Fifty years ago, the Southern California kelp forests, arguably one of the richest marine ecosystems on the planet, were home to a remarkable number of large fish and invertebrates. Four-hundred pound black sea bass, 100-pound groupers, 20-pound lobsters swam through the kelp’s towering fronds, sometimes in great numbers.

The absence of once common marine organisms, especially the scarcity of the largest ones, has prompted marine scientists Paul Dayton and Ed Parnell of Scripps Institution of Oceanography and others to describe Southern California’s kelp forest as a veritable “ghost forest.” Their interest in reversing the trend toward greater depletion of these habitats has led them to study the use of marine protected areas as a tool for restoring marine biodiversity.

This project compiled current and historical records of fishes occurring in the vicinity of the San Diego-La Jolla Ecological Reserve (SDLJER), and assessed the effects of the Reserve on the abundance, diversity and population structure of resident fishes. This was accomplished by collection of quantitative data within the Reserve, immediately adjacent to the Reserve, and at site relatively distant from the Reserve that is not part of any marine reserve and subject to more intense fishing pressure. These assessments included transect surveys of densities and size distributions of conspicuous fishes. This study provides critical, but heretofore absent, baseline data for population monitoring of fishes in the Reserve and adjacent rocky-reef and kelp-forest communities in the San Diego region. In addition, records of fishes recorded within the vicinity of the SDLJER were compiled from the Scripps Institution of Oceanography Marine Vertebrate Collection in order to provide a detailed list of the ichthyofauna recorded in and around the Reserve.

Despite the kelp forest’s biological and economic importance, kelp forest ecology is rich in unanswered, yet basic, scientific questions. What controls the abundance of kelp spores? Do spores from distant kelp beds reseed local beds torn asunder by storms? Are many small kelp beds or fewer large ones better for maintaining healthy fisheries? All these are important questions for managing the state’s marine resources and for preserving its remarkable natural history.

Describing the foraging dynamics of apex predators is crucial to understanding ecosystem function and to effective conservation and management. Leopard seals are conspicuous apex predators in Antarctic coastal ecosystems; however, their foraging ecology is poorly understood. Likely due to a geographical redistribution driven by pack-ice habitat reduction in the western Antarctic Peninsula, leopard seals have been hauling out at Cape Shirreff with increasing frequency in recent years. Utilizing that rare access we implemented an integrated sampling design including morphometrics, biological samples, and bio-logger deployments in January and February between 2008 and 2014. Subsequently, we quantified foraging behavior using: k-means cluster (diving), time-local convex hulls (movement), Bayesian stable isotope mixing models (diet), and linear regression (mass estimation) analyses. While they are typically described as generalist apex predators, video, dive, and movement data suggest they employ specialized foraging patterns. They affect coastal ecosystems through pathways beyond direct predation, including intraspecific kleptoparasitism, predator-induced stress effects, facultative scavenging and food caching. Leopard seal diving behavior is concentrated at night, is both shallow and coastal, and is composed of four distinct dive types. Haul-out probabilities were highest near midday and were positively correlated with available daylight. Video, scat and stable isotope analyses indicate that their summer diet contains four prey groups: Antarctic fur seals, pygoscelid penguins, krill, and demersal notothen fishes. Finally, measurements of body size and mass are fundamental to pinniped population management and research. The recent proliferation of unmanned aerial systems (UAS) in wildlife monitoring has provided a promising new platform for the photogrammetry of free-ranging pinnipeds. Photogrammetric measurements from a single, vertical image obtained using UAS were as accurate as ground measures, and provide a noninvasive approach for estimating the mass and body condition of pinnipeds. This dissertation provides substantial insight into the hunting tactics, foraging behavior, and diet of large adult female leopard seals and provides a viable option for future monitoring.

The kelp forests of California are an important habitat for many species of economically important fish and invertebrates. There has been an alarming downward trend for many of these species over the last two decades to the extent that the kelp forests resemble ghost towns. It is becoming increasingly apparent that these so-called “ghost-forests” are in need of protection. In response to this downward trend in marine populations off California, the state legislature passed the Marine Life Protection Act in 1999. This Act mandates the establishment of a network of marine reserves to reverse these declines. Unfortunately, political pressure based on the dearth of focused science has impeded implementation of the law.

The human capacity to expand niche breadth through cultural evolution has propelled humans into keystone ecological roles in many ecosystems. In particular terrestrial animal assemblages have experienced radical reductions in diversity and size distribution. Oceanic habitats have experienced shorter histories of exploitation and typically retain faunal assemblages that more closely resemble pre-human Pleistocene assemblages. Although the direct harvest of many marine mammal and seabird species has diminished in recent decades, these assemblages now face an onslaught of novel human impacts in marine and oceanic island habitats. Stressors range from noise and chemical pollution to the introduction of invasive mammalian predators on oceanic islands. To develop a better understanding of how these disparate effects will impact the ecologies and conservation statuses of wide-ranging, dynamic, and patchy seabird and marine mammal populations, this dissertation leveraged the use of two extensive observational datasets collected by and in collaboration with the NOAA-NMFS Southwest Fisheries Science Center. In the first section (Chapters 1-3) I used satellite tag and biopsy sampling 1) to describe vertical habitat use and biogeographic distribution patterns, and 2) to develop a systematic framework to better understand foraging ecology trade-offs in seven species of toothed whales from the Bahamas. In the second section (Chapters 4-5) I have applied innovative modeling techniques to estimate population abundance and growth rate parameters using an extensive time series of seabird transect surveys. These parameters play critical roles in assessing population status and developing strategic management decisions.

The energy needs of rorqual whales (f. Balaenopteridae) govern their relationship to marine habitats during the foraging season. However, their cryptic foraging strategies and extreme feeding behaviors complicate our effort to identify and protect habitats “critical” for rorquals. What is the relationship between rorquals and their habitat, and how must that shape conservation strategies? I addressed this question in the case of sympatric humpback (Megaptera novaeangliae) and fin whales (Balaenoptera physalus) in the marine territory of the Gitga’at First Nation in the Kitimat Fjord System of British Columbia. For three summers (2013-2015) I studied whales, their prey, and their environment aboard the RV Bangarang using oceanographic station sampling, systematic transect surveys, and opportunistic focal follows of whales (Chapter 1). Ocean sampling demonstrated the strong coupling of water features with offshore patterns in storm forcing and regional meteorology (Chapter 2). By combining these surveys with a long-term Gitga’at dataset, area humpback whales were found to practice a structured and persistent pattern in seasonal habitat use, which demonstrates how complex and habitat-specific a rorqual’s habitat use can be (Chapter 3). Both humpback and fin whales were found to respond to changes in krill supply in aggregative and behavioral thresholds that are set by a combination of intrinsic energetic needs and the context of local prey supply (Chapter 4). Associations with non-prey habitat features were markedly different in the two species (Chapter 5). Humpback distribution was more closely coupled to that of their prey and other habitat features, while fin whale distribution was driven broadly by site fidelity. Novel spatial analytics were used to identify the most probable environmental cues used by foraging whales (Chapter 6). Both species were found to be particularly sensitive to the depth of prey layers, which is governed largely by oceanographic features (Chapter 7). This coupling of habitat features and feeding performance influences the competitive dynamics of rorqual whales. The findings in this case study advance general theories on marine predator ecology and conservation, and have direct implications for the management of Gitga’at territory and the identification of fin whale critical habitat in Pacific Canada.

The island of Catalina off southern California has been fished recreationally and commercially for over a century. The marine resources of this popular destination are under increasing pressure as the population of southern California expands rapidly. The effects of this pressure have been dramatic for many marine species off Catalina. Clearly, the marine resources on Catalina are limited while human population growth does not appear to be limited in the near future. Therefore, improved management of the marine resources off Catalina is critical. Improved management consists of adaptively changing traditional management practices such as limiting effort, closing species to fishing, limiting sizes that can be taken, etc. However, a new approach to protecting marine resources and rebuilding fisheries is the use of protected areas where fishing is limited or prohibited. Marine protected areas (MPAs) are an increasingly popular though controversial tool for the management of exploited species and marine ecosystems. The California Marine Life Protection Act (MLPA) was signed into law in 1999. The MLPA called for the establishment of a network of marine protected areas throughout the state to help rebuild depleted fisheries, enhance recreational activities, protect marine habitats, and conserve biodiversity. The design of marine reserves is complex because many ecological factors must be taken into account to design effective reserve networks. The purpose of this report is to provide information useful for the design of MPAs off Catalina. Here we, (1) review the efficacy and current science of MPAs, (2) present some of the historical changes to marine resources at Catalina, (3) list and discuss current MPAs off Catalina, (4) discuss ecological criteria for the design of a network of MPAs off Catalina, (5) recommend a specific network of MPAs for Catalina, and (6) recommend future research that would aid the design and monitoring of MPAs off Catalina. There are currently several protected areas off Catalina. The current reserves that limit or exclude fishing, with one exception, are too small to effectively enhance fishery resources, a primary goal of marine protected areas. The goals, governance, and degree of protection vary considerably among these MPAs. Currently, there is no overarching governance or management. Overarching management and governance is needed not only at the scale of Catalina Island but also at the larger scales that are required for MPA networks to achieve the goals of enhancing resources and preserving biodiversity. We recommend such oversight and governance for any network of reserves established at Catalina, recognizing that the MPA network should be considered as a single collective unit for achieving conservation and protection goals. Therefore, we recommend the establishment of an oversight authority in the form of a panel composed of local stakeholders, scientists, and members of state and federal agencies that govern MPAs at larger scales. The panel should be responsible for monitoring the network, gauging its effectiveness, and fine tuning the network as necessary. The panel should also consider the utility of traditional fishery management practices in combination with marine protected areas. We recommend the following actions for the protection of marine resources at Catalina: (1) All of the state waters off Catalina should be designated as an Area of Special Biological Significance to protect water quality throughout the Island. (2) All of the state waters off Catalina should be established as a State Marine Conservation Area. This status permits selected commercial and recreational fishing and establishes the governance to restrict activities that compromise the protection of vulnerable species, communities, habitats or geological features. Nested within this State Conservation Area we recommend the establishment of State Marine Parks and State Marine Reserves to provide higher levels of protection to specific communities and habitats. (3) The front-side of Catalina from Land’s End to Church Rock should be established as a State Marine Park. State Marine Park status protects this area from commercial fishing. (4) Five State Marine Reserves should be established off Catalina. State Marine Reserve Status prohibits extraction of all plants and animals as well as geological and archeological artifacts. Two of these reserves are expansions of current ‘notake’ marine reserves while the rest are new. The State Marine Reserves should extend to either the 100-meter contour or 1.5 nautical miles offshore, whichever is greater. (5) The current boundaries of the Farnsworth Bank reserve should remain unchanged and the area should be established as a State Marine Park to exclude commercial fishing activities. (6) The market squid fishery off Catalina should be limited to vessels based solely in California. (7) The use of all longlines and nets, with the exception of purse seine nets specifically used for squid and baitfish, should be permanently banned in all state waters off Catalina. (8) Current traditional statewide commercial and recreational fishing regulations (e.g., seasonal, size, bag limits, groundfish closures, closed species) should not be changed for state waters off Catalina.