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 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.

This study is an attempt to simulate aspects of human visual perception by automating the detection of specific types of objects in digital images. The success of the methods attempted here was measured by how well results of experiments corresponded to what a typical human’s assessment of the data might be. The subject of the study was images of live fish taken underwater by digital video or digital still cameras. It is desirable to be able to automate the processing of such data for efficient stock assessment for fisheries management. In this study some well known statistical pattern classification techniques were tested and new syntactical/ structural pattern recognition techniques were developed. For testing of statistical pattern classification, the pixels belonging to fish were separated from the background pixels and the EM algorithm for Gaussian mixture models was used to locate clusters of pixels. The means and the covariance matrices for the components of the model were used to indicate the location, size and shape of the clusters. Because the number of components in the mixture is unknown, the EM algorithm has to be run a number of times with different numbers of components and then the best model chosen using a model selection criterion. The AIC (Akaike Information Criterion) and the MDL (Minimum Description Length) were tested.The MDL was found to estimate the numbers of clusters of pixels more accurately than the AIC, which tended to overestimate cluster numbers. In order to reduce problems caused by initialisation of the EM algorithm (i.e. starting positions of mixtures and number of mixtures), the Dynamic Cluster Finding algorithm (DCF) was developed (based on the Dog-Rabbit strategy). This algorithm can produce an estimate of the locations and numbers of clusters of pixels. The Dog-Rabbit strategy is based on early studies of learning behaviour in neurons. The main difference between Dog-Rabbit and DCF is that DCF is based on a toroidal topology which removes the tendency of cluster locators to migrate to the centre of mass of the data set and miss clusters near the edges of the image. In the second approach to the problem, data was extracted from the image using an edge detector. The edges from a reference object were compared with the edges from a new image to determine if the object occurred in the new image. In order to compare edges, the edge pixels were first assembled into curves using an UpWrite procedure; then the curves were smoothed by fitting parametric cubic polynomials. Finally the curves were converted to arrays of numbers which represented the signed curvature of the curves at regular intervals. Sets of curves from different images can be compared by comparing the arrays of signed curvature values, as well as the relative orientations and locations of the curves. Discrepancy values were calculated to indicate how well curves and sets of curves matched the reference object. The total length of all matched curves was used to indicate what fraction of the reference object was found in the new image. The curve matching procedure gave results which corresponded well with what a human being being might observe.

L’évaluation et la gestion des stocks de poissons ont pour objectif d’atteindre une exploitation durable des ressources fournies par les océans. Si les progrès dans ce domaine sont bien réels pour certains stocks de grande importance commerciale, la situation est différente pour les stocks dits à données limitées. Souvent historiquement moins exploités, ces stocks ne bénéficient pas des mêmes ressources, tant économiques qu’humaines, pour réaliser une évaluation de stock permettant par la suite la mise en place de mesures de gestion. Ce travail s’appuie sur deux cas d’étude, le lieu jaune (Pollachius pollachius) et la seiche (Sepia officinalis), afin d’explorer des méthodologies d’évaluation de stocks adaptées aux situations de données limitées. Après une première partie introductive reprenant le contexte de l’évaluation des stocks et présentant les deux cas d’étude, une revue des méthodes d’évaluation de stocks à données limitées est proposée. Une troisième partie compare les résultats d’un modèle de biomasse à deux stades et d’un modèle multi-annuel de déplétion généralisé appliqués au stock de seiche de Manche. Une version améliorée du modèle de biomasse à deux stades codé en Bayésien est également présentée. Le travail se poursuit avec l’application d’un modèle d’analyse intégrée Stock Synthesis au stock de lieu jaune de mer Celtique. Les résultats sont comparés aux résultats de modèles plus simples nécessitant moins de données. Les résultats du modèle Stock Synthesis s’avèrent sensibles aux hypothèses sur la valeur de mortalité naturelle, dont le calcul dépend des paramètres de croissance du stock. La cinquième partie présente l’acquisition et le traitement de nouvelles données qui pourront permettre une meilleure estimation de l’état du stock de lieu jaune. Un modèle hiérarchique Bayésien est construit, permettant un transfert d’information entre trois stocks et la mise à jour des paramètres biologiques du lieu jaune. Le dernier chapitre conclut ce travail en reprenant les principaux résultats obtenus et en élargissant la discussion sur des perspectives de recherche. / The assessment and the management of fish stocks aim at achieving a sustainable exploitation of the resources provided by the oceans. While progress have been made in this field for some stocks of great commercial importance, the situation is different for the so-called “data limited” stocks. Often historically less exploited, these stocks do not benefit from the same economical resources nor workforce to conduct the stock assessments required to set management measures. This work is based on two case studies, pollack (Pollachius pollachius) and cuttlefish (Sepia officinalis). The aim is to investigate the stock assessment methods adapted to data-limited situations. A first introductive part presents the background of fish stock assessment as well as the two case studies. This first chapter is followed by a review of data-limited stock assessment methods. The third part compare the results of a two-stage biomass model with the results of a multi-annual generalized depletion model applied to the English Channel stock of cuttlefish. An improved version of the Bayesian two-stage biomass model is also presented. In the fourth part, a Stock Synthesis model based on integrated analysis methods is applied to the stock of pollack in the Celtic Seas Ecoregion. The results are compared to the results of simpler models which require less data. The Stock Synthesis model results are sensitive to the assumptions on the natural mortality value, which relies on the growth parameters of the stock. The fifth part presents the collection and analysis of new data which will allow a better estimate of pollack stock status. A Bayesian hierarchical model is constructed, allowing information transfer between three stocks and the update of pollack biological parameters. The last chapter concludes this work by summarizing the main results. The discussion is extended to the research perspectives.

Under the growing demand for marine fish resources, and the apparent and expected impacts of global climate change, there is a need to conduct long-term monitoring (LTM) to ensure effective management of resources and conservation of biodiversity. However LTM programmes often suffer from design deficiencies and fail to achieve their objectives. These deficiencies stem from the fact that insufficient consideration is afforded to the design phase, with programmes selecting methods that are not suitable to address the objectives, or are not cost-efficient, compromising the sustainability of the LTM. To facilitate the establishment of LTM programmes along the southern coast of South Africa, background research needed to be conducted to identify which methods were most appropriate for LTM of reef fish. This study presents a detailed field-based assessment of the suitability and cost-efficiency of monitoring methods for long-term monitoring of reef fish in the Agulhas Ecoregion of South Africa. The approach adopted to identify the method, or suite of methods most suited for LTM, involved (i) the selection of methods considered suitable for LTM, (ii) the individual assessment and optimisation of method performance, and (iii) the comparative assessment of the fish community sampled by the different methods. The most suited method(s) were then identified as those that provide the most comprehensive assessment of the fish community and had the highest cost-efficiency. The research was conducted between January 2008 and 2011 in the Tsitsikamma and Table Mountain National Park (TNP and TMNP, respectively) marine protected areas (MPAs) within the Agulhas Ecoregion. The methods selected included fish traps (FT), controlled angling (CA), underwater visual census (UVC), remote underwater video (RUV), baited RUV (BRUV) and remotely operated vehicles (ROV). The individual assessment and optimisation was conducted with the FT, UVC, RUV and BRUV methods. The assessment of the FT method aimed to identify the optimal soak time, and whether or not the size of the funnel entrance to the trap affected the catch. The results identified that larger funnel entrances caught more fish and soak times of 80 minutes produced the highest catches per unit effort. However the data were highly variable and the method detected few of the species typical of the region. Fish traps were also associated with high levels of mortality of fish post-release. The assessment of UVC strip transect method involved directly comparing the precision of data collected by researchers and volunteers using a novel double-observer technique (paired-transects). The results showed considerable error in both the volunteers and researchers data, however the researchers produced significantly higher precision data, compared to the volunteers. The distinction between researchers and volunteers was not evident in the data for the dominant species of fish. For all observers, the abundance of a species in the sample had a significant influence on its detectability, with locally scarce or rare species poorly detected. UVC was able to sample the majority of species typical of reefs in the region, however it appeared plagued by observer and detectability biases. The assessments of RUV and BRUV were conducted simultaneously which enabled the assessment of the effect of bait on the observed fish community. In addition the optimal deployment time for both methods to maximise species richness and abundance was determined. The results showed that BRUV, and to a lesser degree RUV, were able to effectively survey the reef fish community for the region with a 50 minute and 35 minute deployment time, respectively. Baited remote underwater video was especially good at detecting the invertebrate and generalist carnivores, and cartilaginous species. On the other hand, RUV was more effective at surveying the microinvertebrate carnivores. Remote underwater video was characterised by higher data variability, compared to BRUV, and was ultimately considered a less cost-efficient monitoring method. Comparative methods assessments were conducted during two field experiments with the FT, UVC and BRUV methods in the TMNP MPA, and the FT, CA, UVC, RUV, BRUV and ROV methods compared in the TNP MPA. The objectives of the comparison were to investigate differences in the fish communities observed with the different methods, and to determine the power of the data to detect an annual 10% growth in the fish populations over a period of five years. The results from the method comparison were in turn used to conduct the cost-benefit analysis to determine the efficiency of the different methods at achieving monitoring objectives requiring population data from multiple trophic and functional groups with the community, and from species of fisheries importance. The results indicated that FT, CA and ROV were ineffective at monitoring the reef fish community, although CA appeared to provide valuable data for the dominant fisheries species. Both CA and FT required minimal initial investment however, the variability in the data translated into high annual monitoring costs, as the required sampling effort was great. The ROV required the highest initial investment and was identified as the least cost-efficient method. Underwater visual census was able to adequately survey the bony fish within the community, however it did not detect the cartilaginous species. Underwater visual census required a large initial investment and was not cost-efficient, as a many samples were required to account for the variability in the data. Remote underwater video provided a comprehensive assessment of the reef fish community, however it too was associated with high levels of variability in the data, compared to BRUV, reducing its cost-efficiency. BRUV provided the most comprehensive assessment of the reef fish community and was associated with the highest cost-efficiency to address the community and fisheries species monitoring objectives. During the course of this research stereo-BRUV has gained considerable support as an effective reef fish monitoring method. Although not tested during this research, stereo-BRUV is preferred to BRUV as it provides accurate data on the size of fish. However, the initial investment of stereo-BRUV is over three times that required for the BRUV. Although it is recommended that a baited video technique be used for LTM in the Agulhas Ecoregion, the choice between BRUV and stereo-BRUV will depend on the specific objectives of the programme and the available budget at the implementing agency.

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, / KMBT_363 / Adobe Acrobat 9.54 Paper Capture Plug-in

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.

Largespot pompano, Trachinotus botla, is a surf zone carangid with a cosmopolitan distribution in subtropical and tropical waters. Within South Africa, the species occurs along the KwaZulu-Natal coastline where it is a popular recreational fishing target. Recreational fishing in southern Africa has developed significantly in recent years, and is now regarded as an industry with huge economic potential. The long-term contribution of South African recreational fisheries to local economies is reliant upon sustainable exploitation through effective management. Trachinotus botla was found to grow rapidly with maximum observed age of six years. Otolith growth zone deposition was validated using edge analysis. Growth was similar between males and females until ~350 mm FL after which females continued to grow while growth in males slowed. The resulting overall sex ratio was slightly female-biased (1 male: 1.3 females). Trachinotus botla matures early with all fish considered to be mature at 290 mm FL, which corresponds to an age of three years. A protracted spawning season was observed ranging from November to February and there was evidence to suggest that T. botla is a serial spawner. Dietary analysis indicates that T. botla is an opportunistic predator with a catholic diet. The opportunistic utilization of “superabundant” prey items is a fundamental characteristic of the species feeding habits. An ontogenetic dietary shift was observed at approximately 300 mm FL that was linked to a shift in habitat preference. This thesis provided the first evidence that infection by the tongue-replacing isopod, Cymothoa borbonica, reduces the growth rate of wild host fish populations despite not affecting the diet, feeding habits and feeding frequency of their hosts. These results also highlighted the inadequacy of condition factor as a proxy for quantifying the effects of cymothoids on their hosts, and identified the need to incorporate host age when assessing the effects of parasite infection. Information on the life-cycle of C. borbonica, including estimates of the hypothesized “infectious” period and its longevity were obtained through analysis of parasite infection patterns as a function of host age and length. An assessment of the T. botla shore fishery of KwaZulu-Natal using historical catch data revealed that the fishery is stable. Productivity of the T. botla fishery increased towards the north of KwaZulu-Natal. Distinct seasonal variations in the T. botla fishery were also noted with catches peaking in summer months and lowest during winter. A per-recruit assessment revealed that the species is currently underexploited (SBR = 62% of pristine levels), and fishing mortality rate could be doubled before reaching the spawner biomass-per recruit target reference point of FSB₄₀. A combination of the life history characteristics of species, the nature of the recreational shore fishery together with the current management regulation of 5 fish person⁻¹ day⁻¹ has ensured the sustainable utilization of the T. botla resource in KwaZulu-Natal.

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 United States Pacific Northwest is well known for its shellfish farming. Historically, commercial harvests were dominated by the native Olympia oyster, Ostrea lurida, but over-exploitation, habitat degradation, and competition and predation by non-native species has drastically depleted their densities and extirpated many local populations. As a result, shellfish aquaculture production has shifted to the introduced Pacific oyster, Crassostrea gigas. An underlying objective of this dissertation is the use of molecular genetics to improve our ability to accurately identifying optimal oyster broodstock for either restoration of Olympia oysters or farming of Pacific oysters. The ecological benefits provided by oysters as well as the Olympia oyster's historical significance, has motivated numerous restoration/supplementation efforts but these efforts are proceeding without a clear understanding of the genetic structure among extant populations, which could be substantial as a consequence of limited dispersal, local adaptation and/or anthropogenic impacts. To facilitate this understanding, we isolated and characterized 19 polymorphic microsatellites and used 8 of these to study the genetic structure of 2,712 individuals collected from 25 remnant Olympia oyster populations between the northern tip of Vancouver Island BC and Elkhorn Slough CA. Gene flow among geographically separated extant Olympia oyster populations is surprisingly limited for a marine invertebrate species whose free-swimming larvae are capable of planktonic dispersal as long as favorable water conditions exist. We found a significant correlation between geographic and genetic distances supporting the premise that coastal populations are isolated by distance. Genetic structure among remnant populations was not limited to broad geographic regions but was also present at sub-regional scales in both Puget Sound WA and San Francisco Bay CA. Until it can be determined whether genetically differentiated O. lurida populations are locally adapted, restoration projects and resource managers should be cautious of random mixing or transplantation of stocks where gene flow is restricted. As we transition from our Olympia oyster population analysis to our Pacific oyster quantitative analysis, we recognize that traditional quantitative trait locus (QTL) mapping strategies use crosses among inbred lines to create segregating populations. Unfortunately, even low levels of inbreeding in the Pacific oyster (Crassostrea gigas) can substantially depress economically important quantitative traits such as yield and survival, potentially complicating subsequent QTL analyses. To circumvent this problem, we constructed an integrated linkage map for Pacific oysters, consisting of 65 microsatellite (18 of which were previously unmapped) and 212 AFLP markers using a full-sib cross between phenotypically differentiated outbred families. We identified 10 linkage groups (LG1-LG10) spanning 710.48 cM, with an average genomic coverage of 91.39% and an average distance between markers of 2.62 cM. Average marker saturation was 27.7 per linkage group, ranging between 19 (LG9) and 36 markers (LG3). Using this map we identified 12 quantitative trait loci (QTLs) and 5 potential QTLs in the F1 outcross population of 236 full-sib Pacific oysters for four growth-related morphometric measures, including individual wet live weight, shell length, shell width and shell depth measured at four post-fertilization time points: plant-out (average age of 140 days), first year interim (average age of 358 days), second year interim (average age of 644 days) and harvest (average age of 950 days). Mapped QTLs and potential QTLs accounted for an average of 11.2% of the total phenotypic variation and ranged between 2.1 and 33.1%. Although QTL or potential QTL were mapped to all Pacific oyster linkage groups with the exception of LG2, LG8 and LG9, three groups (LG4, LG10 and LG5) were associated with three or more QTL or potential QTL. We conclude that alleles accounting for a significant proportion of the total phenotypic variation for morphometric measures that influence harvest yield remain segregating within the broodstock of West Coast Pacific oyster selective breeding programs. / Graduation date: 2012