Adaptations in allopatric populations of Triakis megalopterus isolated by the Benguela Current: steps towards understanding evolutionary processes affecting regional biodiversity
- Authors: Soekoe, Michelle
- Date: 2016
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5389 , http://hdl.handle.net/10962/d1021264
- Description: This study was initiated to gain a better understanding of evolution and adaptation of elasmobranchs by investigating how a putative biogeographic barrier, the Benguela Current, had influenced populations of a demersal shark species, Triakis megalopterus. It was hypothesized that the Benguela Current formed a biogeographic barrier in the distribution of T. megalopterus and was responsible for the divergence between South African (SA) and Angolan (AN) populations. Since elasmobranchs are generally characterized by a slow rate of evolutionary change and conservative morphology and life history traits, it was hypothesized that there would be limited genetic, morphological and life history divergence between the populations. Both mtDNA Control Region (mtCR) and microsatellites (nDNA) were used to assess population connectivity and structure of T. megalopterus. The mtCR predominantly showed a northern (Angola, AN, and Namibia, NA) versus southern (Western Cape, WC, and Eastern Cape, EC) Benguela subsystem arrangement. This suggested that the formation of the Benguela Current had an influence on the genetic structure of T. megalopterus during the early Pleistocene. The nDNA, however, showed a distinct transoceanic, Atlantic (AN, NA, WC) versus Indian Ocean (EC) arrangement, and this was attributed to the more recent exposure of the Agulhas Bank and reduced rocky shore habitat during the glaciations of the late Pleistocene. Traditional morphological analyses on full body and tooth morphology were used to assess phenotypic plasticity and/or adaptability of T. megalopterus. A novel method of geometric morphology, with potential for non-lethal application, was developed and tested to examine interpopulation divergence in shape. Traditional morphometrics showed significant divergence between populations and this variation was congruous with the mtCR haplotypes. However, the divergence in the truss variables was not concomitant to the haplotypes and suggested that differences in shape may be attributed to phenotypic plasticity. There was limited divergence in the tooth morphology between populations. The divergence in several morphological characters associated with swimming speed and manoeuvrability may be attributed to both habitat structure and dominant prey in the different biogeographic zones. The diet of T. megalopterus consisted primarily of crustaceans, teleosts and molluscs. The significant variation in the diet between populations suggested a generalist tooth configuration and broad trophic adaptability. There was significant divergence in the interpopulation life history parameters. The AN population had the fastest growth, smallest size at maturity, and shortest longevity. Individuals in the EC population had the youngest age at maturity, while the WC population had the earliest parturition. This divergence may be attributed to the contrasting thermal regimes in the three biogeographic regions and the dissimilar exploitation rates of the three populations. The results of this thesis demonstrated that a combination of the formation of the Benguela Current and sea level change most likely contributed to vicariance of three populations of T. megalopterus. The significant interpopulation morphological and life history divergence appeared to be both phenotypic and genetic, and suggested that contrasting environmental drivers can result in relatively rapid change in elasmobranchs.
- Full Text:
- Date Issued: 2016
- Authors: Soekoe, Michelle
- Date: 2016
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5389 , http://hdl.handle.net/10962/d1021264
- Description: This study was initiated to gain a better understanding of evolution and adaptation of elasmobranchs by investigating how a putative biogeographic barrier, the Benguela Current, had influenced populations of a demersal shark species, Triakis megalopterus. It was hypothesized that the Benguela Current formed a biogeographic barrier in the distribution of T. megalopterus and was responsible for the divergence between South African (SA) and Angolan (AN) populations. Since elasmobranchs are generally characterized by a slow rate of evolutionary change and conservative morphology and life history traits, it was hypothesized that there would be limited genetic, morphological and life history divergence between the populations. Both mtDNA Control Region (mtCR) and microsatellites (nDNA) were used to assess population connectivity and structure of T. megalopterus. The mtCR predominantly showed a northern (Angola, AN, and Namibia, NA) versus southern (Western Cape, WC, and Eastern Cape, EC) Benguela subsystem arrangement. This suggested that the formation of the Benguela Current had an influence on the genetic structure of T. megalopterus during the early Pleistocene. The nDNA, however, showed a distinct transoceanic, Atlantic (AN, NA, WC) versus Indian Ocean (EC) arrangement, and this was attributed to the more recent exposure of the Agulhas Bank and reduced rocky shore habitat during the glaciations of the late Pleistocene. Traditional morphological analyses on full body and tooth morphology were used to assess phenotypic plasticity and/or adaptability of T. megalopterus. A novel method of geometric morphology, with potential for non-lethal application, was developed and tested to examine interpopulation divergence in shape. Traditional morphometrics showed significant divergence between populations and this variation was congruous with the mtCR haplotypes. However, the divergence in the truss variables was not concomitant to the haplotypes and suggested that differences in shape may be attributed to phenotypic plasticity. There was limited divergence in the tooth morphology between populations. The divergence in several morphological characters associated with swimming speed and manoeuvrability may be attributed to both habitat structure and dominant prey in the different biogeographic zones. The diet of T. megalopterus consisted primarily of crustaceans, teleosts and molluscs. The significant variation in the diet between populations suggested a generalist tooth configuration and broad trophic adaptability. There was significant divergence in the interpopulation life history parameters. The AN population had the fastest growth, smallest size at maturity, and shortest longevity. Individuals in the EC population had the youngest age at maturity, while the WC population had the earliest parturition. This divergence may be attributed to the contrasting thermal regimes in the three biogeographic regions and the dissimilar exploitation rates of the three populations. The results of this thesis demonstrated that a combination of the formation of the Benguela Current and sea level change most likely contributed to vicariance of three populations of T. megalopterus. The significant interpopulation morphological and life history divergence appeared to be both phenotypic and genetic, and suggested that contrasting environmental drivers can result in relatively rapid change in elasmobranchs.
- Full Text:
- Date Issued: 2016
An assessment of the invasion state and fisheries suitability in four dams and a natural lake in the Western Cape, South Africa
- Authors: Dredge, Brendon Neville
- Date: 2016
- Subjects: Introduced organisms Fishery management -- South Africa -- Western Cape Fishes -- Conservation -- South Africa -- Western Cape Introduced fishes -- South Africa -- Western Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/69114 , vital:29391
- Description: Despite more than a century of introductions, fish invasions are poorly understood in South Africa. This thesis aims to: (1) provide baseline information on the fish fauna in five inland water bodies (four dams: Theewaterskloof, Clanwilliam, Quaggaskloof, and Voelvlei and a natural lake, Groenvlei) in the Western Cape; (2) determine which species were established and provide a baseline of abundance and size structure for monitoring and, (3) make preliminary recommendations for a fishery. First, criteria for determining establishment were developed by undertaking a full biological assessment of bluegill Lepomis macrochirus, a data-poor species in South Africa. This included the assessment of growth rate using validated estimates of age derived from otoliths in two dams (Clanwilliam Dam: Lt=335.9(1−eo.113(t+1.06)); Groenvlei: Lt=287.2(1-e−0.171(t+0.54)). Length at 50% maturity was similar for males (146 mmFL) and females (147 mmFL). Length frequency analysis combined with data on the age and growth and reproduction demonstrated that established populations of bluegill contained several age cohorts as well as mature and juvenile fishes. A meta-analysis was conducted to: (1) compile a list of initial stocking dates for all alien fishes in each waterbody and (2) use angler tournament data to assess for additional species and persistence over time. Data from the meta-analysis was combined with ichthyological survey data to determine establishment success. These data demonstrated that nine non-native species had established in the five water bodies. Clanwilliam Dam had the largest number (7) of non-native species established, Groenvlei (5) and Theewaterskloof, Brandvlei and Voelvlei the lowest with four species. The state of invasion of each species in the province showed that all nine species are categorised as invasive. This information on establishment was then integrated into a framework for rapidly determining what type of fishery would be most suitable for the 5 waterbodies. Potential yield was estimated using morphoedaphic models, were 260 t/yr for Theewaterskloof Dam, 93 t/yr for Voelvlei, 81 t/yr for Brandvlei, 59 t/yr for Groenvlei and 55 t/yr for Groenvlei. The CPUE for Groenvlei was the highest in gill nets with 1.32 ± 1.94 kg/h, then Voelvlei 1.05 ± 1.34 kg/h followed by Brandvlei (0.84 ± 1.48 kg/h), Clanwilliam (0.71 ± 1.55 kg/h) and lastly Theewaterskloof (0.36 ± 0.41 kg/h). Only Theewaterskloof could produce in excess of 100 t/yr but less than 400 t/yr of fish making it suitable for a small scale fishery. The CPUE values of Theewaterskloof were the lowest and a gill net fishery on this water body may not produce sufficient fish for the fishery. All water bodies had a high recreational angling usage, the opening of a small scale fishery could be detrimental to this industry. Subsistence and recreational anglers should be promoted with the possibility of a long line industry targeting Clarias gariepinus.
- Full Text:
- Date Issued: 2016
- Authors: Dredge, Brendon Neville
- Date: 2016
- Subjects: Introduced organisms Fishery management -- South Africa -- Western Cape Fishes -- Conservation -- South Africa -- Western Cape Introduced fishes -- South Africa -- Western Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/69114 , vital:29391
- Description: Despite more than a century of introductions, fish invasions are poorly understood in South Africa. This thesis aims to: (1) provide baseline information on the fish fauna in five inland water bodies (four dams: Theewaterskloof, Clanwilliam, Quaggaskloof, and Voelvlei and a natural lake, Groenvlei) in the Western Cape; (2) determine which species were established and provide a baseline of abundance and size structure for monitoring and, (3) make preliminary recommendations for a fishery. First, criteria for determining establishment were developed by undertaking a full biological assessment of bluegill Lepomis macrochirus, a data-poor species in South Africa. This included the assessment of growth rate using validated estimates of age derived from otoliths in two dams (Clanwilliam Dam: Lt=335.9(1−eo.113(t+1.06)); Groenvlei: Lt=287.2(1-e−0.171(t+0.54)). Length at 50% maturity was similar for males (146 mmFL) and females (147 mmFL). Length frequency analysis combined with data on the age and growth and reproduction demonstrated that established populations of bluegill contained several age cohorts as well as mature and juvenile fishes. A meta-analysis was conducted to: (1) compile a list of initial stocking dates for all alien fishes in each waterbody and (2) use angler tournament data to assess for additional species and persistence over time. Data from the meta-analysis was combined with ichthyological survey data to determine establishment success. These data demonstrated that nine non-native species had established in the five water bodies. Clanwilliam Dam had the largest number (7) of non-native species established, Groenvlei (5) and Theewaterskloof, Brandvlei and Voelvlei the lowest with four species. The state of invasion of each species in the province showed that all nine species are categorised as invasive. This information on establishment was then integrated into a framework for rapidly determining what type of fishery would be most suitable for the 5 waterbodies. Potential yield was estimated using morphoedaphic models, were 260 t/yr for Theewaterskloof Dam, 93 t/yr for Voelvlei, 81 t/yr for Brandvlei, 59 t/yr for Groenvlei and 55 t/yr for Groenvlei. The CPUE for Groenvlei was the highest in gill nets with 1.32 ± 1.94 kg/h, then Voelvlei 1.05 ± 1.34 kg/h followed by Brandvlei (0.84 ± 1.48 kg/h), Clanwilliam (0.71 ± 1.55 kg/h) and lastly Theewaterskloof (0.36 ± 0.41 kg/h). Only Theewaterskloof could produce in excess of 100 t/yr but less than 400 t/yr of fish making it suitable for a small scale fishery. The CPUE values of Theewaterskloof were the lowest and a gill net fishery on this water body may not produce sufficient fish for the fishery. All water bodies had a high recreational angling usage, the opening of a small scale fishery could be detrimental to this industry. Subsistence and recreational anglers should be promoted with the possibility of a long line industry targeting Clarias gariepinus.
- Full Text:
- Date Issued: 2016
An assessment of the small-scale fisheries in the Kogelberg district of the Western Cape, South Africa
- Authors: Jordan, Tia
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/997 , vital:20011
- Description: Small-scale fisheries play a critical role in communities by contributing to food security, poverty alleviation and source of income. The study focused on the Kleinmond small-scale fishery and estimated the current economic value of the fishery as well as exploring the potential for increasing this and also whether it is being used in a way that ensures sustainable harvesting of the marine resources. It was important to evaluate the ecological, economic and social dimensions of the fishing community in order to address the problems currently facing the community. The study draws on previous research done in the Kleinmond area. Data were collected to update and complement previous research and addresses current research. In order to investigate the fisheries catch contribution in the area, data were obtained from the Department of Agriculture, Forestry and Fisheries. Three different questionnaires were developed and conducted in face-to-face formal and informal interviews with the various stakeholders (n=42) in the value-chain. Interviews were also conducted telephonically with other stakeholders and a focus group was formed to supplement previous available data. Simple economic models were developed for the fisheries working from the Kleinmond harbour, which were used to estimate the gross and net economic value of catches for individual right-holders, as well as the Kleinmond area as a whole. The economic models used in this study showed that the West Coast rock lobster Jasus lalandii, fishery was the primary source of income for small-scale fishers. This was due to the rock lobsters being sold to the export market as a high-valued commodity, whereas the linefish were sold to the local market as a lower-valued commodity. However, linefish were found to be more of a commodity to the community as a portion would be retained for personal consumption. The linefishers were concerned in that over the past couple of years, snoek Thrysites atun have been absent the Kleinmond area, resulting in and the fishing effort shifting to a resident species Cape bream Pachymetopon blochii. Whereas West Coast rock lobster were considered to be harvested sustainably under the current total allowable catch strategy, there was concern for the future of the fishery because of the occurrence of illegal fishing, both locally and nationally. Small-scale fisheries in the Kleinmond community are largely dependent on fishing resources, even though the industry is only marginally profitable. Future management measures should concentrate on optimising the value-chain to provide both sustainability for the resources and improve the livelihoods of the community.
- Full Text:
- Date Issued: 2016
- Authors: Jordan, Tia
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/997 , vital:20011
- Description: Small-scale fisheries play a critical role in communities by contributing to food security, poverty alleviation and source of income. The study focused on the Kleinmond small-scale fishery and estimated the current economic value of the fishery as well as exploring the potential for increasing this and also whether it is being used in a way that ensures sustainable harvesting of the marine resources. It was important to evaluate the ecological, economic and social dimensions of the fishing community in order to address the problems currently facing the community. The study draws on previous research done in the Kleinmond area. Data were collected to update and complement previous research and addresses current research. In order to investigate the fisheries catch contribution in the area, data were obtained from the Department of Agriculture, Forestry and Fisheries. Three different questionnaires were developed and conducted in face-to-face formal and informal interviews with the various stakeholders (n=42) in the value-chain. Interviews were also conducted telephonically with other stakeholders and a focus group was formed to supplement previous available data. Simple economic models were developed for the fisheries working from the Kleinmond harbour, which were used to estimate the gross and net economic value of catches for individual right-holders, as well as the Kleinmond area as a whole. The economic models used in this study showed that the West Coast rock lobster Jasus lalandii, fishery was the primary source of income for small-scale fishers. This was due to the rock lobsters being sold to the export market as a high-valued commodity, whereas the linefish were sold to the local market as a lower-valued commodity. However, linefish were found to be more of a commodity to the community as a portion would be retained for personal consumption. The linefishers were concerned in that over the past couple of years, snoek Thrysites atun have been absent the Kleinmond area, resulting in and the fishing effort shifting to a resident species Cape bream Pachymetopon blochii. Whereas West Coast rock lobster were considered to be harvested sustainably under the current total allowable catch strategy, there was concern for the future of the fishery because of the occurrence of illegal fishing, both locally and nationally. Small-scale fisheries in the Kleinmond community are largely dependent on fishing resources, even though the industry is only marginally profitable. Future management measures should concentrate on optimising the value-chain to provide both sustainability for the resources and improve the livelihoods of the community.
- Full Text:
- Date Issued: 2016
An evaluation of sampling and statistical methods for long-term monitoring of subtidal reef fishes : a case study of Tsitsikamma National Park marine protected area
- Authors: Parker, Denham
- Date: 2016
- Subjects: Reef fishes -- South Africa -- Monitoring , Tsitsikamma National Park (South Africa)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5385 , http://hdl.handle.net/10962/d1019991
- Description: Tsitsikamma National Park (TNP) possesses the oldest (established 1954), and one of the largest (350 km2) ‘no-take’ marine protected areas (MPA) in South Africa. A long-term monitoring (LTM) programme to observe the subtidal reef fishes in the TNP MPA was established in 2007. To date, 243 angling replicates have been completed, and a total of 2,751 fish belonging to 41 different species have been caught and released. In an era of unprecedented global biodiversity loss, data that can be used to monitor ecosystems and gauge changes in biodiversity through time are essential. This thesis aims to improve the methodological and statistical processes currently available for LTM of subtidal reef fish by providing an evaluation of the TNP MPA LTM programme. Angling data revealed definitive spatial structuring, in the form of spatial autocorrelation, and a shift in viewing spatial dependency as a statistical obstacle to a source of ecological information created a new avenue of data inference. Species-specific distribution maps identified localized habitat as the main predictor variable for species abundance, emphasizing the need for accurate a priori bathymetric information for subtidal monitoring. ‘Random forest’ analyses confirmed spatial variables are more important than temporal variables in predicting species abundance. The effectiveness of Generalized Linear Mixed Models (GAMMs) to account for spatial autocorrelation was highlighted, and evidence that disregarding spatial dependencies in temporal analyses can produce erroneous results was illustrated in the case of dageraad (Chrysoblephus cristiceps). Correlograms indicated that the current sampling strategy produced spatially redundant data and the sampling unit size (150 m2) could be doubled to optimize sampling. Temporal analyses demonstrated that after 50 years of ‘no take’ protection the TNP MPA ichthyofauna exhibits a high level of stability. Species-specific size structure was also found to be highly stable. Dageraad was the only species to exhibit a definitive temporal trend in their size structure, which was attributed to recruitment variation and the possibility that large individuals may migrate out of the study area. The inadequacy of angling as a method for monitoring a broad spectrum of the fish species was highlighted, particularly due to its selectivity towards large predators. As a result, a new sampling technique known as Stereo Baited Remote Underwater Videos (stereo-BRUVs) was introduced to the LTM programme in 2013. Stereo-BRUVs enabled sampling of 2640 fish belonging to 52 different species, from 57 samples collected in less than two years. A comparison of the sampling methods concluded that, compared to angling, stereo-BRUVs provide a superior technique that can survey a significantly larger proportion of the ichthyofauna with minimal length-selectivity biases. In addition, stereo-BRUVs possess a higher statistical power to detect changes in population abundance. However, a potential bias in the form of ‘hyperstability’ in sites with unusually high fish densities was identified as a possible flaw when using stereo-BRUVs. In an attempt to provide a more rigorous method evaluation, simulation testing was employed to assess the ability of angling and stereo-BRUVs to accurately describe a decreasing population. The advantage of this approach is that the simulated population abundances are known, so that each sampling method can be tested in terms of how well it tracks known abundance trends. The study established that stereo- BRUVs provided more accurate data when describing a distinct population decline of roman (Chrysoblephus laticeps) over 10- and 20-year periods. In addition, spawner-biomass was found to be a more accurate population estimate than relative abundance estimates (CPUE and MaxN) due to the inclusion of population size structure information, highlighting the importance of length-frequency data. The study illustrated that an evaluation framework that utilizes simulation testing has the potential to optimize LTM sampling procedures by addressing a number of methodological questions. This includes developing a procedure that aligns data collected from different sampling methods by applying correction factors, thus ensuring LTM programmes are able to adapt sampling strategies without losing data continuity.
- Full Text:
- Date Issued: 2016
- Authors: Parker, Denham
- Date: 2016
- Subjects: Reef fishes -- South Africa -- Monitoring , Tsitsikamma National Park (South Africa)
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5385 , http://hdl.handle.net/10962/d1019991
- Description: Tsitsikamma National Park (TNP) possesses the oldest (established 1954), and one of the largest (350 km2) ‘no-take’ marine protected areas (MPA) in South Africa. A long-term monitoring (LTM) programme to observe the subtidal reef fishes in the TNP MPA was established in 2007. To date, 243 angling replicates have been completed, and a total of 2,751 fish belonging to 41 different species have been caught and released. In an era of unprecedented global biodiversity loss, data that can be used to monitor ecosystems and gauge changes in biodiversity through time are essential. This thesis aims to improve the methodological and statistical processes currently available for LTM of subtidal reef fish by providing an evaluation of the TNP MPA LTM programme. Angling data revealed definitive spatial structuring, in the form of spatial autocorrelation, and a shift in viewing spatial dependency as a statistical obstacle to a source of ecological information created a new avenue of data inference. Species-specific distribution maps identified localized habitat as the main predictor variable for species abundance, emphasizing the need for accurate a priori bathymetric information for subtidal monitoring. ‘Random forest’ analyses confirmed spatial variables are more important than temporal variables in predicting species abundance. The effectiveness of Generalized Linear Mixed Models (GAMMs) to account for spatial autocorrelation was highlighted, and evidence that disregarding spatial dependencies in temporal analyses can produce erroneous results was illustrated in the case of dageraad (Chrysoblephus cristiceps). Correlograms indicated that the current sampling strategy produced spatially redundant data and the sampling unit size (150 m2) could be doubled to optimize sampling. Temporal analyses demonstrated that after 50 years of ‘no take’ protection the TNP MPA ichthyofauna exhibits a high level of stability. Species-specific size structure was also found to be highly stable. Dageraad was the only species to exhibit a definitive temporal trend in their size structure, which was attributed to recruitment variation and the possibility that large individuals may migrate out of the study area. The inadequacy of angling as a method for monitoring a broad spectrum of the fish species was highlighted, particularly due to its selectivity towards large predators. As a result, a new sampling technique known as Stereo Baited Remote Underwater Videos (stereo-BRUVs) was introduced to the LTM programme in 2013. Stereo-BRUVs enabled sampling of 2640 fish belonging to 52 different species, from 57 samples collected in less than two years. A comparison of the sampling methods concluded that, compared to angling, stereo-BRUVs provide a superior technique that can survey a significantly larger proportion of the ichthyofauna with minimal length-selectivity biases. In addition, stereo-BRUVs possess a higher statistical power to detect changes in population abundance. However, a potential bias in the form of ‘hyperstability’ in sites with unusually high fish densities was identified as a possible flaw when using stereo-BRUVs. In an attempt to provide a more rigorous method evaluation, simulation testing was employed to assess the ability of angling and stereo-BRUVs to accurately describe a decreasing population. The advantage of this approach is that the simulated population abundances are known, so that each sampling method can be tested in terms of how well it tracks known abundance trends. The study established that stereo- BRUVs provided more accurate data when describing a distinct population decline of roman (Chrysoblephus laticeps) over 10- and 20-year periods. In addition, spawner-biomass was found to be a more accurate population estimate than relative abundance estimates (CPUE and MaxN) due to the inclusion of population size structure information, highlighting the importance of length-frequency data. The study illustrated that an evaluation framework that utilizes simulation testing has the potential to optimize LTM sampling procedures by addressing a number of methodological questions. This includes developing a procedure that aligns data collected from different sampling methods by applying correction factors, thus ensuring LTM programmes are able to adapt sampling strategies without losing data continuity.
- Full Text:
- Date Issued: 2016
Biology and ecology of Glossogobius callidus (Smith 1937) in irrigation impoundments in the Sundays River Valley of the Eastern Cape
- Authors: Mofu, Lubabalo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1136 , vital:20023
- Description: The River Goby Glossogobius callidus (Smith, 1937) is a native abundant fish in both freshwater and estuarine habitats in the Cape Fold Ecoregion, yet little information is available on its life-history. This study aims to contribute to knowledge on the age and growth, reproductive biology and the diet and feeding habits of G. callidus in irrigation impoundments. Glossogobius callidus was sampled monthly from August 2013 till March 2015; from the irrigation ponds in the Sundays River Valley, Eastern Cape Province, South Africa. To determine sex, gonads were visually assessed under a dissecting microscope to confirm the sex based on the shape of the urogenital papillae. Fish were then dissected to confirm sex and gonads were categorised into five macroscopic stages which were histologically validated. Microscopic stages of gonadal development were discerned based on nuclear and cytoplasmic characteristics of the oocyte or sperm. Ovaries and sperms were assigned stages based on the most advanced type of oocyte present. In total 2054 fishes ranging in length from 21.1 mm to 137.2 mm TL were sampled. The sex ratio (1.1 males: 1 females) did not differ from unity (x2 = 0.027, df = 1, p = 0.87). Length at 50% maturity (Lm) was 70 mm TL females and 72 mm TL for males. Spawning season was mid-spring and mid-summer and mean ± S.D absolute fecundity was estimated at 1028.2 ± 131.7 ova/fish. Relative fecundity (number of vitellogenic oocytes per gram of eviscerated fish mass) were estimated at 50 ± 18 ova/fish gram. Otoliths from 560 fish were used for ageing. Growth zone deposition rate was validated using edge analysis. As a unimodal periodic regression model best described the temporal proportion of opaque zone deposition on the edge of otoliths over a one-year period, growth zone deposition rate was validated as annual. The oldest female fish was a 4-year old 84.4 mm TL fish and the oldest male was a 7-year old 100.5 mm TL fish. The length-at-age for the entire population of 560 G. callidus provided von Bertalanffy parameters of Lt = 92 (1 - e -0.58(t + 0.4)) mm TL for the entire population, Lt = 70 (1 - e -1.8 (t + 0.06)) mm TL for males and Lt = 65 (1 - e -1.8 (t + 0.05)) mm TL for females. Converting length at maturity to age at maturity demonstrated that G. callidus attained maturity at an age of 2-years. Growth performance described using the phi-prime index showed that G. callidus had lower growth performance compared to the invasive Neogobius melanostomus. Using age structure, natural mortality was estimated at 1.31 yr-1 using catch curve analysis. Diet of G. callidus comprised of ten taxonomic groups. Among these, aquatic invertebrates were the most diverse group but while relative contribution of the dietary components varied across all size classes and seasons, the key prey items were consistently found in all size classes. These were Diptera, Hemiptera, Trichoptera, Odonata, Cladocera, Copepoda, Hydracarina, Amphipoda, Crustacea, and Mollusca. While dietary differences were observed between the size classes and throughout the seasons, G. callidus can be regarded as a generalist feeder preying on an array of different species. Given its abundance and diet, I suggest that G. callidus contribute considerably to the invertebrate predation pressure in these artificial aquatic environments in an arid region. In summary, medium fecundity, fast growth, moderate maturity, and a generalist feeding behaviour demonstrate that G. callidus is an equilibrium life strategist. In comparison with other species, the life-history traits of G. callidus from irrigation impoundments resemble those of other freshwater goby species, some of which are global invaders.
- Full Text:
- Date Issued: 2016
- Authors: Mofu, Lubabalo
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1136 , vital:20023
- Description: The River Goby Glossogobius callidus (Smith, 1937) is a native abundant fish in both freshwater and estuarine habitats in the Cape Fold Ecoregion, yet little information is available on its life-history. This study aims to contribute to knowledge on the age and growth, reproductive biology and the diet and feeding habits of G. callidus in irrigation impoundments. Glossogobius callidus was sampled monthly from August 2013 till March 2015; from the irrigation ponds in the Sundays River Valley, Eastern Cape Province, South Africa. To determine sex, gonads were visually assessed under a dissecting microscope to confirm the sex based on the shape of the urogenital papillae. Fish were then dissected to confirm sex and gonads were categorised into five macroscopic stages which were histologically validated. Microscopic stages of gonadal development were discerned based on nuclear and cytoplasmic characteristics of the oocyte or sperm. Ovaries and sperms were assigned stages based on the most advanced type of oocyte present. In total 2054 fishes ranging in length from 21.1 mm to 137.2 mm TL were sampled. The sex ratio (1.1 males: 1 females) did not differ from unity (x2 = 0.027, df = 1, p = 0.87). Length at 50% maturity (Lm) was 70 mm TL females and 72 mm TL for males. Spawning season was mid-spring and mid-summer and mean ± S.D absolute fecundity was estimated at 1028.2 ± 131.7 ova/fish. Relative fecundity (number of vitellogenic oocytes per gram of eviscerated fish mass) were estimated at 50 ± 18 ova/fish gram. Otoliths from 560 fish were used for ageing. Growth zone deposition rate was validated using edge analysis. As a unimodal periodic regression model best described the temporal proportion of opaque zone deposition on the edge of otoliths over a one-year period, growth zone deposition rate was validated as annual. The oldest female fish was a 4-year old 84.4 mm TL fish and the oldest male was a 7-year old 100.5 mm TL fish. The length-at-age for the entire population of 560 G. callidus provided von Bertalanffy parameters of Lt = 92 (1 - e -0.58(t + 0.4)) mm TL for the entire population, Lt = 70 (1 - e -1.8 (t + 0.06)) mm TL for males and Lt = 65 (1 - e -1.8 (t + 0.05)) mm TL for females. Converting length at maturity to age at maturity demonstrated that G. callidus attained maturity at an age of 2-years. Growth performance described using the phi-prime index showed that G. callidus had lower growth performance compared to the invasive Neogobius melanostomus. Using age structure, natural mortality was estimated at 1.31 yr-1 using catch curve analysis. Diet of G. callidus comprised of ten taxonomic groups. Among these, aquatic invertebrates were the most diverse group but while relative contribution of the dietary components varied across all size classes and seasons, the key prey items were consistently found in all size classes. These were Diptera, Hemiptera, Trichoptera, Odonata, Cladocera, Copepoda, Hydracarina, Amphipoda, Crustacea, and Mollusca. While dietary differences were observed between the size classes and throughout the seasons, G. callidus can be regarded as a generalist feeder preying on an array of different species. Given its abundance and diet, I suggest that G. callidus contribute considerably to the invertebrate predation pressure in these artificial aquatic environments in an arid region. In summary, medium fecundity, fast growth, moderate maturity, and a generalist feeding behaviour demonstrate that G. callidus is an equilibrium life strategist. In comparison with other species, the life-history traits of G. callidus from irrigation impoundments resemble those of other freshwater goby species, some of which are global invaders.
- Full Text:
- Date Issued: 2016
Effect of lipid inclusion levels in aquafeed on carcass composition, quality change during storage and nutrient excretion in dusky kob (Argyrosomus japonicus)
- Authors: Ginindza, Nhlanhla Joseph
- Date: 2016
- Subjects: Aquaculture
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5387 , http://hdl.handle.net/10962/d1020854
- Description: Dusky kob, Argyrosomus japonicus, is an aquaculture species in South Africa that is in pilot commercial production. While the major nutrient requirements of the species are known, the advantages of incorporating formulated feeds into the diet of the species has yet to be fully explored. Research on formulated feed composition is required to: minimise input costs; improve the organoleptic properties and meat quality; and minimise nutrient loss, which contributes to environmental pollution. This study sought to test the impact of different lipid levels in aquafeeds fed to dusky kob juveniles by determining: (i) growth performance, feeding efficiency, proximate and fatty acid composition; (ii) chemical changes and shelf-life of refrigerated fish fillets; and (iii) metabolic rates and nitrogen excretion of juvenile dusky kob. And more...
- Full Text:
- Date Issued: 2016
- Authors: Ginindza, Nhlanhla Joseph
- Date: 2016
- Subjects: Aquaculture
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5387 , http://hdl.handle.net/10962/d1020854
- Description: Dusky kob, Argyrosomus japonicus, is an aquaculture species in South Africa that is in pilot commercial production. While the major nutrient requirements of the species are known, the advantages of incorporating formulated feeds into the diet of the species has yet to be fully explored. Research on formulated feed composition is required to: minimise input costs; improve the organoleptic properties and meat quality; and minimise nutrient loss, which contributes to environmental pollution. This study sought to test the impact of different lipid levels in aquafeeds fed to dusky kob juveniles by determining: (i) growth performance, feeding efficiency, proximate and fatty acid composition; (ii) chemical changes and shelf-life of refrigerated fish fillets; and (iii) metabolic rates and nitrogen excretion of juvenile dusky kob. And more...
- Full Text:
- Date Issued: 2016
Genetic structure and biogeography of three wrasse species (Labridae) within the Western Indian Ocean
- Authors: Mayekiso, Sisanda
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1114 , vital:20021
- Description: The biogeography of wrasses within the Western Indian Ocean (WIO) is poorly understood, with regard to origins and genetic differentiation or connectivity among the regions of the WIO. This region is a good model for studying the influence of physical complexities and biogeographic breaks in shaping patterns of differentiation in wrasses. Three reef-associated fish species, Cheilio inermis, Thalassoma hebraicum and T. lunare, were selected to examine the factors that have influenced patterns of differentiation across the WIO. Each species was sampled from various localities of the WIO, the Red Sea and Indo-West Pacific Islands. Sequence data were generated from two mitochondrial gene fragments (cytochrome b and ATPase 6) and one nuclear locus (the first intron of the ribosomal protein S7 gene). Genetic analyses were used to calculate genetic diversity indices within species, which were then compared among species. The relationships among haplotypes and alleles were constructed using median-joining networks. Where necessary, neighbour-joining trees (NJ) were constructed to examine relationships among haplotypes and alleles for the Thalassoma species. Population structure was analysed using AMOVA and pairwise ФST to compare and calculate differentiation between the WIO localities. Mismatch distributions were used to examine population growth and decline or stability, and demographic parameters were used to calculate time of population expansion. There was high haplotype (h = 0.88 to 0.98) and low nucleotide diversities (π = 0.003 to 0.008) among all species for mitochondrial markers. For S7 intron I, high allelic (A = 0.95 to 0.98) and low nucleotide diversities (π = 0.002 to 0.014) were observed for all species. The pairwise ФST values revealed little to great (ФST = -0.02 to 0.67) genetic differentiation between localities, across all species for the three gene regions. The pairwise comparisons indicated the differentiation in C. inermis of Tanzania and Kenya from Mozambique and Nosy Be (Madagascar). The widespread C. inermis also revealed the differentiation of Kenya and Tanzania. For C. inermis, the AMOVAs of ATPase 6 and cytochrome b data indicated high differentiation among defined locality groups. The groups were defined according to geographic proximity. However, the AMOVA of the nuclear gene (S7 intron I) did not find variation among defined locality groups. Cheilio inermis revealed a sequence divergence of 0.4%. The divergence that was found in C. inermis was not enough to suggest a cryptic species within the WIO. Overall, the widespread and monotypic C. inermis revealed genetic differentiation within the WIO. Thalassoma hebraicum generally revealed little genetic differentiation across the WIO. The AMOVAs of the three gene regions showed no variation among specimens of the defined locality groups. However, some differentiation was found between localities. The pairwise comparisons of T. hebraicum revealed the differentiation of Seychelles from the African mainland and Madagascar. Southern Africa was observed to be differentiated from Nosy Be and Zanzibar. The observed differentiation could be caused by oceanic barriers such as the South Equatorial Current (SEQC), East African Coastal Current (EACC), and the Comoros Gyres and eddies in the Mozambique Channel, and Agulhas Current. Thalassoma lunare revealed genetic isolation between the WIO and the Red Sea as well as within the WIO. The genetic isolation between the WIO and the Red Sea is probably due to the historical isolation by the Bab al Mandab and contemporary barriers such as the cold upwelling cells in Somalia. The differentiation of Maldives from the African mainland and Seychelles could be due to distance and the upwelling cells created by monsoon winds. Mismatch distributions suggested that C. inermis and T. hebraicum had undergone demographic expansion during the Pleistocene (92 678 to 40 219 years ago). The results of the current study are similar to those from previous studies of WIO reef fish species, and the results of the present study could have potential implications for conservation and fisheries management. Single genetic markers and single species studies do not detect all barriers to dispersal in the WIO, thus they are insufficient to inform conservation management. Thus, the use of multispecies and genetic markers in the current study can be adopted by other studies of the marine taxa of the WIO.
- Full Text:
- Date Issued: 2016
- Authors: Mayekiso, Sisanda
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1114 , vital:20021
- Description: The biogeography of wrasses within the Western Indian Ocean (WIO) is poorly understood, with regard to origins and genetic differentiation or connectivity among the regions of the WIO. This region is a good model for studying the influence of physical complexities and biogeographic breaks in shaping patterns of differentiation in wrasses. Three reef-associated fish species, Cheilio inermis, Thalassoma hebraicum and T. lunare, were selected to examine the factors that have influenced patterns of differentiation across the WIO. Each species was sampled from various localities of the WIO, the Red Sea and Indo-West Pacific Islands. Sequence data were generated from two mitochondrial gene fragments (cytochrome b and ATPase 6) and one nuclear locus (the first intron of the ribosomal protein S7 gene). Genetic analyses were used to calculate genetic diversity indices within species, which were then compared among species. The relationships among haplotypes and alleles were constructed using median-joining networks. Where necessary, neighbour-joining trees (NJ) were constructed to examine relationships among haplotypes and alleles for the Thalassoma species. Population structure was analysed using AMOVA and pairwise ФST to compare and calculate differentiation between the WIO localities. Mismatch distributions were used to examine population growth and decline or stability, and demographic parameters were used to calculate time of population expansion. There was high haplotype (h = 0.88 to 0.98) and low nucleotide diversities (π = 0.003 to 0.008) among all species for mitochondrial markers. For S7 intron I, high allelic (A = 0.95 to 0.98) and low nucleotide diversities (π = 0.002 to 0.014) were observed for all species. The pairwise ФST values revealed little to great (ФST = -0.02 to 0.67) genetic differentiation between localities, across all species for the three gene regions. The pairwise comparisons indicated the differentiation in C. inermis of Tanzania and Kenya from Mozambique and Nosy Be (Madagascar). The widespread C. inermis also revealed the differentiation of Kenya and Tanzania. For C. inermis, the AMOVAs of ATPase 6 and cytochrome b data indicated high differentiation among defined locality groups. The groups were defined according to geographic proximity. However, the AMOVA of the nuclear gene (S7 intron I) did not find variation among defined locality groups. Cheilio inermis revealed a sequence divergence of 0.4%. The divergence that was found in C. inermis was not enough to suggest a cryptic species within the WIO. Overall, the widespread and monotypic C. inermis revealed genetic differentiation within the WIO. Thalassoma hebraicum generally revealed little genetic differentiation across the WIO. The AMOVAs of the three gene regions showed no variation among specimens of the defined locality groups. However, some differentiation was found between localities. The pairwise comparisons of T. hebraicum revealed the differentiation of Seychelles from the African mainland and Madagascar. Southern Africa was observed to be differentiated from Nosy Be and Zanzibar. The observed differentiation could be caused by oceanic barriers such as the South Equatorial Current (SEQC), East African Coastal Current (EACC), and the Comoros Gyres and eddies in the Mozambique Channel, and Agulhas Current. Thalassoma lunare revealed genetic isolation between the WIO and the Red Sea as well as within the WIO. The genetic isolation between the WIO and the Red Sea is probably due to the historical isolation by the Bab al Mandab and contemporary barriers such as the cold upwelling cells in Somalia. The differentiation of Maldives from the African mainland and Seychelles could be due to distance and the upwelling cells created by monsoon winds. Mismatch distributions suggested that C. inermis and T. hebraicum had undergone demographic expansion during the Pleistocene (92 678 to 40 219 years ago). The results of the current study are similar to those from previous studies of WIO reef fish species, and the results of the present study could have potential implications for conservation and fisheries management. Single genetic markers and single species studies do not detect all barriers to dispersal in the WIO, thus they are insufficient to inform conservation management. Thus, the use of multispecies and genetic markers in the current study can be adopted by other studies of the marine taxa of the WIO.
- Full Text:
- Date Issued: 2016
Mesopredator release and the effectiveness of camera traps for estimating mammal abundances in the Eastern Cape, South Africa
- Authors: Taylor, Jonathan Michael
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3587 , vital:20527
- Description: Remotely operated cameras (camera traps) have become an indispensable tool for many ecologists, particularly those studying rare and elusive animals. A plethora of camera trap makes and models are now commercially available, yet the effects of their varying design features on the quality and quantity of data recorded remains principally unknown. Better understanding of differing camera trap designs is needed before adequate management policies can be implemented, especially when the aim is to protect vulnerable and endangered species such as many carnivores. Habitat loss and human conflict has prompted worldwide declines of apex predator populations. Following this, many smaller predators have undergone population ‘explosions’ due to the lack of top-down forcing, a phenomenon known as mesopredator release. Land use changes in the Eastern Cape of South Africa have caused extensive degradation and fragmentation of the Subtropical Thicket Biome. In addition, coupled with anthropogenic persecution, apex predators including lions (Panthera leo), leopards (P. pardus), and brown hyaenas (Hyaena brunnea) have been extirpated from large areas of their historic range. Removal of these apex predators may provide opportunity for mesopredators, such as black-backed jackals (Canis mesomelas) and caracals (Caracal caracal), to be released from top-down forcing and possibly initiate trophic cascade effects. Therefore, using randomly distributed camera traps, my study aimed to explore the quality and quantity of data collected by different camera trap designs, and to investigate the mesopredator release hypothesis in the Eastern Cape of South Africa. A total of 2,989 trap nights was used to compare camera trap designs. Camera traps with narrow detection zones and fast trigger speeds (≤ 0.25 seconds) recorded a higher diversity of carnivores, but there was no significant difference in the relative abundances of carnivore species recorded by different camera trap models. A total of 19,659 trap nights was used to assess mesopredator relative abundance, occupancy, distribution and daily activity patterns at one site with, and one site without, apex predators. Consistent with the mesopredator release hypothesis, black-backed jackal relative abundance was significantly higher in the absence of apex predators, and this was supported by occupancy analyses. Further, black-backed jackal distribution was significantly concentrated in areas where apex predator activity was low, possibly indicating spatial avoidance. There was no significant difference in caracal relative abundance, occupancy, distribution, or daily activity between sites. These results provide the first indication of mesopredator release of blackbacked jackals in the Eastern Cape. The implications of black-backed jackal release including prey population structure, local extinctions, altered seed dispersal and disease dynamics are discussed.
- Full Text:
- Date Issued: 2016
- Authors: Taylor, Jonathan Michael
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3587 , vital:20527
- Description: Remotely operated cameras (camera traps) have become an indispensable tool for many ecologists, particularly those studying rare and elusive animals. A plethora of camera trap makes and models are now commercially available, yet the effects of their varying design features on the quality and quantity of data recorded remains principally unknown. Better understanding of differing camera trap designs is needed before adequate management policies can be implemented, especially when the aim is to protect vulnerable and endangered species such as many carnivores. Habitat loss and human conflict has prompted worldwide declines of apex predator populations. Following this, many smaller predators have undergone population ‘explosions’ due to the lack of top-down forcing, a phenomenon known as mesopredator release. Land use changes in the Eastern Cape of South Africa have caused extensive degradation and fragmentation of the Subtropical Thicket Biome. In addition, coupled with anthropogenic persecution, apex predators including lions (Panthera leo), leopards (P. pardus), and brown hyaenas (Hyaena brunnea) have been extirpated from large areas of their historic range. Removal of these apex predators may provide opportunity for mesopredators, such as black-backed jackals (Canis mesomelas) and caracals (Caracal caracal), to be released from top-down forcing and possibly initiate trophic cascade effects. Therefore, using randomly distributed camera traps, my study aimed to explore the quality and quantity of data collected by different camera trap designs, and to investigate the mesopredator release hypothesis in the Eastern Cape of South Africa. A total of 2,989 trap nights was used to compare camera trap designs. Camera traps with narrow detection zones and fast trigger speeds (≤ 0.25 seconds) recorded a higher diversity of carnivores, but there was no significant difference in the relative abundances of carnivore species recorded by different camera trap models. A total of 19,659 trap nights was used to assess mesopredator relative abundance, occupancy, distribution and daily activity patterns at one site with, and one site without, apex predators. Consistent with the mesopredator release hypothesis, black-backed jackal relative abundance was significantly higher in the absence of apex predators, and this was supported by occupancy analyses. Further, black-backed jackal distribution was significantly concentrated in areas where apex predator activity was low, possibly indicating spatial avoidance. There was no significant difference in caracal relative abundance, occupancy, distribution, or daily activity between sites. These results provide the first indication of mesopredator release of blackbacked jackals in the Eastern Cape. The implications of black-backed jackal release including prey population structure, local extinctions, altered seed dispersal and disease dynamics are discussed.
- Full Text:
- Date Issued: 2016
Movement patterns of Cape stumpnose, Rhabdosargus holubi (Sparidae), in the Kowie Estuary, South Africa
- Authors: Grant, Gareth Neil
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/982 , vital:20010
- Description: Rhabdosargus holubi is an ubiquitous estuary-dependent fishery species endemic to southern Africa. Although aspects of its recruitment dynamics from sea to estuary have received considerable research attention, little is known about its movement behaviour within estuarine systems. Fishery surveys have also revealed that R. holubi is a dominant species in catches within several temperate estuaries in South Africa. Therefore, investigating movement behaviour is fundamental to understanding the ecology of this species and providing a means for implementing effective fisheries management strategies. This study made use of passive acoustic telemetry to quantify the movement patterns of juvenile R. holubi in the Kowie Estuary, in the Eastern Cape Province of South Africa. Previous studies have revealed that surgically implanted transmitters may have adverse effects on the physiology and behaviour of tagged fish. Therefore, due to the small size of juvenile R. holubi, an a priori transmitter-effect experiment was undertaken. This experiment revealed that juvenile R. holubi (146-217 mm fork length) were not adversely affected by the surgical implantation of acoustic transmitters (7 mm Ø, 1.6 g out of water) and hence acoustic telemetry was well suited to monitoring the movements of this species. A 4-month telemetry study evaluated the movement patterns of 21 juveniles (140-190 mm fork length) tagged in three equal batches along the length of the estuary. Specific aspects of their movement included space use patterns, habitat connectivity, and the influences of geophysical cycles and environmental variables. Tagged fish exhibited high residency, which varied between each release site area. The mean length of estuary used was greater for the upper batch (15.65 ± 6.49 km) than the middle and lower batches (7.36 ± 3.68 and 2.67 ± 2 km, respectively). In terms of habitat connectivity, once the tagged fish left the estuary, they generally did not return. Tagged R. holubi spent the majority (83%) of their monitoring periods within the estuarine environment, with the sea (16%) and riverine (1%) environments being utilised to a lesser extent. Diel and tidal cycles influenced the movement patterns of juvenile R. holubi. However, the high levels of residency meant that fine-scale movements were difficult to detect due to the acoustic receiver deployment configuration (i.e. receivers moored one kilometer apart). The influence of environmental variables on the movement of individuals, modelled with general linear mixed models (GLMMs), revealed that the effects of river inflow and water temperature were greatest. Increased river inflow caused individuals to use larger portions of the estuary. Increased water temperature, particularly river temperature, caused individuals to shift their distributions downstream (towards the mouth of the estuary). This study highlighted the importance of estuarine nursery habitats to R. holubi, suggesting that a loss or reduction of healthy estuarine habitats may lead to significant declines in the abundance of this species. Furthermore, extreme resident behaviour suggests that no-take area closures (estuarine protected areas) would be an effective management strategy for this important fishery species.
- Full Text:
- Date Issued: 2016
- Authors: Grant, Gareth Neil
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/982 , vital:20010
- Description: Rhabdosargus holubi is an ubiquitous estuary-dependent fishery species endemic to southern Africa. Although aspects of its recruitment dynamics from sea to estuary have received considerable research attention, little is known about its movement behaviour within estuarine systems. Fishery surveys have also revealed that R. holubi is a dominant species in catches within several temperate estuaries in South Africa. Therefore, investigating movement behaviour is fundamental to understanding the ecology of this species and providing a means for implementing effective fisheries management strategies. This study made use of passive acoustic telemetry to quantify the movement patterns of juvenile R. holubi in the Kowie Estuary, in the Eastern Cape Province of South Africa. Previous studies have revealed that surgically implanted transmitters may have adverse effects on the physiology and behaviour of tagged fish. Therefore, due to the small size of juvenile R. holubi, an a priori transmitter-effect experiment was undertaken. This experiment revealed that juvenile R. holubi (146-217 mm fork length) were not adversely affected by the surgical implantation of acoustic transmitters (7 mm Ø, 1.6 g out of water) and hence acoustic telemetry was well suited to monitoring the movements of this species. A 4-month telemetry study evaluated the movement patterns of 21 juveniles (140-190 mm fork length) tagged in three equal batches along the length of the estuary. Specific aspects of their movement included space use patterns, habitat connectivity, and the influences of geophysical cycles and environmental variables. Tagged fish exhibited high residency, which varied between each release site area. The mean length of estuary used was greater for the upper batch (15.65 ± 6.49 km) than the middle and lower batches (7.36 ± 3.68 and 2.67 ± 2 km, respectively). In terms of habitat connectivity, once the tagged fish left the estuary, they generally did not return. Tagged R. holubi spent the majority (83%) of their monitoring periods within the estuarine environment, with the sea (16%) and riverine (1%) environments being utilised to a lesser extent. Diel and tidal cycles influenced the movement patterns of juvenile R. holubi. However, the high levels of residency meant that fine-scale movements were difficult to detect due to the acoustic receiver deployment configuration (i.e. receivers moored one kilometer apart). The influence of environmental variables on the movement of individuals, modelled with general linear mixed models (GLMMs), revealed that the effects of river inflow and water temperature were greatest. Increased river inflow caused individuals to use larger portions of the estuary. Increased water temperature, particularly river temperature, caused individuals to shift their distributions downstream (towards the mouth of the estuary). This study highlighted the importance of estuarine nursery habitats to R. holubi, suggesting that a loss or reduction of healthy estuarine habitats may lead to significant declines in the abundance of this species. Furthermore, extreme resident behaviour suggests that no-take area closures (estuarine protected areas) would be an effective management strategy for this important fishery species.
- Full Text:
- Date Issued: 2016
The effect of kelp supplementation in formulated feed on the production performance and gut microbiota of South African abalone (Haliotis midae)
- Authors: Nel, Aldi
- Date: 2016
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/899 , vital:20001
- Description: Formulated feeds with a relatively low (< 5 % of dry mass) kelp (Ecklonia maxima) inclusion level are widely used on commercial abalone (Haliotis midae) farms in South Africa. Although the use of kelp, a major constituent of the natural diet of H. midae, as a dietary supplement is considered to enhance abalone growth and feed utilisation, there are no published studies which quantify the effects of kelp inclusion in formulated feeds. Furthermore, the physiological mechanisms by which kelp supplementation may positively influence abalone digestive physiology and growth are largely unknown. As the kelp supplement is comprised mostly of soluble fibres and abalone gut bacteria associated with macroalgae (and its fibrous polysaccharides) are known to play a key role in digestion, it was hypothesised that the kelp supplement influences the gut-bacterial community profiles of cultured abalone through prebiotic and other metabolic effects. The present thesis thus examined the effect of kelp supplementation on the performance of abalone (Haliotis midae) fed formulated feeds and explored the influence of a kelp supplement on the abalone gut microbiota and its function in the gastrointestinal tract. The key hypotheses of the study were that kelp supplementation in formulated feed: 1) enhances abalone growth; 2) causes a shift in abalone gut-bacterial community composition through a prebiotic-like effect; 3) may induce changes in crop morphology as a result of potential bacterial-associated increases in volatile short-chain fatty acids, and 4) alters digestive enzyme activities in the abalone gut through changes in bacterial-derived (exogenous) digestive enzymes. The growth-promoting efficacy of low-level kelp supplementation was tested by feeding isonitrogenous and isoenergetic experimental feeds containing 0.00 – 3.54 % kelp (dry mass) to sub-adult abalone (~43 mm shell length) for eight months under commercial farm conditions. The growth trial established that kelp supplementation (0.44 – 3.54 % of dry mass) promoted faster growth and improved feed conversion and protein efficiency ratios in cultured abalone compared to abalone fed the non-supplemented control diet, while there were no significant differences in growth for abalone fed the different kelp-supplemented diets (0.44, 0.88, 1.76 and 3.54 % of dry mass). Feed conversion and protein efficiency ratios displayed significant correlations with kelp level in the range of 0.00 – 3.54 % dry mass, and it is therefore recommended that kelp be included in the formulated feeds of cultured South African abalone at a rate of up to 3.54 % of dry mass. A kelp-supplemented (0.88 % dry weight inclusion) feed was fed to abalone under farm conditions to compare gut physiological parameters (crop morphology, digestive enzyme activities and the gut microbiota) in abalone against that of abalone fed an isonitrogenous and isoenergetic non-supplemented control feed. To establish if the observed higher abalone growth rates were related to improved gastrointestinal tract epithelium activity and integrity, as reflected by epithelial cell growth in response to potential changes in bacterial-derived short-chain fatty acid production, crop epithelial morphology was compared between abalone fed the kelp-supplemented and control feeds. Kelp supplementation did not induce any observable changes in crop epithelial cell height for farm-reared sub-adult abalone fed the experimental diets on-farm for seven weeks. This was attributed to the similar macronutrient compositions of kelp-supplemented and control diets and/ or the common diet history of experimental abalone from weaning to the initiation of the experiment. Digestive enzyme activity was compared between abalone fed a kelp-supplemented and a control feed during an on-farm feeding trial with sub-adult abalone. Gut samples were collected after seven weeks and colorimetric enzyme assays were performed for the polysaccharide-degrading enzymes amylase, alginate lyase, laminarinase and fucoidanase, and for acid protease, trypsin and chymotrypsin activity. Amylase and alginate lyase activities were relatively high, compared to the other enzymes. Polysaccharidase and acid protease activity levels did not differ significantly between abalone fed kelp-supplemented and control feeds, but a greater variability in enzyme activity levels was observed in abalone fed the control diet. It was hypothesised that this might be due to the kelp supplement promoting a more stable and less opportunistic gut-bacterial community than the control diet. Pooled gut samples of abalone fed the kelp-supplemented diet were used for proteomic analyses to identify the composition of enzyme proteins of both endogenous and exogenous origin in the abalone digestive system. The key polysaccharidases and proteases in the gut samples of kelp-supplemented formulated feed-fed abalone were all of abalone origin, whereas the bacterial enzymes were of the types that form part of intermediate reactions in metabolic pathways. The results suggested that bacterial enzymes play a different role to abalone endogenous enzymes in the digestion of formulated feed. While abalone enzymes appear to be the main degraders of carbohydrate and protein macromolecules, the profile of exogenous enzymes suggests that they perform bioconversions of smaller organic compounds. The profiles of gut-bacterial communities of farm-reared sub-adult abalone fed kelpsupplemented and control feeds on-farm for seven weeks were analysed with metagenomic pyrosequencing and DGGE analyses, using 16S rDNA-targeted amplified DNA. The results indicated a shift in gut-bacterial composition with a higher abundance of Mollicutes in abalone fed kelp-supplemented feed compared to those fed the control feed. DGGE band patterns displayed a greater within-group similarity in gut bacteria for abalone fed the kelpsupplemented diet and the presence of unique and variable bands for bacteria in the guts of abalone fed the control diet. It was concluded that when cultured abalone are fed kelpsupplemented formulated feeds, more stable gut bacterial communities are present compared to a more opportunistic gut-bacterial community in abalone fed non-supplemented feeds, and that the observed increase in Mollicutes could reflect the restoration of the abalone gut microbiota to a more natural state. The novel application of proteomics to abalone nutrition in the present study demonstrated that gut-bacterial enzymes may form part of many different metabolic pathways and suggests that the metabolism of the gut microbiota serves as an extension of the abalone’s digestive metabolism. Future studies should quantify the contribution of commensal gut-bacteria to cultured abalone nutrition by employing metabolomic studies to characterize the utilisation of bacterial-derived metabolites by the abalone host.
- Full Text:
- Date Issued: 2016
- Authors: Nel, Aldi
- Date: 2016
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/899 , vital:20001
- Description: Formulated feeds with a relatively low (< 5 % of dry mass) kelp (Ecklonia maxima) inclusion level are widely used on commercial abalone (Haliotis midae) farms in South Africa. Although the use of kelp, a major constituent of the natural diet of H. midae, as a dietary supplement is considered to enhance abalone growth and feed utilisation, there are no published studies which quantify the effects of kelp inclusion in formulated feeds. Furthermore, the physiological mechanisms by which kelp supplementation may positively influence abalone digestive physiology and growth are largely unknown. As the kelp supplement is comprised mostly of soluble fibres and abalone gut bacteria associated with macroalgae (and its fibrous polysaccharides) are known to play a key role in digestion, it was hypothesised that the kelp supplement influences the gut-bacterial community profiles of cultured abalone through prebiotic and other metabolic effects. The present thesis thus examined the effect of kelp supplementation on the performance of abalone (Haliotis midae) fed formulated feeds and explored the influence of a kelp supplement on the abalone gut microbiota and its function in the gastrointestinal tract. The key hypotheses of the study were that kelp supplementation in formulated feed: 1) enhances abalone growth; 2) causes a shift in abalone gut-bacterial community composition through a prebiotic-like effect; 3) may induce changes in crop morphology as a result of potential bacterial-associated increases in volatile short-chain fatty acids, and 4) alters digestive enzyme activities in the abalone gut through changes in bacterial-derived (exogenous) digestive enzymes. The growth-promoting efficacy of low-level kelp supplementation was tested by feeding isonitrogenous and isoenergetic experimental feeds containing 0.00 – 3.54 % kelp (dry mass) to sub-adult abalone (~43 mm shell length) for eight months under commercial farm conditions. The growth trial established that kelp supplementation (0.44 – 3.54 % of dry mass) promoted faster growth and improved feed conversion and protein efficiency ratios in cultured abalone compared to abalone fed the non-supplemented control diet, while there were no significant differences in growth for abalone fed the different kelp-supplemented diets (0.44, 0.88, 1.76 and 3.54 % of dry mass). Feed conversion and protein efficiency ratios displayed significant correlations with kelp level in the range of 0.00 – 3.54 % dry mass, and it is therefore recommended that kelp be included in the formulated feeds of cultured South African abalone at a rate of up to 3.54 % of dry mass. A kelp-supplemented (0.88 % dry weight inclusion) feed was fed to abalone under farm conditions to compare gut physiological parameters (crop morphology, digestive enzyme activities and the gut microbiota) in abalone against that of abalone fed an isonitrogenous and isoenergetic non-supplemented control feed. To establish if the observed higher abalone growth rates were related to improved gastrointestinal tract epithelium activity and integrity, as reflected by epithelial cell growth in response to potential changes in bacterial-derived short-chain fatty acid production, crop epithelial morphology was compared between abalone fed the kelp-supplemented and control feeds. Kelp supplementation did not induce any observable changes in crop epithelial cell height for farm-reared sub-adult abalone fed the experimental diets on-farm for seven weeks. This was attributed to the similar macronutrient compositions of kelp-supplemented and control diets and/ or the common diet history of experimental abalone from weaning to the initiation of the experiment. Digestive enzyme activity was compared between abalone fed a kelp-supplemented and a control feed during an on-farm feeding trial with sub-adult abalone. Gut samples were collected after seven weeks and colorimetric enzyme assays were performed for the polysaccharide-degrading enzymes amylase, alginate lyase, laminarinase and fucoidanase, and for acid protease, trypsin and chymotrypsin activity. Amylase and alginate lyase activities were relatively high, compared to the other enzymes. Polysaccharidase and acid protease activity levels did not differ significantly between abalone fed kelp-supplemented and control feeds, but a greater variability in enzyme activity levels was observed in abalone fed the control diet. It was hypothesised that this might be due to the kelp supplement promoting a more stable and less opportunistic gut-bacterial community than the control diet. Pooled gut samples of abalone fed the kelp-supplemented diet were used for proteomic analyses to identify the composition of enzyme proteins of both endogenous and exogenous origin in the abalone digestive system. The key polysaccharidases and proteases in the gut samples of kelp-supplemented formulated feed-fed abalone were all of abalone origin, whereas the bacterial enzymes were of the types that form part of intermediate reactions in metabolic pathways. The results suggested that bacterial enzymes play a different role to abalone endogenous enzymes in the digestion of formulated feed. While abalone enzymes appear to be the main degraders of carbohydrate and protein macromolecules, the profile of exogenous enzymes suggests that they perform bioconversions of smaller organic compounds. The profiles of gut-bacterial communities of farm-reared sub-adult abalone fed kelpsupplemented and control feeds on-farm for seven weeks were analysed with metagenomic pyrosequencing and DGGE analyses, using 16S rDNA-targeted amplified DNA. The results indicated a shift in gut-bacterial composition with a higher abundance of Mollicutes in abalone fed kelp-supplemented feed compared to those fed the control feed. DGGE band patterns displayed a greater within-group similarity in gut bacteria for abalone fed the kelpsupplemented diet and the presence of unique and variable bands for bacteria in the guts of abalone fed the control diet. It was concluded that when cultured abalone are fed kelpsupplemented formulated feeds, more stable gut bacterial communities are present compared to a more opportunistic gut-bacterial community in abalone fed non-supplemented feeds, and that the observed increase in Mollicutes could reflect the restoration of the abalone gut microbiota to a more natural state. The novel application of proteomics to abalone nutrition in the present study demonstrated that gut-bacterial enzymes may form part of many different metabolic pathways and suggests that the metabolism of the gut microbiota serves as an extension of the abalone’s digestive metabolism. Future studies should quantify the contribution of commensal gut-bacteria to cultured abalone nutrition by employing metabolomic studies to characterize the utilisation of bacterial-derived metabolites by the abalone host.
- Full Text:
- Date Issued: 2016
The trophic and spatial ecology of juvenile porcupine rays Urogymnus asperrimus at the remote St. Joseph Atoll
- Authors: Elston, Chantel
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/965 , vital:20007
- Description: Little information exists for the widely occurring but rare porcupine ray Urogymnus asperrimus. This is a concern given that it is a vulnerable species and likely plays an important ecological role in tropical atoll ecosystems. The aims of this thesis were to investigate the trophic and spatial ecology of juvenile porcupine rays within the St. Joseph Atoll, which is hypothesized to be functioning as a nursery for this species. Specific objectives were to determine i) the dietary composition and resource selectivity displayed by juvenile porcupine rays, ii) residency to the atoll, space use, and seasonality in movements, and iii) whether environmental factors affect short-term movements. Gastric lavage was used to collect stomach contents from 55 juveniles and sediment samples were collected. Thirteen juveniles were implanted with acoustic transmitters and monitored for a year by an array of 88 acoustic receivers situated in and around the St. Joseph Atoll. Porcupine rays appeared to be generalist and opportunistic feeders, foraging predominantly on annelids with the highest environmental availability. Polychaetes of the family Capitellidae were the most important prey item (Index of Importance = 35%). Rays only fed on deep infaunal prey, likely because of their foraging behaviour, suggesting they may influence this community. There was a size-related shift in the crustacean families consumed. The tagged rays displayed high residency to the atoll (mean residency index of 64%) and restricted movements, with small core use and activity space areas (mean of 0.5km² and 3km² respectively) and the majority of detections were recorded within 1km of their tagging locations. The rays favoured the sand ats where 88% of detections occurred. Transient use of the lagoon and fringe reef peaked in the north-west monsoon season, indicating a seasonal usage of these habitats. The effects of temperature and water depth on movements were manifested as diel and tidal cyclical patterns in presence. Evidence illustrates that the St. Joseph Atoll constitutes an important nursery for this species, which has been declared a Marine Protected Area. A major determinant behind the dependence of this nursery habitat is related to predator avoidance. Thermoregulatory behaviours were identified, suggesting that this species is vulnerable to climate change.
- Full Text:
- Date Issued: 2016
- Authors: Elston, Chantel
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/965 , vital:20007
- Description: Little information exists for the widely occurring but rare porcupine ray Urogymnus asperrimus. This is a concern given that it is a vulnerable species and likely plays an important ecological role in tropical atoll ecosystems. The aims of this thesis were to investigate the trophic and spatial ecology of juvenile porcupine rays within the St. Joseph Atoll, which is hypothesized to be functioning as a nursery for this species. Specific objectives were to determine i) the dietary composition and resource selectivity displayed by juvenile porcupine rays, ii) residency to the atoll, space use, and seasonality in movements, and iii) whether environmental factors affect short-term movements. Gastric lavage was used to collect stomach contents from 55 juveniles and sediment samples were collected. Thirteen juveniles were implanted with acoustic transmitters and monitored for a year by an array of 88 acoustic receivers situated in and around the St. Joseph Atoll. Porcupine rays appeared to be generalist and opportunistic feeders, foraging predominantly on annelids with the highest environmental availability. Polychaetes of the family Capitellidae were the most important prey item (Index of Importance = 35%). Rays only fed on deep infaunal prey, likely because of their foraging behaviour, suggesting they may influence this community. There was a size-related shift in the crustacean families consumed. The tagged rays displayed high residency to the atoll (mean residency index of 64%) and restricted movements, with small core use and activity space areas (mean of 0.5km² and 3km² respectively) and the majority of detections were recorded within 1km of their tagging locations. The rays favoured the sand ats where 88% of detections occurred. Transient use of the lagoon and fringe reef peaked in the north-west monsoon season, indicating a seasonal usage of these habitats. The effects of temperature and water depth on movements were manifested as diel and tidal cyclical patterns in presence. Evidence illustrates that the St. Joseph Atoll constitutes an important nursery for this species, which has been declared a Marine Protected Area. A major determinant behind the dependence of this nursery habitat is related to predator avoidance. Thermoregulatory behaviours were identified, suggesting that this species is vulnerable to climate change.
- Full Text:
- Date Issued: 2016
The use of treated brewery effluent as a water and nutrient source in crop irrigation
- Authors: Taylor, Richard Peter
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5390 , http://hdl.handle.net/10962/d1021265
- Description: Brewery effluent (BE) needs to be treated before it can be released into the environment, reused or used in down-stream activities. Current technologies used to address this concern at the experimental wastewater treatment plant at Ibahyi Brewery (SAB Ltd) include anaerobic digestion (AD), primary facultative ponds (PFP), high rate algal ponds (HRAP) and constructed wetlands (CW). The aim of this work was to determine if BE treated in these systems might be suitable for crop irrigation. A test crop, cabbage (Brassica oleracea cv. Star 3301), grew best on post-AD and post-PFP BE compared to those irrigated with post-HRAP or post-CW effluent. However, the yield was 13% lower than cabbage plants irrigated with a commercial nutrient solution and fresh water. The relatively high conductivity (3019.05 ± 48.72 μs/cm2) of BE may be the main factor reducing the cabbage yields. Post-HRAP and post-CW BE were the least suitable for irrigated crop production due to the higher conductivity and lower nutrient content of these treated effluents. After three months, soils irrigated with post-AD and post-PFP BE had a significantly higher sodium content and sodium adsorption ratio (3919 ± 94.77 mg/kg & 8.18 ± 0.17) than soil irrigated with a commercial nutrient solution (920.58 ± 27.46 mg/kg & 2.20 ± 0.05; p<0.05). However, this was not accompanied by a deterioration in the soil’s hydro-physical properties, nor a change in the metabolic community structure of the soil (p>0.05). After prolonged irrigation with treated BE, sodium is likely to build up in the soil and this can be expected to be accompanied by a deterioration in the soil physical structure. However, crops species such as millet (Echinochloa esculenta), lucerne (Medicago sativa) and saltbush (Atriplex nummularia) reduced the build-up of sodium in the soil. The results suggest that sodium was mainly removed from the soil through plant-assisted leaching. Of the crops grown, lucerne showed the most promise because it improved the soil physical properties, is able to grow well in alkaline environments, is a popular fodder crop and can be harvested multiple times from a single stand. Brewery effluent is more suitable for soil production systems than hydroponic production systems because the soil was able to act as a buffer against the high pH of post-AD BE, whereas in a hydroponics systems the high pH reduced the availability of key minerals to plants. In conclusion brewery effluent contains sufficient plants nutrients to support the growth of cabbages, saltbush, lucerne and millet. However the sodium content of BE is a concern as it accumulates in the soil, and in the long-term it may lead to soil degradation. It is suggested that the brewery change the pH neutralising treatment of BE from sodium hydroxide to potassium hydroxide, or dolomitic lime (calcium and magnesium carbonate) because this would reduce the introduction of sodium into the system, and would increase the suitability of BE for crop production, given potassium and calcium are plant nutrients. The benefits of developing this nutrient and water resource could contribute to cost-reductions at the brewery, more efficient water, nutrient and energy management, create job opportunities with the potential of improving food security in the local community.
- Full Text:
- Date Issued: 2016
- Authors: Taylor, Richard Peter
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5390 , http://hdl.handle.net/10962/d1021265
- Description: Brewery effluent (BE) needs to be treated before it can be released into the environment, reused or used in down-stream activities. Current technologies used to address this concern at the experimental wastewater treatment plant at Ibahyi Brewery (SAB Ltd) include anaerobic digestion (AD), primary facultative ponds (PFP), high rate algal ponds (HRAP) and constructed wetlands (CW). The aim of this work was to determine if BE treated in these systems might be suitable for crop irrigation. A test crop, cabbage (Brassica oleracea cv. Star 3301), grew best on post-AD and post-PFP BE compared to those irrigated with post-HRAP or post-CW effluent. However, the yield was 13% lower than cabbage plants irrigated with a commercial nutrient solution and fresh water. The relatively high conductivity (3019.05 ± 48.72 μs/cm2) of BE may be the main factor reducing the cabbage yields. Post-HRAP and post-CW BE were the least suitable for irrigated crop production due to the higher conductivity and lower nutrient content of these treated effluents. After three months, soils irrigated with post-AD and post-PFP BE had a significantly higher sodium content and sodium adsorption ratio (3919 ± 94.77 mg/kg & 8.18 ± 0.17) than soil irrigated with a commercial nutrient solution (920.58 ± 27.46 mg/kg & 2.20 ± 0.05; p<0.05). However, this was not accompanied by a deterioration in the soil’s hydro-physical properties, nor a change in the metabolic community structure of the soil (p>0.05). After prolonged irrigation with treated BE, sodium is likely to build up in the soil and this can be expected to be accompanied by a deterioration in the soil physical structure. However, crops species such as millet (Echinochloa esculenta), lucerne (Medicago sativa) and saltbush (Atriplex nummularia) reduced the build-up of sodium in the soil. The results suggest that sodium was mainly removed from the soil through plant-assisted leaching. Of the crops grown, lucerne showed the most promise because it improved the soil physical properties, is able to grow well in alkaline environments, is a popular fodder crop and can be harvested multiple times from a single stand. Brewery effluent is more suitable for soil production systems than hydroponic production systems because the soil was able to act as a buffer against the high pH of post-AD BE, whereas in a hydroponics systems the high pH reduced the availability of key minerals to plants. In conclusion brewery effluent contains sufficient plants nutrients to support the growth of cabbages, saltbush, lucerne and millet. However the sodium content of BE is a concern as it accumulates in the soil, and in the long-term it may lead to soil degradation. It is suggested that the brewery change the pH neutralising treatment of BE from sodium hydroxide to potassium hydroxide, or dolomitic lime (calcium and magnesium carbonate) because this would reduce the introduction of sodium into the system, and would increase the suitability of BE for crop production, given potassium and calcium are plant nutrients. The benefits of developing this nutrient and water resource could contribute to cost-reductions at the brewery, more efficient water, nutrient and energy management, create job opportunities with the potential of improving food security in the local community.
- Full Text:
- Date Issued: 2016
Towards an alternative spatial-based management approach for estuarine fisheries in South Africa, with a case study from the Sundays Estuary
- Authors: Kramer, Rachel
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1007 , vital:20012
- Description: Estuaries are productive habitats and biologically important ecosystems which serve as juvenile nursery areas and feeding grounds for adults from a host of fish species. They are, however, threatened habitats, increasingly exposed to human disturbance and exploitation. The stocks of several South African estuary-dependent linefish species are now considered as either overexploited or collapsed. It is clear that their dependence on estuaries would warrant the inclusion of these ecosystems into marine reserve planning exercises. Since traditional management strategies (e.g. bag and size limit restrictions) have proven ineffective for estuarine fisheries, there is a need for alternative management measures, such as spatial and temporal restrictions, to ensure increased survival of juveniles and recovery of adult breeding populations. This thesis explored the potential for an ecosystem-based approach through the application of a rapid sustainability assessment technique, and a spatial-based management approach for an important fishery species, using conservation planning software. The Sundays Estuary, Eastern Cape, South Africa falls within the footprint of the Addo Elephant National Park, with a proposed expansion to include a marine protected area (MPA). However the estuaries resources were not considered during the planning of the proposed MPA. This study conducted an indicator-based sustainability assessment based on the principles of sustainable development. The results showed that present levels of exploitation, due to non-compliance and a lack of law enforcement are unsustainable. The sustainability of the Sundays Estuary had a low overall sustainability score of only 23.8%. With limited enforcement of estuarine fisheries regulations in South Africa, alternative management measures such as spatial regulations may provide a viable option forward. The sustainability of fishery resources depends on the comprehensive understanding of the fishery resource. Acoustic telemetry is a technique that has been widely adopted to infer habitat and area use patterns of fish species. The second component of this study made use of high resolution telemetry data collected on juvenile dusky kob Argyrosomus japonicus movements within the Sundays Estuary to conduct a scenario-based approach using Marxan conservation planning software. The best solution given by Marxan, in the form of a protected area for the conservation of juvenile A. japonicus in the Sundays Estuary was identified in the middle (starting 7km from the mouth) to the upper reaches (approximately 16km from the mouth) of the estuary, ultimately providing protection to tagged individuals for 61% of their time in the estuary. Although Marxan presented a best solution, the Sundays Estuary’s small size and shape, and minimal features used, was too simplistic to be included into a Marxan analysis. However, new methods and tools to analyse and plan spatial-based management options at this scale are currently being developed. Using the Sundays Estuary as a case study, a decision tree was then developed as a protocol to assist management address the challenges of effective estuarine management depending on the unique biological and socio-economic characteristics of individual estuaries in South Africa.
- Full Text:
- Date Issued: 2016
- Authors: Kramer, Rachel
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1007 , vital:20012
- Description: Estuaries are productive habitats and biologically important ecosystems which serve as juvenile nursery areas and feeding grounds for adults from a host of fish species. They are, however, threatened habitats, increasingly exposed to human disturbance and exploitation. The stocks of several South African estuary-dependent linefish species are now considered as either overexploited or collapsed. It is clear that their dependence on estuaries would warrant the inclusion of these ecosystems into marine reserve planning exercises. Since traditional management strategies (e.g. bag and size limit restrictions) have proven ineffective for estuarine fisheries, there is a need for alternative management measures, such as spatial and temporal restrictions, to ensure increased survival of juveniles and recovery of adult breeding populations. This thesis explored the potential for an ecosystem-based approach through the application of a rapid sustainability assessment technique, and a spatial-based management approach for an important fishery species, using conservation planning software. The Sundays Estuary, Eastern Cape, South Africa falls within the footprint of the Addo Elephant National Park, with a proposed expansion to include a marine protected area (MPA). However the estuaries resources were not considered during the planning of the proposed MPA. This study conducted an indicator-based sustainability assessment based on the principles of sustainable development. The results showed that present levels of exploitation, due to non-compliance and a lack of law enforcement are unsustainable. The sustainability of the Sundays Estuary had a low overall sustainability score of only 23.8%. With limited enforcement of estuarine fisheries regulations in South Africa, alternative management measures such as spatial regulations may provide a viable option forward. The sustainability of fishery resources depends on the comprehensive understanding of the fishery resource. Acoustic telemetry is a technique that has been widely adopted to infer habitat and area use patterns of fish species. The second component of this study made use of high resolution telemetry data collected on juvenile dusky kob Argyrosomus japonicus movements within the Sundays Estuary to conduct a scenario-based approach using Marxan conservation planning software. The best solution given by Marxan, in the form of a protected area for the conservation of juvenile A. japonicus in the Sundays Estuary was identified in the middle (starting 7km from the mouth) to the upper reaches (approximately 16km from the mouth) of the estuary, ultimately providing protection to tagged individuals for 61% of their time in the estuary. Although Marxan presented a best solution, the Sundays Estuary’s small size and shape, and minimal features used, was too simplistic to be included into a Marxan analysis. However, new methods and tools to analyse and plan spatial-based management options at this scale are currently being developed. Using the Sundays Estuary as a case study, a decision tree was then developed as a protocol to assist management address the challenges of effective estuarine management depending on the unique biological and socio-economic characteristics of individual estuaries in South Africa.
- Full Text:
- Date Issued: 2016
Towards determining the dietary lysine requirement in the South African abalone, Haliotis midae
- Authors: Lloyd, Kyle Everett
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1024 , vital:20014
- Description: Animals generally do not have a requirement for protein, but instead have a requirement for specific essential amino acids (EAAs) and non-essential amino acids (NEAAs). The NEAAs are those that can be synthesised by the animal, however, EAAs cannot be synthesised and must therefore be supplied as part of the diet. When these amino acids (AAs) are supplied in the correct ratios and with the correct level of digestible energy, nutritionists can maximise somatic growth from proteins. This has resulted in increased research into the use of crystalline AAs as a tool in feed formulation research in order to quantify the AA requirements in aquaculture species, and allow for alternative protein sources (other than fishmeal) to be utilised. In common with other water soluble nutrients, leaching of crystalline AAs from diets prior to ingestion is of concern in an aquatic environment. Microencapsulation techniques have been successfully employed to restrict micronutrient leaching, and improve ingestion rates. In this research, LysiPEARL™ (Kemin®) was used as a means to determine the lysine requirement in Haliotis. midae. This encapsulated lysine product is used in the dairy cattle industry as an effective source of rumen bypass for intestinal release of lysine. It has previously been proposed that crystalline AAs are not suitable for AA studies in H. midae due to the slow feeding rates of the species as well as the solubility of these AAs. However, 90.00 % of supplemented lysine was maintained in this study after a six hour period of leaching, showing that if effective microencapsulation techniques are used, it is possible to use crystalline amino acids to supplement protein bound lysine in abalone feeds. Six isoenergetic (15.90 MJ/kg), isolipidic (6.00 %) and isonitrogenous (29.00 %) diets enriched with 5.52, 6.40, 7.28, 8.14, 9.00 and 9.86 % lysine (as a % of protein) were fed to triplicate groups of 20 H. midae (20.41 ± 1.95 mm SL 1.51 ± 0.44 g w.wt) for 90 days. Wet weight and shell length measurements were taken every 30 days and specific growth rate (SGR) (% body weight.day-1), feed conversion ratio (FCR), protein efficiency ratio (PER), feed consumption (% body weight.day-1) and condition factor were calculated for each dietary treatment. Linear regression showed that FCR increased as dietary lysine increased (Regression analysis, p=0.031), and that PER reduced as dietary lysine increased (Regression analysis, p=0.026). Feed consumption also increased as dietary lysine increased (Regression analysis, p<0.001). The inclusion of lysine at 7.28 % of the total protein in the diet resulted in significantly superior SGR (0.57±0.01 % body weight.day-1) to that of 5.52 % (0.42±0.05 % body weight.day-1), FCR (1.51±0.05) to that of 8.14 % (1.99±0.21) and PER (2.45±0.07) to that of 8.14 % (1.99±0.18; ANOVA, p<0.05). There was a significant difference found in feed consumption (% body wt.d-1), with consumption increasing significantly between the first three dietary treatments and the last three dietary treatments (ANOVA, p<0.001). There was no significant improvement in SGR when dietary lysine increased above 7.28 % of the dietary protein in the diet, indicating that dietary lysine requirement was being met at 7.28 %, after which excess lysine promoted no growth response. The diet producing the best SGR, PER and FCR in this study was diet 3 which had a measured lysine content of 6.90 %. The results of the present study suggest that the lysine requirement in H. midae is in the range of 6.00 - 7.00 % of dietary protein. From these data amino acid ratios were used to estimate optimum inclusion levels of other essential amino acids. However, lysine availability in LysiPEARL™ may have resulted in over estimations due to the lipid encapsulation technique used, and haliotids limited ability to efficiently digest lipids. For this reason EAA requirements were suggested based on three different hypothetical scenarios of lysine availability from LysiPEARL™.
- Full Text:
- Date Issued: 2016
- Authors: Lloyd, Kyle Everett
- Date: 2016
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/1024 , vital:20014
- Description: Animals generally do not have a requirement for protein, but instead have a requirement for specific essential amino acids (EAAs) and non-essential amino acids (NEAAs). The NEAAs are those that can be synthesised by the animal, however, EAAs cannot be synthesised and must therefore be supplied as part of the diet. When these amino acids (AAs) are supplied in the correct ratios and with the correct level of digestible energy, nutritionists can maximise somatic growth from proteins. This has resulted in increased research into the use of crystalline AAs as a tool in feed formulation research in order to quantify the AA requirements in aquaculture species, and allow for alternative protein sources (other than fishmeal) to be utilised. In common with other water soluble nutrients, leaching of crystalline AAs from diets prior to ingestion is of concern in an aquatic environment. Microencapsulation techniques have been successfully employed to restrict micronutrient leaching, and improve ingestion rates. In this research, LysiPEARL™ (Kemin®) was used as a means to determine the lysine requirement in Haliotis. midae. This encapsulated lysine product is used in the dairy cattle industry as an effective source of rumen bypass for intestinal release of lysine. It has previously been proposed that crystalline AAs are not suitable for AA studies in H. midae due to the slow feeding rates of the species as well as the solubility of these AAs. However, 90.00 % of supplemented lysine was maintained in this study after a six hour period of leaching, showing that if effective microencapsulation techniques are used, it is possible to use crystalline amino acids to supplement protein bound lysine in abalone feeds. Six isoenergetic (15.90 MJ/kg), isolipidic (6.00 %) and isonitrogenous (29.00 %) diets enriched with 5.52, 6.40, 7.28, 8.14, 9.00 and 9.86 % lysine (as a % of protein) were fed to triplicate groups of 20 H. midae (20.41 ± 1.95 mm SL 1.51 ± 0.44 g w.wt) for 90 days. Wet weight and shell length measurements were taken every 30 days and specific growth rate (SGR) (% body weight.day-1), feed conversion ratio (FCR), protein efficiency ratio (PER), feed consumption (% body weight.day-1) and condition factor were calculated for each dietary treatment. Linear regression showed that FCR increased as dietary lysine increased (Regression analysis, p=0.031), and that PER reduced as dietary lysine increased (Regression analysis, p=0.026). Feed consumption also increased as dietary lysine increased (Regression analysis, p<0.001). The inclusion of lysine at 7.28 % of the total protein in the diet resulted in significantly superior SGR (0.57±0.01 % body weight.day-1) to that of 5.52 % (0.42±0.05 % body weight.day-1), FCR (1.51±0.05) to that of 8.14 % (1.99±0.21) and PER (2.45±0.07) to that of 8.14 % (1.99±0.18; ANOVA, p<0.05). There was a significant difference found in feed consumption (% body wt.d-1), with consumption increasing significantly between the first three dietary treatments and the last three dietary treatments (ANOVA, p<0.001). There was no significant improvement in SGR when dietary lysine increased above 7.28 % of the dietary protein in the diet, indicating that dietary lysine requirement was being met at 7.28 %, after which excess lysine promoted no growth response. The diet producing the best SGR, PER and FCR in this study was diet 3 which had a measured lysine content of 6.90 %. The results of the present study suggest that the lysine requirement in H. midae is in the range of 6.00 - 7.00 % of dietary protein. From these data amino acid ratios were used to estimate optimum inclusion levels of other essential amino acids. However, lysine availability in LysiPEARL™ may have resulted in over estimations due to the lipid encapsulation technique used, and haliotids limited ability to efficiently digest lipids. For this reason EAA requirements were suggested based on three different hypothetical scenarios of lysine availability from LysiPEARL™.
- Full Text:
- Date Issued: 2016
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