Includes bibliographical references. / The two-species South African hake fishery (deep-water Merluccius paradoxus and shallow-water M. capensis) has been managed using Operational Management Procedures (OMPs) since 1990. This thesis summarises the development of two OMPs: OMP-2007, which was the basis for the 2007 to 2010 Total Allowable Catch (TAC) recommendations, and OMP-2011, which was first used for the 2011 TAC recommendation and which is intended to extend to 2014. The Operating Models (OMs) used for simulation testing of OMP-2007 were based on the first fully species-disaggregated coast wide assessment of the South African hake resource.

This thesis presents four marine resource assessments; three concern the Southern Hemisphere (SH) humpback whale (Megaptera novaeangliae) and one the South African east coast rock lobster Palinurus delagoae. It also sets out the statistical background to the methodology employed in the assessments, including an outline of the Bayesian approach, Bayes' theorem, and the sampling-importance re-sampling (SIR) as well as the Markov Chain Monte Carlo (MCMC) methods.

Includes bibliographical references (leaves 89-97). / Although two monkfish species (Lophius vomerinus and L. vaillanti) are caught off the Namibian coast, the less abundant of the two (L. vaillanti, contributing only 1 % to total landings) is not explicitly dealt with in this thesis, and the resource is treated as one species. The purpose of this thesis is to undertake a Bayesian assessment of the resource, and to use this as the basis to develop an Operational Management Procedure (OMP) for the resource. First, the biology, history of the fishery, and the history of monkfish stock assessment and management are reviewed briefly. Then the reasons for using an Age-Structured Production Model (ASPM) for assessment are discussed.

Bibliography: pages 162-178. / The two species of Cape hake, Merluccius capensis (shallow-water hake) and M paradoxus (deepwater hake), fomi the mainstay of the bottom trawl industry off South Africa and constitute the country's most valuable fishery. It is therefore important that the status of this resource be assessed regularly to ensure that exploitation is at a sustainable level. The two Cape hake species are morphologically similar and no distinction is made between them in commercial catch statistics. Consequently, for assessment purposes, the Cape hakes are treated as a single species. It is assumed that two stocks of Cape hake exist, one off the West Coast and another off the South Coast of South Africa. Central to the assessments of these stocks are the catch per unit effort (CPUE) data because it assumed that CPUE is proportional to abundance. The nominal CPUE (hake catch divided by actual time trawled) for both the West and South Coast stocks has shown a steady growth over the period 1978 - 1994, increasing at a rate of 3.8% per annum on the West Coast and 4.2% per annum on the South Coast. The bulk of this thesis is concerned with determining whether these increases in CPUE are the result of an increasing biomass, or are rather, in part, the result of improved vessel efficiency due to technological advancement or of changes in fishing strategy. The existing CPUE time series had previously been standardised by means of applying power factors which were crudely estimated in the early 1970s and which are likely inappropriate for the current fishing fleets. These CPUE series have therefore been re-standardised by applying the internationally accepted approach of General Linear Modelling (GLM).

The Cape Vulture Gyps coprotheres is one of the world's largest avian scavengers and was once widely distributed in southern Africa, to which it is endemic. It has suffered major changes of fortune in recorded history and has, at least twice, undergone large range contractions and expansions in the Cape Province. It has variously been classified as 'rare', 'vulnerable' or 'threatened'. It is currently thought, by some, to be in decline. The central aim of these researches is to answer the 'Grand Question': What is the probability that the Cape Vulture will survive well into the twenty-first century as a free-flying bird? This is followed by a secondary question: What is the stability of the population in space, time and age-structure?

The hake fishery is South Africa's most valuable and harvests two morphologically similar species, the shallow- water Cape hake Merluccius capensis and the deep-water Cape hake M. paradoxus. Since 1948, annual catches have exceeded 50 000 tons and the current total allowable catch (TAC) is about 150 000 tons, a quantity informed by assessments of the hake resource. Current assessments on which management is based use single-stock models that ignore food-web effects. Usually including such interactions in assessments is problematic because of the complexity of food webs. In the case of Cape hake, however, cannibalism and inter-species predation form a very large component of hake mortality and food consumption, thus making a multi-species model not only more feasible but also likely more reliable. A comprehensive multi-species model incorporating these interactions was last investigated in 1995. Since then, substantially more data have become available, and hake single-species assessments have developed considerably, inter alia now including the ability to take careful account of species differentiation. Additionally, with increased computer processing power, more sophisticated modelling can now be attempted than was possible 20 years ago, rendering an update and refinement of the 1995 analyses timeous. The thesis uses mathematical methods to model hake-on-hake predation and cannibalism in hake populations explicitly by incorporating an additional mortality term to account for these interactions. Information from stomach samples obtained on hake research surveys on predator and prey lengths, as well as on the proportion of hake in the diet of hake predators, is then included when fitting the model to data. Chapter 1 contains a brief introduction to the work. Chapter 2 provides background information on the Cape hake fishery and its management, as well as pertinent information on the biology and diet of the hake (and related fish) from the literature that is relevant to the development of the model constructed in this thesis. Chapter 3 lays out the data available for assessing the Cape hake populations: abundance indices together with catch and catch-at-size data for the standard non-predation model, and hake stomach content data for the years 1999-2013 to inform the predation component of multi-species model developed. Chapter 4 provides the details for the standard hake assessment model used at present to inform management of the stocks. This model forms the basis for the multi-species model developed incorporating predation, which is presented in Chapter 5. The remaining Chapters of the thesis present the results and discussions (Chapter 6), possible future development of this model (Chapter 7) and a brief summary of the main findings of the thesis (Chapter 8).

Includes abstract. Includes bibliographical references (leaves 92-111). / Many species of baleen whales and seals in the Southern Hemisphere were subject to intensive overexploitation by commercial harvesting in the last two centuries, and many populations were reduced to very low levels. Krill is the dominant prey item of these species. Harvesting (to near extinction) of the large baleen whales (blue, humpback and fin whales) from the start of the 20th century led to a likely increase in the availability of krill to other krill predators such as the Antarctic minke whales and crabeater seals. This phenomenon is referred to as the “krill surplus” hypothesis and has been a central hypothesis of Antarctic ecosystem studies. This thesis aims to better understand species interactions in the Antarctic through developing and extending multispecies models of the system. The study considered only Region A (IWC Management Areas II, III and IV, 60°W to 130°E) because the numbers of baleen whales harvested in Atlantic/Indian Oceans were far greater than in other Oceans, so that the impacts on the dynamics of these species are likely greater. The simple models of competition between blue and fin whales developed give qualitatively similar results to the Mori-Butterworth Antarctic ecosystem model of an initial number of fin whales before exploitation began that is much lower than single species models suggest. However, there are important features of blue and fin whale CPUE data off Durban over the middle decades of the last century that are not reflected by the model results, and a number of possible reasons for this are advanced. In particular, the introduction of competition in the models predicts a steady fin whale population until 1950, but cannot reproduce the feature in the CPUE data of an increase from the 1920’s to 1950’s. The study then extends the Mori-Butterworth Antarctic ecosystem model by adding squid, which has fast dynamics compared to whales and seals. The model estimates population trends in terms of numbers or biomass. This study indicates that results are particularly sensitive to the density dependence assumed for natural mortality and/or birth rate. The results highlight that the squid biomass trajectory is relatively insensitive to initial squid abundance but depends strongly on the density dependence assumed for squid. Generally, the estimated historical trajectories suggest that the inclusion of squid in the model hardly impacts the maxima reached by other species that benefited from the krill surplus. The model predicts that squid started to increase at about the same time (1920) that the reduction of large baleen whales (blue, humpback and fin whales) commenced under heavy harvesting. This suggests that species with fast dynamics such as squid were possibly the first to benefit from krill surplus, even before minke whales and crabeater seals, which started to increase only about a decade later. The study provides a potential framework for understanding the interplay between species with slow and fast dynamics.

Includes bibliographical references (leaves 105-109). / This thesis comprises two sections. The first deals with the analysis of observer data from pelagic commercial vessels with a particular focus being to examine whether there is any indication of dumping (discarding) that is provided by these data. The second section investigates the ability of constraints associated with the ECOPATH mass-balance equations to improve knowledge on estimates of parameters in the southern Benguela ecosystem. Sardine and anchovy are the most valued and carefully managed species of small pelagic fish in South Africa. The problem of dumping in this pelagic fishery has been recognised for some time. The reasons for dumping are thought to arise, inter alia, from large bycatches of sardine (counting against a bycatch allowance) with anchovy and unsuitable sizes of sardine caught for canning purposes. As there were no data that could be used as a basis to investigate the claims, little was done to substantiate them. The Observer Programme to collect data from commercial vessels was instituted in 1999. These data are analyzed to establish whether there are any appreciable differences in catch rates between vessels with observers and those without. General Linear Models (GLMs) are used to adjust for the effects of other factors that could confound comparisons because of the non-random nature of observer placement. Central to the analyses of these data are different catch rate measures. The first measure used is catch per time at sea, which is referred to as CPUETS: the catch of the species concerned made by a vessel on a trip divided by the total number of hours it takes for the vessel to steam from port to the fishing ground, fish and then return to the port. The second measure is catch per haul, which is referred to as CPUEH. This measure divides catch by the total number of hauls made by the vessel during that trip. The CPUETS was the preferred measure due to concerns related to the CPUEH measure (essentially greater reliability of the data and less potential for bias being introduced through other effects which influence haul size). Catch rates were modelled with errors assumed to follow either a log normal or a Poisson distribution. The Poisson error model was the preferred model based on features of the standardized residuals.

Bibliography: p. 309-319. / Pilchard and anchovy are the main targets of the pelagic fishery, South Africa's second most valuable fishery in monetary terms, but producing the highest annual yield in terms of landed mass. It is the most dynamic of South Africa's major commercial fisheries, because the species it targets are relatively short-lived, often occur in mixed shoals and experience large fluctuations in abundance. Mixed shoaling causes operational problems for the pelagic fishery because of the inevitability of juvenile pilchard by catch (more valued as adults for canning) in the anchovy directed fishery. The operational interactions imply a trade-off between these species, and necessitate that they are managed together. The thesis describes the development of a joint management procedure, which provides a framework for quantifying this trade-off such that acceptable levels of risk of resource ""collapse"" are not exceeded for either resource. A management procedure in this context is essentially a computer-simulation tested set of formulae used to recommend catch levels based upon the results of two research surveys of resource abundance, one based on adult fish, and the other on recruitment (juveniles). Parameter estimates for the underlying models used in these simulation tests are derived from assessments of each resource, which fit models to the observations from research surveys and commercial catches using maximum likelihood estimation. Assessment results indicate adult and juvenile natural mortality values of 0.4 and 1.0.year-1 for pilchard, and 0.9.year-1 each for anchovy. They also suggest that recruitment surveys for pilchard are much less precise than sampling CVs alone indicate, but this may be an artefact of problems in the age data, which require further investigation. A range of alternative assessments for pilchard and anchovy is selected for the purpose of performing management procedure robustness trials as part of the simulation tests. The thesis presents two methods for incorporating a trade-off decision between pilchard and anchovy into management procedures. The first develops the trade-off decision as ""external"" (the external trade-off decision, or ETD method), where the responsible Minister makes a trade-off decision for the industry as a whole. This method is problematic because it requires a compromise between those rights holders that prefer pilchard (for canning), and those that prefer anchovy (for reduction). The trade-off decision is then developed as ""internal"" (the internal trade-off decision or lTD method), where rights holders make their own trade-off decision based on their particular preferences. The ETD method specifies a pilchard anchovy ratio for the whole industry, calculates TACs (total allowable catches) on the basis of this selection, and then allocates quotas to each rights holder on the basis of a percentage right for each fishery (pilchard and anchovy). In contrast, the lTD method collapses separate rights for pilchard and anchovy into a single right for the pelagic fishery, and allocates quotas on the basis of trade-off decisions made by individual rights holders, thus avoiding an overall compromise choice. The introduction of non-linear adjustment factors ensures that (over time) allocations to individual rights holders would be near identical, whichever of the two methods is used. The lTD method is currently (2002) being used by Marine and Coastal Management as the basis to set pilchard and anchovy TACs and to allocate individual quotas. The thesis analyses two further aspects of management procedures. The first looks at whether the performance of management procedures can be improved if they incorporate information about regime shifts, modified as sinusoidal cycles. Results indicate that improvement is possible, but that, surprisingly, one would do better using a running mean of research survey estimates of abundance to track a regime cycle, than direct measurements of the actual position in the cycle. The second investigates the benefits of using environmental indices in management procedures, where these indices are used as short-term predictors of recruitment and replace the assumption (made because of lack of information) that forthcoming recruitment will be average. Results indicate that, given the uncertainties related to using such indices, they would need to explain at least 50% of the variation in recruitment before management procedures start showing appreciably improved performance. Priorities for future work include: investigating the implications of a possible changed perception of the bias associated with pilchard adult surveys than that adopted to test the present management procedure; developing the daily egg production method to provide unbiased estimates of pilchard abundance; and performing a thorough investigation of pilchard age data to isolate any problems.

Includes bibliographical references (p. 281-303). / The main objective of this thesis is to model the krill-predator dynamics of the Antarctic ecosystem so as to determine whether predator-prey interactions alone can broadly explain observed population trends of the species considered in the model without any appeal to systematic effects possibly caused by environmental change. The history of human harvesting in the Antarctic is summarized briefly, and the central role played by krill is emphasized. The background to the hypothesis of a krill surplus in the mid 20th Century is described, and the information, particularly regarding population trends, that has become available since the postulate was first advanced is discussed. By reviewing the consumption and abundance estimates for various species in the Antarctic, it is evident that among the baleen whales, blue, fin, humpback and minke whales feed mainly on krill, and could collectively be consuming up to 120 million tons of krill in this region for each of the years around 1990. Of the seals, the Antarctic fur seals and crab-eater seals also feed mainly on krill, and these two species could be consuming up to 70 million tons of krill each year. Consumption estimates for other krill predators (birds, fish and cephalopods) are relatively poorly determined by comparison. Of these four baleen whale species, minke whales currently make the greatest impact on krill due to their large number at present compared to the other larger whale populations which are still depleted. Trend information suggests that the large baleen whales that were heavily depleted during the commercial whaling period are now recovering at rates in the vicinity of 10% per year, but there are some indications of a recent decrease in minke whale numbers. Thus, the consumption of krill by these large baleen whales has probably been increasing over recent years, though decreasing for minke whales. Updated and refined catch-at-age analyses of minke whales for the International Whaling Commission (IWC) Management Areas IV and V suggest an increase in abundance of this species in the middle decades of the 20th Century to peak at about 1970, followed by a decline for the next three decades. Fitting the recruitment time trend obtained from these analyses to a stock-recruitment model suggests that minke whale carrying capacity first increased from about 1940 to 1960 followed by a 60% decrease from the 1960s to the present. General trends in the biological parameters of this species are consistent with such a decline. A predator-prey interaction model is developed including krill, four baleen whale (blue, fin, humpback and minke) and two seal (Antarctic fur and crab-eater) species. The model commences in 1780 (the onset of fur seal harvests) and distinguishes the Atlantic/Indian and Pacific sectors in view of the much larger past harvests in the former. A reference case and six sensitivities are fit to available data on predator abundances and trends, and the plausibility of the results and the assumptions on which they are based is discussed, together with suggested areas for future investigation. Amongst the key inferences of the study are that: i) species interaction effects alone can explain observed predator abundance trends, though not without some difficulty; ii) it is necessary to consider other species in addition to baleen whales and krill to explain observed trends, with crab-eater seals seemingly playing an important role and constituting a particular priority for improved abundance and trend information; iii the Atlantic/Indian region shows major changes in species abundances, in contrast to the Pacific which is much more stable; iv) baleen whales have to be able to achieve relatively high growth rates to explain observed trends; v) species interaction effects impact the dynamics of these predators in ways that differ from what might be anticipated in a conventional single-species harvesting context, and they need to be better understood and taken into account in management decisions, and vi) Laws' (1977) estimate of some 150 million tons for the krill surplus may be appreciably too high as a result of his calculations omitting consideration of density dependent effects in feeding rates. . A priority for future work is to obtain improved estimates of the amount of krill consumed by other species, such as birds, cephalopods and fish as well as to obtain consensus on current abundance estimates for crab-eater seals and baleen whales (especially minke whales and also the associated abundance trend). Once such information is improved, more thorough sensitivity tests to the assumptions of the model and uncertainties in the abundance estimates of the species considered need to be explored. With such further development, it is hoped that such a model may ultimately assist in providing scientific advice for appropriate sustainable harvesting strategies for the Antarctic marine ecosystem taking species interactions into account, as this is a matter of key importance for the IWC and for the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR).