Thesis (M.S.)--Oregon State University, 2010. / Printout. Includes bibliographical references (leaves 124-131). Also available on the World Wide Web.

Seagrass beds are highly valuable ecosystems with a potential nursery function for rockfishes in British Columbia. Understanding how the nursery value of seagrass habitats differs for rockfish species, and what factors create this variability in habitat value, is important for effective conservation planning. In this study, the use of Zostera marina beds in Barkley Sound by juvenile rockfishes (Sebastes spp.) was investigated. Rockfish have been observed in Z. marina beds by many researchers, however, their abundance and distribution between beds has been shown to be variable. The abundance of juvenile rockfishes in five beds was assessed in 2005 and 2006 using visual surveys. Environmental and biological variables that could potentially influence this abundance were measured concurrently. These included supply of settling fish (hereafter “settlers”), biotic and abiotic habitat characteristics. The eelgrass beds that I studied were found to differ significantly in their habitat characteristics, the abundance of settlers arriving to them, as well as the abundance of juvenile recruits in the beds. Sebastes melanops and S. caurinus were found at the sites between June and September. There was no significant relationship between the abundance of settlers arriving at a bed, and the abundance of juveniles using it. However, many of the eleven habitat characteristics investigated were significantly correlated with the abundance of either S. melanops, or S. caurinus. It is likely that these relationships arose from multiple causes which acted both pre- and post-settlement. Habitat features that were identified as correlates with high juvenile abundance value included lower epiphyte biomass, nearness to kelp habitats, lower water temperature, lower shoot density, and higher leaf width.

Seagrass beds are highly valuable ecosystems with a potential nursery function for rockfishes in British Columbia. Understanding how the nursery value of seagrass habitats differs for rockfish species, and what factors create this variability in habitat value, is important for effective conservation planning. In this study, the use of Zostera marina beds in Barkley Sound by juvenile rockfishes (Sebastes spp.) was investigated. Rockfish have been observed in Z. marina beds by many researchers, however, their abundance and distribution between beds has been shown to be variable. The abundance of juvenile rockfishes in five beds was assessed in 2005 and 2006 using visual surveys. Environmental and biological variables that could potentially influence this abundance were measured concurrently. These included supply of settling fish (hereafter “settlers”), biotic and abiotic habitat characteristics. The eelgrass beds that I studied were found to differ significantly in their habitat characteristics, the abundance of settlers arriving to them, as well as the abundance of juvenile recruits in the beds. Sebastes melanops and S. caurinus were found at the sites between June and September. There was no significant relationship between the abundance of settlers arriving at a bed, and the abundance of juveniles using it. However, many of the eleven habitat characteristics investigated were significantly correlated with the abundance of either S. melanops, or S. caurinus. It is likely that these relationships arose from multiple causes which acted both pre- and post-settlement. Habitat features that were identified as correlates with high juvenile abundance value included lower epiphyte biomass, nearness to kelp habitats, lower water temperature, lower shoot density, and higher leaf width.

Thesis (Ph. D.)--Oregon State University, 2006. / Printout. Includes bibliographical references (leaves 109-115). Also available on the World Wide Web.

Seagrass beds are highly valuable ecosystems with a potential nursery function for rockfishes in British Columbia. Understanding how the nursery value of seagrass habitats differs for rockfish species, and what factors create this variability in habitat value, is important for effective conservation planning. In this study, the use of Zostera marina beds in Barkley Sound by juvenile rockfishes (Sebastes spp.) was investigated. Rockfish have been observed in Z. marina beds by many researchers, however, their abundance and distribution between beds has been shown to be variable. The abundance of juvenile rockfishes in five beds was assessed in 2005 and 2006 using visual surveys. Environmental and biological variables that could potentially influence this abundance were measured concurrently. These included supply of settling fish (hereafter “settlers”), biotic and abiotic habitat characteristics. The eelgrass beds that I studied were found to differ significantly in their habitat characteristics, the abundance of settlers arriving to them, as well as the abundance of juvenile recruits in the beds. Sebastes melanops and S. caurinus were found at the sites between June and September. There was no significant relationship between the abundance of settlers arriving at a bed, and the abundance of juveniles using it. However, many of the eleven habitat characteristics investigated were significantly correlated with the abundance of either S. melanops, or S. caurinus. It is likely that these relationships arose from multiple causes which acted both pre- and post-settlement. Habitat features that were identified as correlates with high juvenile abundance value included lower epiphyte biomass, nearness to kelp habitats, lower water temperature, lower shoot density, and higher leaf width. / Science, Faculty of / Botany, Department of / Graduate

Some fish produce sounds for a variety of reasons, such as to find mates, defend their territory, or maintain cohesion within their group. These sounds could be used to non-intrusively detect the presence of fish and potentially to estimate their number (or density) over large areas and long time periods. However, many fish sounds have not yet been associated to specific species, which limits the usefulness of this approach. While recording fish sounds in tanks is reasonably straightforward, it presents several problems: many fish do not produce sounds in captivity or their behavior and sound production is altered significantly, and the complex acoustic propagation conditions in tanks often leads to distorted measurements. The work presented in this thesis aims to address these issues by providing methodologies to record, detect, and identify species-specific fish sounds in the wild. A set of hardware and software solutions are developed to simultaneously record fish sounds, acoustically localize the fish in three-dimensions, and record video to identify the fish and observe their behavior. Three platforms have been developed and tested in the field. The first platform, referred to as the large array, is composed of six hydrophones connected to an AMAR acoustic recorder and two open-source autonomous video cameras (FishCams) that were developed during this thesis. These instruments are secured to a PVC frame of dimension 2 m x 2 m x 3 m that can be transported and assembled in the field. The hydrophone configuration for this array was defined using a simulated annealing optimization approach that minimized localization uncertainties. This array provides the largest field of view and most accurate acoustic localization, and is well suited to long-term deployments (weeks). The second platform, referred to as the mini array, uses a single FishCam and four hydrophones connected to a SoundTrap acoustic recorder on a one cubic meter PVC frame; this array can be deployed more easily in constrained locations or on rough/uneven seabeds. The third platform, referred to as the mobile array, consists of four hydrophones connected to a SoundTrap recorder and mounted on a tethered Trident underwater drone with built-in video, allowing remote control and real-time positioning in response to observed fish presence, rather than long-term deployments as for the large and mini arrays. For each array, acoustic localization is performed by measuring time-difference of arrivals between hydrophones and estimating the sound-source location using linearized (for the large array) or non-linear (for the mini and mobile arrays) inversion. Fish sounds are automatically detected and localized in three dimensions, and sounds localized within the field of view of the camera(s) are assigned to a fish species by manually reviewing the video recordings. The three platforms were deployed at four locations off the East coast of Vancouver Island, British Columbia, Canada, and allowed the identification of sounds from quillback rockfish (Sebastes maliger), copper rockfish (Sebastes caurinus), and lingcod (Ophiodon elongatus), species that had not been documented previously to produce sounds. While each platform developed during this thesis has its own set of advantages and limitations, using them in coordination helps identify fish sounds over different habitats and with various budget and logistical constraints. In an effort to make passive acoustics a more viable way to monitor fish in the wild, this thesis also investigates the use of automatic detection and classification algorithms to efficiently find fish sounds in large passive acoustic datasets. The proposed approach detects acoustic transients using a measure of spectrogram variance and classifies them as “noise” or “fish sounds” using a binary classifier. Five different classification algorithms were trained and evaluated on a dataset of more than 96,000 manually annotated examples of fish sounds and noise from five locations off Vancouver Island. The classification algorithm that performed best (random forest) has an Fscore of 0.84 (Precision = 0.82,Recall = 0.86) on the test dataset. The analysis of 2.5 months of acoustic data collected in a rockfish conservation area off Vancouver Island shows that the proposed detector can be used to efficiently explore large datasets, formulate hypotheses, and help answer practical conservation questions. / Graduate

Nearshore marine habitats provide critical nursery grounds for juvenile fishes, but their functional role requires the consideration of the impacts of spatial connectivity. This thesis examines nursery function in seagrass habitats through a marine landscape (“seascape”) lens, focusing on the spatial interactions between habitats, and their effects on population and trophic dynamics associated with nursery function to rockfish (Sebastes spp.). In the temperate Pacific Ocean, rockfish depend on nearshore habitats after an open-ocean, pelagic larval period. I investigate the role of two important spatial attributes, habitat adjacency and complexity, on rockfish recruitment to seagrass meadows, and the provision of subsidies to rockfish food webs. To test for these effects, underwater visual surveys and collections of young-of-the-year (YOY) Copper Rockfish recruitment (summer 2015) were compared across adjacent seagrass, kelp forest, and sand habitats within a nearshore seascape on the Central Coast of British Columbia. Recruitment was positively influenced by the structural complexity of seagrass and adjacency to kelp forest sites, however a negative interaction between seagrass complexity and kelp forest adjacency suggests that predation modifies Copper Rockfish recruitment densities. In addition, using δ13C and δ15N isotopes to determine the basal contributions to seagrass food webs, kelp-derived nutrients were on average 47% ± 0.4 of YOY Copper Rockfish diets, which was 3x and 67x greater than the contribution of autochthonous seagrass production (seagrass epiphyte and seagrass blades, respectively). YOY Copper Rockfish diets in seagrass adjacent to sand habitats had the greatest amounts of kelp-derived nutrients and harpacticoid copepods, and concurrently had lower body condition compared to rockfish in the seagrass kelp edges and interior, feeding predominantly on seagrass epiphytes and calanoid copepods. This thesis provides further evidence that temperate seagrasses are nurseries for rockfish and that spatial elements of seascapes, including connectivity via habitat adjacency and variability in habitat structure, alter the recruitment and diets of rockfish in seagrass habitats. These seascape nursery effects are important considerations for marine planning, especially given the global decline of nearshore habitats. / Graduate

Precise and accurate species abundance and distribution data are important for making effective ecological conservation and management decisions. These data are often challenging to obtain, especially in marine environments where the logistical and technical difficulties of working underwater can limit the precision and accuracy of detection. The chosen survey methodology, along with the study design, will determine the extent to which species’ spatial or temporal variability in abundance and distribution may be investigated. Different observational methods may yield different results. I explore how the methodology used to collect sample measurements of fish abundance and diversity in marine environments can influence your understanding of the focal population and the effectiveness of spatial marine conservation measures. I compare inshore rockfish abundance and fish diversity estimates between paired towed video and baited video surveys and between dive and baited video surveys conducted on temperate rocky-reefs in the nearshore Northeast Pacific on the coast of British Columbia, Canada. I test if the baited video survey data yield equivalent insight to those data derived from the methods commonly used in shallow (dive surveys) and deeper waters (towed video surveys). Paired dive and baited video surveys took place inside and outside of spatial marine conservation areas designated for inshore rockfish called Rockfish Conservation Areas. I test whether the baited video data generate the same conclusions about Rockfish Conservation Area effectiveness as data derived from the dive surveys, and whether the Rockfish Conservation Areas have greater inshore rockfish abundance and fish diversity than paired locations outside the conservation areas. I find similar inshore rockfish abundance estimates between towed and baited video, but baited video surveys detect a greater number of unique species than the towed video surveys. The dive surveys detect greater inshore rockfish abundance and fish diversity than the baited video surveys, but the baited video data yield equivalent insight on Rockfish Conservation Area effectiveness to data derived from the dive surveys. I find little evidence that inshore rockfish recovery is influenced by Rockfish Conservation Area protection. When data were combined across all sites sampled, Rockfish Conservation Areas did not produce more inshore rockfish, bigger rockfish, or greater fish diversity than paired sites outside of Rockfish Conservation Areas, whether measured using a dive survey or a baited video survey. However, I did observe a positive effect of Rockfish Conservation Area protection for some of the individual Rockfish Conservation Areas surveyed that rated as having a high Conservation Score. This suggests certain Rockfish Conservation Areas may be effective conservation areas for inshore rockfish recovery. The differences I observe in inshore rockfish abundance and fish diversity between the paired surveys reveals the methodology used can influence species abundance and diversity estimates. Baited video surveys are a low cost and effort methodology that can be used to examine inshore rockfish abundance and fish diversity over rocky reefs from nearshore waters down to depths greater than 20 m, and to monitor the effectiveness of spatial marine conservation areas. / Graduate

Synthetic marine habitats such as artificial reefs (ARs) are deployed to offset marine habitat losses and aid conservation of marine communities, including species at risk. Though environmental benefit is often assumed, AR’s ability to support northern temperate marine fish communities has rarely been tested. The structural orientation and location of a reef can strongly influence biodiversity and productivity of faunal communities inhabiting it. For ARs, understanding how reef characteristics affect species and community composition are key in optimizing their use in conservation initiatives. I used ROV and sonar to survey threatened rockfish (Sebastes spp.) and other groundfish species associated with 18 ARs and natural reefs (NRs) along the northeast Pacific coastal shelf, along the coast of BC, Canada. In my second chapter, I investigate how ARs compare to NRs in achieving conservation objectives as measured by fish abundance and species richness. I found that community composition significantly differed between NRs and ARs. ARs had high variability in rockfish abundance, while NRs consistently supported intermediate rockfish abundances. Groundfish diversity was markedly greater on NRs. Depth and relief significantly explained variability in abundance and species richness. Interestingly, rockfish abundance was negatively associated with proximity to nearest rockfish conservation area. In my third chapter, I assess variation between AR fish communities on six reefs to better understand efficacy of meeting conservation objectives. I quantified structural characteristics of each reef using high-definition sonar data to create three-dimensional models and calculate measurements of reef structure. I also examined the effects of surrounding habitat associated with reef locations. I found that depth, conservation status, rugosity, and reef age significantly explained rockfish abundance. Groundfish species richness was significantly associated with conservation status, relief, reef size, and an interaction between depth and reef age. This research is a first step in proposing underlying mechanisms for differences between fish communities on ARs in BC, and which reef attributes facilitate successful contributions to conservation. Though ARs show promise in the conservation of some threatened species, the maintenance of diverse fish communities may depend on protection of heterogeneous natural reef communities. Given that a critical component of AR success is structure, using three-dimensional technologies can be used as a tool to understand species-habitat association on existing reefs and help predict the success of future reefs. / Graduate

Concerns about declines in marine biodiversity led to the creation of marine protected areas and spatial fishery closures as tools for recovery. Yet many marine conservation areas suffer low levels of compliance from diverse fishing populations, including recreational fishers. Little research quantifies levels of recreational fisher compliance and its drivers, especially in temperate marine environments, despite the prevalence of this kind of fishing in some regions. This thesis addresses this knowledge gap through a study of recreational fisher compliance in Rockfish Conservation Areas (RCAs) in British Columbia, Canada. One hundred and sixty four RCAs were implemented between 2003 and 2007 and now cover 4847.2 km2. These conservation areas were created in response to widespread concern from fishers and non-governmental organizations about inshore rockfish population declines. However, recent research suggested that recreational fisher compliance might be low. This thesis had two goals: 1) contribute to knowledge about, and develop methods of assessing, non-compliance within marine conservation areas, and 2) address the immediate problem of suspected recreational non-compliance in RCAs. I had the following objectives: 1) Assess ecological and social RCA effectiveness to date, using a framework for improving governance from the literature on common pool resources; 2) Assess recreational fisher knowledge and perceptions of RCAs, and 3) Quantify non-compliance and social and ecological compliance drivers in RCAs. Methods included a literature review, structured surveys with 325 recreational fishers at 16 locations in the Salish Sea (Southern Gulf Islands and Victoria area), and trail camera monitoring in 42 coastal locations (both RCAs and unprotected sites). Results show that recreational fisher knowledge and compliance to RCA regulations is low. The assessment of social and ecological effectiveness shows much room for management improvement for recreational fisheries. This finding is supported by my survey and trail camera data. I found that 25.5% of recreational fishers had never heard of RCAs and ~60% were unsure of RCA locations. The total non-compliance rate was 23% in RCAs. Seventy nine percent of trail camera monitored RCA sites showed confirmed or probable fishing activity, with no significant difference between fishing effort inside and outside RCAs. However, 77% of fishers surveyed believed that rockfish conservation is necessary with advertising, fisher education, and increased monitoring offered as solutions to non-compliance. I recommend managers implement a public outreach and education campaign to address low levels of compliance. This study suggests that positive perceptions of marine conservation areas and conservation initiatives are not enough to create high compliance. Educating stakeholders and creating high levels of awareness should be an essential first step when creating marine conservation areas. My research offers important insights into the study of non-compliance, and the immediate problem of recreational non-compliance in BC’s RCAs. My successful use of a simple and cost/time efficient multiple methods approach to assessing compliance provides robust tools for future compliance analyses, and hence provides a valuable contribution to the compliance literature. The study also suggests that trail camera monitoring could be a promising new method for monitoring coastal conservation areas. / Graduate / 0768 / 0792 / 0306