The master's thesis focuses on Slapy valley reservoir which is first described as a suitable location for fishing and recreation. Special attention is also paid to its history. The main body of the thesis features the enumeration and characteristics of individual fish species which occur in the reservoir. Furthermore, the thesis deals with the evaluation of the fishing management of the reservoir from 1962 to 2016 considering fish stock and catches of individual species. Factors influencing the development and dynamics of the fish stock are also evaluated. The summary management of Slapy valley reservoir is analyzed in terms of fish stocking and fishing yields. In addition, the population dynamics trends of predatory and non-predatory fish species are analyzed on the basis of fishing catches. In the conclusion, the current condition of the fish stock is evaluated and some minor recommendations for optimizing the fishing management of the reservoir are proposed. KEYWORDS: fish, Slapy, valley reservoir, sport fishing, catch, fish stock, fishing management

I studied the influence of fishpond management and environmental characteristics on diving beetles (Coleoptera: Dytiscidae), which are important predators in aquatic systems. In 2014 I used live traps to study diving beetle communities in 117 ponds in South Bohemia. The ponds were divided in three categories: intensively managed, extensively managed, and without fish. In total 26 species of diving beetles were found (N=1346). Overall, the beetles prefered shallow litoral zones with cattail (Typha), manna grass (Glyceria) and reed (Phragmites). The number of species declined with increasing alttitude and depth near the trap, while their abundance increased with pond area and amount of detritus near the trap. Beetles occured more in ponds with lower pH, lower conductivity and higher oxygen content. More beetles were found in fishless ponds. On the other hand, some ponds with high density of fishes but well preserved littoral zone had similar communities of diving beetles to the fishless ponds. This shows that high density of fish in ponds decreases the diversity and abundance of diving beetles, most likely because it decreases the vegetation in littoral zone. During the survey, four new localities of Graphoderus bilineatus were found; the species is protected by NATURA 2000 and has been known from very few recent localities in the Třeboň area.

Biodiversity of planktonic crustaceans, cladocerans and copepodans in southbohemian Naděje fishponds system were studied. Both fishpond and non-fishpond (pools, canals, sand-pits, river) localities were observed. Samples were taken from pelagic and littoral zones. Total of 21 species of copepodans and 44 species of cladocerans were recorded over whole area. Hypothesis {\clq}qA higher fish management intensity and higher fish stock cause a lower diversity of zooplankton in a pelagic zone`` was proven. Suppressed species are able to survive in a smaller space (littoral zones, pools, canals, fishponds with a lower fish stock and other non-fishpond localities), where predation pressure is not so strong. None or mild decline of a species diversity can be observed in large areas rich in different water ecosystems, with a reasonable management and production intensity. Different methods of sampling were also compared, those of {\clq}qprolovení litorálních partií`` proved good with the view of effectiveness.

Poenskop Cymatoceps nasutus (Pisces: Sparidae), an endemic South African sparid, is an important angling species being predominantly targeted by the recreational shore and skiboat sector. This species is slow-growing, long-lived, late-maturing and sex-changing, making poenskop acutely sensitive to over-exploitation. Despite interventions, such as the imposition of size and bag limits (currently 50 cm TL and one per licensed fisher per day) by authorities, catch-per-unit-effort trends reflect a severe and consistent stock decline over the last two decades. Poenskop has been identified as a priority species for research and conservation. Although the biology and population dynamics of this species have been well-documented, little is known about the movement behaviour of poenskop. Furthermore, there is a complete lack of information on its genetic stock structure. This thesis aimed to address the current knowledge gaps concerning movement behaviour and genetic stock structure of poenskop, making use of a range of methods and drawing on available information, including available fishery records as well as published and unpublished survey and research data, and data from long-term monitoring programmes. Analysis of available catch data (published and unpublished) revealed a decline in the number of poenskop caught as well as size of fish taken over the last two decades, ultimately reflecting the collapse of the stock (estimated to be at 20% of their pristine level). Improved catch-per-unit-effort data from the Tsitsikamma National Park Marine Protected Area (MPA), and larger poenskop being caught in the no-take areas than adjacent exploited areas of the Pondoland MPA confirmed that MPAs can be effective for the protection and management of poenskop. The current MPA network in South Africa is already wellestablished, and encompasses considerable reef areas, being preferable for poenskop habitation. Conventional dart tagging and recapture information from three ongoing, long-term fishtagging projects, conducted throughout the poenskop’s distribution, indicated high levels of residency at all life-history stages. Coastal region, seasonality and time at recapture did not appear to have a significant effect on the level of movement or distance moved. However, on examining the relationship among coastal movements and fish size and ages, larger and older fish (adults) moved greater distances, with juveniles and sub-adults showing high degrees of residency. An estimation of home-range size indicated smaller poenskop to hold smaller home-ranges, while larger poenskop hold larger home-ranges. Large easterly displacements of a number of adult poenskop is in accordance with previous findings that this species may undertake a unidirectional migration up the coastline of South Africa where they possibly settle in Transkei waters for the remainder of their lives. This high level of residency makes poenskop vulnerable to localised depletion, although they can be effectively protected by suitable MPAs. Despite considerable tagging effort along the South African coastline (2 704 poenskop tagged with 189 recaptures, between 1984 and 2010), there remains limited information on the connectivity of different regions along the South African coastline. This was addressed using mitochondrial DNA sequencing. The mitochondrial DNA control region was used due to its high substitution rate, haploid nature, maternal inheritance and absence of recombination. The mtDNA sequencing showed no evidence of major geographic barriers to gene flow in this species. Samples collected throughout the core distribution of poenskop showed high genetic diversity (h = 0.88, π = 0.01), low genetic differentiation among regions, no spatial structure (ɸST = 0.012, p = 0.208) and no evidence of isolation by distance. The collapsed stock status of poenskop as well as the fact that it is being actively targeted by recreational and commercial fishers suggests that this species requires improved management, with consideration given to its life-history style, residency and poor conservation status. Management recommendations for poenskop, combined with increasing South Africa’s existing MPA network, include the possibility of setting up a closed season (during known spawning periods) as well as the decommercialisation of this species. The techniques used and developed in this study can also be adopted for other overexploited linefish species.

Marine Protected Areas (MPAs), the Ecosystem Approach to Fisheries management (EAF) and Integrated Coastal Management (ICM) have been identified as possible alternatives to traditional linefish management measures, which have largely failed. Monitoring and assessment of fish communities on a long-term basis is necessary, and will provide a means to evaluate the effectiveness of such management measures. Therefore, standardised protocols and optimal sampling methods for long-term monitoring (LTM) and assessment of coastal fish communities are essential. This study aimed to identify suitable methods and develop a protocol for assessment of inshore reef fish communities. A suitable location for evaluation of proposed methods was identified in the warm temperate biogeographical region of South Africa, encompassing the well-established Tsitsikamma Coastal National Park MPA and an adjacent exploited area. Chrysoblephus laticeps (roman) was identified as an indicator species for the study, as it has been well-studied and is well represented in the area. Underwater visual census (UVC) and controlled fishing were identified as suitable methods. UVC transects were found to be superior to point counts, in terms of sampling efficiency, variability, bias and required sample size. An effort of two angler hours per fishing station was shown to provide low catch variability, while at the same time a representative catch and low overall cost and required time. The methods were incorporated in a proposed sampling protocol, and evaluated. The methods were able to detect known differences between protected and exploited communities. It is recommended that LTM within protected areas, for detection of natural change, be focused on community-level indicators, while LTM in exploited areas, aimed at detection of anthropogenic change, be focused on species-level indicators. The proposed protocol with standardised methods will allow for comparisons across a network of LTM sites and provide the opportunity for a broad-scale assessment of the effects of environmental variables on reef fish stocks. The protocol developed in this study has application in other biogeographical regions in South Africa, and other parts of the world. Shift in the focus of much marine research, in South Africa and elsewhere, to LTM, highlights the relevance and timeous nature of this study.

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.

White steenbras Lithognathus lithognathus (Pisces: Sparidae) has been a major target species of numerous fisheries in South Africa, since the late 19th century. Historically, it contributed substantially to annual catches in commercial net fisheries, and became dominant in recreational shore catches in the latter half of the 20th century. However, overexploitation in both sectors resulted in severe declines in abundance. The ultimate collapse of the stock by the end of the last century, and the failure of traditional management measures to protect the species indicate that a new management approach for this species is necessary. The species was identified as a priority for research, management and conservation in a National Linefish Status Report. Despite knowledge on aspects of its biology and life history, little is known about juvenile habitat use patterns, home range dynamics and movement behaviour in estuaries. Similarly, the movement and migration of larger juveniles and adults in the marine environment are poorly understood. Furthermore, there is a complete lack of information on its genetic stock structure. Such information is essential for effective management of a fishery species. This thesis aimed to address the gaps in the understanding of white steenbras movement patterns and genetic stock structure, and provide an assessment of its current conservation status. The study adopted a multidisciplinary approach, incorporating a range of methods and drawing on available information, including published literature, unpublished reports and data from long-term monitoring programmes. Acoustic telemetry, conducted in a range of estuaries, showed high site fidelity, restricted area use, small home ranges relative to the size of the estuary, and a high level of residency within estuaries at the early juvenile life stage. Behaviour within estuaries was dominated by station-keeping, superimposed by a strong diel behaviour, presumably based on feeding and/or predator avoidance, with individuals entering the shallow littoral zone at night to feed, and seeking refuge in the deeper channel areas during the daytime. Conventional dart tagging and recapture data from four ongoing, long-term coastal fish tagging projects, spread throughout the distribution of this species, indicated high levels of residency in the surf zone at the late juvenile and sub-adult life stages. Consequently, juvenile and sub-adult white steenbras are vulnerable to localised depletion, although they can be effectively protected by suitably positioned estuarine protected areas (EPAs) and marine protected areas (MPAs), respectively. It has been hypothesized that adult white steenbras undertake large-scale coastal migrations between summer aggregation areas and winter spawning grounds. The scale of observed coastal movements was correlated with fish size (and age), with larger fish undertaking considerably longer-distance coastal movements than smaller individuals, supporting this hypothesis. Given the migratory behaviour of adults, and indications that limited spawning habitat exists, MPAs designed to protect white steenbras during the adult life stage should encompass all known spawning aggregation sites. The fishery is plagued by problems such as low compliance and low enforcement capacity, and alternative management measures, such as seasonal closure, need to be evaluated. Despite considerable conventional dart tagging effort around the coastline (5 782 fish tagged) with 292 recaptures there remains a lack of empirical evidence of fish migrating long distances (> 600 km) between aggregation and spawning areas. This uncertainty in the level of connectivity among coastal regions was addressed using mitochondrial DNA sequencing and genotyping of microsatellite repeat loci in the nuclear genome, which showed no evidence of major geographic barriers to gene flow in this species. Samples collected throughout the white steenbras core distribution showed high genetic diversity, low genetic differentiation and no evidence of isolation by distance or localised spawning. Although historically dominant in several fisheries, analysis of long-term commercial and recreational catch data for white steenbras indicated considerable declines and ultimately stock collapse. Improved catch-per-unit-effort in two large MPAs subsequent to closure confirmed that MPAs can be effective for the protection of white steenbras. However, the current MPA network encompasses a low proportion of sandy shoreline, for which white steenbras exhibits an affinity. Many MPAs do not prohibit recreational shore angling, which currently accounts for the greatest proportion of the total annual catch. Furthermore, EPAs within the juvenile distribution protect a negligible proportion of the total available surface area of estuaries – habitat on which white steenbras is wholly dependent. Despite some evidence of recent increases in abundance in estuaries and the surf zone in certain areas, white steenbras meets the criteria for “Endangered” on the IUCN Red List of Threatened Species, and for “Protected species” status on the National Environmental Management: Biodiversity Act of South Africa. The species requires improved management, with consideration for its life-history style, estuarine dependency, surf zone residency, predictable spawning migrations and its poor conservation status. The multidisciplinary approach provides valuable information towards an improved scientific basis for the management of white steenbras and a framework for research that can be adopted for other overexploited, estuarine-associated coastal fishery species.

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.

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.

The thesis was chosen on the basis of the continuation of the bachelor´s work. This thesis is focused on the literature search of problems of the conflicts between the protection of cormorants and the interest of fishery, further on the media analysis in the Czech Republic and finally on the processing of opinions of various groups of respondents (holidaymakers in the area called ´Třeboňsko´ and Czech fishermen). The opinions of questioned people were obtained from controlled interviews written down and processed in the questionnaires. The available information shows that a number of the protected cormorants is increasing not only in the Czech Republic but all over the world. The increase of the number of cormorant population causes problems especially to fishery, because cormorants cause the damage by catching fish stock. These conflicts in the problem area are mostly promoted in the media. In the problem area there are important opinions of the key groups of inhabitants. Groups of questioned people demonstrated their knowledge: holidaymakers in the area called ´Třeboňsko´ have basic knowledge in cormorants and problems caused by cormorants. On the contrary, fishermen are well-informed about the problem. The fishermen are more interested in the problem. Media are very important for solving conflicts and forming opinions of various groups of people. Media analysis showed that most spokesmen, who initiated writing newspaper articles were just fishermen. Therefore the articles on the cormorants are negative and without opinions on the spokesmen as member of general public or academics. Results of the sociological analysis have feed back on the results of the media analysis. It was found out that in the Czech Republic there had not been drawn up any management of fish protection againts cormorants. That is why I prefer to suggest the management in the near future. I recommend to follow the existing foreign management, forexample, in Great Britain. Further, I propose to change the Czech legislation for lower payment of the compensation for the damage caused by cormorants.