Thesis (Ph. D.)--University of Washington, 1998. / Vita. Includes bibliographical references (leaves [184]-194).

In the marine realm, there has been considerable habitat degradation caused by multiple human disturbances that often act synergistically, strongly affecting fish and invertebrate populations and, consequently, one of the major stakeholders of these resources, fishers. However, the mechanisms underlying how marine habitats support fisheries remain understudied. In this dissertation I examined the importance of fish habitat at global, regional and local scales in two distinct systems (mangrove habitats in the tropics and rockfish habitats in inshore waters of Vancouver Island) combining a suite of different approaches. First, I explored the mangrove-fishery linkage relationship by conducting a global meta-analysis. I found strong evidence supporting the importance of mangrove area to enhance fisheries. This relationship, however, varied across countries, likely based on regional geomorphological settings and fishery management policies. Subsequently, I determined the use of mangrove and adjacent habitats by fish in a tropical lagoon system in the continental Caribbean (Colombia), systems often overlooked in the Caribbean when analyzing mangroves as fish habitat. I collected fish with gillnets at different distances from mangroves and at different sites within the same lagoon system. While fish used mangroves, fish abundance was not higher in these habitats compared to adjacent ones, as predicted. However, diversity tended to be higher in mangroves. Nevertheless, the major driver affecting abundance, diversity and biomass was salinity. That is, diversity and abundance decreased as salinity increased. Next, I used a Local Ecological Knowledge approach to explore the mangrove-fishery linkage relationship because fishers are seldom incorporated into such relationships. By conducting semi-structured interviews I found that fishers fish close to their village and to mangroves, that in addition to fishing they use mangroves for firewood and as construction material. Fishers also agreed that mangroves are important for their fishing activity, as these habitats are critical for fish and crustaceans caught in the system. Finally, I examined the importance of derived benthic parameters for rockfish abundance and distribution at large spatial scales (100s km) in inshore waters of Vancouver Island. I established that higher complexity better explains presence and higher abundance of rockfish. Furthermore, the results provided valuable information for fishery and spatial management and habitat conservation to help recover rockfish populations. All together, these findings highlight the urgency to preserve coastal marine habitats for both juvenile and adult marine organisms to sustain small-scale fisheries as a food source and for traditional purposes. While conserving habitats is a key component of a broader and more complex ecosystem approach that includes overfishing and other anthropogenic pressures, in the absence of a holistic approach the chances of success are minimal. / Graduate / 2019-04-18

Marine Protected Areas (MPAs) are a management tool used to protect and sustain many ecologically and economically important fish species from overexploitation by recreational and commercial fishing. Lingcod (Ophiodon elongatus) and some of its prey species, such as rockfish (Sebastes spp.), are species that are protected from fishing in some California MPAs. Lingcod is an apex predator that consumes a variety of fish and invertebrate species. In this study, I sought to assess the effect of an MPA on the abundance, size and diet of Lingcod. I hypothesized that Lingcod in a no-take MPA would be more abundant and larger than Lingcod in an adjacent reference site (REF) that was open to fishing. Furthermore, I hypothesized that diet would differ between Lingcod in caught the MPA and Lingcod in the REF. I collected Lingcod from the Point Buchon State Marine Reserve (MPA) and an adjacent REF site that was open to fishing. I measured, weighed, sexed, and collected stomach contents from Lingcod using the gastric lavage (stomach pumping) technique. Then, I identified prey items from Lingcod stomach contents down to the lowest taxonomic level possible and quantified diet composition by percent by occurrence, percent by number, and percent by mass. Lingcod in the MPA consumed more fish prey items than Lingcod in the REF site. Lingcod in the REF consumed more cephalopod prey items than Lingcod in the MPA. I analyzed the four most common prey items (rockfish, anchovies, flatfish, and octopus) for nutritional content. My data suggest that Lingcod increased in size and abundance in a no-take MPA because they do not suffer from fishing mortality. However, a more nutritious diet could also contribute to a biologically significant advantage for Lingcod in the MPA. To address this would require further research focused on calculating the net energy (gross energy extracted from the prey item minus the energetic costs of handling and digesting the prey item) obtained by Lingcod from consuming different fish and cephalopod prey items. MPAs can be an effective management tool for protecting fish stocks, although, it is important to understand the interspecific interactions between predator and prey species to adaptively mange MPAs and the species that reside within them.

Recent studies have shown environmental factors influence life history traits in fishes. Understanding intraspecific variability of life history characteristics and condition is necessary to determine local fisheries management strategies. Gopher rockfish, Sebastes carnatus, comprise 50% of the estimated shallow nearshore recreational rockfish catch in California, yet insufficient local data exist regarding life history traits and condition of this species. Our study locally defines growth parameters (maximum size and age), size (age) at reproductive maturity, and condition (hepatosomatic indices) for gopher rockfish in south central California. The growth parameter values of gopher rockfish from our study are similar to previously published research. However, our data also indicate that the current local gopher rockfish stock in south central California reaches reproductive maturity at a larger size and an older age when compared to gopher rockfish sampled throughout central California (primarily in Monterey) between 1977-1982. Furthermore, we examined spatial and temporal differences in life history information, within and outside of two south central California Marine Protected Areas (MPAs) established in 2007, between two time periods. Our data show that the size and longevity of fish has increased after the establishment of MPAs.

Stock assessments are statistical models which characterize the state of a population of fish. Data for stock assessment models of West Coast nearshore groundfish come largely from fisheries-dependent sources. Incorporating fisheries-independent data would increase data availability. A potential source of fisheries-independent data which is comparable to existing fisheries-dependent data is the California Collaborative Fisheries Research Program (CCFRP), a Marine Protected Area (MPA) monitoring study. We are interested in understanding the context in which CCFRP could be implemented into assessments of nearshore groundfish, specifically rockfish. To investigate this, we used management-relevant metrics to examine three questions concerning the implementation of CCFRP as a data source: whether the scope of the project captures the core depth distribution of a species, whether the methodology of the project affects assessment metrics, and how the presence of data from MPAs affects assessment metrics. Comparisons were made for three species with different life histories and desirability in the recreational groundfish fishery: Blue rockfish (Sebastes mystinus), Vermilion rockfish (S. miniatus), and Gopher rockfish (S. carnatus). Based on these metrics and comparisons, we found that the specific method of potential implementation of fisheries-independent data into stock assessments is highly species dependent, but all species could benefit. Implementing this data will lead to better-informed management, ensuring that these populations persist.

Resolving diversity patterns and their underlying drivers has application for both ecological theory and ocean management. Because seafloor characteristics are often used to assess bottom habitat, I examined the relationship between deep-sea benthic (bottom-living) diversity and multi-scale topographic heterogeneity. Most work occurred on the Canadian Pacific continental shelf at Learmonth Bank with additional sites in Strait of Georgia (BC) and Gulf of Maine (Atlantic shelf). High-resolution species distribution and seafloor data were annotated from remotely operated vehicle benthic imagery surveys while large-scale seafloor data were derived from multibeam sonar. New method development to address problems of current methods and to facilitate comparison among ecosystems is a major outcome. My new MiLS method (microtopographic laser scanning) can profile the deep seafloor at a resolution of ~1-2 cm with high accuracy and precision. I also developed a new ACR (arc-chord ratio) rugosity index as a measure of 3-D topographic heterogeneity that is simple, accurate and highly versatile. Model systems and scales vary among my studies but results consistently yield a positive relationship between diversity and topographic heterogeneity and identify bottom hydrodynamics as an important underlying driver. Rockfish Sebastes spp. associate with higher seafloor rugosity non-randomly and select for deep-sea corals and sponges over inert substrata alone. Data indicate that degradation of biogenic structures is a long-term detriment to rockfish species. Gorgonian coral- and sponge-dominant biotopes strongly associate with a single substratum type. These relationships were used to map coral and sponge distributions. This work, which collectively adds new information on the ecological relevance and distribution of corals and sponges, is pertinent to the conservation and management of fish stocks and vulnerable marine ecosystems. Epibenthic community variables abundance, richness, and Shannon diversity positively correlated with both the local microtopographic heterogeneity on a scale of 10 m2 and with the surrounding regional large-scale topographic heterogeneity on scales of 25 to 250,000 m2. Relationships were strongest between epibenthic community variables and the largest scale rugosity and were used to generate and test predictive diversity models. Where management strategies rely on surrogate measures in data-poor areas, mapping benthic diversity using ACR rugosity will provide good indicators. Although bottom hydrodynamics is consistently identified as an underlying driver of epibenthic patterns related to topographic heterogeneity, data suggest the nature of the relationship varies across spatial scales. At small scales, high topographic heterogeneity likely increases diversity by increasing the number of available niches (including hydrodynamic gradients; e.g., the abrupt vertical rugosity created by tall corals and sponges provides rockfish refuge from currents) while at large scales, high topographic heterogeneity increases local diversity less directly through distant hydraulic events that alter bottom flow hydrodynamics. / Graduate / 0329 / 0416 / 0799 / cdupreez@uvic.ca

Management strategies to prevent overfishing while achieving optimum yield vary according to the available data and life history of the fished stock. I evaluated two sets of management strategies for Pacific coast rockfish: strategies to set harvest limits for data-poor stocks, and strategies intended to protect the age structure of fished stocks. Setting Harvest Limits for Data-poor Stocks - The collapse of canary rockfish, Sebastes pinniger, in the northeast Pacific began more than two decades before the stock was officially declared overfished. The 2006 reauthorization of the Magnuson-Stevens Fishery Conservation and Management Act requires a scientifically-based harvest limit for all fished stocks, including those with data limited to catch. Two such "data-poor" methods are currently in use for the management of west coast stocks, depletion-corrected average catch (DCAC) and depletion-based stock reduction analysis (DB-SRA). To evaluate the performance of each method when challenged with catch and biological uncertainty, I retrospectively applied the methods to the catch and biological data available at the time of the first and second canary rockfish stock assessments in 1984 and 1990. In 1980 canary rockfish would be classified as "data-poor", and in 1990 as "data-rich". To evaluate the sensitivity of DCAC and DB-SRA to error in the catch data, harvest limits were estimated using both the historic catch data from each assessment, and the reconstructed catch data from the most recent stock assessment. In addition, harvest limits were estimated using simulated catch data sets for the years 1916 to 1983 with increasing variability around the true catch. DCAC and DB-SRA estimated harvest limits were significantly lower than the catch recommended in both the data-poor and data-rich stock assessments, but higher than the "true" overfishing limit. Use of current catch data improved the estimated harvest limit when the stock was data-poor, but not when the stock was data-rich. The simple methods responded to increasing error in the catch time series with decreasing mean estimates of the harvest limit, indicating that these methods are highly precautionary for this species, when the catch time series is the only source of error. Age Structure Management Strategies - In a variable oceanographic environment, a population with many reproductive age classes benefits not only from the increased fecundity of older fish; but also, in some species, an increase in larval fitness. Older females may also spawn at different times or over longer periods than younger females, increasing the probability of larvae encountering favorable environmental conditions. Despite the accumulating evidence for the importance of age structure to long-term population viability in harvested fish populations, long-lived west coast rockfish (Genus Sebastes) are managed with a biomass-based harvest control rule. I compared three strategies for age structure management, and evaluated the strategies relative to the status quo, biomass-based harvest control rules, across three rockfish life histories. I examined the tradeoff between yield and traditional management reference points, as well as performance measures that could serve as management reference points for age structure. Yield was reduced by strategies that maintain "old growth" age structure, but annual variation in the catch and the probability of becoming overfished were also reduced. The longest-lived rockfish benefited the most from strategies that maintained older fish in the population through dome-shaped selectivity. The shorter-lived rockfish benefited from adjustments in the catch limit based on the age composition of the catch one year previous. Achieving "pretty good yield" with management strategies that also decrease the potential for overexploitation is an important goal for stocks that are well-studied and those that are poorly understood; these investigations contribute to a growing literature on alternative approaches to sustainable fisheries management. / Graduation date: 2012

The nearshore waters off the Oregon coast (< 73 meters) are a region of high productivity and economic value, with a variety of habitats that include rock outcrops. Temperate reef habitats are important to many commercially important fishes inhabiting the Pacific coast, including canary rockfish (Sebastes pinniger) and yelloweye rockfish (Sebastes ruberrimus), which are currently listed as "overfished" by the Pacific Fishery Management Council. Along the Pacific coast of North America, nearshore rocky reefs have been designated as essential fish habitat (EFH), while comprising approximately just seven percent of Oregon's territorial sea. Despite this EFH designation, the use of visual (SCUBA, remotely operated vehicles (ROVs), human occupied vehicles (HOVs)) and non-visual (bottom trawl) survey methods within this region has been infrequent and scattered, providing limited information on species-habitat associations and species assemblages within nearshore waters. It is logistically difficult and costly to survey nearshore reefs. The factors that have led to the paucity of surveys include the depth (too deep for SCUBA surveys but too shallow for larger survey vessels), high seas limiting available days for field work, and the high-relief nature of the habitat (precluding the use of bottom trawls). In an effort to better understand species-habitat associations and community structure of Oregon's nearshore reefs, an autonomous underwater drop-camera termed the "video lander" was employed at the Three Arch Rocks reef, a nearshore reef off of Oceanside, Oregon. Video lander footage was used to identify and groundtruth habitat types, as well as species assemblages over two distinct seasons: spring/summer (n=272) and winter (n=108). Many species-habitat associations were statistically significant: yelloweye rockfish (large boulder p<0.0073), canary rockfish (small boulder p<0.0006), kelp greenling (Hexagrammos decagrammus) (bedrock outcrop p<0.0162), and quillback rockfish (Sebastes maliger) (large boulder p<0.0016). Summer and winter surveys revealed similar habitat associations and distributions for these species. I found no significant difference in species composition between the northern and southern regions of the reef (Bray-Curtis dissimilarity index (BCDI) = 71.71, ANOSIM p>0.1447), but a significant difference between spring/summer and winter seasons was identified on the outer section of the reef, due to the presence of spotted ratfish (Hydrolagus colliei) in the winter (BCDI =76.41, ANOSIM p < 0.0155). My study shows that data provided by the video lander can fill existing gaps in our understanding of nearshore distribution and habitat associations of temperate rocky-reef fishes off the Oregon coast. / Graduation date: 2013