that proposed projects, with eastern projects deriving from “top-down” approaches and western from “bottom-up”. Finally, we found that management region, applicant type, fishery, and size of project were positively associated with success in EFP projects, with Alaska and West Coast regions accounting for the highest proportion of successful projects.

The spatial distributions of benthic organisms within a coral reef ecosystem are structured by biological and physical mechanisms such as coral competition, reproduction, and reef structure. By examining the neighborhood patterns between scleractinian coral, soft coral, and algae, we can understand who typically lives near who and vice versa in a coral reef ecosystem. This brings insight into how organisms’ interactions, life histories, and the reef’s physical processes all impact the spatial distributions of colonies within their environment. Past coral spatial pattern studies relied on spatial point pattern (SPP) techniques such as nearest neighbor analysis. SPPs utilize the centroid of a colony, which poorly represents benthic organisms due to their variability in shape and size. In this study, we used an in-situ imaging technique to produce 14 plots of the reef based around Palmyra Atoll, covering 1400 m2 of benthic habitat in total. All colonies within these plots were identified to the lowest taxonomic classification possible. The utilization of GIS programming allowed us to take the shape of organisms into account and calculate the percent occupancy in 10 cm buffer regions around each colony. A bootstrapping approach was used to determine if the observed average neighborhood of each taxon and morphological type was more or less frequent compared to that of a null of equal occupancy. Few significant co-occurrence patterns were found due to the high abundance of a few taxa and competition between colonies. Of those significant neighbor patterns found, most positive patterns were intraspecific and biologically driven (via competition, reproduction, and partial mortality), and negative patterns were interspecific and were habitat driven (via physical processes and structure of the physical environment).

Species of branching Acropora, once dominant, complex coral species, have experienced major decline over the last several decades due to physical and anthropogenic disturbances. Following this decline, species of Acropora have been a direct focus of coral monitoring and restoration efforts across the Caribbean, in hopes of recovering populations of these threatened species. Measuring growth in the field presents countless challenges, including inaccuracy and imprecision of measurements due to intricate branching morphologies, the amount of time a diver can spend underwater measuring aspects of coral health, and unpredictable diving conditions. Here we used large-scale 3D imagery derived using Structure from Motion photogrammetric techniques to quantify branching Acropora species across multiple reef terrace sites on Palmyra Atoll. We estimated branch density (number of branches per thicket) and various metrics of linear and areal size of colonies within imagery which facilitates a direct comparison of commonly used metrics to track growth. We were able to monitor growth based on initial size through larger thicket form for six Acropora thickets through multiple time points from 2012-2019. The use of large area imaging technology provides a permanent record and a powerful tool to quantify growth using a variety of metrics, not constrained by in situ logistics. Gaining access to and perfecting methods that account for accurate size and growth measurements for reef accretion can hold the key to long-term successful ecological monitoring and restoration efforts.

Most organisms shift between different ecological niches or habitats throughout their lives. These shifts are prompted by growth and changing resource needs. In the marine realm, understanding why and when fish shift habitats is particularly important due to the increasing use of spatial management as a conservation strategy. Effective spatial management requires understanding how a species habitat usage changes throughout its’ lifespan.

Within the Southern California Bight (SCB)Yellowtail (Seriola lalandi) are iconic gamefish and widely targeted throughout the region, both in U.S. and Mexican territorial waters. Their cross-border movements mean these fish encounter a diverse array of anthropogenic pressures, ranging from ocean-warming to agricultural and urban run-off to significant recreational, artisanal, and commercial fishing.

This work attempts to understand and quantify how yellowtail use the Southern California Bight and how that usage affects their biology. This was carried out in 3 separate chapters dealing with analysis of long-term recreational catch records, conventional tagging, passive acoustic telemetry as well as spatially-explicit analysis of age, growth, diet and trophic position.

The primary differences detected across all investigated parameters were size-mediated. Thus, one contiguous population with distinct ontogenetic shifts in habitat and diet is the most parsimonious explanation for the results from each chapter presented in this thesis. Recreational catch data showed inshore and offshore catch sizes were different between years and across seasons and fish size, rather than tagging season best explained detection rates of acoustically tagged fish. These findings supported claims by recreational anglers that large fish caught inshore are potentially year-round SCB residents. The conclusion of one, panmictic, SCB yellowtail population is further supported by results from life-history analysis as fish size again was the only source of significant differences in age/growth, diet, or trophic position regardless of sampling location or region.

Results from tag returns, acoustic telemetry and life-history analysis indicate that there is likely one contiguous population of yellowtail in the SCB and that due to high

levels of fishing pressure, this population may be reliant on seasonal influxes of fish from the south to sustain current fishing levels.

Coral reefs, and particularly the study of coral reef fishes, have provided fundamental contributions to our understanding of community ecology in part due to their spectacular diversity of life. This dissertation seeks to evaluate facets of the community ecology of fish communities at reefs in the south and central Pacific Ocean via a variety of classical and new approaches, including traditional visual surveys and new techniques in genetics. Collectively, the results of my dissertation address outstanding questions regarding the communities of fishes on coral reefs at islands and atolls in the south and central Pacific, including both well-studied inhabited islands with intimate associations between humans and environments and others from remote environments that have seen only sporadic human visitation and presence. I begin with an investigation of a potential stabilizing mechanism of coexistence through the application of metagenomics to assess dietary niche-partitioning in a guild of hawkfish from remote reefs in the central equatorial Pacific. We observe previously unidentified relationships in this cryptic species complex at its proposed center of distribution and separate clustering of species for both the microbial community of the gut and presumed prey sequences. I next calculate length–weight relationships for abundant coral reef fish species from eight different islands in French Polynesia. These region-specific biological parameters are important for assessing accurate metrics of biomass for coral reef fish communities from underwater visual surveys. I focus on members of the community that are often overlooked and understudied in such contexts, including species of importance for the aquarium trade. I then assess temporal patterns in trophic groups of coral reef fishes via remote video surveys on forereefs of Moorea, French Polynesia. I conclude by investigating the “paradox of planktivores”—that is, the substantial number of co-occurring reef fishes that are presumably relying on similar resources. I use metagenomic sequencing and underwater visual surveys to assess the evidence for niche-partitioning and changes in observed abundance through time that could indicate coexistence in a guild of closely related planktivorous reef fishes.

Time and energy are finite resources in any environment, and how and when organisms use their available resources to survive and reproduce is the crux of life history theory (Gadgil and Bossert 1970; Balon 1975; Stearns 1976). The different survival strategies used by animals are often shaped by their environment in addition to their biology (Winemiller and Rose 1992), which allows for exploration into biological variability when environmental factors are known. For this reason, the Line Islands in the Central Pacific provide an ideal location to perform observational studies due to their unique productivity gradient and fish assemblage structures across the island chain (Sandin et al. 2008; DeMartini et al. 2008; Fox et al. 2018; Zgliczynski et al. 2019). Many of the world’s coral reefs are in remote regions that lack monitoring programs or even local populations, so conducting ecological surveys on fish communities in these regions can require extensive amounts of time, energy, resources and people. The inherent variability an environment exerts on the many factors that contribute to growth over a lifetime make it difficult to generate a directly proportional formula that calculates age. A novel age estimation method was developed that utilizes in-situ visual census data to estimate the age of fishes, and as a case study, several fish were chosen as representative species to explore its capabilities. Through this process, new ecological information and insight can be gained about the age structures of fish populations both between and throughout the Line Islands.