Thesis (M.S.)--Oregon State University, 2000. / Typescript (photocopy). Includes bibliographical references (leaves 50-54). Also available on the World Wide Web.

The development of assays for stress in marine fishes is vital for studying the impacts of bycatch in fisheries and for determining the health of fish being cultured or used in research. This research developed behavioral and physiological assays for stress in juvenile sablefish, Anoplopoma fimbria, a species that comprises a valuable North Pacific fishery and is often a substantial part of incidental discard. The effects of conditions, intrinsic or extrinsic to the fish, on the variability of the stress response were also investigated. A moderate stress of 15 minutes in air was used to elicit an acute stress response. Behavioral responses and physiological values were evaluated at 1, 5, and 24 hours after the 15 minute air stress, and were compared with control fish that received only a minimal air stress. In the first series of experiments, behavioral patterns and changes in behavior over time of stressed and control fish were determined, and the protocols and time course for measuring behavioral effects of stress were established. In the second series of experiments, physiological assays were added to the behavioral protocols developed during the first series of experiments. The behavioral assays included activity levels, swimming speed at capture, and appetitive behavioral patterns in response to a chemical food stimulus (squid extract), and to a visual food stimulus (squid without odor). These behaviors are ecologically relevant in terms of performance and survival. All of these behaviors were sensitive to stress. In general, behavioral responses were depressed by stress at 1 hour, followed by recovery to control levels by 5 hours. However, the intensity of behavioral responses was affected by feeding history (1 or 5 days of food deprivation) and group influence (recovering alone or in visual contact with 3 conspecifics), which therefore affected the ability of the behavioral responses to assess stress. The behavioral assays were less capable of detecting differences between stressed and control fish when the responses of control fish were depressed as a consequence ofbeing fed the day before. Visual contact with conspecifics facilitated recovery of activity in stressed fish, but therefore also resulted in apparent activity responses to chemical food stimulus that were more likely attributable to activity increases of conspecifics than to appetitive behavior. The focus of attention of isolated fish on activity of conspecifics often interfered with visual detection of food. The physiological assays included plasma concentrations of cortisol, glucose, and lactate, all of which proved to be sensitive measures of stress in sablefish. These parameters were elevated by stress at 1 hour, followed by a decreasing trend to 5 and 24 hours. The physiological assays were affected by feeding history, and an effect of group influence was also indicated. Cortisol and lactate levels in stressed fish fed the day before recovered faster than for stressed fish that were deprived of food for 5 days. Glucose levels in stressed fish fed the day before were not elevated above controls. These results suggested an alleviating effect of feeding on the biochemical stress response. At 5 hours, cortisol and glucose were elevated above baseline levels in both solitary stressed fish and in stressed fish influenced by a group, but also for controls influenced by a group, suggesting an exacerbating effect of isolated fish being in visual contact with groups. There were critical cortisol, glucose and lactate thresholds (180 ng/ml, 140 mg/dl, and 175 mg/dl, respectively) above which no appetitive behavioral responses occurred. These clear demarcation levels are extremely valuable for linking behavioral and physiological responses. These results indicate that behavioral and physiological assays are sensitive indicators of stress in sablefish, although the magnitude, time courses, and correlation of responses may be affected by factors intrinsic and extrinsic to the fish that may vary before and during recovery. There was a correspondence between behavioral and physiological indications of stress shortly after the stressor had been removed and levels of stress were still severe. However, there was a temporal discrepancy after partial recovery had occurred, at which time recovery of physiological norms had not yet been established although behavioral responses had recovered. While behavioral patterns may readjust quickly, the persistence of an energetic load during recovery from stress, as indicated by continued physiological perturbations, may compromise ability to respond to additional stressors. / Graduation date: 2001

Graduation date: 1986

Carbohydrates have variable digestibilities and metabolizable energy values in carnivorous fish. Simple sugars are generally more digestible than complex polysaccharides, and low levels of dietary carbohydrate may contribute more metabolizable energy than high levels. Two experiments were conducted to study the effects of dietary level and processing treatment of wheat starch on the digestibility of diets fed to sablefish (Anoplopoma fimbria), in different regions of the digestive tract. Moreover, an experiment was undertaken to determine if the dietary concentration of an indigestible external marker (chromic oxide) influenced its motility, relative to other ingredients in the ingesta, as it passed through the digestive tract. Lastly, a growth experiment was undertaken to compare the performance of sablefish fed formulated diets containing one of two levels of carbohydrate to that of fish fed a natural fish diet. The gastric evacuation of a formulated and a natural diet were also investigated. Apparent digestibility values for the nutrients in a formulated diet (containing 44.4% cooked wheat and 0.1% chromic oxide) fed to sablefish were noted to increase progressively from the anterior to the posterior regions of the intestinal tract. Within each region of the gut, the apparent digestibility values for most nutrients declined over three sample periods. Carbohydrate (nitrogen-free extract) digestibility down to the distal section of the intestine ranged from 51.0 to 82.8%. An experiment designed to assess the effect of carbohydrate treatment on the digestibility of four isonitrogenous, isocaloric diets met with partial failure. It was determined that the 1.0% chromic oxide marker flowed at a differential rate to the rest of the ingesta in the digestive tract, which violated the criteria for an effective marker. Consequently, diet digestibility was not determined in this experiment. Hepatic glycogen levels in fish receiving the dietary treatments were compared, and these values were used to estimate the relative availability (digestibility) of carbohydrate from the respective diets. According to this index, the sequence for digestibility was as follows: pregelatinized starch > cooked wheat > pregelatinized starch/cooked wheat > unprocessed wheat. Differential movement of chromic oxide relative to other ingesta was observed in sablefish fed on alternate days regardless of the dietary concentration of the indigestible marker (0.1 or 1.0%). It was surmised that the feeding protocol established the circumstances from which marker 'streaming' was observed in the results. Differential transport of Cr₂O₃ through the gut by ingested seawater was suggested as a possible mechanism for the phenomenon. Sablefish fed a natural fish diet had the highest growth rates, condition factors, liver lipid levels and the lowest feed conversion ratios and liver glycogen levels. Sablefish fed a diet containing 22.2% cooked wheat had a higher growth rate, condition factor, and a lower food conversion ratio, than those fed a diet containing 44.4% cooked wheat. Ingestion of the 44.4% cooked wheat diet resulted in the highest values for liver glycogen and hepatosomatic index. It was concluded that sablefish have a limited ability to metabolically utilize digestible carbohydrate and that most of the dietary non-protein energy should originate from high quality lipid for maximum protein sparing. / Science, Faculty of / Resources, Environment and Sustainability (IRES), Institute for / Graduate

As two species diverge, much of their genomes begin to differentiate. In many lineages, however, the genomic structure remains remarkably intact, with orthologous gene content maintained across millions of years and significant changes to their biological characteristics. The maintenance of gene content is defined as conserved synteny while the preservation of gene order is defined as conserved linkage; the conservation of both can be incredibly informative when interrogating and comparing two genomes. In non-model organisms, linkage conservation to a well-developed model allows informed, cost-effective and rapid answers to fundamental biological questions without generation of equivalent resources. With the development of new model organisms, we can begin to discuss more fundamental evolutionary concepts, such as the maintenance of chromosomal gene content across larger evolutionary time-scales, or the reorganization that occurs in chromosomes following major genomic events such as whole-genome duplications. In this work, I utilized the rapid development of primary genomic resources in the non-model teleost sablefish (Anoplopoma fimbria) to demonstrate that conserved linkage to a model genomic reference can identify the gene most likely responsible for genetic sex-control. I then assembled the first genome for a non-duplicated member of the teleost lineage Protacanthopterygii, the northern pike (Esox lucius), and demonstrated the conservation of synteny between three major lineages of teleosts, the Protacanthopterygii, the Acanthopterygii and the Ostariophysi. I further showed that the genome of northern pike retains an ancestral teleost organization and pre-duplicated genome in comparison to the economically important Salmoniformes. Finally, with continued improvements of the genome to the chromosome level, I demonstrated the degree of conserved linkage maintained between Atlantic salmon and northern pike and explained how conserved linkage through both genomes could be used to improve the genome assembly of the other, even with over 125 million years of separation. As genomic technology continues to advance and new genomic resources become available, the continued refinement of genome re-organization post duplication will be revealed, and this pre-duplication outgroup will continue to push our understanding of the effects of genome duplication, as we transition from genome organization to functional modifications of gene duplicates following duplication. / Graduate / 2018-12-01

The three components of the aerobic respiratory metabolism of sablefish, digestion (SDA), activity, and standard metabolism, were examined separately and together as dependent variables responding to the independent variable, feeding frequency. All fish were similar in size and held within a temperature range of 8.5 - 9.5 C on a 12 hr photoperiod. Fish were studied in both 4000 L mass respirometers equipped with activity meters and in a tunnel respirometer. Identical meals were given every 4, 7, and 14 days. A fourth series of starved fish served as controls. In the mass respirometers, oxygen consumption, ammonia nitrogen excretion, and activity were monitored continuously before, during, and after acclimation to the different feeding frequencies. This permitted estimation of total metabolism, the activity and feeding components of total metabolism, standard metabolism, and protein and lipid catabolism. In the tunnel respirometer, energy expenditures at similar levels of Imposed activity were compared before and after eating to examine repartitioning of locomotor and feeding metabolism. It was found that swimming energy expenditures and standard metabolism are a sigmoid functions of ration frequency. The lowest metabolic rates are associated with the least frequent feedings and the greatest with the most frequent meals. Consequently, total and routine metabolic rates are also direct functions of ration history. The lowest metabolic rates are based on lipid oxidation as an energy source. The fish primarily oxidize proteins to meet metabolic needs when on higher rations. It is also shown that apparent specific dynamic action (SDA) results to a greater extent from catabolic rather than anabolic processes. When the dual metabolic load of locomotion and digestion threatens to exceed the aerobic metabolic scope of the fish, a physiological mechanism exists whereby oxygen supply is preferentially shunted to locomotor requirements. When spontaneously active in the mass respirometers, the activity component of metabolism is generally less than 25% of the standard metabolic rate and digestion and locomotion can proceed synchronously. When swimming spontaneously, the sablefish move at a single, probably optimal velocity regardless of ration history. The better fed fish in the experiments were active most of the day despite the low contribution of the activity component to the routine metabolic rate. These results have significance regarding assumptions often made in bioenergetic models, specifically that activity energy expenditures and standard metabolic rates are independent of ration. They reveal an adaptable physiology which applies different energy partitioning strategies to meet the changing metabolic needs of fish in a dynamic environment with a variable food supply. / Science, Faculty of / Zoology, Department of / Graduate

Light regulates many biological processes through light-sensitive proteins called opsins. Opsins are involved in vision, but they are also expressed in extraretinal tissue, where their roles are far less clear. Fish have large opsin repertoires, derived from a long history of gene duplication and divergence, making them useful models to study opsin diversity and function. I introduce the deep-sea sablefish (Anoplopoma fimbria) as a model for opsin research for three main reasons: i) the availability of a draft genome and transcriptome, simplifying the characterization of this species’ opsin repertoire, ii) the proximity of the only sablefish aquaculture facility in the world, providing exclusive access to a large number of individuals at all developmental stages, iii) the observation that sablefish occupy very different light environments during the course of development, ranging from well-lit shallow waters to the aphotic zone, which provides a light environment context for opsin gene expression data. My survey of the genome showed that sablefish have 36 distinct opsin genes (7 visual and 29 non-visual), even though they spend most of their lives in the dark. The sablefish opsin sequences and repertoire are similar to those of other teleost fish. To test the hypothesis that the sablefish opsin repertoire is being expressed/transcribed during the comparatively brief period of time when this species is exposed to light (the free-swimming larval stage through to the juvenile stage), I quantified the expression of five paralogous genes from a well-studied non-visual opsin family (OPN4’s) in the brain across life stages. Data show statistically stable expression of Opn4m1 and Opn4m3 among life stages, a rough association of Opn4x1 and Opn4m2 expression with age and light environment, and little-to-no expression of Opn4x2. I localized proteins encoded by the most highly expressed class of OPN4 genes in the brain, the Opn4m genes, to the surface of the optic tectum just below a cranial ‘window’; a zone that has been shown to express dozens of opsins in zebrafish (a distant relative, with their ancestor diverging more than 230 million years ago). Thus, in some cases, expression appears to be correlated with light exposure not only temporally, but also spatially. By studying non-visual opsins in sablefish, I have challenged and broadened the current understanding of opsin evolution and function in fish and provided the foundation for future studies to test brain regions for light-sensitivity, perform opsin gene knock-outs, and explore potential light-independent processes. / Graduate / 2023-09-06

Average global ocean temperatures and the frequency and intensity of marine heat waves have been increasing over the last century. Temperature plays a critical role in defining the geographical range of the majority of marine species. Some species may respond to ocean warming trends by shifting their latitudinal and depth ranges, while others may be able to cope with changes in temperature through phenotypic plasticity and local adaptations. If a species is unable to shift its distribution or has limited thermal plasticity, it may face severe population declines or local extinction. Therefore, describing thermal tolerance limits is a useful tool for predicting how a given species will respond to ocean warming. Due to its commercial importance, sablefish (Anoplopoma fimbria) is a fish species of particular interest in British Columbia. Sablefish are semi-demersal and spawn along the continental slopes of the Pacific coast from California to Alaska. Their various life history stages occupy different depth strata and thus experience substantially different environments with respect to temperature (as well as salinity, oxygen, etc.). Adult sablefish spawn at depths that exceed 300 m and embryos sink to depths of ~1,000 m after fertilization. Embryos hatch into yolk-sac larvae until they become mobile at the post-yolk-sac larvae stage. The latter migrate to near-surface waters (<3 m) at which temperatures are approximately 12-15°C in the late spring. Heart rate is a temperature-dependent performance measure and has been used to gain insight into the thermal tolerance of many adult fishes. However, few studies have used this approach with the early life stages of fishes such as embryos and yolk-sac larvae (YSL). The purpose of this study was to assess whether sablefish embryos and YSL have the potential for cardiac acclimation by examining changes in their thermal tolerance limits when incubated at temperatures outside of what they experience in a natural setting (~5°C). Cardiac performance was assessed during an acute temperature challenge from 2.0° to 12.0°C in increments of 1.0°C (at a rate of 1°C 40 min-1) for individuals incubated at 3.0°C, 5.0°C (control), and 7.0°C. Embryos were video recorded at each 1.0°C increment and videos were viewed at a later date to determine heart rate at each temperature. This study attempted to use temperature breakpoint analysis, commonly used in studies of adults, on these early life stages to assess cardiac performance. It was hypothesized that sablefish embryos and yolk-sac larvae incubated at warmer temperatures would have a higher thermal tolerance than sablefish embryos and YSL incubated at colder temperatures, as seen in other fish species. There was some degree of thermal compensation of cardiac function with temperature in sablefish embryos and YSL as mean heart rate increased with incubation temperature throughout acute warming. YSL had consistently higher mean heart rate values at any given temperature of the acute temperature challenge when compared to embryos incubated at the same temperature. TAR is the temperature at which the heart first becomes arrhythmic is considered a sub-lethal index because the organism is expected to experience cardiac collapse soon after. TAR was reached for 100% of embryos incubated at 3.0°C at an average temperature of 8.6 ± 1.0°C. In contrast, only 18% and 33% of embryos incubated at 5.0° and 7.0°C exhibited arrhythmia (mean TAR were 9.0 ± 3.0 and 8.5± 1.5°C, respectively). The lower thermal limit for embryos incubated at 7.0°C was likely near 1.0°C, which was determined during preliminary testing. Neither the upper or lower limits were reached for YSL during the acute temperature challenge. No mortalities were observed during any acute temperature challenges. Overall percent mortality throughout the entirety of the experiment could not be determined due to limitations in the experimental setup and reduced staff working on this project due to COVID-19 safety protocols. This study is also the first to investigate whether transporting sablefish embryos from a hatchery to a research facility at different stages of development had an effect on their cardiac performance during acute warming. Embryos were transported in a cooler from the sablefish hatchery on Salt Spring Island to UVic via ferry and vehicular transport. Time of transportation did not significantly change the temperature at which heart rate reaches its maximum or TAR. There was also consistent overlap in mean heart rate ± standard error at each temperature of the acute temperature challenge between these two groups. Therefore, there appears to be no indication that transportation affected the heart rate response of sablefish embryos when incubated at the same temperature. However, future studies may want to confirm this by identifying and comparing other breakpoint temperatures that characterize physiological performance. Determining whether transportation has effects on cardiac performance may be of interest to other researchers who need to transport fish embryos from the field to the laboratory. Heart rate measurements during an acute temperature challenge of sablefish embryos and yolk-sac larvae (YSL) incubated at various temperatures provided initial insight to their overall success in a warming climate. Currently, it is projected that waters at depths of 1,000 m will warm on average by less than a degree by the end of the 21st century. The results of this study suggest that the early life stages of sablefish may not be exposed to critical temperatures in the near future, but future impacts on overall physiological decline remain unknown. The novel data presented here lay the groundwork for future researchers to continue to characterize the thermal tolerances of the early life stages of sablefish, and the likely response of this important species to ocean warming. / Graduate

Sablefish (Anoplopoma fimbria) is a scarcely represented species in Northwest Coast archaeology, but its remains are abundant at Tse-whit-zen, a large, Lower Elwha Klallam village in modern Port Angeles, WA that was occupied over the past 2,800 years. Because sablefish flesh has high nutritional value and it can be easily captured from nearshore waters in its juvenile form, sablefish should have been pursued where it was available. Therefore, the scarcity of sablefish in many Northwest Coast archaeological sites could indicate this species was not abundant in past fisheries. However, current zooarchaeological reports do not contain sufficient information on taphonomic histories, sampling, or zooarchaeological methods to determine whether patterns of sablefish scarcity could actually explained by differential destruction of sablefish remains, sample size effects, screen size effects, or misidentification. In this thesis, I examine how each of these factors may have affected the abundance of sablefish remains in Northwest coast archaeological sites. I evaluate four hypotheses that attribute sablefish representation to zooarchaeological identification methods, screen size, sample size, and post-depositional destruction of fishbone. While I do not explicitly test whether social and ecological factors affect sablefish abundance, sociocultural and environmental variation can be considered likely explanations for the observed patterns of sablefish representation if the other hypotheses are rejected. I test my hypotheses using three scales of archaeological records. First, I reanalyzed six previously analyzed Salish Sea assemblages to assess whether criteria for sablefish identification exist, are valid, and have been applied consistently. Second, I synthesized fishbone data from 35 previously analyzed Northwest Coast assemblages to evaluate the effects of screen size, sample size, and post-depositional destruction on sablefish representation. Finally, I integrate previously unreported fishbone data from the analysis of Tse-whit-zen into the synthesis of previous studies. The Tse-whit-zen materials I report on here represent six discrete time periods in the 1,800-year history of one large area of the site, which encompasses part of a plankhouse, providing a unique opportunity to examine the effects of screening, sample size, and post-depositional destruction at an extremely fine scale. I also use data from the reanalysis of a portion of the Tse-whit-zen fishbone to verify the consistency of sablefish identification for this site. I reject all four hypotheses and conclude that the uneven distribution of sablefish is likely a true reflection of ecological factors, human decision-making, or both factors. Whether sablefish scarcity is related to distributions of sablefish in past environments, or whether humans chose not to pursue sablefish is not known from the current study. Connecting sablefish capture to specific seasons with body-size regression methods may reveal associations between sablefish acquisition and other seasonal fisheries and activities, and help evaluate whether they conflicted with sablefish procurement in some contexts. Although zooarchaeological identification and reporting methods do not appear to account for sablefish scarcity, zooarchaeologists need to include more information about their methods so that the validity of inter-assemblage comparisons can be assessed. Zooarchaeologists maximize the value of their contributions to anthropology, biological sciences, and human ecodynamics when they explicitly report the methods they use to identify animal remains. By reporting the methodological and analytic procedures they used in detail, zooarchaeologists enhance the reader's confidence in their conclusions and provide future researchers with the information that is required to replicate their results. Which elements were recorded, and the criteria that were used to make taxonomic attributions, fundamentally affect the primary faunal data that researchers use. This study is part of a growing interest among zooarchaeologists in data quality assurance and quality control, which constitute a critical part of every large-scale comparative analysis.