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The effect of dietary vitamin E and dietary lipids on growth and immune parameters of juvenile turbot (Scophthalmus maximus) were investigated in a series of experiments. The aims of the studies were to maximise immune function through dietary modulation to counteract stress induced immunodepression resulting from high stocking densities. In the first experimental trial, the vitamin E requirement for an optimum immune response was studied and revealed that vitamin E depletion induced poor health status, lower growth with some mortalities occurring at the end of the trial. However, supplementation of the diets with high levels of α-tocopherol although ensuring better growth did not significantly enhance most of the parameters measured at the end of the trial. The second trial aimed to test regimes coupling fresh or oxidised oil and low or high vitamin E supplementation. The results showed that vitamin E had a role in preventing peroxidation as high vitamin E supplementation improved some of the immunological parameters measured compared to fish fed with the same oxidised oil but low levels of vitamin E. By contrast low levels of vitamin E did not induce pathological conditions in fish fed with fresh oil showing the importance of dietary lipid in the evaluation of vitamin E requirements. Following this investigation another feeding trial was designed to look at the interaction of polyunsaturated fatty acids (PUFAs) and α-tocopherol on the immune parameters of juvenile turbot. Although liver lipid composition was affected by the diets and growth was enhanced by high vitamin E levels and a high ratio of (n-3)/(n-6) PUFAs no significant differences could be attributed to the lipid quality in the immunological parameters measured. Vitamin E supplementation enhanced the proliferation of kidney leucocytes when stimulated with lipopolysaccharide. These studies give some information on the requirements for vitamin E and lipid quality of juvenile turbot.

The life history traits, population dynamics, and community ecology of marine fishes vary along spatio-temporal gradients in environmental conditions and habitat (i.e. physical conditions). Accordingly, incorporating physical drivers into fisheries assessments can improve fishery management advice, and thus the sustainability of fisheries. However, collective inferences on the effects that physical conditions have on fishes can be difficult to draw due to confounding effects of scale, sampling procedure, gear type, and other aspects of methodology. Here, I examined the role of physical drivers and methodological biases in explaining variation in aspects of fish populations and communities across levels of biotic organization. In the first study contained in this dissertation, I employed simulations to demonstrate the influence of sample distribution on growth parameter estimates and per-recruit assessment for the Gulf Corvina (Cynoscion othonopterus) in the Gulf of California. Sample distribution could confound growth parameter estimates in conventional assessments, and is especially important to account for when documenting spatio-temporal variation in growth, as sample distributions are rarely consistent over time and space. In the second, I described the effects – or lack thereof – of physical conditions on the distributions of common petroleum platform-associated fish species in the Gulf of Mexico through large-scale submersible camera sampling. In the third, I combined camera and hydroacoustic data to characterize water-column fish communities at petroleum platforms and identified the dominant physical drivers that shape them. In the fourth, I examined the challenges of assessing fish community size spectra with hydroacoustics in rugose marine habitats. Assessing the size spectra of fish communities over time and space is useful for understanding the effects of physical conditions and anthropogenic activities on community structure, and using hydroacoustic technology allows size spectra to be assessed more rapidly and efficiently than conventional methods. The findings and approaches described in this dissertation may be used to understand variation in fish growth, distribution, abundance, and community structure in response to physical drivers, thereby making spatial and ecosystem considerations more accessible to fisheries assessment and management frameworks

The biological characteristics of fisheries stocks that are assessed for management considerations are rarely homogeneous over time or space. However, stock assessment scientists largely ignore this heterogeneity in their models. This thesis addresses the effects of spatial and temporal heterogeneity on stock assessment models using Atlantic Weakfish (Cynoscion regalis) as a case study. First, spatial and temporal variation was incorporated into length-, weight-, and maturity-at-age estimates using mixed-effects models (Chapter Two). The resulting heterogeneous weight and maturity parameters then were applied to per-recruit analyses to examine the sensitivity of biological reference points to spatial and temporal variation in life history attributes (Chapter Three). Mixed-effects life history models incorporating spatial and temporal variation revealed distinct regional and annual trends that were not visible from standard homogeneous models. In several instances, the homogeneous modelling approach produced life history estimates that varied significantly from the spatial and temporal means produced by the heterogeneous models. In some cases, this difference was so great that the homogeneous means were much higher or lower than the heterogeneous means for all regions or years. Minimized AIC statistics revealed that spatially and temporally integrated mixed-effects models were more robust and descriptive of Atlantic Weakfish life history than the standard homogeneous models. Per-recruit and biological reference points derived from these life history estimates in Chapter Three were found to be highly sensitive to spatial and temporal variations in weight parameters. In several cases, reference points used as management targets were so significantly different that ignoring spatial and temporal heterogeneity in Atlantic Weakfish life history would likely cause overfishing and decline of Weakfish in certain regions and years.

Climate variability can affect fish populations and fisheries production in numerous ways, including inducing measurable fluctuations in fish growth, condition, and fisheries production. Unfortunately, mechanisms driving these linkages are poorly understood for most exploited species, which hinders effective management. The purpose of this study was to use the Gulf Corvina (Cynoscion othonopterus), a heavily exploited marine fish in the Gulf of California, Mexico, as a model to investigate relationships between El Niño Southern Oscillation (ENSO) as measured by the Multivariate ENSO Index (MEI), sea surface temperature (SST), precipitation, drought as measured by the Palmer Drought Severity Index (PDSI), and river flow from the Morelos Dam with three parameters: adult fish condition, growth rate, and fisheries production. Adult fish condition was assessed by comparing annual variations in weight-length relationships of fish captured by the commercial fishery to each climate and environmental variable using an exponential model. Fish growth rate was measured using otolith chronologies for juveniles (years 0-2) and adult (years 3-10). Lastly, annual catch data from the commercial fishery was compared to each climate and environmental variable to examine relationships between climate and fisheries production. Results indicate that adult condition, juvenile growth rate and fisheries production are enhanced during El Niño conditions and increased SST. El Niño conditions during the birth year showed a positive relationship with fisheries landings at peak age of capture five years later, suggesting a possible linkage between juvenile recruitment, survivorship and future fisheries production. A weak positive relationship between river flow and growth rate in juveniles and adults was also found, which indicated that growth rate of both life history stages may be enhanced during strong El Niño years with high river flow. However, no relationship was found between precipitation and our parameters. Lastly, a positive relationship between decreased drought during the birth year and fisheries landings five years later indicated a freshwater influence on fisheries production. Our results indicate climate variability acting through El Niño events has a positive effect on growth, condition, fisheries production, and potentially juvenile recruitment suggesting the importance of both ocean climate variability and freshwater input on the Gulf Corvina.

It is rare to have longitudinal data on the somatic growth of fish, that is, how their body length changes over time. In most temperate fish, scales or other hard parts, like otoliths or other bones, form annual rings or increments. Growth of the hard part can be measured, thereby giving a longitudinal record of hard part growth from cross-sectional data. Methods such as back-calculation and linear mixed-effects models have used the growth of hard parts to infer somatic growth. At times, it is not feasible to obtain the measurements of the hard part. Body length at time of capture is much easier to measure and reflects somatic growth, which is usually of more interest. In this thesis, I present a model that is based on a longitudinal approach but models length at time of capture, rather than the yearly body growth. It also allows for estimation of environmental impact on growth.

The Staunton River is a high gradient, second order stream approximately 6 km in length located on the eastern slope of the Blue Ridge Mountains in Shenandoah National Park, VA. In June 1995, a catastrophic flood and debris flow altered the instream habitat and Salvelinus fontinalis population of the Staunton River. The debris flow scoured the streambed, deposited new substrate materials, removed trees from the riparian zone, and eliminated fish from a 1.9km section of the stream. By June 1998, both young-of-year (YOY) and age 1+ S. fontinalis had recolonized the debris flow affected area. The event provided a rare opportunity to examine recovery of the S. fontinalis population and instream habitat in addition to addressing potential effects of the debris flow on movement, activity, and growth of fish in the debris flow affected and unaffected areas of the stream. Post-recolonization movement and activity were monitored using two-way fish traps (weirs), mark-recapture techniques, and radio telemetry. The weirs failed to produce any movement data. Most fish (91%) in the mark-recapture study had range sizes less than 100m, however biases common to mark-recapture study designs (low recapture rate, flawed logic, etc.) hampered interpretation of results. For example, subsequent recapture of individually marked fish indicated that as many as 54% of marked fish confirmed to have been alive at the time of a recapture session were not recaptured. Radio telemetry provided information on S. fontinalis movement and activity at seasonal and diel scales during summer and fall. Differences in movement and activity between the debris flow affected and unaffected areas were minimal when compared to seasonal variations. During summer, range sizes were near 0m and crepuscular activity patterns were observed. During the fall range size increased and diel activity was concentrated in the mid-afternoon with a much higher peak than during summer. Basin-wide visual estimation technique (BVET) fish population surveys performed each spring and fall from 1993 = 1999 provided pre- and post-event fish population abundance and density estimates. Post-event fish growth in the debris flow affected and unaffected areas was monitored using mark-recapture techniques. Abundance and density of both YOY and age 1+ S. fontinalis exceeded pre-event levels within 2-3 years. Growth of YOY and age 1+ fish was significantly greater in the debris flow affected area until spring 1999. Population density appeared to have a strong negative influence on growth. The observed changes in fish growth and differences in fish size associated with population density would be of minimal importance to the typical angler but may suggest a mechanism by which S. fontinalis populations can quickly recover from catastrophic events. BVET habitat surveys provided information on total stream area, number of pools and riffles, pool and riffle surface area and depth, substrate composition, and large woody debris (LWD) before (1993), immediately following (1995), and four years post-event (1999). Immediately following the debris flow, the stream channel was highly disordered which resulted in an increase in the total number of habitat units and a decrease in average habitat unit surface area, total stream area, and average depth when compared with pre-event conditions. In addition, substrate composition had shifted from small to large diameter particles and LWD loading had increased in both debris flow affected and unaffected areas. Four years after the event, the total number of habitat units, average habitat unit surface area, total stream area, and average depth had all returned to near pre-debris flow levels and substrate composition had begun to shift towards smaller particle sizes. Changes in LWD loading from 1995-1999 reflected changes in the riparian zone following the debris flow. In the unaffected area, where riparian trees remained intact, LWD loading increased, whereas in the debris flow affected area, where riparian trees were eliminated, LWD loading decreased. For the most part the effects of the debris flow, although immediately dramatic, were in the long term minimal. The debris flow affected area was recolonized rapidly and abundance and density quickly rebounded past pre-event levels. Differences in fish growth between the affected and unaffected area were short lived. Any effect the debris flow affected area may have had on movement or activity was minimal when compared with seasonal variations. Most habitat characteristics reverted to near pre-event levels just four years after the flood and debris flow. Although a number of factors will influence recovery time from such events, these results indicate that immediate management action, such as stocking or habitat modifications, are not necessary in all cases.

This study is another phase of the overall research program designed to furnish basic information for the management of East Texas lakes and has as its specific purpose the determination of the age and growth characteristics of two valuable species on these waters. The species to be considered are the black crappie, Pomoxis nigro-maculatus (Le Sueur) and the white crappie, Pomoxis annularis Rafinesque. Both species are highly regarded as food fish and have for many years offered recreational outlets for Texas fishermen.