Dissertations / Theses on the topic 'Aquaculture and fisheries stock assessment'

For years bluefin tuna has been the poster child for overfishing and poor management. However, recent improvements in data collection, catch monitoring and international cooperation are providing an opportunity to reverse the perception of a fishery that is doomed to collapse. Stock assessments are conducted routinely to monitor the abundance and productivity of exploited fish stocks so managers can determine how many fish can be sustainably harvested each year. Should a stock be declared overfished or under-going overfishing, the science behind stock assessments also equip managers with the knowledge necessary to make decisions about what short-term and long-term management measures should be taken to help reverse these trends. in that light, the goal of my research has been to use newly available age data to improve the quality and reliability of assessments for Atlantic bluefin tuna by reducing uncertainty about the data and methods used to infer growth and age composition. A secondary goal has been to provide managers with the knowledge necessary to implement effective stock rebuilding programs for Pacific bluefin tuna. Chapter 2 is focused on cohort slicing, a method routinely used in the Atlantic bluefin tuna assessment to estimate catch-at-age from catch-at-size information. This chapter explores how errors in cohort sliced catch-at-age data can bias estimates of total mortality rate derived from catch curve analysis. Recommendations are provided concerning the appropriate mortality estimator and plus group to use depending on the parameters characterizing the stock. Chapter 3 provides updated growth estimates for western Atlantic bluefin tuna, which were adopted in 2017 as the basis for defining growth in the assessment. Chapter 4 provides an overview of the theory behind age-length keys with particular emphasis on the assumptions that govern each method and provides notes of caution concerning their applications to real data. Chapter 5 evaluates through simulation the relative performance of different methods for estimating age composition of western Atlantic bluefin tuna catches and applies the best performing technique, the combined forward-inverse age-length key, to actual western Atlantic bluefin tuna data. Chapter 6 moves over to the Pacific and focuses on evaluating the potential impacts of different minimum size regulations on the stock of Pacific bluefin tuna and explores ways in which to minimize short-term pain to the industry while still achieving long-term yield and conservation goals. Overall, this work has contributed major improvements to the stock assessment process of Atlantic bluefin tuna and implications of this work resonate beyond the bluefin tuna world to other highly migratory species faced with similar problems.

Young sandeels (0- and 1-group fish) form a substantial part of the total stock biomass at Shetland. As well as forming the basis for a local fishery at Shetland, they are also an extremely important prey item for many seabird species which breed around Shetland coasts. Improving our understanding of recruitment dynamics is vital for managing the Shetland fishery whilst minimizing adverse affects on breeding seabirds. Therefore, this thesis has concentrated on analyzing recruitment patterns and developing models to simulate hypothetical recruitment scenarios. Various models were developed and/or parameterised to simulate recruitment. Firstly, as there appeared to be no clearly defined stock-recruit relationship, time series models were applied to expose and improve understanding of patterns in the data. However, the relationship between stock and recruitment cannot be ignored if spawning stock biomass changes through exploitation. Therefore, Shepherd (1982) and Ricker (1954, 1975) stock-recruit models are parameterised using bootstrap analysis. For the Shepherd model, which is the more complex of the two, bootstrap analysis identified models which could be considered as "constant recruitment" models - that is no influence of spawning stock biomass on recruitment. It was found that four very low recruit years, which occurred in the late 1980s when spawning stock biomass was generally high or moderate, were strongly influencing model fit. This prompted the question: are these low recruit years typical of the range of recruitment for the given spawning stock biomasses or can they be considered outliers? In the face of uncertainty (although there is no biological reasoning) these data points were removed and the stock-recruit models re-parameterised. This enabled curves with 95% confidence intervals to be parameterised for both stock-recruit models (Shepherd & Ricker). The autoregressive model parameterised earlier was combined with the stock-recruit models so recruitment in any year was expressed as a function of SSB and of recruitment in the previous year.

Modern fishing fleets have the capacity to over-exploit fish stocks. Inaccurate assessments could overestimate the stock size and as a result Total Allowable Catches (TAC) are set too high for sustainable stock conservation. Fisheries management need robust and reliable stock assessments to ensure that the species and environmental effect of fishing is sustainable. Since the demand for ecosystem based approaches to management has increased, the needs for improved estimates of un-assessed abundance have risen. Managers simply need to know how many fish left in the see and how much to limit the fishermen to fish to have sustainable fisheries. Therefore, accurate assessment of the market as well as by-catch stocks and records of true landings and discards are critical aspects of the scientific advice to the fisheries managers to accurately set TACs. Here, we consider the marine species that are left un-assessed. That is because they cannot be assessed by the existing methods. We therefore sought to fill the key gap with this matter. This thesis has five key elements. First we reviewed the stock assessment method with the emphasis on the length-structured models. Second, we produced a population model (so called survey-landings model) to make the use of survey frequency data extracted from International Bottom Trawl Survey and total annual landed biomass from commercial reports. Third, within a twin-experiment context and sensitivity analysis the model was assessed for accuracy and robustness in variability in initial parameter values and observational noise. Forth, applying the survey-landings model the population dynamics of the North Sea haddock was assessed and the results were compared with the International Council for Exploitation of the Sea assessment. Fifth, after the model proved to be reliable it is used as an alternative for age- or catch-at-length model, the population of the North Sea grey gurnards were modelled with confidence. This model enabled un-assessed species such as grey gurnards to be modelled and assessed for the first time.

Growth and mortality of the chinese clam (chione gnidia) were examined in the Estuary of La Cruz, Sonora, Mexico from 1987 to 1989. Clams were reared in trays in two habitats of the Estuary of La Cruz, the pool and the canal, where four experiments were carried out. In experiment 1 growth and mortality under two densities and two environments was assessed. Experiment 2 yielded information on growth and mortality of clams growing on four different substrates and at two densities. Experiment 3 assessed growth and mortality in high density conditions, and experiment 4 assessed growth after a period of growth stagnation. In all cases, highly significant differences in growth and mortality were observed between environments. The pool was found to be the place where higher total growth and least mortality occurred. However, the sizes achieved by clams in the pool suggest that the Estuary of La Cruz is not a suitable environment for the cultivation of this clam, and that the introduction of C. gnidia in this area is not feasible under present habitat conditions.

Riverine fisheries in England are under pressure from a variety of activities, including increasing intensification of land-use, urbanisation, rising demands for water abstraction, pollution, proliferation of exotic species, climate change and recreational activities. As a result, the integrity of English rivers has changed. In this study, an attempt was made to measure the ecological health of 22 English lowland rivers from the Thames, Trent and Yorkshire Ouse catchments using a variety of tools. The objective was to modify the Index of Biotic Integrity (IBI) for use on English lowland rivers and compare it with existing indices. A number of diversity indices, Margalef (DMg), Simpson (Dsm) and ShannonWiener (H') were used to evaluate the status of fisheries in the study rivers. The Abundance / Biomass (ABC) method and computer-based multivariate analyses, UPGMA, TWINS PAN, DECORANA, were also used to evaluate the status of fish communities. In addition to these indices, the ABC method and multivariate analyses, the IBI, a multimetric index was also used to evaluate the ecological health of study rivers. The IBI is based on structural and functional attributes of fish communities and is capable of evaluating health and condition of an aquatic ecosystem. The IBI requires a reference condition with which to compare the output. In English rivers, no pristine (reference) sites were considered available, consequently best available data were used to develop a reference condition. In this study, the IBI was modified from Karr (1981), which was based on 12 metrics (community characteristics) of fish assemblages. For the study rivers, 15 metrics which described the status of the fish communities were selected to calculate the IBI. Each metric was scored on a simple scale from 0 (absence) to 5 (high quality). The sum of all the metrics (range 0 - 75) was used to assign sites to qualitative classes of biotic integrity. Six integrity classes on a continuous scale were chosen with the following class boundaries: Excellent (56 - 75), Good (42 - 55), Fair (28 - 41), Poor (16 - 27), Very Poor (1 - 15) and No Fish (0). In the study rivers, the DMg, Dsm and H' indices were unable to measure anthropogenic impacts on fish communities as all these indices were based on structural properties of fish communities. These indices also failed to take account of the presence of juveniles in the fish community in a river. Moreover, these indices were influenced by dominant species abundance and sampling strategies, giving an inaccurate assessment of the status of the fisheries. The ABC method was better at evaluating fish communities than diversity indices as the method considered fish abundance and biomass. However, the method did not include functional components of the fish community and was over influenced by juvenile fishes. Consequently, the ABC method was not considered a good indicator of ecosystem health based on fish assemblages. The UPGMA, TWINSPAN and DECORANA analyses, successfully grouped and separated river reaches with rich or poor fish stocks. These analyses however, did not take into account the functional attributes of the fish communities and were not sufficient to explain the status of a fishery without support from other indices. The IBI assessed the ecological health of the middle and lower reaches of the study rivers more accurately than the other diversity indices, ABC method and multivariate analyses. The selected IBI metrics were able to evaluate many perturbations and disturbances as the metrics represented both structural and functional attributes of fish communities. The DMg, Dsm, H', ABC, UPGMA, TWINSPAN and DECORANA were designed to highlight a specific attribute and lost information during calculation but the IBI included a greater variety of information and produced an appropriate index. Spearman's rank correlation indicated the IBI outputs were more similar to diversity indices than other measures, as significant relationships were found between the IBI and DMg, the IBI and Dsm, and the IBI and H' at a = 0.01 level. Significant relationships were probably due to the use of fish density and abundance in the models. However, this did not mean that all diversity indices and the IBI were similar in measuring ecological conditions of a river, rather it was probably numerical similarity. No significant relationship was found between the IBI and ABC, as the ABC index was a ratio of abundance and biomass while the IBI used absolute values of biomass and abundance separately. All the diversity indices, ABC method and multivariate analyses mentioned reinforced the view that the IBI developed in this study was an appropriate index at evaluating ecological health of the middle and lower reaches of the study rivers. The IBI, however, failed to predict the quality of the fisheries in headwater streams because of the exclusion of salmonid species, minor species and general low species diversity found in these zones. Consequently, it was identified that reference conditions and metrics chosen for the middle and lower reaches of the study rivers were not appropriate to assess the ecological health of headwaters. The existing monitoring programmes of the Environment Agency (EA) for fishery data collection, were considered appropriate for calculating IBIs. Sampling strategies of the EA, i.e. daytime, electric fishing both in summer and winter periods irrespective of lunar cycle and breeding season were also considered acceptable to calculate the IBI. Further research was recommended to test the IBI on a wide range of rivers to assess whether the IBI is appropriate for assessing ecological health of middle and lower reaches of rivers in all regions of the UK. Separate IBIs for headwaters, still waters and estuaries were proposed as these zones / waterbodies have different fish communities. Investigation should be directed at developing a simplified IBI using other cost-effective data sources if suitable resources are not available. It is also recommended that the possibility of including the IBI in wider aquatic resource monitoring programmes (e.g. WFD) be investigated. It is also recommended that the possibility of using the IBI to detect change in the pre and post implementation periods of any management action or anthropogenic activity be investigated. Research is also needed to integrate the IBI with other bioassessment methods (e.g. Habitat index, Diatom index, Microinvertebrate index, Chemical index and GQA index). For more effective application and understanding, the IBI may be built into a GIS (Geographical Information System) environment. It is suggested that a suitable computer package be developed to simplify calculations of the IBI. The interpretation should however, be carried out by the fishery manager or scientist.

A problem commonly encountered in stock assessments of tropical marine resources in developing countries is data paucity, which invariably results from the lack of both human and economic capacity within the government to implement and maintain programmes for data collection and analysis. With special reference to the demersal fishery of Brunei Darussalam, this thesis examines approaches for extracting useful information from data-poor fisheries to assess the state of resources and inform fishery management actions. By using official fishery statistics, augmented by local ecological knowledge (LEK) obtained from fishers engaged in either the large-scale (LS) or small-scale (SS) fisheries in Brunei, changes in demersal fishery resources over the years were assessed. The sustainability of Brunei’s demersal capture fishery was evaluated in the face of its ongoing development and climate change. Using trophodynamic indicators such as mean trophic level (MTL), Fishing-in- Balance (FiB), trophic spectra (TS) and community structure analyses, LS fishery catches of Brunei between 2000 and 2009 revealed a deteriorating state of the coastal demersal ecosystem. Closer examination of the abundance of overall demersal finfish stocks, using the Catch-Per-Unit-Effort (CPUE) index – standardised for other factors not related to abundance – indicated a declining trend, even when total catches remained stationary, although trends in abundance of the different demersal fish families varied. This rapid significant change in recent years is further supported by fishers’ LEK on relative abundance of Brunei marine resources. The study on LEK has also revealed the ‘shifting baseline syndrome’ (SBS) among currently active fishers and their exploited populations, a phenomenon not previously reported for Brunei fisheries. Findings from the study are synthesised with other information, where a number of key issues and policy options are discussed, and recommendations for the management of the fishery are made. This thesis demonstrates that researchers in data-poor fisheries can utilise different assessment tools, given the resources at their disposal, to assist in the management of marine resources.

For data-limited fisheries, length-based mortality estimators are attractive as alternatives to age-structured models due to the simpler data requirements and ease of use of the former. This dissertation develops new extensions of mean length-based mortality estimators and applies them to federally-managed stocks in the southeastern U.S. and U.S. Caribbean. Chapter 1 presents a review of length-based methods from the literature. Common themes regarding the methodology, assumptions, and diagnostics in these length-based methods are discussed. In Chapter 2, a simulation study evaluates the performance of the length-converted catch curve (LCCC), Beverton-Holt equation (BHE), and Length Based-Spawner Potential Ratio (LB-SPR) over a range of scenarios. Although the LCCC and BHE are older methods than LB-SPR, the former outperformed LB-SPR in many scenarios in the simulation. Overall, it was found that the three length-based mortality estimators are less likely to perform well for low M/K stocks (M/K is the ratio of the natural mortality rate and the von Bertalanffy growth parameter; this ratio describes different life history strategies of exploited fish and invertebrate populations), while various decision rules for truncating the length data for the LCCC and BHE were less influential. In Chapter 3, a multi-stock model is developed for the non-equilibrium mean length-based mortality estimator and then applied to the deepwater snapper complex in Puerto Rico. The multispecies estimator evaluates synchrony in changes to the mean length of multiple species in a complex. Synchrony in mortality can reduce the number of estimated parameters and borrows information from more informative species to lesser sampled species in the model. In Chapter 4, a new method is developed to estimate mortality from both mean lengths and catch rates (MLCR), which is an extension of the mean length-only (ML) model. to do so, the corresponding behavior for the catch rate following step-wise changes in mortality is derived. Application of both models to Puerto Rico mutton snapper shows that the MLCR model can provide more information to support a more complex mortality history with the two data types compared to the ML model. In Chapter 5, a suite of mean length-based mortality estimators is applied to six stocks (four in the Gulf of Mexico and two in the U.S. Atlantic) recently assessed with age-structured models. There was general agreement in historical mortality trends between the age-structured models and the mean length-based methods, although there were some discrepancies which are discussed. All models also agreed on the overfishing status in the terminal year of the assessment of the six stocks considered here when the mortality rates were compared relative to reference points. This dissertation develops new length-based assessment methods which consider multiple sources of data. The review guides prospective users on potential choices for assessment with length-based methods. Issues and diagnostics associated with the methods are also discussed in the review and highlighted in the example applications.

Overexploitation of many fish stocks underlines the need for more effort directed towards stock management so that the sustainability of resources is assured. To avert the tragic consequences of overfishing in coastal waters, a growing body of theoretical and empirical research provides evidence in support of cooperation among resource users to manage their commons. This study aimed to investigate the factors that contribute to the emergence and evolution of collective action in fishermen's communities to manage their coastal fish resources in South Al-Batinah, Sultanate of Oman. The study emphasises the importance of a collective action approach to fish resource management with examples from three fishing towns.In order to understand why fishermen choose to participate (or not to participate) in local collective action to manage fish resources, the researcher focuses on six main sets of issues that influence fishermen's decisions: economic factors; awareness of resource exploitation problems; institutional rules in use; social identity, group size and heterogeneity among resource users. Social and demographic factors as well as vessel configuration were also considered.Data collection for the study was carried out using three methods: questionnaire, semi-structured interview and observations of fishermen's activities. Statistical reports and other research papers carried out in Oman were also reviewed. The study found that there is a management institution that governs the fishing activities of the fishermen in the study area. Fishermen in the area inherited an indigenous management institution, which was established hundreds of years ago. It was also found that fishermen were very aware of the resource exploitation problems. High awareness of the resource exploitation problems coupled with high interdependence among users might induce them to work collectively to mitigate harm to their long-term welfare.The results of testing a number of hypotheses indicated that among the reasons which may influence collective action, are high economic dependence on the fishery,individuals' social identity as fishermen, awareness of the resources exploitation problems, risk aversion and heterogeneity (differences in objectives and interests).The study findings indicated that individuals using common resources are faced by various "assurance" and "chicken" problems. In both the PD game and the Assurance game, the preferred outcome is mutual cooperation. Whereas the predicted outcome of the former is defection, the latter suggests the possibility that the preferred outcome (i.e., cooperation) will occur, because individuals' decisions in the commons are influenced by a complex set of factors, rather than strictly materialistic self-interest. The analysis presented in this study examined several of those factors for their influence on individual behaviour. The findings of this study strongly suggest that the presence of local management institutions to coordinate the fishermen's activities in the study area is the key factor in avoiding the worst outcome (universal defection). The game structure has been changed from a Prisoner's dilemma to a Privileged game or a game of Chicken where the benefits from cooperation are maximized. It is the role of the institutions to determine how the cost of providing the public goods might be shared among participants.

The statistical assessment of harvested fish populations, such as the Atlantic-Iberian sardine (AIS) stock, needs to deal with uncertainties inherent in fisheries systems. Uncertainties arising from sampling errors and stochasticity in stock dynamics must be incorporated in stock assessment models so that management decisions are based on realistic evaluation of the uncertainty about the status of the stock. The main goal of this study is to develop a stock assessment framework that accounts for some of the uncertainties associated with the AIS stock that are currently not integrated into stock assessment models. In particular, it focuses on accounting for the uncertainty arising from the catch data sampling process. The central innovation the thesis is the development of a Bayesian integrated stock assessment (ISA) model, in which an observation model explicitly links stock dynamics parameters with statistical models for the various types of data observed from catches of the AIS stock. This allows for systematic and statistically consistent propagation of the uncertainty inherent in the catch sampling process across the whole stock assessment model, through to estimates of biomass and stock parameters. The method is tested by simulations and found to provide reliable and accurate estimates of stock parameters and associated uncertainty, while also outperforming existing designed-based and model-based estimation approaches. The method is computationally very demanding and this is an obstacle to its adoption by fisheries bodies. Once this obstacle is overcame, the ISA modelling framework developed and presented in this thesis could provide an important contribution to the improvement in the evaluation of uncertainty in fisheries stock assessments, not only of the AIS stock, but of any other fish stock with similar data and dynamics structure. Furthermore, the models developed in this study establish a solid conceptual platform to allow future development of more complex models of fish population dynamics.

The role of inland fisheries as contributors to local and national economies in developing African countries is well documented. In South Africa, there is increasing interest in inland fisheries as vehicles for achieving national policy objectives including food security, livelihoods provision, poverty alleviation and economic development but there is surprisingly little literature on the history, current status, and potential of inland fishery resources. This lack of knowledge constrains the development of management strategies for ensuring the biological sustainability of these resources and the economic and social sustainability of the people that are dependent on them. In order to contribute to the knowledge base of inland fisheries in South Africa this thesis: (1) presents an exhaustive review of the available literature on inland fisheries in South Africa; (2) describes the organisation of recreational anglers (the primary users of the resource); (3) compiles recreational angling catch records and scientific gill net survey data, and assesses the applicability of these data for providing estimates of fish abundance (catch-per-unit effort [CPUE]); and finally, (4) determines the potential for models of fish abundance using morphometric, edaphic, and climatic factors. The literature review highlighted the data-poor nature of South African inland fisheries. In particular information on harvest rates was lacking. A lack of knowledge regarding different inland fishery sectors, governance systems, and potential user conflicts was also found. Recreational anglers were identified as the dominant user group and catch data from this sector were identified as potential sources of fish abundance and harvest information. Formal freshwater recreational angling in South Africa is a highly organised, multi-faceted activity which is based primarily on angling for non-native species, particularly common carp Cyprinus carpio and largemouth bass Micropterus salmoides. Bank anglers constituted the largest number of formal participants (5 309 anglers affiliated to formal angling organisations) followed by bass anglers (1 184 anglers affiliated to formal angling organisations). The highly structured nature of organised recreational angling and dominant utilisation of inland fisheries resources by this sector illustrated not only the vested interest of anglers in the management and development of inland fisheries but also the role that anglers may play in future decision-making and monitoring through the dissemination of catch data from organised angling events. Generalised linear models (GLMs) and generalised additive models (GAMs) were used to standardise CPUE estimates from bass- and bank angling catch records, which provided the most suitable data, and to determine environmental variables which most influenced capture probabilities and CPUE. Capture probabilities and CPUE for bass were influenced primarily by altitude and conductivity and multiple regression analysis revealed that predictive models incorporating altitude, conductivity, surface area and capacity explained significant (p<0.05) amounts of variability in CPUE (53%), probability of capture (49%) and probability of limit bag (74%). Bank angling CPUE was influenced by conductivity, surface area and rainfall although an insignificant (p>0.05) amount of variability (63%) was explained by a predictive model incorporating these variables as investigations were constrained by small sample sizes and aggregated catch information. Scientific survey data provided multi-species information and highlighted the high proportion of non-native fish species in Eastern Cape impoundments. Gillnet catches were influenced primarily by species composition and were less subject to fluctuations induced by environmental factors. Overall standardised gillnet CPUE was influenced by surface area, conductivity and age of impoundment. Although the model fit was not significant at the p<0.05 level, 23% of the variability in the data was explained by a predictive model incorporating these variables. The presence of species which could be effectively targeted by gillnets was hypothesised to represent the most important factor influencing catch rates. Investigation of factors influencing CPUE in impoundments dominated by Clarias gariepinus and native cyprinids indicated that warmer, younger impoundments and smaller, colder impoundments produced higher catches of C. gariepinus and native cyprinids respectively. A predictive model for C. gariepinus abundance explained a significant amount of variability (77%) in CPUE although the small sample size of impoundments suggests that predictions from this model may not be robust. CPUE of native cyprinids was influenced primarily by the presence of Labeo umbratus and constrained by small sample size of impoundments and the model did not adequately explain the variability in the data (r² = 0.31, p>0.05). These results indicate that angling catch- and scientific survey data can be useful in providing predictions of fish abundance that are biologically realistic. However, more data over a greater spatial scale would allow for more robust predictions of catch rates. This could be achieved through increased monitoring of existing resource users, the creation of a centralised database for catch records from angling competitions, and increased scientific surveys of South African impoundments conducted by a dedicated governmental function.

The South African demersal longline experiment is assessed with emphasis on the target species, kingklip Genypterus capensis. The hypothesis that kingklip on the South African coast comprise a unit stock is tested. Recommendations for the management of the fishery are made. Longlining was found to be commercially viable. Techniques have been developed to target on either kingklip or the Cape hakes, Herluccius capensis and H. paradoxus. Longline fishermen exploit the kingklip spawner stock from August to No v ember by taking advantage of prespawning aggregations on the South-East Coast . Effort switches to the West Coast in late summer and early winter where kingklip are less abundant and a larger proportion of hake is caught. Catch rates of kingklip on the South Coast have declined sharply and the resource there has been exploited at a rate greater than that required to retain 50% of the unexploited biomass . There is a 17,6% probability that the spawner biomass on the South Coast has already been depleted below its pristine level. On the West Coast the catch rates of kingklip are lower than on the South Coast and have not changed significantly, although within the 95% confidence limits there is a possibility that the resource there has also been depleted below 50% of its pristine level. Genypterus capensis on the South African coast comprise a unit stock. Comparison of kingklip morphology using multivariate and discriminant function analysis and of otolith morphology using univariate statistics shows that there are no significant differences between the fish on the West and South Coasts. They are a slow growing species and were aged up to 25 years. Kingklip on the West Coast are smaller and have a lower L~ than those on the South Coast, but this is not a characteristic of discrete stocks. Kingklip on the South Coast mature earlier than those on the West Coast and aggregate to spawn on the South - East Coast in spring. There is no obvious spawning period on the West Coast. It is hypothesized that kingklip spawning on the South-East Coast is in response to favourable environmental conditions that enhances the survival of their eggs and larvae. It is recommended that demersal longlining be established as a permanent kingklip-directed fishery but that effort should not be allowed to increase. The West and South Coasts should be managed .separately. A TAC of 5 OOOt for kingklip should be introduced for 1989 of which 2 OOOt should be allocated to the West Coast and 3 OOOt to the South Coast . A closed season for kingklip from 1 August to 30 September on the South-East Coast is recommended. Hake-directed longlining should not be allowed as its effect on the hake spawner stocks are unknown and could be a potential threat to the stability of the demersal trawl fishery.

Length-based stock assessment models estimating mortality rates are attractive choices for assessing fisheries with data deficiencies. The U.S. Caribbean is exploring using these models and trying to optimize their commercial sampling program for such a model.

A simulation model was constructed to compare two length-based mortality estimators, the Beverton-Holt and Gedamke-Hoenig models. The simulations also tested aspects of the Gedamke-Hoenig model previously not thoroughly addressed, such as the effects of varied life history parameters, violating the assumptions of constant growth and recruitment, sample sizes (n), and sampling program length (Ys) on total mortality rate estimates (Z).

Given the scenarios investigated, the Beverton-Holt model produced consistently biased, but more stable results when n was low, variation was high for both growth and recruitment, and sampling began after the change in Z took place. The Gedamke-Hoenig model was generally less biased and detected changes in Z, but produced variable results of the current Z, especially with low sample sizes and high variability. In those situations, both models can be carefully interpreted together for management advice.

In the Gedamke-Hoenig model results, a clear pattern emerged in the mean accuracy and precision of the model where after an asymptote was reached, increasing n did not improve the means. The variance of the model improved with both increasing n and increasing Ys. Outliers were predictable and could be accounted for on a case-by-case basis.

The model developed here can be a tool for guiding future stock assessment model choice and sample design in the U.S. Caribbean and other regions.
Master of Science

The conservation of marine ecosystems is at least 20 years behind terrestrial and freshwater ecosystems due to the difficulties in studying and monitoring these dynamic and complex environments. Furthermore, marine environment receive less attention because human impacts are less visible in the sea, and oceans are viewed as global commons. The purpose of the present dissertation is to contribute to the knowledge of marine conservation through the development of three components in natural resources management: inventory, monitoring, and assessment of impacts. I elaborate a multi-taxa inventory, identify key species to monitor, characterize one of the key species, and assess the impacts of the most important fishery in the community-based controlled marine area of the Seri Indians along the Sonoran desert coast of Mexico. A total 657 species of mollusks, echinoderms, sharks, rays, bony fish, sea turtles, sea snake, aquatic birds and marine mammals were recorded in the Seri territory through review of 30 scientific collections housed in museums and universities, literature, and field collections. The fish information was improved through the analysis of 151 traditional Seri names. Fifty species were identified for monitoring ecosystem health. They represent species with a legal status, rare, commercially important, taxa that dominate or characterize entire communities, common taxa, and species recognized in the Seri culture. The annual eelgrass (Zostera marina atam) was selected as a key species inside the Canal de Infiernillo in the Seri territory. Coverage of the eelgrass beds was estimated using aerial photographs, field mapping, and Seri traditional ecological knowledge. The total extent of the eelgrass beds was approximately 6687 ha, which regrew in the same areas during the three-year study, maintaining the same general shapes and sizes. Twenty-six percent of the eelgrass beds overlap with the swimming crab (Callinectes bellicosus) fishing zones. Major impact on this fishery are caused by "ghost" fishing traps, which continue to capture crabs and animals and modify the substrate as they are moved around by currents and accumulate on the sea bottom. Efforts to standardize the use of traps will reduce these impacts on this fishery in the long term.

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.

Statistical age-structured models are widely used in fisheries stock assessment. These models have been become increasingly complex over recent decades, allowing them to incorporate a larger variety of fisheries data. These typically include information regarding annual fishery yields, indices of abundance and catch composition data, which reflect the distribution of ages in the harvested population each year. In some fisheries, age composition can be determined annually through the examination of annuli on hard parts, such as otoliths or scales. These methods are, however, costly, time consuming and require a relatively high level of expertise on the part of data collectors. Alternatively, length frequency distributions within the annual catch are relatively simple and inexpensive to acquire, and can be employed to extrapolate age structure given that some information regarding age length relationships in the population is known. This type of data is therefore critical for many age-structured fisheries models. Length frequency data are compiled from length measurements of a sub-sample of the commercial catch. Even when they derive from a relatively large sample size, however, these data depend on a number of biological, economic and logistical factors. In some fisheries, for example, larger, more valuable fish may be separated from the overall catch and sold quickly, before port samplers have chance to gather sub-samples (Burns et al. 1983). This can reduce the relative frequency of large individuals in length frequency data. Alternatively, fish may become stratified in holding bins or storage containers according to size, due to their slippery texture and body shape (Hilborn and Walters 1992). With smaller, shorter individuals falling to the bottom where they are less likely to be picked up and measured, length frequency data may contain a disproportionately high frequency of large fish. This study used simulations to examine the impact of these two types of bias in length frequency data on a statistical age-structured model. The model, which was similar to those used in stock assessments for black sea bass (Centropristis striata) and gag (Mycteroperca microlepis) in the southeastern United States, produced erroneous population estimates when given biased data. Length frequency data that contained too many small fish caused stock status estimates to became overly pessimistic, indicating that populations were more heavily depleted than was actually the case. This type of bias supported overly conservative management measures, which posed an unnecessary cost to fishermen. Conversely, when the data included too many large fish, estimates of stock status were overly optimistic, and supported management actions that did not effectively protect the stock from overfishing. These results indicate that the quantity of length frequency data alone does not protect against bias when using complex age-structured models. The likelihood and magnitude of bias in these must also be examined in order to determine whether results are likely to be biased. For a given fishery, it is therefore critical that potential sources of bias in length frequency data be thoroughly inspected, and that the modeling approach used to assess the stock be appropriate based on the availability and accuracy of the data.
Master of Science

Large catfishes (Clarias gariepinus & Clarias ngamensis) are not exploited commercially in the Okavango Delta, Botswana. They however constitute a large proportion of the gill net fishery catch (23 %) albeit as by-catch, coming second after cichlids (70 %). Monthly experimetal gill net sampling over 8 years showed that C. gariepinus was the most abundant species in the Okavango Delta by mass making up 37 % of the catch composition by fresh weight. Despite the relatively high abundance of C. gariepinus in the Okavango Delta, its status has never been fully assessed. For this reason, this study aimed to assess the status of C. gariepinus in the Okavango Delta with the particular goal to determine if the species could support a directed commercial gill net fishery. Investigation of the effects of the flood pulse on abundance of C. gariepinus showed that variability in water levels was the major driver of population abundance for this species. Three biological variables: (1) catch per unit effort (CPUE); (2) % catch composition and (3) Shannon's diversity index (H') exhibited a negative and significant relationship with the flood index within a year. The variation in these variables was statistically significant between months. There was a weak positive relationship between water levels and the biological variables between years suggesting increase in productivity of the system at high water levels without a lag period. Age and growth were determined using sectioned otoliths. Edge analysis showed that growth zone deposition occurred during the drawdown period in summer when water temperature and day length were increasing. The maximum recorded age was 15 years. Growth of this species was best described by the linear models (y = 21.50x + 427.39 mm LT; r² = 0.35) for females and (y = 23.79x + 440.83 mm LT; r² = 0.38) for males. The von Bertalanffy growth model described growth as Lt = 10000(1- exp(-0.002(t + 18.07))) mm LT for combined sexes Lt = 10000(1- exp( -0.002(t + 18.50))) mm LT , for females and Lt =908(1-exp(-0.076(t+7.95)))mmLT for males. Age at 50 % maturity was attained in the first year of life. Spawning occurred throughout the year with an apparent peak between November and April. The mean total annual mortality rate (Z) was 0.25 per year. The mean annual natural mortality rate (M) was 0.20 per year and fishing mortality (F) was calculated at 0.05 per year. The life history strategy of C. gariepinus was in between the periodic and opportunistic strategies. Therefore management of this species should be aimed at maintaining a healthy adult population and age structure. Since a large portion of the Okavango Delta is already protected and most other parts are also inaccessible to fishers there are enough spatial refugia for the species and the status quo should be maintained. Under this scenario, there is no need for regulation of the current mesh sizes because the species is harvested after maturity and replenishment of exploited populations will always occur from other parts of the system. Per recruit analyses indicate that the current fishing mortality maintains spawner biomass at levels greater than 90 % of pristine levels. Therefore a commercial fishery may be established using mesh 93 mm to maximize yield with a rotational harvesting strategy. Close monitoring is essential to ensure that re-colonization of overexploited habitats does indeed occur. Recreational angling and commercial gill net fishing need to be separated on a spatial and temporal scale during the feeding run to minimize potential conflicts.

An understanding of the population structure of commercially exploited species is essential for effective fisheries management. Fish stocks are typically identified based on the observation of differences in genetic and/or phenotypic characteristics between fish from discrete units. Recent deliberations on the management of the South African purse-seine sardine fishery recognises the likely existence of two stocks, one on the west and another on the south coasts, following studies that have documented spatial variability in several phenotypic characteristics of this species around South Africa. Those studies typically examined spatial variability in a single characteristic (e.g. gill raker morphology and meristics, body shape, otolith shape, vertebral count, parasite loads), but the application of multiple stock identification methods to the same individual fish has been recommended in order to maximize the likelihood of correctly inferring and identifying fish stocks. This study seeks to assess the population structure of South African sardine Sardinops sagax using a combination of stock identification methods including meristic, morphometric and parasite markers. Most of the sardine samples used in this study were obtained off the west and south coasts of South Africa during pelagic surveys conducted in 2013 and 2014 by Fisheries Branch of the Department of Agriculture, Forestry and Fisheries, with some additional samples obtained from commercial fisheries. Fish caught from the west and south coasts are presumed to be part of the putative western and southern stocks respectively. The variables examined included body shape, gill arch length, gill raker spacing, number of gill rakers, otolith shape indices (otolith circularity and form factor), the number of vertebrae, and the abundance of a 'tetracotyle' type metacercarian parasite found in the eyes of sardine; these were first analysed individually and then collectively (excluding body shape data) in a multivariate analysis to test their effectiveness in discriminating between sardine from the putative western and southern sardine stocks. Analysis using geometric morphometrics revealed significant differences in body shape between sardine from the putative western and southern stocks. Results of GLM analyses indicated that gill arch length, the number of gill rakers, otolith form factor and circularity, and parasite abundance were effective univariate discriminators of sardine stocks. No significant difference in gill raker spacing and the number of vertebrae was found between individuals from the two stocks. A Stock Identification Index (SDI) of 0.75 derived from the univariate analyses, as well as results of the multivariate analysis of data provided strong evidence for the existence of two mixing stocks, therefore, supporting the two-stock hypothesis. The five multivariate classification models used in the study showed varying degree of allocation success. Overall classification accuracy ranged from a low 47% in the Linear Discriminant Analysis model to highs of 82% and 91% in the Classification Tree Analysis and Random Forest models, respectively. Both CTA and RF revealed the combination of variables with the strongest spatial discriminatory power to be the number of vertebrae and abundance of the 'tetracotyle' type metacercarian parasite. These results agree with those of previous studies and further support the inclusion of sardine population structure into management strategies for the purse-seine fishery for South African sardine. Given the importance of the 'tetracotyle' type metacercaria in the discrimination of South African western and southern sardine stocks, further studies were undertaken to identify and describe this parasite using light and scanning microscopy, as well as molecular tools. Such information will assist in the definitive identification of the first intermediate host of the parasite, presently hypothesized to be a sub-tidal gastropod occurring off the west coast only. Definitive identification of the first intermediate host (or hosts) will enable the full life cycle of this parasite to be determined and the parasite endemic area to be identified; a critical knowledge gap in application of the parasite biotag approach to stock discrimination using this 'tetracotyle' type metacercarian parasite. Metacercariae collected from fresh sardine sampled from a commercial landing in Gans Baai, South Africa, were manually excysted, relaxed in warm water, fixed in 70% ethanol and stained with haematoxylin for light microscopy. The metacercarial body is oval-shaped, measuring 762 - 967 x 512 - 677μm. It is divided by transverse folds into a forebody, midbody and hindbody. Diagnostic features include the unique, large excretory bladder lobes situated on the lateral sides of the body; two large pseudosuckers in the anterior part of the midbody; an acetabulum which is larger than the oral sucker; and a large lobulated holdfast organ in the posterior half of the midbody. These features are those of the metacercariae of the genus Cardiocephaloides, confirming the previous hypothesis regarding the genus of this digenean biotag. Analysis of partial 28S rDNA region sequence data showed that the metacercariae and the adult Cardiocephaloides found in the African penguin Spheniscus demersus are of the same species, likely C. physalis. This study is the first documentation of the morphological and molecular characterization of the stock-discriminating Cardiocephaloides metacercaria found in the eyes of Sardinops sagax in South Africa.

Small-scale fishers are often identified as key players in the recovery of overexploited fish and invertebrate stocks supplying food for rural people and contributing to achieving healthy marine ecosystems. Stocks harvested by small-scale fisheries tend to be largely unassessed, but methods based on the data-limited toolbox exist that help provide information on exploitation status for fished stocks that do not have historical time series of catches, as usually occur in small-scale fisheries. Many of the data-limited methods follow length-based assessment approaches, which assume steady state, use at least length structure derived from fishery and knowledge on the life history parameters of the fished species. Accordingly, this thesis aimed at addressing the reliability of data-poor stock assessment methods in providing advice on the status of small-scale fisheries lacking knowledge of catch history. The data-rich bottom trawl fishery for European hake (Merluccius merluccius) in GSA 06 (Northwest Mediterranean Sea) was assumed as data-limited. This case study allowed me to test the performance of the pseudo-cohort Virtual Population Analysis (VPA) when input data are considered well known and unbiased. The same fishery but held in GSA 01 (Southwest Mediterranean Sea) was used as data-limited case study to introduce the uncertainty derived from parameterizing the length-based spawning potential ratio (LB-SPR) model with two contrasting growth hypotheses. Acknowledging challenges faced by stock assessment of small-scale fisheries around the world, I considered high input-data bias and large outputs uncertainty. The effect of biases in fishery data and uncertainty in life-history parameters on the outputs of the pseudo-cohort VPA model was explored by assessing the small-scale Wayuu fisheries for lane snapper (Lutjanus synagris) and white grunt (Haemulon plumierii) in the northern Colombian Caribbean Sea. An extreme, but common, case of uncertainty in small-scale fisheries was explored through assessing the beach fishery of the Peruvian grunt (Anisotremus scapularis) in the central coast of Peru on the Pacific Ocean, holding poor information on life-history parameters and catches. My findings indicate that the pseudo-cohort VPA may offer useful information regarding the exploitation trend but the absolute values of the indicators do not accurately express the fishing mortality and stock size among years for the European hake. The SPR estimates for this species is not specially linked to the growth hypothesis, and estimates of the ratio of fishing mortality to natural mortality (F/M) and the SPR value depend on the sample size and representation of the stock structure. The contribution of the information derived from the participatory monitoring of small-scale fisheries in Colombia, instead of using only official fishery data, largely demonstrated an improving picture of the exploitation of the lane snapper and white grunt. The uncertainty related to estimates of the von Bertalanffy growth parameters and natural mortality of the Peruvian grunt could be addressed but an accurate definition of SPR was not straightforwardly achieved. This thesis highlights that the data-limited methods assuming a steady state might contribute to defining the status of the small-scale fisheries. However, the stock status is importantly affected by bias in the input data, the available knowledge on the assessed fisheries and how fishery fit the model assumptions.
Los pescadores artesanales se identifican generalmente como actores claves en la recuperación de poblaciones sobreexplotadas, en el suministro de alimento a poblaciones rurales y en contribuir a alcanzar ecosistemas marinos saludables. Las poblaciones que son extraídas por las pesquerías artesanales (denominadas pesquerías de pequeña escala) tienden a carecer de evaluación. Sin embargo, algunos métodos de evaluación que se incluyen en el grupo “datos limitados” ayudan a suministrar información sobre el estado de estas pesquerías cuando no poseen información histórica de capturas. Muchos de los métodos limitados en datos y basados en estructura de tallas asumen estado de equilibrio. Estos métodos usan al menos como datos de entrada la estructura de tallas que provienen de la pesquería y el conocimiento disponible sobre los parámetros de historia de vida de las especies pescadas. Por todo lo expuesto anteriormente, el propósito de esta tesis es direccionar la fiabilidad de los métodos limitados en datos para proporcionar información sobre el estado de poblaciones que no cuentan con información histórica de capturas. La pesquería de merluza (Merluccius merluccius) de arrastre en GSA 06 (Mar Mediterráneo noroeste) “rica en datos” se asumió limitada en datos. Este caso de estudio me permitió probar el desempeño del Análisis de Población Virtual (VPA por sus siglas en inglés) basado en pseudo cohortes cuando los datos de entrada se asumen bien conocidos y libres de sesgos. Esta misma pesquería pero llevada a cabo en GSA 01 (suroeste del Mar Mediterraneo) también fue usada como un estudio de caso limitado en datos. Esto con el propósito de explorar la incertidumbre producida por el modelo que determina la proporción del potencial reproductor que es basada en tallas (LB-SPR por sus siglas en inglés) cuando son consideradas dos hipótesis de crecimiento contrastantes. Reconociendo los desafíos que enfrenta la evaluación de las pesquerías artesanales alrededor del mundo, yo consideré el análisis de sesgos relevantes en los datos que alimentan el modelo así como una gran incertidumbre en los resultados de evaluación. De esta manera, el efecto de los sesgos en la información proveniente de las pesquerías y la incertidumbre en los parámetros de historia de vida sobre los resultados del VPA basado en pseudo cohortes se exploró a través de la evaluación de las pesquerías Wayuu del pargo rayado (Lutjanus synagris) y la boca colorada (Haemulon plumierii) en el norte del Mar Caribe colombiano. Posteriormente, un extremo pero común caso de incertidumbre en pesquerías artesanales se consideró a través de la evaluación de la pesquería de playa de la chita (Anisotremus scapularis) en la costa central de Perú en el Océano Pacífico. Esta pesquería posee limitada información sobre la historia de vida de la especie y sobre las capturas producidas por la pesquería. Mis hallazgos indican que el VPA basado en pseudo-cohortes puede ofrecer información útil respecto a la tendencia de explotación de la pesquería, pero los valores absolutos no expresan apropiadamente la mortalidad por pesca ni el tamaño de la población entre años para la merluza. El valor de SPR para esta misma especie no se vincula a la hipótesis de crecimiento asumida y las estimaciones de la proporción de mortalidad por pesca respecto a la mortalidad natural (F/M) y el valor de SPR dependen del tamaño de la muestra y de la representación de la estructura de tallas del stock. La contribución de la información derivada del monitoreo participativo de la pesca artesanal en Colombia demuestra mejoramiento de la imagen de explotación del pargo rayado y la boca colorada que no cuando solo se usa información oficial. De otro lado, encontré que la incertidumbre relacionada con los parámetros de crecimiento de von Bertalanffy y la mortalidad natural de la chita puede ser direccionada pero una definición precisa del valor de SPR no se obtiene fácilmente. Esta tesis resalta que lo métodos limitados en datos que asumen estado de equilibrio pueden contribuir a definir el estado de explotación de las pesquerías artesanales. Sin embargo, el estado de la población se encuentra afectado de manera importante por los sesgos de los datos que alimentan el modelo, el conocimiento disponible sobre la pesquería evaluada y el cómo la pesquería se ajusta a los supuestos de los modelos de evaluación.

The panga, Pterogymnus laniarius (Cuvier, 1830), is a South African endemic sparid fish species. On the Agulhas Bank, South Africa it is a commercially important species, caught as bycatch in the hake directed trawlfisheries and targeted by offshore hook-and-linefishers. Recently there has been considerable interest shown in directing further fishing effort on this species. The lack of a suitable management procedure for teleost bycatch in South Africa was the principal reason for undertaking this study. This thesis investigates aspects the panga's life history, particularly those aspects that have management implications. A full knowledge of this species' distribution and abundance was necessary as this could highlight the existence of any nursery areas, ontogenetic migratory patterns and areas of high spawner biomass. The derived parameter estimates were then included as inputs into stock assessment models to determine the status and productivity of the resource. Growth studies based on sectioned sagittal otoliths revealed that the panga was a relatively slow growing fish with ages of 16 years being recorded. Growth was best described by the von Bertalanffy growth model as Lt=379.4(1-e⁻°·¹³⁽t ⁺ ¹·⁷⁸⁾). Total, natural and fishing mortalities were estimated at 0.36 year⁻¹, 0.28 year⁻¹ and 0.08 year ⁻¹, respectively. Detailed histological examination of the gonads revealed that panga is a late gonochorist, males and females maturing after a non-functional intersexual stage. Females mature at approximately 200 mm fork length or 4 years of age. Reproduction occurs throughout the year although there is a slight peak in winter. Gametogenesis was found to be similar to that of other sparid fishes and marine teleosts in general. The panga feeds predominantly on crustaceans with a distinct ontogenetic shift in feeding habits. Juvenile fish feed predominantly in the water column on mysids after which they move to the benthos. Subadult fish feed principally on ophiuroids and amphipods. Adult fish remain on or near the benthos, feeding predominantly on crabs, and on polychaetes, ophiuroids and fishes to a lesser extent. Several aspects of the panga's biology contribute to its ability to sustain a higher fishing pressure than other sympatric sparid species. These include its late gonochoristic reproductive style, protracted spawning season, maturation before recruitment and preference for soft substratum prey that enables it to utilise large areas of the Agulhas Bank. The panga's longevity, slow growth and low natural mortality rate, however, mitigated against these factors and were considered in the stock assessments. A heterogeneous Geographical Information System (GIS) was developed to analyse the distribution and abundance patterns of the panga. The GIS developed in this thesis makes a significant contribution towards the development of a South African Fisheries Information System to analyse and manage fish resources in general and bycatch resources in particular. The GIS developed in this study combines statistical Generalized Additive Modelling and standard GIS methods. Analysis of fourteen biannual fishery independent biomass surveys, disaggregated by life history stage, revealed that a nursery area for immature fish (<23 cm TL or < 4 years of age) exists on the Central Agulhas Bank. After sexual maturation, approximately 40% of the biomass migrated eastwards, colonising large areas of the Eastern Agulhas Bank.ilie location of the nursery area appears to be a result of the pelagic eggs and larvae being advected towards the coast in an anti-cyclonic gyre, stemming off the Agulhas current and later deposited over the Central Agulhas Bank. The weak bottom currents on the Central Agulhas Bank prevented juvenile loss to the Benguela system. The eurytopy of adult fish to various physical variables such as temperature, dissolved oxygen and stronger currents enabled it to reduce conspecific competition and migrate eastwards with distribution primarily determined by depth. Relative biomass estimates revealed a gradual increase in biomass of 5.5% per annum between 1988 and 1995. Predictions from yield-per-recruit, biomass-per-recruit and spawner biomass-per-recruit analyses showed that there was scope for further exploitation. A FSB₅₀ fishing strategy was considered to be the most appropriate fishing strategy as it did not reduce the spawner biomass-per-recruit to less than 50% of unexploited levels. Effort control was considered the most effective management tool as the age-at-50%-selectivity occurred after age-at-sexual maturity and releasing undersized fish was undesirable due to heavy mortalities resulting from severe barotrauma. The panga resource was also assessed using an age-structured production model. The values for the free parameters of the model were estimated using biomass indices derived from fishery-independent trawl surveys. Although the data were fairly uninformative about the productivity of the resource, the results indicated robustly, that the population has recovered from low levels in the mid-1970's and could sustain higher levels of fishing intensity. Risk analysis calculations were used to assess the sustainability of different catch scenarios. The level of sustainable catch was found to be sensitive to the selectivity pattern of the gear utilised. Both stock assessment methods used in this study to investigate the status of the panga resource showed that the resource could theoretically sustain higher catches. It was found that although the stock could be harvested using available fishing methods, the sympatry of this species with other commercial species was of concern as the latter would form a significant bycatch in a panga directed fishery. The failure of current harvesting methods to address the bycatch problem highlights the management problem in South Africa and stresses the need for creativity by both scientists and fishers in designing new and improved methods for selectively harvesting bycatch fish resources. Considering that no suitable method is currently available to fish the panga stock in a directed fishery the fishery should be managed as status quo until some suitable and efficient gear is developed.

Quantitative population dynamics modeling is needed to evaluate the stock status and fisheries management plans to provide robust model and management strategies. Atlantic Weakfish (Cynoscion regalis), one important commercial and recreational fish species along the west coast of Atlantic Ocean that was found to be declining in recent years, was selected as an example species. My study aimed to explore the possible spatial heterogeneity of CPUE (catch per unit effort) year trend based on three fishery independent surveys and explore the influence of nonstationary natural mortality on the fisheries management through a MSE (Management Strategy Evaluation) algorithm based on the Weakfish stock assessment results. Five models for catch rate standardization were constructed based on the NEAMAP (NorthEast Area Monitoring and Assessment Program) survey data and the ‘best' two models were selected based on the ability to capture nonlinearity and spatial autocorrelation. The selected models were then used to fit the other two survey data to compare the CPUE year trend of Weakfish. Obvious differences in distribution pattern of Weakfish along latitude and longitude were detected from these three surveys as well as the CPUE year trend. To test the influence of the model selection on the MSE, five stock-recruitment models and two forms of statistical catch-at-age models were used to evaluate the fishery management strategies. The current biomass-based reference point tends to be high if the true population dynamics have nonstationary natural mortality. A flexible biomass based reference point to match the nonstationary process is recommended for future fisheries management.
Master of Science

Two dimensional stocks of fish can be assessed with methods that mimic the analysis of research survey data but that use commercial catch-effort data. This finite population approach has scarcely been used in fisheries science though it brings about very large sample sizes of local fish density with models of only moderate levels of complexity. The extracted information about the status of the stock can be interpreted as biomass indices. Statistical inference on finite populations has been the locus of a highly specialized branch of sampling-distribution inference, unique because observable variables are not considered as random variables. If statistical inference is defined as "the identification of distinct sets of plausible and implausible values for unobserved quantities using observations and probability theory" then it is shown that Godambe's paradox implies that the classical finite populations approach is inherently contradictory as a technique of statistical inference. The demonstration is facilitated by the introduction of an extended canonical form of an experiment of chance, that apart from the three components identified by Birnbaum, also contains the time at which the experiment is performed. Realization of the time random variable leaves the likelihood function as sole data-based mathematical tool for statistical inference, in contradiction with sampling-distribution inference and in agreement with direct-likelihood and Bayesian inference. A simple mathematical model is introduced for biomass indices in the spatial field defined by the fishing grounds. It contains three unknown parameters, the natural mortality rate, the probability of observing the stock in the area covered by the fishing grounds, and mean fish density in the sub-areas where the stock was present. A new theory for the estimation of mortality rates is introduced, using length frequency data, that is based on the population ecology analogue of Hamilton-Jacobi theory of classical mechanics. The family of equations require estimations of population growth, individual growth, and recruitment pattern. Well known or new techniques are used for estimating parameters of these processes. Among the new techniques, a likelihood-based geostatistical model to estimate fish density is proposed and is now in use in fisheries science (Roa-Ureta and Niklitschek, 2007, ICES Journal of Marine Science 64:1723-1734), as well as a new method to estimate individual growth parameters (Roa-Ureta, In Press, Journal of Agricultural, Biological, and Environmental Statistics). All inference is done only using likelihood functions and approximations to likelihood functions, as required by the Strong Likelihood principle and the direct-likelihood school of statistical inference. The statistical model for biomass indices is a hierarchical model with several sources of data, hyperparameters, and nuisance parameters. Even though the level of complexity is not low, a full Bayesian formulation is not necessary. Physical factors, mathematical manipulation, profile likelihoods and estimated likelihoods are used for the elimination of nuisance parameters. Marginal normal and multivariate normal likelihood functions, as well as the functional invariance property, are used for the hierarchical structure of estimation. In this manner most sources of information and uncertainty in the data are carried over up the hierarchy to the estimation of the biomass indices.

Baited remote underwater video (BRUV) is becoming an increasing popular tool for examining reef fish assemblages in depths less than 100m. This sampling technique is relatively new in the literature and several gaps remain to be filled. Scientists using this technique have selected bait based on results from trapping experiments. Therefore the first objective of the study was to compare commonly used baits and test if different fish species and fish assemblages were recorded. I planned to apply results from the first study towards further research using BRUV. Management at Jervis Bay Marine Park, located in southeast Australia, have applied a strategy to protect a comprehensive and representative sample of local habitats and associated flora and fauna. In doing so, sanctuary “no take” zones have been put in place. Surprisingly, there are no patch reefs afforded this protection. My second objective was to provide the Jervis Bay Marine Park management with baseline data on deep patch reef locations and to draw comparisons between deep patch, deep coastal, and shallow coastal reefs. I compared three different baits (pilchard, abalone, and urchin) at three locations in two separate years. A total of 63 “drops” (30 min recordings) were conducted in two years and a total of 47 species were recorded. There were no differences in the diversity and abundance of fish recorded while baited with pilchard and abalone. In contrast, in the second year of sampling I detected a greater species richness and abundance using pilchard, compared to urchin, at most locations (p<0.05). The two most speciose families recorded in the study were Labridae and Monacanthidae. These families, as well as several individual fish species, were examined but there were no significant differences in their relative abundance among bait treatments. Additionally, in the second year of sampling I detected differences in H′ and time of first arrival among locations (p<0.05). Surprisingly, large differences between the baits were greatly reduced at one location - Plantation Point. I interpret this finding as there being a high density of fish at Plantation Point that masks the differences in the attraction of these baits. I concluded that as the behaviour and structure of the fish assemblage can vary in space, pilchard was the best choice of bait for consistently detecting species richness and abundance. A total of 144 BRUV “drops” (30 min recordings) in 9 locations in 2005 and 2006 were completed in the second study. The composition of fish assemblage at shallow and deep water habitats was different (p<0.05). Indeed, depth related differences for temperate reef fish are well documented and my findings emphasise the need for the Marine Park management to maintain protection of reef habitats across abroad range of depths. I did not detect any differences in the composition of the fish assemblage or the relative abundance of fish between the two deep habitats (p>0.05), although the presence of several rarely encountered species including Bodianus unimaculatus, Coris sandageri, Meuschenia scaber, Caesioperca lepidoptera, and Eubalichthys mosaicus were recorded in the deep patch reef habitat. I concluded that the inclusion of the deep habitat in the sanctuary zoning plan is important for protecting fish biodiversity. By generating permanent baseline data, this study aims to assist Marine Park management in making sound decisions on future zoning plans.

It is currently hypothesised that the chokka squid (Loligo reynaudi) consist of a single stock. This was tested through a spatial comparison of the morphology of this species. Forty three morphometric characters were measured from 1079 chokka squid collected from three regions: the south coast of South Africa, the west coast of South Africa, and southern Angola. While no significant differences were found for the hard body parts, results from discriminant function analyses showed the soft body morphometric characters from each of the three regions differed, with an overall correct classification rate of 100% for males and 99% for females in all three regions. Due to the existing model being used to assess the resource currently being updated it was not feasible to apply this model to the area-disaggregated data from this study. Rather, the CPUE trends and catches from the area-disaggregated data were compared against those of the area-aggregated data, as a first attempt to discern any appreciable differences which would suggest the use of disaggregated data in future assessments. Both the trawl and jig CPUE trends from the area-disaggregated analysis differed only slightly from those of the area-aggregated data. Similarly, the spring and autumn biomass trends for the main spawning area (east of 22°E) followed the same trends as for the full area. It is therefore concluded that there is currently no need to assess the resource on an area-disaggregated basis.

Three hammerhead sharks (Sphyrna spp.) are currently managed as part of the large coastal shark complex in the United States. Including multiple species in an assessment ignores the different stock dynamics of each individual species within the complex due to different life histories. This study completed individual assessments of scalloped (S. lewini), great (S. mokarran), and smooth (S. zygaena) hammerhead sharks in the U.S. Atlantic Ocean and Gulf of Mexico. Combined data for all three species and unclassified hammerhead sharks were also used to produce a stock assessment of the hammerhead shark complex. Depletions of 83%, 96%, and 91% were estimated for scalloped, great, and smooth hammerhead sharks, respectively, between 1981 and 2005. When modeled as a single stock, the hammerhead shark complex experienced a 90% decline over the same time period. All three stocks, and the complex were overfished (below population size associated with maximum sustainable yield (MSY)), and overfishing (fishing level above that associated with MSY) occurred in 2005. We found that scalloped hammerhead shark population recovery is likely to occur within 10 years if catch remains at or below 2005 levels. Great and smooth hammerhead sharks will likely still be overfished in 30 years unless catches are reduced. It appears that the species composition could be changing in this hammerhead shark complex. The faster-growing scalloped hammerhead sharks are able to withstand fishing pressure better than great or smooth hammerhead sharks. However, it is difficult to target any single large coastal shark species while fishing; hence they are subject to similar fishing pressure. The result is a greater decline in great and smooth hammerhead sharks than experienced by scalloped hammerhead sharks. Therefore, the proportion of scalloped hammerhead sharks increased between 1981 and 2005. Species-specific stock assessments, such as those presented here, allow managers to more closely monitor populations of slower-growing species and reduce the risk of overexploitation of those species.
Master of Science

Cephalopods constitute an important faunistic group in marine ecosystems, representing keystone elements in marine food webs. Additionally, they are an important fishing resource, and their contribution to worldwide fishery landings has been rising significantly over the last decades. In the Mediterranean Sea, several local short-term studies on cephalopod abundance and distribution exist, but few integrate longer time scales and larger areas. The present thesis work combines large-scale, long-term studies on cephalopods community composition, diversity and abundance (Part I) with small-scale, local case studies around the Balearic Islands (Part II). First, a community analysis was conducted at the whole Mediterranean scale in order to describe the present status and reveal possible differences between the western and the eastern Mediterranean sub-basins (Chapter 2). The aim was to compare assemblage structures between sub-basins together with the influence of large-scale environmental gradients on species composition. While basins did not differ significantly in cephalopod species composition, relative species contributions varied. Cephalopods are very sensitive to environmental changes, and adapt quickly due to their short life cycle and typically seasonal semelparity impeding generation buffering. Therefore sea surface temperature (SST) and chlorophyll a (Chl a) were hypothesised and documented as important drivers of cephalopod assemblages. While their importance differed between sub-basins, depth was confirmed as the most important factor structuring cephalopod communities. At the same spatial scale, cephalopod diversity was analysed during two decades (Chapter 3). Results revealed the absence of clear longitudinal or latitudinal gradients in cephalopod diversity, combined with no distinct temporal trends over the last twenty years. Besides, temporal changes in diversity varied between various Mediterranean sub-regions. Location, depth, SST and productivity regime resulted to influence diversity. To assess whether environmental variability impacts cephalopod populations at species level, the influence of SST and surface primary production on the spatial structuring and the population dynamics of two commercially important cephalopod species was investigated (Chapter 4). Although Octopus vulgaris and Illex coindetii exhibit contrasting life history traits and inhabit different habitats, long-term abundance trends and synchronic behaviour of their populations was similar, and population sub-structuring across the Mediterranean Sea were revealed. In consistency with former chapters, SST and Chl a regimes were shown to be significant drivers of distribution patterns and inter-annual abundance fluctuations. The motivation for the second part of the thesis was fuelled by the present situation in the Mediterranean Sea, where cephalopod stocks are presumably overexploited, but where their ad-hoc assessment and management is far from being implemented. To contribute to existing knowledge of the current situation in the Balearic Sea, a case study on cuttlefish fishery, life-history and population dynamics was conducted using short-term and intra-annual data (Chapter 5). Possible drivers of cuttlefish abundance fluctuations were analysed, revealing significant influences of SST and local climatic variability. While the study provided an overview of possible intrinsic and extrinsic drivers of cuttlefish population fluctuations in the Balearic Sea, the next step was applying stock assessment techniques to cuttlefish and squid fisheries of this area (Chapter 6). Being the first application of depletion methods to Mediterranean cephalopod stocks, the study combined information of those two fisheries with the evaluation of this stock assessment method for short life cycle species. Results uncovered existing problems and suggested that the current sampling scheme under the EU-Data Collection Framework is inadequate for cephalopods in view of the assessment´s data requirements. Consequently, a modification of the existing scheme was proposed.
Los cefalópodos constituyen un grupo faunístico importante en los ecosistemas marinos, representando elementos clave en la estructura y dinámica de las redes tróficas. Además, son un importante recurso pesquero y su contribución a los desembarcos pesqueros mundiales se ha incrementado significativamente en las últimas décadas. En el Mar Mediterráneo existen varios estudios locales sobre la abundancia y distribución de cefalópodos, pero pocos integran escalas temporales largas y áreas extensas. Esta tesis combina estudios sobre la estructura de la comunidad, la diversidad y la abundancia de cefalópodos a gran escala espacio-temporal (Parte I) con estudios a escala local alrededor de las Islas Baleares (Parte II). En primer lugar, se realizó un análisis de la comunidad de cefalópodos a escala de todo el Mediterráneo para describir el estado actual y determinar posibles diferencias entre las sub-cuencas occidental y oriental (Capítulo 2). El objetivo fue comparar la estructura de las comunidades faunísticas entre estas dos sub-cuencas y analizar la influencia de gradientes ambientales a gran escala sobre la composición específica. Aunque no se observaron diferencias significativas en la composición específica, las contribuciones relativas de las diferentes especies variaron entre ambas cuencas. Debido a su corto ciclo vital y estrategia reproductiva semélpara, los cefalópodos son muy sensibles a los cambios ambientales, adaptándose a ellos con relativa rapidez. Se esperaba, por tanto, que factores ambientales como la temperatura superficial del mar (SST) y el contenido de clorofila a (Chl a) fueran factores importantes en la estructuración de las comunidades de cefalópodos. Si bien su importancia difirió entre las dos sub-cuencas, se confirmó que la profundidad era el factor estructural más importante en dichas comunidades. Se analizaron también cambios en la diversidad específica de las comunidades de cefalópodos a escala de todo el Mediterráneo durante los últimos 20 años (Capítulo 3). Los resultados no mostraron ninguna tendencia temporal ni espacial (latitud, longitud) clara y homogénea en la diversidad. Las únicas tendencias temporales observadas variaron entre diferentes sub-regiones, siendo la posición geográfica, profundidad, SST y productividad los principales factores determinantes de estas tendencias. Para confirmar la importancia de la variabilidad ambiental a nivel específico, se analizó la influencia de la SST y la producción primaria en la estructura espacial y la dinámica poblacional de dos especies de cefalópodos de importancia comercial (Capítulo 4). Aunque Octopus vulgaris e Illex coindetii exhiben diferentes estrategias vitales y viven en diferentes hábitats, las tendencias temporales a largo plazo en su abundancia y el comportamiento sincrónico de sus poblaciones fueron similares, observándose sub-poblaciones temporalmente persistentes a lo largo de todo el Mediterráneo. En consonancia con los capítulos anteriores, la SST y Chla resultaron ser factores significativos en la definición de patrones de distribución y fluctuaciones interanuales de la abundancia. La segunda parte de la tesis estaba motivada por la situación actual de los cefalópodos en el Mar Mediterráneo, donde no existen medidas de evaluación y gestión específica para este grupo y algunas de sus poblaciones se encuentran sobreexplotadas. Para contribuir al conocimiento de la situación actual en el Mar Balear, se analizó la pesquería, ciclo vital y dinámica poblacional de la sepia utilizando series temporales intra-anuales (Capítulo 5). El análisis de diferentes factores ambientales reveló que la SST y la variabilidad climática local influían significativamente en las fluctuaciones de abundancia de la especie. En un trabajo posterior (Capítulo 6) se aplicaron técnicas de evaluación de stocks a las pesquerías de sepia y calamar de las Islas Baleares utilizando datos procedentes de la EU Data Collection Framework (DCF). Hasta donde sabemos, este trabajo constituye la primera aplicación de los Lesly-Delury Depletion Methods a stocks de cefalópodos del Mediterráneo. Los resultados demostraron que el esquema actual de muestreo de la DCF es inadecuado para la evaluación de cefalópodos y se proponen posibles modificaciones.
Els cefalòpodes constitueixen un grup faunístic important als ecosistemes marins, essent elements clau a les xarxes tròfiques. A més, són importants recursos pesquers i la seva contribució als desembarcs pesquers mundials s’ha incrementat en les últimes dècades. representant al voltant del 30% de la captura desembarcada a nivell mundial. Al Mar Mediterrani existeixen varis estudis locals sobre l’abundància i distribució de cefalòpodes, però pocs integren escales temporals llargues i àrees extenses. Aquesta tesi combina estudis sobre la composició de la comunitat, la diversitat i l’abundància de cefalòpodes a gran escala espaciotemporal (Part I) amb estudis a escala local al voltant de les Illes Balears (Part II). En primer lloc, es va realitzar un anàlisi de les comunitats de cefalòpodes a escala de tot el Mediterrani per descriure l’estat actual i determinar possibles diferències entre les sub-conques occidental i oriental (Capítol 2). L’objectiu fou comparar l’estructura de les comunitats faunístiques entre sub-conques i analitzar la influència de gradients ambientals a gran escala sobre la composició específica. Tot i que no s’observaren diferències significatives en la composició específica, les contribucions relatives de les diferents espècies variaren entre sub-conques. Degut al seu cicle vital curt i estratègia reproductiva semèlpara els cefalòpodes són molt sensibles als canvis ambientals, adaptant-se a ells amb relativa rapidesa. S’esperava, per tant, que factors ambientals com la temperatura superficial del mar (SST) i el contingut de clorofil·la a (Chla) fossin factors importants en l’estructuració de les comunitats de cefalòpodes. Si bé la seva importància va diferir entres les dues sub-conques, es va confirmar que la profunditat era el factor estructural més important en aquestes comunitats. S’analitzaren també canvies en la diversitat específica de les comunitats de cefalòpodes a escala de tot el Mediterrani durant els últims 20 anys (Capítol 3). Els resultats no mostraren cap tendència temporal ni espacial (latitud, longitud) clara i homogènia en la diversitat. Les úniques tendències temporals observades variaren entre diferents sub-regions, essent la posició geogràfica, profunditat, SST i productivitat els principals factors determinants d’aquestes tendències. Per tal de confirmar la importància de la variabilitat ambiental a nivell específic, es va investigar la influència de la SST i la producció primària en l’estructuració espacial i la dinàmica poblacional de dues espècies de cefalòpodes d’importància comercial (Capítol 4). Tot i que Octopus vulgaris i Illex coindetii tenen característiques vitals diferents i viuen en hàbitats diferents, les tendències temporals a llarg plaç en la seva l’abundància i el comportament sincrònic de les seves poblacions va ser similar, observant-se sub-poblacions temporalment persistents al llarg del Mediterrani. En consonància amb els capítols anteriors, la SST i Chla resultaren ser factors significatius en la definició de patrons de distribució i fluctuacions interanuals de l’abundància. La segona part de la tesi estava motivada per la situació actual dels cefalòpodes al Mar Mediterrani, on no existeixen mesures d’avaluació i gestió específica per aquest grup i algunes de les seves poblacions es troben sobre-explotades. Per contribuir al coneixement de la situació actual al Mar Balear, es va analitzar la pesqueria, cicle vital i dinàmica poblacional de la sípia utilitzant sèries temporals intra-anuals (Capítol 5). L’anàlisi de diferents factors ambientals va revelar que la SST i la variabilitat climàtica local influïen significativament en les fluctuacions d’abundància de l’espècie. En un treball posterior (Capítol 6) s’aplicaren tècniques d’avaluació d’stocks a les pesqueries de sípia i calamar de les Illes Balears utilitzant dades procedents de la EU Data Collection Framework (DCF). Fins on sabem, aquest treball constitueix la primera aplicació dels Lesly-Delury Depletion Methods a stocks de cefalòpodes del Mediterrani. Els resultats demostraren que l’esquema actual de mostratge de la DCF és inadequat per a l’avaluació de cefalòpodes i es proposen possibles modificacions.

Bangweulu Wetlands is a 6000 km² public-private-partnership conservation area in northeastern Zambia, lying on the south-eastern margins of the Bangweulu Swamps, Congo River system. The area is important for wildlife conservation, tourism and as a fishing ground for the local inhabitants. This study provides a baseline of the fish and fisheries of this area. The conservation area is situated on the transition zone between woodland, floodplain and swamp. A total of 42 fish species representing 12 taxonomic families were collected. The fish fauna of the area was characterised by a diversity of small cyprinids (14 species), cichlids (9 species), clariid catfishes (4 species) and mormyrids (4 species). Species such as Clarias gariepinus, C. ngamensis, Marcusenius macrolepidotus, Tilapia rendali, T. sparrmanii and several small Barbus species were shared with adjacent floodplain systems such as the upper Zambezi and Kafue rivers. Fishing was undertaken by fishing groups consisting of a fisherman and his family, or a group of men fishing together. Access to the fishing grounds was controlled by traditional fishing leaders, who collected tribute from fishermen. Fishing groups utilised fixed, distinct fishing areas determined by ancestry. The most important time for fishing was during the drawdown phase of the floodplains, from March until June. During the dry season fewer groups were engaged in fishing, with many having returned to farming activities. The main fishing methods of the floodplain fishery were basket traps and mosquito-mesh funnel nets set into earth fish barriers (fish weirs) constructed on the plains, various mesh sizes of gillnets, hook longlines and seine nets. The use of fish spears, drag baskets and piscicides was of lesser importance. Most fishing gears were constructed of a variety of natural and modern, manufactured materials. The fishery was multi-species and 23 fish species were recorded from in catch. The three most important species in the catches were C. gariepinus, T. rendalli and M. macrolepidotus. Together these contributed 67% by weight to the catch. Catch-per-unit-effort (CPUE) for the different gears was 0.4 ± 0.3 kg.trap.night⁻¹ for basket traps, 2.7 ± 4.6 kg.net.night⁻¹ for funnel nets, 0.3 ± 0.5 kg.50 m net.night⁻¹ for gill nets, 3.5 ± 6.3 kg.100 hooks.night⁻¹ for longlines, 1.79 ± 1.11 kg.haul⁻¹ for mosquito-mesh seine nets and 6.87 ± 6.27 kg.haul⁻¹ for larger-mesh seine nets. The weight of average daily landings of fishing groups, using a variety of gears was 7.8 ± 7.4 kg. Fishermen were able to maintain the same catch rate between dry and wet seasons, with no significant differences (p < 0.05) in daily landings between seasons. Yield per fisherman for a seven month season, which required 2-3 relocations due to falling water level, was 1.64 t based on catch assessment, and 1.9 t from a socio-economic survey. A tentative yield per area estimate for the area was 2I7 kg.ha⁻¹ over the three month shallow-floodplain fishing season. Most fish landed in the fishery were processed into sundried or smoke-dried products. These were used for 1) home consumption, 2) trade with village farmers (from up to 70 km inland of the fishing grounds) in exchange for staple starch meal, and 3) sold to urban fish traders, reaching markets as distant as Lubumbashi in Democratic Republic of Congo. Fish traders toured fishing camps to buy fish, supporting auxiliary industries such as transport and accommodation services. The price for dried fish at source was 3.14 ± 1.34 USDlkg and the market price reported for the Zambian Copperbelt was 6.14 ± 2.54 USD/kg. Typical returns on investment in fish trading were estimated as 68-77%. The fishery was considered to be biologically and socially sustainable. By harvesting a seasonally transient assemblage of species with high productivity and biological turnover rates and with life histories adapted to high mortality, fishermen were able to maintain a stable and viable livelihood. Management recommendations for the area were that a fisheries management plan be developed that would seek to strengthen the traditional system of rights-allocation, address problems between fishing and tourism activities, and enhance communication between fisheries and conservation stakeholders. To do this it was recommended that: 1) conservation authorities recognise the importance of the fishery, 2) no changes to current effort levels and fishing methods were necessary, 3) points 1 and 2 above be used to improve communication and trust between conservation authorities and fishermen, 4) customary resource-access mechanisms be understood and strengthened so that local inhabitants' rights to the resource are protected, 5) fishermen help formulate and accept conservation and tourism rules, 6) tourists and guides be made aware of the function of the fishery, 7) a fisheries management forum of key community, government and conservation stakeholders be formed to shape and implement the fisheries management plan, 8) locally-adapted bylaws be created to legitimise crucial floodplain gears currently considered illegal (e.g. mosquito-net gears, fish weirs), 9) no intervention to formalise fish trading be made, and 10) a trained person with a fisheries background be hired oversee the implementation of the recommendations.

Recent U.S. legislation applies a precautionary approach to setting catch regulations in federal fisheries management. A transparent approach to complying with federal guidelines involves calculating the catch recommendation that corresponds to a specified probability, P*, of exceeding the "true" overfishing limit (OFL) located within an estimated distribution. The P* methodology aims to manage the risk of overfishing explicitly, but choice of P* alone does not provide sufficient information on all of the risks associated with a control rule—both the probability of overfishing and the severity of overfishing. Rather, the ramifications of P* choices depend on the amount of uncertainty in the stock assessment and on the life history of the species in question. To evaluate these effects on the risks associated with P* rules, my study simulated fishing three example species under three levels of uncertainty. Trends identified among example species were consistent with predictions from life history. Periodic strategists, which have highly variable recruitment, experienced probabilities of overfishing which exceeded P* and which increased in time. Equilibrium strategists showed more predictable risks of overfishing but may have less capacity to recover from depleted biomass levels. Differences in the size of the OFL distribution—representing differences in levels of uncertainty—led to mixed results depending on whether the distribution was biased or whether uncertainty was fully characterized. Lastly, because OFL distributions are themselves estimates and subject to uncertainty in their shape and size, lower P* values closer to the tails of the estimated distribution produced more variable resulting risks.
Master of Science

Since the study on the Port Alfred/Kenton-on-Sea/Boknes linefishery by Hecht and Tilney (1989) there have been substantive changes to the linefish management environment in South Africa. Using the Port Alfred linefishery as a model, the aim of this study was to evaluate the effectiveness of the linefish management regulations that were implemented by Marine and Coastal Management (MCM) since 1992, and to assess the behaviour and 'status' of the fishery in response to these changes. Changes to both the licensing structure and catch regulations have had a significant effect on the functioning of many aspects of the Port Alfred linefishery (fishing effort, catch composition, cpue) as well as on the structure of the fishery and its socio-economic profile. Overall commercial cpue decreased from 1985 to 1998. Since 1998 there has been a significant increase in cpue (from 2.3 Kg.fisher⁻¹ hour⁻¹ to a peak of 4.8 Kg.fisher⁻¹.hour⁻¹ in 2005. This was attributed to good catches of geelbek, particularly in 2005, 2007 and 2008 (during these years geelbek contributed an average of 35% to the total landings in comparison to a mean contribution of II % between 1985 and 2004). However, size spectra analysis suggests that the increase in overall cpue since 1998 misrepresents the actual status of the fishery. If geelbek is excluded from the analysis on the grounds that it is the only species in the fishery that is highly migratory, susceptible to recruitment fluctuations and it does not contribute to the catches on a year round basis, then the results suggest that the fishery is still in a declining phase despite the 80% reduction in commercial effort and numerous stricter catch regulations (e.g. size/bag limits). Furthermore, the cpue of silver kob, which has been the "mainstay" species of the fishery, has consistently declined over the last 23 year period (from 1.69 Kg.fisher⁻1 .hour1 in 1986 to 0.86 Kg.fisher⁻1.hour⁻1in 2007). The substantial reduction in commercial effort in the fishery from 33 vessels in 2001 to 13 in 2002 resulted in a shift from commercial to recreational fishing. The number of active commercial vessels in Port Alfred alone decreased from 29 in 1989 (Hecht 1993) to four in 2008. During the same timeframe, the number of regularly active recreational vessels had almost doubled (16 in 1989 to 26 in 2008). Despite the greater number of recreational boats in the fishery they only landed approximately half the average yearly tonnage of the commercial vessels (21,5 and 44,7 tonnes,annum-I , respectively) between 2006 and 2008, This was ascribed to the differences in catch regulations for the two sectors, Furthermore, it was speculated that increasing operating costs and narrowing profit margins have contributed to lower levels of compliance in both the commercial and recreational sectors since 2006, For example, 16% of silver kob landed during 2006-08 were under the minimum size, Despite the changes made to the regulations since 1998 and the 60,6% reduction In legislated commercial effort in the fishery between 2001 and 2002 it was concluded that the fishery has continued to decline, Except for the good recruitment of geelbek (which may be due to regulatory changes made in 1992) the changes in the management environment have had no measurable positive effect on this fishery, It is recommended that commercial effort should not be allowed to increase beyond the current number of active boats, that there should be an area restriction on all commerciallinefish vessels, that the current recreational bag limit for silver kob should be re-assessed, there should also be a concerted and nationally funded effort to educate recreational anglers about the merits of catch and release, and the frequency of catch inspections of both sectors should be increased,
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The catchability coefficient is used in most marine stock assessment models, and is usually assumed to be stationary and density-independent. However, recent research has shown that these assumptions are violated in most fisheries. Violation of these assumptions will cause underestimation of stock declines or recoveries, leading to inappropriate management policies. This project assesses the soundness of stationarity and density independence assumptions using multi-species data for seven stocks and four gears in the U.S. Gulf of Mexico. This study also develops a multi-species methodology to compensate for failures of either assumption. To evaluate catchability assumptions, abundance-at-age was reconstructed and compared with catch-per-unit-effort data in the Gulf. Mixed-effects, Monte Carlo, and bootstrap analyses were applied to estimate time-varying catchability parameters. Gulf data showed large and significant density dependence (0.71, s.e. 0.07, p<0.001) and increasing trends in catchability (2.0% annually compounding, s.e. 0.6%, p < 0.001). Simulation modeling was also used to evaluate the accuracy and precision of seven different single-species and multi-species estimation procedures. Imputing estimates from similar species provided accurate estimates of catchability parameters. Multi-species estimates also improved catchability estimation when compared with the current assumptions of density independence and stationarity. This study shows that multi-species data in the Gulf of Mexico have sufficient quantity and quality to accurately estimate catchability model parameters. This study also emphasizes the importance of estimating density-dependent and density-independent factors simultaneously. Finally, this study shows that multi-species imputation of catchability estimates decreases errors compared with current assumptions, when applied to single-species stock assessment data.
Master of Science

L'aquaculture et la pêche impactent l'environnement, les ressources et le fonctionnement des écosystèmes. L’un des enjeux en écologie est de placer ces activités anthropiques dans un cadre de développement durable. Afin de quantifier et de limiter ces impacts, différentes méthodes d’évaluation environnementale ont vu le jour. L’Analyse de Cycle de Vie (ACV) est une méthode pertinente pour évaluer le bilan environnemental d'un produit en prenant en compte l’ensemble de ses étapes de vie, "du berceau à la tombe", depuis l’extraction des matières premières et leurs transformations pour l'élaboration du produit, jusqu’à la fin de vie. Cette thèse porte sur l’adaptation de l’ACV au domaine de l'aquaculture et de la pêche en Tunisie. Son objectif est d'explorer les perspectives offertes par cette méthodologie afin de mieux caractériser le fonctionnement des systèmes de production de poissons et leur lien avec l’environnement. Cette étude a montré que les pratiques aquacoles et la production d'aliment de poisson sont les contributeurs majeurs aux impacts environnementaux, ceci est expliqué par l'utilisation de farine et d'huile de poisson dans la fabrication de l'aliment. Les résultats ont également montré que les impacts du chalutage de fond sont proportionnels à la quantité de carburant nécessaire pour la production. Ce travail a permis d'étudier et comparer les impacts environnementaux de l'activité aquacole et de la pêche au chalutage de fond en Tunisie. Les résultats de cette thèse ont un intérêt pour les gestionnaires en proposant des voies d'amélioration et des recommandations stratégiques de gestion pour améliorer les deux secteurs afin de les placer dans un contexte de développement durable
The main goal of ecology is to place human activities within a framework of sustainable development by enhancing their economic benefits, their social attractiveness and their environmental performances. Ecosystems that support fisheries and aquaculture are subject to several alterations of significant relevance to their functioning and to their abilities to provide goods and services. Therefore, the long-term sustainability of fishing and aquaculture is a major concern from an environmental and ecological viewpoint. Both activities carry risks of negative environmental impacts because of its close relation with the immediate environment. To better understand environmental impacts and ensure the sustainability of fishing and aquaculture, it is necessary to develop an integrative sciencebased approach to impact assessment. Life Cycle Assessment (LCA) has emerged as a robust method to estimate potential environmental impacts associated with a product. It allows the assessment of environmental impacts “from cradle to grave”, taking into account all stages of a product’s life. This thesis focuses on the adaptation of LCA to demersal trawling and aquaculture in Tunisia. The goal is to explore how LCA improves the environmental evaluation of seafood production systems and how it helps to better understand their links with the environment. Results revealed that rearing practices and fish feed were the greatest contributors to the impacts studied due to the production of fish meal and oil and the low efficiency of feed use. The study also showed that impact intensity of demersal trawling was proportional to the amount of fuel consumed. LCA is a valuable tool for assessing how to improve environmental sustainability of demersal trawling and aquaculture

The Roe’s abalone (Haliotis roei) fishery near Perth, Western Australia, is uniquely accessible, and highly vulnerable to overexploitation. The sustainability of this intensively utilized fishery requires robust assessment. To facilitate an assessment, this research aimed to provide rigorous and detailed biological information with appropriate interpretation. Four critical aspects of the species’ biology and population dynamics were investigated: (1) the stock structure; (2) the recreational catch; (3) an appropriate growth curve and description of size at age; and (4) abundance measures against which to assess the impact of fishing mortality. Allozyme electrophoresis was used to investigate stock structure across the species’ distribution. Standardized variance in allelic frequencies between 10 sites in south-western Australia indicated high levels of gene flow across the 3000 km sampled (mean FST = 0.009). An isolation-by-distance was evident when pairwise measures of GST were related to geographic distance (r=0.45, P<0.001). The area of complete genetic mixing was estimated from samples within the Perth fishery to be less than the distance between the two nearest sites, or 13 km. Consequently, the Perth fishery comprises numerous discrete stocks, each requiring independent assessment. A possible mechanism for this population structure is the retention of larvae in the wind driven currents oscillating in the near-shore lagoons, with rare pulses of long distance dispersal via the southerly Leeuwin current, running further offshore. The presumed impact of intensive recreational fishing, combined with substantial commercial quotas for the Perth fishery, had led to tight restrictions on fishing effort, without any quantitative measure of the recreational catch. A stratified creel survey was adapted to estimate the effort, catch rate and mean weight of abalone harvested by the recreational sector. Catches were estimated for reef complexes, or stocks, of less than 10 nautical miles (18.5 km) of coast. Between 1997 and 2000 the recreational catch varied from 30 to 45 tonnes whole weight, approximately equivalent to the commercial quota of 36 tonnes. On average 88% of the recreational catch came from two stocks, while 98% of the commercial catch came from these two, and one additional, stocks. The incidental mortality from recreational fishing, measured as the number of abalone left dead on the reef as a proportion of the estimated catch, was approximately 7% and 20% at two sites surveyed. Spatial and temporal patterns of growth were examined on the west coast of Western Australia. Growth increments were measured for abalone larger than about 30 mm from tagging studies at five sites in the Perth fishery, a site at the northern extent of the species’ distribution and a site in the southwest. Mean annual growth increments of the 0+ year class were obtained by fitting components to length frequencies from five sites in the Perth fishery, and combined with growth increments from each Perth tag site for model fitting. A von Bertalanffy growth curve provided a slightly better fit to the tag data, but a Gompertz growth curve was a much better fit when the mean increment from the 0+ to 1+ cohort was included, with the inflection occurring at about 40 mm, the size at sexual maturity. There was no difference in annual growth between the two years studied. There was significant variation in growth between the reef platform and adjacent sub-tidal reef, but this variation was site specific and faster growth rates were not consistently associated with either habitat. There was no latitudinal trend in growth rate. Growth at the Perth sites was the fastest and similar at all five sites with growth increments greater in summer than in winter. Size and abundance of abalone were measured using fixed transects and quadrats. Abalone densities were highest on the outer edge of the platform, intermediate in the middle of the reef platform, and lowest on both the inner platform and the sub-tidal reef. The pattern of mean lengths of abalone was the inverse of the density. Mean length and abundance were driven by the presence of post-settlement juveniles on the outer and middle reef habitats. There was a high spatial variation in abundance, with densities varying between transects at the same site, but the trend between years for each transect at a site was not significantly different. Abalone abundances, by size class, were examined from sites sampled between 1996 and 2002. A low density of post-settlement juveniles at all sites in 1997 was reflected in low densities of the 1+ and 2+ year classes in subsequent years. Abalone abundances at an unfished site were steady over the seven years. Two sites were located within each of the main stocks utilised by the recreational fishery. Abundance was stable or increasing in one stock, corresponding to a stable total catch. In the second stock the total catch increased over time and abundances declined. Perth is the focus of the Roe’s abalone fishery, with recreational and commercial fishers take about equal shares of the annual catch. Stocks are highly subdivided, with most of this catch coming from only 3 stocks occupying about 20 nautical miles of coast. Growth rates were found to be lower than previous estimates, and more similar to other commercial species of abalone. All life history stages are highly habitat specific, particularly the recruits, and the distribution and abundance through time indicate that the main stocks are near, or slightly over, the limit of sustainable fishing.

Animal behaviour is a state variable of the individual that deserves special attention given its determinant role in eco-evolutionary processes (Wolf et al. 2007 in Nature). The decomposition of the behavioural variation in between- and within-individual variability has revealed the existence of consistent between-individual differences referred to as personality or behavioural types (Dall et al. 2004 in Ecology Letters). Five axes of personality are usually recognized (exploration, aggressiveness, activity, sociability and boldness), and individual specificities along them tend to be correlated leading to what is known as behavioural syndromes. Recently, these patterns of covariation have been enlarged to accommodate movement behaviour within a personality-dependent spatial ecology theory (Spiegel et al. 2017 in Ecology Letters). Most animals tend to forage, reproduce and develop any activity within specific bounded space, which leads to the formation of home range (HR) areas (i.e., HR behaviour, Börger et al. 2008 in Ecology Letters). The increasing development of animal tracking technology is providing a huge amount of movement data revealing that HR behaviour is widespread among taxa and shows a large consistent variability, both at within- and between-individual level, which allows to define the existence of well-contrasted spatial behavioural types (SBTs). SBTs, as other personality traits, play an important role in selective processes as those impelled by harvesting activities. The Pace-of-Life-Syndrome (POLS) theory (Réale et al. 2010 in Philos. Trans. R. Soc. B Biol. Sci), hypothesises on how personality traits are expected to be correlated with life history (LH) traits along the fast-slow continuum (Stearns 1992 in Oxford Univ. Press) in the broadest sense. Accordingly, patterns of covariation between specific SBTs, physiology-related features and LHs would be expected to exist whenever they maximize the animal performance in a given environment. However, the way in which behavioural variation at the within-species level is translated to the wide range of LH traits remains a fundamental yet unresolved question, mainly due to the lack of a proper theoretical framework (Mathot & Frankenhuis, March 2018 in Behavioral Ecology and Sociobiology). Thus, unrevealing the mechanisms behind is certainly scientifically very exciting but also socially relevant. In such a context, this PhD thesis aimed to address from conceptual, empirical and theoretical perspectives cornerstone questions in behavioural ecology: what are the feasible mechanisms underpinning the establishment of HR areas and within-species variation, what are their consequences for animal functioning and performance (i.e., in. LH traits) at the individual and eco-evolutionary levels, or what are the implications for the assessment and conservation of wildlife of the existence of SBTs. The PhD thesis focusses in a fish heavily exploited by recreational fishers but it aims to provide general reasoning applicable to a wide range of wild animals. First, the PhD thesis proposes a mechanistic theory of personality-dependent movement behaviour based on dynamic energy budget models (i.e., a behavioural-bioenergetics theoretical model). Second, integrated in the field of animal personality (i.e., decomposition of behavioural variability into within- and between-individual’s components), it addresses empirically the study of behavioural variability in the main axis of personality for a marine fish species and looked for evidences of whether personality-mediated differences in energy acquisition may exist. Aiming to support empirically the possible connections between personality traits and space-use behaviour, the thesis provides some insights on the application of a novel-tracking algorithm to analyse the movement of individual fish submitted to different experimental conditions. Third, it provides two examples of how applying HR-related theoretical concepts may improve the management of natural resources: attending the properties of HR may facilitate the assessment of wildlife using fixed monitoring sampling stations, and considering SBTs may influence the assessment of the status of wild fish stocks. Finally, the adaptive value of the proposed behavioural-bioenergetics theory is explored by means of dynamic optimization to understand the eco-evolutionary consequences related with HR variability. In summary, this PhD thesis makes an important contribution to behavioural ecology by developing a unifying theory to test the generality and adaptive value of POLS based on dynamic energy budgets. This behavioural-bioenergetics model connects (1) personality traits (2) HR behaviour, (3) physiology and (4) LH traits through an interwoven of mass/energy fluxes, within which they interact and feedback with the ecological context. Overall, from an eco-evolutionary perspective, the proposed framework constitutes a powerful tool for exploring the ecological role of HR behaviour and predicting what combination of behavioural traits would be evolutionally favoured in a given ecological context. Moving forward to including managerial scenarios, this unifying theory provides scientifically founded knowledge that would promote to improve natural resource management by attending the behavioural component of animal populations.

The Pacific Coastal ecoregion contains large tracts of economically important forestlands that also serve as critical stream habitat for endangered Salmonids. Excessive fine sediment deposition in streams of this region is a major environmental concern in the region but difficult to measure directly. The use of stream invertebrates to monitor fine sediment conditions in streams requires careful consideration of several important factors that complicate their use as bioindicators including high spatial and temporal variability and covariance with other environmental variables.

To evaluate the use of stream invertebrates as bioindicators of excessive fine sediment, three hypotheses were tested. The first hypothesis was that invertebrates would be related to broad-scale climate variables (Chapter 2). The second hypothesis was that functional aspects of the invertebrate community would serve as useful indicators of excessive fine sediment condition. (Chapter 3). The third hypothesis was that invertebrates in streams with naturally high levels of sediment would be tolerant to fine sediment (<2 mm, Chapter 4). Hypotheses were tested using a temporal data set at two streams in western Oregon, spatial data from 214 sites across the Oregon Coast Range, and in-situ experiment conducted in streams with erosive or resistant geologies.

In the temporal study, both invertebrate density and functional traits were positively related to El Niño strength (R² range = 0.22–0.36, ρ range = 0.008–0.04) and air temperature (R ² range = 0.32–0.49, ρ range = 0.002–0.01). The spatial study identified several environmental and hydrological factors that exhibited strong negative controls on both fine sediment (Mantel r range 0.14–0.25, ρ range = 0.001–0.01) and invertebrate Scrapers (R² range = 0.11–0.14, ρ range = 0.001–0.04). The result of the experimental study provide evidence that invertebrates in streams with erosive geologies exhibit tolerance to sediment addition when compared to invertebrates in resistant geologies (mean loss=15%, ρ <0.01) and that invertebrate grazing traits were most strongly associated with fine sediment dosing frequency (ρ <0.05).

The findings of this research demonstrate the role of geology in shaping invertebrate communities and their functional response to fine sediment addition and identify functional indicators that may be useful in different geologic settings. For environmental managers in the Pacific Coastal ecoregion, these findings are of potential value in assisting with the identification of biologically-relevant changes in stream fine sediment conditions and support efforts to balance economic needs in the region while protecting critical Salmonid habitat.

This thesis draws on David Harvey’s concept of “accumulation by dispossession” and an international political economy (IPE) approach centred on the institutional arrangements and power structures that privilege certain actors and values, in order to critique current capitalist practices of primitive accumulation by the global corporate extractive industry. The thesis examines how accumulation by dispossession by the global extractive industry is facilitated by the “free entry” or “free mining” principle. It does so by focusing on Canada as a leader in the global extractive industry and the spread of this country’s mining laws to other countries – in other words, the transnationalisation of norms in the global extractive industry – so as to maintain a consistent and familiar operating environment for Canadian extractive companies. The transnationalisation of norms is further promoted by key international institutions such as the World Bank, which is also the world’s largest development lender and also plays a key role in shaping the regulations that govern natural resource extraction. The thesis briefly investigates some Canadian examples of resource extraction projects, in order to demonstrate the weaknesses of Canadian mining laws, particularly the lack of protection of landowners’ rights under the free entry system and the subsequent need for “free, prior and informed consent” (FPIC). The thesis also considers some of the challenges to the adoption and implementation of the right to FPIC. These challenges include embedded institutional structures like the free entry mining system, international political economy (IPE) as shaped by international institutions and powerful corporations, as well as concerns regarding ‘local’ power structures or the legitimacy of representatives of communities affected by extractive projects. The thesis concludes that in order for Canada to be truly recognized as a leader in the global extractive industry, it must establish legal norms domestically to ensure that Canadian mining companies and residents can be held accountable when there is evidence of environmental and/or human rights violations associated with the activities of Canadian mining companies abroad. The thesis also concludes that Canada needs to address underlying structural issues such as the free entry mining system and implement FPIC, in order to curb “accumulation by dispossession” by the extractive industry, both domestically and abroad.

The main aim of the study is to assess the productivity and supply chain of aquaculture projects in Gauteng Province, South Africa. The research adopted the use of quantitative method; and collected data and information from the five regions that make up the province. Both primary and secondary data were collected. The study used correlation analyses to determine the perfect fit or negative fit of some variables to supply chain as well as the consumers‟ reactions to the questionnaires. Gross margin analysis as well as gross profit margin ratio was used to determine the profitability of aquaculture production in the province. Findings of the study revealed underutilization of production capacities of the established fish farms. The fish farmers in the study are currently using 36% of the capacities of the established aquaculture projects in the study area. The profit margin was in excess of 40% in all the projects surveyed. The study further revealed lack of proper, effective and efficient supply chain for aquaculture projects which adversely affect aquaculture growth and sustainability in Gauteng Province
Agriculture, Animal Health and Human Ecology
M. Sc. (Agriculture)

Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, Discipline of Environmental Biology, 2006.
"January 2006" Bibliography: pages 188-209. Also available in print form.

With the increasing global population, providing sufficient food to meet the rising demand has become a great challenge to food-producing sectors. Aquaculture is one of the food sources which produces varieties of seafood. Shrimp is the most popular seafood in the US, and its production plays an important role in the aquaculture industry. However, shrimp farming causes various types of pollution to damage the environment and aquatic biodiversity, the associated impacts must be mitigated to ensure the sustainability of shrimp production. This study performed a life cycle assessment (LCA) on different shrimp production chains from cradle to the market in Midwestern US covering three farming systems and eight shrimp feed formulas. Midpoint environmental impacts including acidification potential (AP), eutrophication potential (EP) and global warming potential (GWP) were determined. Feed production was identified as the main contributor to the AP and GWP for both the intensive and semi-intensive production systems (SPS), regardless of the feed formula. While the environmental performance of feed production highly depended on the feed conversion ratio, feed ingredient was another determining factor in which animal protein sources, including poultry by-product meal and fishmeal, showed high contributions to the AP and GWP. However, plant proteins such as soybean, wheat, and corn gluten meals produced higher EP, therefore, substituting plant-based ingredients for animal-based ones in shrimp feeds did not all result in positive environmental consequences. Shrimp farming was the hotspot of all the three impacts, especially accounting for the highest EP. Among the three farming systems studied here, the SPS caused the highest environmental burdens due to the intensive uses of chemicals and fertilizers. On the contrary, the extensive farming was found to be the most sustainable system because no inputs of feeding and additional materials and energy are required for its operation. The LCA model developed in this study is expected to serve as US shrimp farmers’ decision-making guidelines to adapt farming practices with lower environmental footprint.

Tese de doutoramento, Biologia (Biologia Marinha), 2009, Universidade de Lisboa, Faculdade de Ciências
Resumo alargado em português disponível no documento
Fundação para a Ciência e Tecnologia (FCT), SFRH/BD/19319/2004 and the European Union FEDER-Fisheries Programme (MARE)

Aquaponics is the combination of aquaculture and hydroponic technology to grow both fish and plants together in a closed-loop system. While aquaponics can play a role in increasing food security, it may also be a potential educational tool because of its interdisciplinary nature and required technological skill set. With aquaponics, students could conduct hands-on activities involving chemistry, physics and biology to solidify their understanding of a range of theories. Beyond standard science, technology, engineering and mathematics (STEM) principles, aquaponics may be related to projects on sustainability, environmental science, agriculture, the food system, health, economics, business and marketing. The interdisciplinary nature of aquaponics may make it an appealing tool for education, yet that same aspect may also make an aquaponics system challenging to implement and manage. Given this paradox, this exploratory research assesses challenges, solutions and success of aquaponics in education with a specific focus on implementation. Qualitative data were collected through phone interviews with educators (n=10) who currently, or had in the past, used an aquaponics system in an educational setting in North America. The most frequently described uses for aquaponics were flexible, hands-on teaching and learning of STEM and food-related concepts. Participants reported two broad challenges to implementing aquaponics: technical difficulties as a result of the nature of aquaponics and restrictions as a result of their school settings. Solutions given by participants were physical aquaponics system modifications and the development of intangible characteristics, especially community connections and support, passion for aquaponics and expertise. In this study, success in aquaponics in education emerged as a cyclical pattern: participants valued the overall learning experiences of aquaponics and the continued application of these learning experiences. Ultimately, these exploratory findings will help educators manage their expectations for aquaponics while establishing objectives for their particular educational settings.

With the world's fisheries in crisis, most fisheries fully- or over-fished, and world catches perhaps exceeding sustainable limits, our capability to monitor and manage fisheries is uncertain. I reviewed these problems, and described ways that spatial complexity compromises monitoring and assessment. Monitoring/ management combinations that are robust to fine-scale dynamics are needed. I developed a closed-loop simulation framework, using the disc equation to distribute fishing effort. A suite of small, spatially-complex fisheries were simulated, and fishery performance was measured, under different monitoring/ management arrangements. Spatial dynamics interacted with monitoring/ control systems, engendering fine scale effects such as biomass erosion, and serial depletion. Performance depended upon control and monitoring information quality. It deteriorated as capacity and hyperstability increased. Poor information / control combinations (CPUE/ TAC) produced poor performance, especially where the stock and effort were concentrated. Effort control with monitoring fishing rates (F) by tagging was risk-averse, performing consistently well across all scenarios. I used a single-stock, age-structured model to assess the Northern Territory Spanish mackerel fishery. This fishery's status is grossly uncertain: available abundance and composition data were uninformative; catch and effort history, biological parameters and stock structure were all uncertain. There was no evidence supporting any increase of the current limit reference point. Genetic mark-recapture might overcome the limitations of conventional tagging. It is suggested for direct F measurement, for routine monitoring. This would entail in situ collection of tissue ("tagging") and subsequent screening of catch samples for matches ("recaptures"), using DNAfingerprinting. I present device designs for in situ tissue collection. Success rates (proportions of strikes yielding tissue) relative to design features were examined. Design and the line on the test vessel on which the tool was deployed interacted strongly. Predicted success rates of the best design are 44-85%, depending upon the line used. Industry participation, entailing daily genetic tagging a set number of fish, would ensure that all members of the fished population have a similar probability of being tagged. In further simulations, genetic tagging outperformed other monitoring methods. Performance improved with small concurrent conventional tagging programs. This methodology could be developed to monitor F in many fisheries.
Science, Faculty of
Zoology, Department of
Graduate

Recent years have seen an explosion of interest in the use of freely available DNA present in aquatic systems, otherwise known as environmental DNA (eDNA), as a tool for monitoring aquatic organisms. However, much remains unknown about the behavior of eDNA over a range of environmental conditions. This is particularly true in high gradient headwater streams, which have received less attention than other types of water bodies. In the summer of 2011, a headwater stream system with well established species distributions was sampled using eDNA techniques. Though species were detected where known to be present, detections also occurred where traditional techniques failed to detect species. This suggests that a cautious approach to positive eDNA detections is advisable. In 2012 a second study was conducted to better understand the dynamics of eDNA concentration in lotic systems. Caged brook trout (Salvelinus fontinalis) were introduced into two otherwise fishless headwater streams, and eDNA samples were collected at evenly spaced intervals downstream of the cage. This was repeated 19 times from mid-summer through autumn, over flows ranging from approximately 1 to 96 l/sec. Quantitative PCR was used to relate DNA copy number to distance from source for each of these 19 sampling events. In all cases, DNA was detectable at 239.5 m from the cage. Increasing flows generally decreased eDNA copy number near the cage but had relatively little effect at downstream sites. Additionally, the presence of leaf biomass during the fall period had the potential to completely erase otherwise high DNA levels.

The New Zealand Ministry of Fisheries relies on fishery assessments to determine suitable catch quotas for exploited fisheries. Currently, 628 fish stocks are managed in New Zealand using the Quote Management System, which includes the 8 com- mercial flatfish species caught within the Exclusive Economic Zone. These eight species of flatfish, which includes four species of flounder, two species of sole, brill and turbot, are currently managed using a combined catch quota. Since these eight species are managed using a common catch quota, there is concern that some of the individual species may be under or over-fished. This thesis describes work involving the flatfish species caught in the FLA3 man- agement area, around the south island of New Zealand. The FLA3 management area contains three key species: New Zealand sole, lemon sole, and sand flounder. Due to the nature and limitations of the data available, simple biomass dynamic models were applied to these species. The maximum likelihood and Bayesian goodness of fit techniques were used to estimate the model parameters. Three models were used: the Fox model, the Schaefer model and the Pella-Tomlinson model with m = 3. As a mathematical/statistical exercise, these models were used to conduct a risk analysis to analyse the advantages and disadvantages of six management options for setting a TACC. However, because of issues over the way that the parameter K has been modelled (due to necessity caused by the lack of data), this should not be seen as an appropriate method for estimating the fish stock. Conclusions were drawn from the results regarding suitable future action for the assessment and management of flatfish stock in FLA3.

In 1988, the red snapper fishery in the Gulf of Mexico was declared severely overfished. Since then, the daily bag limit has been reduced from 7 to 2, the minimum size limit has increased from 13 to 16 inches, and the year-round recreational season has been reduced to one lasting 53 days. Despite NOAA's recommendations that the Gulf States match these regulations, Texas has enforced a 4 bag limit and no seasonal restrictions. In 2009 alone, the total recreational catch exceeded the allocated quota by 1.7 million pounds. The lack of consistency between state and federal regulations and the drastic changes in management schemes have affected anglers' confidence in management, and limited the ability of the fishery to successfully adapt. This study provides an innovative assessment that measures fishers' knowledge and determines their support for current fishery regulations and for the scientific rationale behind the regulatory system. Over 150 interviews of red snapper anglers at charter and head boat docks were conducted along the Texas coast. The majority of respondents were 20-50 year old (74.5%), male (89.3%), four-year college graduates (34.9%), who resided near the coast (65.3%), and were targeting red snapper (92.5%). Results showed that 72.5 percent of respondents agree with the science behind red snapper management, 63.4 percent believe that the stock has improved since 2008, 89.5 percent agree that a bag limit in general is an appropriate management tool, and 78.2 percent agree with the Texas state management of red snapper. However, 51.7 percent of respondents disagree with the federal management of red snapper, and 90.1 percent of all respondents did not know that red snapper live to be 41-60 years old. The lack of support for the federal management may be due to the lack of knowledge of red snapper life span. Applications of this research will be imperative for managers - who already address biological, ecological, and economic aspects of a fishery - to expand their multi-disciplinary approach to include social analysis for the successful evolution of recreational fisheries management. Future research should explore improved management approaches that involve greater communication between the stakeholders and managers.