Assessing the genetic diversity of catface rockcod epinephelus andersoni in the subtropical Western Indian Ocean and modelling the effects of climate change on their distribution
- Authors: Coppinger, Christine Rose
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54499 , vital:26570
- Description: The catface rockcod Epinephelus andersoni is a range-restricted species that is endemic to the southeast coast of Africa from Quissico in Mozambique (subtropical) to Knysna in South Africa (warmtemperate). Its complex life-history, long-lived nature and high residency make E. andersoni potentially vulnerable to over-exploitation. Epinephelus andersoni is an important fishery species and has shown signs of depletion. Due to inadequate information necessary for management and conservation, further research is vital, particularly in the face of potentially significant climatic changes which could put further pressure on E. andersoni. The aim of the study was to provide information for the management of E. andersoni, with considerations for the possibly detrimental effects of future climate change. The objectives of this study were to describe the genetic structure and diversity of E. andersoni and to determine possible range shifts of E. andersoni with future changes in sea surface temperature. Genetic samples were collected throughout the distribution of E. andersoni. Standard DNA extraction and PCR using universal primers were conducted and nuclear (RPS7-1) and mitochondrial (cytochrome b) data were analysed to determine genetic diversity. A combination of nuclear and mitochondrial markers was used to ensure that the results were robust. RPS7-1 haplotype diversity was high (0.801) and an AMOVA on the RPS7-1 data showed significantly high among group variation (ΦCT = 0.204, p < 0.05) between five groups: 1. Quissico to Inhaca; 2. Cape Vidal to Port Edward; 3 Port St Johns to Coffee Bay; 4. Mbashe; 5. Port Alfred. This geographic structuring could be attributed to low gene flow across barriers such as the Port Alfred upwelling cell, the Mozambique Channel eddies and smaller more localised upwelling cells such as the Port St Johns cell. The cytochrome b results contrastingly indicate low haplotype diversity (0.309) and no differentiation (ΦCT = 0.265, p = 0.074) between groups and support the hypothesis of a historical population bottleneck. This may be due to an unusually slower mutation rate of the cytochrome b region than the RPS7-1 region, resulting in the RPS7-1 data showing a more recent picture of diversification. To complement the genetic results, niche modelling techniques were used to determine range shifts of E. andersoni with future temperature trends using species distribution and climatic data. The model illustrated a contraction of the E. andersoni distribution as well as future intensification of various upwelling cells along the south-east African coast including the Port Alfred upwelling cell. Due to the low gene flow across these barriers this intensification could decrease the resilience of E. andersoni, as its range becomes more limited with global change. The genetic data and modelling results combined provide useful information on which to base future fisheries management.
- Full Text:
- Date Issued: 2014
- Authors: Coppinger, Christine Rose
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54499 , vital:26570
- Description: The catface rockcod Epinephelus andersoni is a range-restricted species that is endemic to the southeast coast of Africa from Quissico in Mozambique (subtropical) to Knysna in South Africa (warmtemperate). Its complex life-history, long-lived nature and high residency make E. andersoni potentially vulnerable to over-exploitation. Epinephelus andersoni is an important fishery species and has shown signs of depletion. Due to inadequate information necessary for management and conservation, further research is vital, particularly in the face of potentially significant climatic changes which could put further pressure on E. andersoni. The aim of the study was to provide information for the management of E. andersoni, with considerations for the possibly detrimental effects of future climate change. The objectives of this study were to describe the genetic structure and diversity of E. andersoni and to determine possible range shifts of E. andersoni with future changes in sea surface temperature. Genetic samples were collected throughout the distribution of E. andersoni. Standard DNA extraction and PCR using universal primers were conducted and nuclear (RPS7-1) and mitochondrial (cytochrome b) data were analysed to determine genetic diversity. A combination of nuclear and mitochondrial markers was used to ensure that the results were robust. RPS7-1 haplotype diversity was high (0.801) and an AMOVA on the RPS7-1 data showed significantly high among group variation (ΦCT = 0.204, p < 0.05) between five groups: 1. Quissico to Inhaca; 2. Cape Vidal to Port Edward; 3 Port St Johns to Coffee Bay; 4. Mbashe; 5. Port Alfred. This geographic structuring could be attributed to low gene flow across barriers such as the Port Alfred upwelling cell, the Mozambique Channel eddies and smaller more localised upwelling cells such as the Port St Johns cell. The cytochrome b results contrastingly indicate low haplotype diversity (0.309) and no differentiation (ΦCT = 0.265, p = 0.074) between groups and support the hypothesis of a historical population bottleneck. This may be due to an unusually slower mutation rate of the cytochrome b region than the RPS7-1 region, resulting in the RPS7-1 data showing a more recent picture of diversification. To complement the genetic results, niche modelling techniques were used to determine range shifts of E. andersoni with future temperature trends using species distribution and climatic data. The model illustrated a contraction of the E. andersoni distribution as well as future intensification of various upwelling cells along the south-east African coast including the Port Alfred upwelling cell. Due to the low gene flow across these barriers this intensification could decrease the resilience of E. andersoni, as its range becomes more limited with global change. The genetic data and modelling results combined provide useful information on which to base future fisheries management.
- Full Text:
- Date Issued: 2014
Assessment of the Lake Liambezi fishery, Zambezi region, Namibia
- Authors: Simasiku, Evans Kamwi
- Date: 2014
- Subjects: Fishery management -- Namibia -- Lake Liambezi , Seines -- Namibia -- Lake Liambezi , Gillnetting -- Namibia -- Lake Liambezi , Fishes -- Namibia -- Lake Liambezi , Fisheries -- Catch effort -- Namibia -- Lake Liambezi
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5366 , http://hdl.handle.net/10962/d1013036
- Description: Lake Liambezi in the Zambezi Region of Namibia, formerly known as the Caprivi Region, is shallow (<6m deep) and characterised by cyclic episodes of filling and drying. When full the lake supports a highly productive fishery and when dry the lake is completely dry and used for agriculture and grazing. In 2000 the lake filled, and between May 2011 and April 2012 was surveyed using beach seine, experimental gillnets and catch landing surveys to obtain information for conservation and management recommendations for the fishery. Littoral fishes in Lake Liambezi and the Kavango floodplain were sampled using seine net and physicochemical properties were measured. Seine net surveys demonstrated that Lake Liambezi littoral zones were dominated by fishes of the family Alestidae (59.7%) while Cichlids constituted the most diverse family. Juvenile Tilapia rendalli and Oreochromis macrochir were among the five most important species in the littoral zone, indicating that these commercially important species use the littoral zone as a nursery ground. Since T. rendalli and O. macrochir are commercially important species, because of this, it is advised that seine nets should not be used. Catch efficiency between monofilament and multifilament gillnets in Lake Liambezi offshore waters were assessed. Catch efficiency experimental fishing trials showed that monofilament gillnets catch per unit effort (CPUE) was three times higher than that of multifilament gillnets for Oreochromis andersonii, O. macrochir, T. rendalli, Serranochromis macrocephalus and Clarias spp. Oreochromis andersonii comprised over 66% of the overall CPUE for both net types combined indicating the importance of this species in the gillnet fishery on the lake. A fishery has been established on the lake with more than 300 canoes and 120 fishermen using monofilament and multifilament gillnets. CPUE was 15 kg/canoe/day and was significantly (P < 0.05) associated with monthly temperature and moon phase parameters indicating that the fishery of Lake Liambezi may be altered by climate and environmental factors. Annual catch from Lake Liambezi was estimated at 3193t with an estimated productivity of 106kg/ha, suggesting that Lake Liambezi makes a significant contribution to the fish supply in the Zambezi Region. Recommendations were made to manage the Lake Liambezi fishery by imposing restrictions on effort (number of fishing boats), gear type, mesh sizes and access. Proper fisheries management and monitoring should incorporate climatic and environmental factors such as temperature and moon phase to meet the challenges of global climatic changes as well as other environmental issues.
- Full Text:
- Date Issued: 2014
- Authors: Simasiku, Evans Kamwi
- Date: 2014
- Subjects: Fishery management -- Namibia -- Lake Liambezi , Seines -- Namibia -- Lake Liambezi , Gillnetting -- Namibia -- Lake Liambezi , Fishes -- Namibia -- Lake Liambezi , Fisheries -- Catch effort -- Namibia -- Lake Liambezi
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5366 , http://hdl.handle.net/10962/d1013036
- Description: Lake Liambezi in the Zambezi Region of Namibia, formerly known as the Caprivi Region, is shallow (<6m deep) and characterised by cyclic episodes of filling and drying. When full the lake supports a highly productive fishery and when dry the lake is completely dry and used for agriculture and grazing. In 2000 the lake filled, and between May 2011 and April 2012 was surveyed using beach seine, experimental gillnets and catch landing surveys to obtain information for conservation and management recommendations for the fishery. Littoral fishes in Lake Liambezi and the Kavango floodplain were sampled using seine net and physicochemical properties were measured. Seine net surveys demonstrated that Lake Liambezi littoral zones were dominated by fishes of the family Alestidae (59.7%) while Cichlids constituted the most diverse family. Juvenile Tilapia rendalli and Oreochromis macrochir were among the five most important species in the littoral zone, indicating that these commercially important species use the littoral zone as a nursery ground. Since T. rendalli and O. macrochir are commercially important species, because of this, it is advised that seine nets should not be used. Catch efficiency between monofilament and multifilament gillnets in Lake Liambezi offshore waters were assessed. Catch efficiency experimental fishing trials showed that monofilament gillnets catch per unit effort (CPUE) was three times higher than that of multifilament gillnets for Oreochromis andersonii, O. macrochir, T. rendalli, Serranochromis macrocephalus and Clarias spp. Oreochromis andersonii comprised over 66% of the overall CPUE for both net types combined indicating the importance of this species in the gillnet fishery on the lake. A fishery has been established on the lake with more than 300 canoes and 120 fishermen using monofilament and multifilament gillnets. CPUE was 15 kg/canoe/day and was significantly (P < 0.05) associated with monthly temperature and moon phase parameters indicating that the fishery of Lake Liambezi may be altered by climate and environmental factors. Annual catch from Lake Liambezi was estimated at 3193t with an estimated productivity of 106kg/ha, suggesting that Lake Liambezi makes a significant contribution to the fish supply in the Zambezi Region. Recommendations were made to manage the Lake Liambezi fishery by imposing restrictions on effort (number of fishing boats), gear type, mesh sizes and access. Proper fisheries management and monitoring should incorporate climatic and environmental factors such as temperature and moon phase to meet the challenges of global climatic changes as well as other environmental issues.
- Full Text:
- Date Issued: 2014
Ecological consequences of non-native fish invasion in Eastern Cape headwater streams
- Authors: Ellender, Bruce Robert
- Date: 2014
- Subjects: Fishery management -- South Africa -- Eastern Cape Fishes -- Conservation -- South Africa Introduced fishes -- South Africa -- Eastern Cape Introduced organisms
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/69065 , vital:29380
- Description: The introduction, spread and concomitant impacts of non-native species are a global problem. Fish are among the most widely introduced vertebrate groups, with their impacts affecting multiple levels of organisation- from individuals, populations and communities, to entire ecosystems. In South Africa, the largest perceived threat to range-restricted endemic headwater stream fishes is said to be invasion by non-native fishes, however, as is the case elsewhere, invasive impacts are often a case of risk perception rather than actual risk analysis. Two range-restricted headwater species, the Eastern Cape redfin Pseudobarbus afer and the Border barb Barbus trevelyani are redlisted by the International Union for the Conservation of Nature (IUCN) as ‘Endangered’, primarily due to invasion by non-native fishes. To investigate invasions in South Africa, and provide a quantitative estimate of the impact of non-native fishes on the two imperilled endemics, P. afer and B. trevelyani, the overall aims of this thesis were to: (A) Provide a literature review on non-native fish invasions in South Africa; (B) Using two case studies on the headwaters of the perennial Keiskamma and episodic Swartkops River systems, investigate the naturalisation-invasion continuum to provide a holistic view of the invasion process in these variable environments. The specific thesis objectives were: (1) Reviewing current knowledge of invasive impacts of non-native fishes in South Africa; (2) Investigating invasibility of headwater stream environments by non-native fishes; (3) Determining the establishment success of non-native fishes, (4) Assessing the spatial and temporal impacts of invasion; (5) Understanding mechanisms responsible for non-native fish impacts; (6) Investigating the threat of non-native fish invasion on the genetic diversity of two the two headwater fishes, P. afer and B. trevelyani. Results from the literature review of fish invasions (Chapter 1) showed that South Africa has a long history of non-native fish introductions, spanning two and a half centuries. Currently, 55 species have been introduced or translocated. Many of these introduced species have become fully invasive (36%). Their impacts also span multiple levels of biological organisation. There was a general paucity of studies on fish invasions (38 studies), however, of those conducted, reviewed studies placed emphases on invasive impacts (25 studies) and the transport, introduction, establishment and spread stages of the invasion process were largely ignored. The two study systems, the Swartkops and Keiskamma Rivers, were heavily invaded and numbers of introduced species surpassed that of natives (Chapter 2, 3 and 5). Headwater streams had varying invasibility and a number of non-native species were successfully established (Chapter 2, 3, 5 and 6). The remainder of the invasions were casual incursions into headwater streams from source populations in mainstream and impoundment environments which were invasion hotspots. Irrespective of establishment, four predatory invaders (largemouth bass Micropterus salmoides, smallmouth bass M. dolomieu, brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss) impacted heavily on native fish communities (Chapter 3, 4 and 5). Two broad types of invasion were documented, top down invasion by non-native O. mykiss and S. trutta and upstream invasion by M. salmoides and M. dolomieu (Chapter 3 and 5). Their impacts included changes in community structure, extirpation from invaded stream reaches resulting in contracted distribution, and isolation and fragmentation of native fish populations. The impacts of non-native predatory fishes were particularly acute for P. afer and B. trevelyani. Where non-native predatory fish occurred, P. afer and B. trevelyani had been extirpated (Chapter 3 and 5). As a result both native species exhibited contracted distributions (>20% habitat loss due to invasion). Upstream invasion by centrarchids isolated and fragmented P. afer populations into headwater refugia, while top down invasion by salmonids excluded B. trevelyani from invaded, more pristine stream reaches, by forcing the species into degraded unsuitable lower stream reaches. Predation also disrupted population processes such as adult dispersal for P. afer, and centrarchid-invaded zones acted as demographic sinks, where adults dispersing through invaded reaches were rapidly depleted. While the Mandela lineage of P. afer exhibited little within or between drainage genetic structuring, B. trevelyani was >4% divergent between drainages, and up to 2% divergent between streams within the Keiskamma River system (Chapter 7). The distribution of genetic diversity for B. trevelyani also indicated that the loss of diversity was imminent without immediate conservation interventions. This thesis has provided conclusive evidence that native fishes are vulnerable to invasion and that non-native predatory fishes have significant impacts on native fishes in Eastern Cape headwater streams. If management and conservation measures are implemented, the unwanted introduction and spread of non-native fishes may be restricted, allowing native fishes opportunities for recovery.
- Full Text:
- Date Issued: 2014
- Authors: Ellender, Bruce Robert
- Date: 2014
- Subjects: Fishery management -- South Africa -- Eastern Cape Fishes -- Conservation -- South Africa Introduced fishes -- South Africa -- Eastern Cape Introduced organisms
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/69065 , vital:29380
- Description: The introduction, spread and concomitant impacts of non-native species are a global problem. Fish are among the most widely introduced vertebrate groups, with their impacts affecting multiple levels of organisation- from individuals, populations and communities, to entire ecosystems. In South Africa, the largest perceived threat to range-restricted endemic headwater stream fishes is said to be invasion by non-native fishes, however, as is the case elsewhere, invasive impacts are often a case of risk perception rather than actual risk analysis. Two range-restricted headwater species, the Eastern Cape redfin Pseudobarbus afer and the Border barb Barbus trevelyani are redlisted by the International Union for the Conservation of Nature (IUCN) as ‘Endangered’, primarily due to invasion by non-native fishes. To investigate invasions in South Africa, and provide a quantitative estimate of the impact of non-native fishes on the two imperilled endemics, P. afer and B. trevelyani, the overall aims of this thesis were to: (A) Provide a literature review on non-native fish invasions in South Africa; (B) Using two case studies on the headwaters of the perennial Keiskamma and episodic Swartkops River systems, investigate the naturalisation-invasion continuum to provide a holistic view of the invasion process in these variable environments. The specific thesis objectives were: (1) Reviewing current knowledge of invasive impacts of non-native fishes in South Africa; (2) Investigating invasibility of headwater stream environments by non-native fishes; (3) Determining the establishment success of non-native fishes, (4) Assessing the spatial and temporal impacts of invasion; (5) Understanding mechanisms responsible for non-native fish impacts; (6) Investigating the threat of non-native fish invasion on the genetic diversity of two the two headwater fishes, P. afer and B. trevelyani. Results from the literature review of fish invasions (Chapter 1) showed that South Africa has a long history of non-native fish introductions, spanning two and a half centuries. Currently, 55 species have been introduced or translocated. Many of these introduced species have become fully invasive (36%). Their impacts also span multiple levels of biological organisation. There was a general paucity of studies on fish invasions (38 studies), however, of those conducted, reviewed studies placed emphases on invasive impacts (25 studies) and the transport, introduction, establishment and spread stages of the invasion process were largely ignored. The two study systems, the Swartkops and Keiskamma Rivers, were heavily invaded and numbers of introduced species surpassed that of natives (Chapter 2, 3 and 5). Headwater streams had varying invasibility and a number of non-native species were successfully established (Chapter 2, 3, 5 and 6). The remainder of the invasions were casual incursions into headwater streams from source populations in mainstream and impoundment environments which were invasion hotspots. Irrespective of establishment, four predatory invaders (largemouth bass Micropterus salmoides, smallmouth bass M. dolomieu, brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss) impacted heavily on native fish communities (Chapter 3, 4 and 5). Two broad types of invasion were documented, top down invasion by non-native O. mykiss and S. trutta and upstream invasion by M. salmoides and M. dolomieu (Chapter 3 and 5). Their impacts included changes in community structure, extirpation from invaded stream reaches resulting in contracted distribution, and isolation and fragmentation of native fish populations. The impacts of non-native predatory fishes were particularly acute for P. afer and B. trevelyani. Where non-native predatory fish occurred, P. afer and B. trevelyani had been extirpated (Chapter 3 and 5). As a result both native species exhibited contracted distributions (>20% habitat loss due to invasion). Upstream invasion by centrarchids isolated and fragmented P. afer populations into headwater refugia, while top down invasion by salmonids excluded B. trevelyani from invaded, more pristine stream reaches, by forcing the species into degraded unsuitable lower stream reaches. Predation also disrupted population processes such as adult dispersal for P. afer, and centrarchid-invaded zones acted as demographic sinks, where adults dispersing through invaded reaches were rapidly depleted. While the Mandela lineage of P. afer exhibited little within or between drainage genetic structuring, B. trevelyani was >4% divergent between drainages, and up to 2% divergent between streams within the Keiskamma River system (Chapter 7). The distribution of genetic diversity for B. trevelyani also indicated that the loss of diversity was imminent without immediate conservation interventions. This thesis has provided conclusive evidence that native fishes are vulnerable to invasion and that non-native predatory fishes have significant impacts on native fishes in Eastern Cape headwater streams. If management and conservation measures are implemented, the unwanted introduction and spread of non-native fishes may be restricted, allowing native fishes opportunities for recovery.
- Full Text:
- Date Issued: 2014
Effect of diet and sex-sorting on growth and gonad development in farmed South African abalone, Haliotis midae
- Authors: Ayres, Devin William Philip
- Date: 2014
- Subjects: Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalone culture -- South Africa , Abalones -- Physiology -- South Africa , Abalones -- South Africa -- Growth , Abalones -- Feeding and feeds -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5357 , http://hdl.handle.net/10962/d1010856 , Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalone culture -- South Africa , Abalones -- Physiology -- South Africa , Abalones -- South Africa -- Growth , Abalones -- Feeding and feeds -- South Africa
- Description: Abalone, Haliotis midae, farmers in South Africa that feed formulated diets reported a periodic drop in abalone growth during periods of increased gonad development. A large drop in abalone biomass was noticed after presumed spawning events. This study was aimed to determine the effect of diet and sex-sorting on gonad development in abalone. Experiments were conducted on a commercial abalone farm from July 2012 to the end of June 2013. Isonitrogenous and isoenergetic diets were formulated with two protein sources. A fishmeal and soybean meal (S-diet) diet and a fishmeal only (F-diet) diet were fed to abalone (50 - 70 g abalone⁻¹) over 12 months. Weight and length gain, gonad bulk index (GBI), visceral index (%) and meat mass index (%) were determined monthly and seasonally. A histological study on the female gonads was conducted. This study also included an experiment to test the effect of sex-sorting (70 - 80 g abalone⁻¹) on growth and body composition with treatments including males (M), females (F) and equal numbers of males and females (MF). Weight gain and length gain were faster in S-diet-fed abalone (RM-ANOVA, F ₍₁, ₁₆₎ = 7.77, p = 0.01; F ₍₁, ₆₉₎ = 49.9, p < 0.001, respectively). Gonad development was significantly affected by the inclusion of soybean meal with S-diet-fed abalone showing higher GBI-values than F-diet-fed abalone (RM-ANOVA, F ₍₁, ₃₃)= 16.22, p = 0.0003). Male abalone had higher GBI-values than females (RM-ANOVA, F ₍₁, ₃₃₎ = 39.87, p < 0.0001). There was no significant difference in average feed conversion ratio (FCR) between diets over time (RM-ANOVA, F ₍₁, ₂₁₎ = 0.008, p = 0.97). However, average FCR-values were significantly highest between November 2012 and March 2013, the presumed spawning season. The visceral mass (gut and gonad) as a proportion of whole mass (visceral index, %) was significantly higher in abalone fed the S-diet (RM-ANOVA; F ₍₁, ₆₉₎ = 68.06, p < 0.0001). There was no difference in meat mass index (%) between diets for both male and female abalone (RM-ANOVA; F ₍₇, ₂₄₈₎ = 0.80, p = 0.60; F ₍₇, ₂₄₁₎ = 1.7, p = 0.11,respectively). Meat mass index significantly decreased from September 2012 to February 2013 coinciding with the period of high GBI-values. The distribution of oocyte maturity stages differed between diets. The majority of oocytes within S-diet-fed abalone were fully mature stage 8 oocytes compared to a majority of stage 7 oocytes in F-diet-fed abalone. Histology corroborated peaks in GBI-values for abalone fed both diets. There was no significant difference in growth, GBI, visceral index (%) and meat mass index (%) between abalone sorted into monosex and mixed-sex populations. Thus, the presence of the opposite sex did not have an effect on growth and gonad mass in H. midae. The phytoestrogens daidzin, glycitin, genistin, daidzein, glycitein and genistein were present in soybean meal and only traceable amounts were found in the F-diet. This study provided evidence that soybean meal present in formulated feed affected growth and gonad development in H.midae. The difference in the distribution of the maturity stages of oocytes was affected by diet. Sex-sorting abalone into monosex and mixed-sex populations had no influence on weight and length gain and gonad development.
- Full Text:
- Date Issued: 2014
- Authors: Ayres, Devin William Philip
- Date: 2014
- Subjects: Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalone culture -- South Africa , Abalones -- Physiology -- South Africa , Abalones -- South Africa -- Growth , Abalones -- Feeding and feeds -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5357 , http://hdl.handle.net/10962/d1010856 , Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalone culture -- South Africa , Abalones -- Physiology -- South Africa , Abalones -- South Africa -- Growth , Abalones -- Feeding and feeds -- South Africa
- Description: Abalone, Haliotis midae, farmers in South Africa that feed formulated diets reported a periodic drop in abalone growth during periods of increased gonad development. A large drop in abalone biomass was noticed after presumed spawning events. This study was aimed to determine the effect of diet and sex-sorting on gonad development in abalone. Experiments were conducted on a commercial abalone farm from July 2012 to the end of June 2013. Isonitrogenous and isoenergetic diets were formulated with two protein sources. A fishmeal and soybean meal (S-diet) diet and a fishmeal only (F-diet) diet were fed to abalone (50 - 70 g abalone⁻¹) over 12 months. Weight and length gain, gonad bulk index (GBI), visceral index (%) and meat mass index (%) were determined monthly and seasonally. A histological study on the female gonads was conducted. This study also included an experiment to test the effect of sex-sorting (70 - 80 g abalone⁻¹) on growth and body composition with treatments including males (M), females (F) and equal numbers of males and females (MF). Weight gain and length gain were faster in S-diet-fed abalone (RM-ANOVA, F ₍₁, ₁₆₎ = 7.77, p = 0.01; F ₍₁, ₆₉₎ = 49.9, p < 0.001, respectively). Gonad development was significantly affected by the inclusion of soybean meal with S-diet-fed abalone showing higher GBI-values than F-diet-fed abalone (RM-ANOVA, F ₍₁, ₃₃)= 16.22, p = 0.0003). Male abalone had higher GBI-values than females (RM-ANOVA, F ₍₁, ₃₃₎ = 39.87, p < 0.0001). There was no significant difference in average feed conversion ratio (FCR) between diets over time (RM-ANOVA, F ₍₁, ₂₁₎ = 0.008, p = 0.97). However, average FCR-values were significantly highest between November 2012 and March 2013, the presumed spawning season. The visceral mass (gut and gonad) as a proportion of whole mass (visceral index, %) was significantly higher in abalone fed the S-diet (RM-ANOVA; F ₍₁, ₆₉₎ = 68.06, p < 0.0001). There was no difference in meat mass index (%) between diets for both male and female abalone (RM-ANOVA; F ₍₇, ₂₄₈₎ = 0.80, p = 0.60; F ₍₇, ₂₄₁₎ = 1.7, p = 0.11,respectively). Meat mass index significantly decreased from September 2012 to February 2013 coinciding with the period of high GBI-values. The distribution of oocyte maturity stages differed between diets. The majority of oocytes within S-diet-fed abalone were fully mature stage 8 oocytes compared to a majority of stage 7 oocytes in F-diet-fed abalone. Histology corroborated peaks in GBI-values for abalone fed both diets. There was no significant difference in growth, GBI, visceral index (%) and meat mass index (%) between abalone sorted into monosex and mixed-sex populations. Thus, the presence of the opposite sex did not have an effect on growth and gonad mass in H. midae. The phytoestrogens daidzin, glycitin, genistin, daidzein, glycitein and genistein were present in soybean meal and only traceable amounts were found in the F-diet. This study provided evidence that soybean meal present in formulated feed affected growth and gonad development in H.midae. The difference in the distribution of the maturity stages of oocytes was affected by diet. Sex-sorting abalone into monosex and mixed-sex populations had no influence on weight and length gain and gonad development.
- Full Text:
- Date Issued: 2014
Genetic and morphometric variation of Octopus vulgaris in the Benguela Current region
- Authors: De Beer, Chénelle Lesley
- Date: 2014
- Subjects: Common octopus -- Africa, Southern , Common octopus -- Genetics , Common octopus -- Morphology , Common octopus -- Geographical distribution , Variation (Biology) , Benguela Current
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5362 , http://hdl.handle.net/10962/d1012971
- Description: The Benguela Current is a cold eastern boundary current located on the south-western coast of the African continent. The establishment of its present day features approximately two million years ago has triggered allopatric events which have driven genetic and/or phenotypic differentiation in many of the warm-temperate organisms that previously had continuous distributions along the south and west coast of southern Africa. However, since many of these species have responded differently, despite similar isolation times, research in this region provides a unique opportunity to increase our understanding of evolutionary processes. The common octopus (Octopus vulgaris, Cuvier 1797) is a coastal, sedentary species, inhabiting coral reefs or rocky environments at depths of up to a 100m. It is considered to be one of the most extensively studied cephalopod species due to its worldwide distribution. However, very little research has been conducted on O. vulgaris in southern Africa. In order to gain a holistic understanding of the effects of the Benguela Current on population connectivity, genetic and phenotypic diversity, and evolutionary history of O. vulgaris, a comparative genetic and morphological study was conducted across the Benguela region. A total of 168 specimens of O. vulgaris were collected from four different regions across the Benguela system. A small tissue sample was preserved in ethanol for molecular analysis, and the specimen was frozen whole for morphometric analysis in the laboratory. Octopus vulgaris genetic population structure and evolutionary history was investigated using a 580bp fragment of the mitochondrial cytochrome b (cytb) gene for 76 individuals located within the Benguela region, yielding 10 different haplotypes. AMOVA and pairwise FST analyses revealed significant genetic differentiation suggesting a northern-southern Benguela divergence. Estimates of time since most recent common ancestor, based on biogeographical calibrators and coalescent analyses, indicated that isolation between the Angolan and South African population occurred between ~231 Ka and 1 Ma. Mismatch distribution analyses revealed a past population expansion within the South African O. vulgaris roughly 129.31 Ka, whilst Bayesian skyline plots were indicative of gradual demographic growth within the Angolan population in the last ~100 Ka. Observed O. vulgaris population structure and demographic history was likely the result of historical climate-induced change within the system. Reconstruction of phylogenetic relationships within the Octopus genus, using cytb and COI suggest that O. vulgaris is not a monophyletic group and a major systematic revision is required. Furthermore, unidentified individuals from South Africa were found to group with species from Indo-West Pacific Oceans and were therefore considered to have been translocated through ballast water from Asia. While the molecular analysis indicated a significant northern-southern Benguela structure results from the principle component analysis (PCA) and discriminate function analysis (DFA) were unable to distinguish between O. vulgaris from different sampling localities throughout the Benguela Current region based on soft-parts, hard-parts and meristic characters. The lack of phenotypic variation, despite significant genetic divergence, highlights the importance of multi-method approaches in gaining a holistic understanding of the taxonomy and biogeography of species.
- Full Text:
- Date Issued: 2014
- Authors: De Beer, Chénelle Lesley
- Date: 2014
- Subjects: Common octopus -- Africa, Southern , Common octopus -- Genetics , Common octopus -- Morphology , Common octopus -- Geographical distribution , Variation (Biology) , Benguela Current
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5362 , http://hdl.handle.net/10962/d1012971
- Description: The Benguela Current is a cold eastern boundary current located on the south-western coast of the African continent. The establishment of its present day features approximately two million years ago has triggered allopatric events which have driven genetic and/or phenotypic differentiation in many of the warm-temperate organisms that previously had continuous distributions along the south and west coast of southern Africa. However, since many of these species have responded differently, despite similar isolation times, research in this region provides a unique opportunity to increase our understanding of evolutionary processes. The common octopus (Octopus vulgaris, Cuvier 1797) is a coastal, sedentary species, inhabiting coral reefs or rocky environments at depths of up to a 100m. It is considered to be one of the most extensively studied cephalopod species due to its worldwide distribution. However, very little research has been conducted on O. vulgaris in southern Africa. In order to gain a holistic understanding of the effects of the Benguela Current on population connectivity, genetic and phenotypic diversity, and evolutionary history of O. vulgaris, a comparative genetic and morphological study was conducted across the Benguela region. A total of 168 specimens of O. vulgaris were collected from four different regions across the Benguela system. A small tissue sample was preserved in ethanol for molecular analysis, and the specimen was frozen whole for morphometric analysis in the laboratory. Octopus vulgaris genetic population structure and evolutionary history was investigated using a 580bp fragment of the mitochondrial cytochrome b (cytb) gene for 76 individuals located within the Benguela region, yielding 10 different haplotypes. AMOVA and pairwise FST analyses revealed significant genetic differentiation suggesting a northern-southern Benguela divergence. Estimates of time since most recent common ancestor, based on biogeographical calibrators and coalescent analyses, indicated that isolation between the Angolan and South African population occurred between ~231 Ka and 1 Ma. Mismatch distribution analyses revealed a past population expansion within the South African O. vulgaris roughly 129.31 Ka, whilst Bayesian skyline plots were indicative of gradual demographic growth within the Angolan population in the last ~100 Ka. Observed O. vulgaris population structure and demographic history was likely the result of historical climate-induced change within the system. Reconstruction of phylogenetic relationships within the Octopus genus, using cytb and COI suggest that O. vulgaris is not a monophyletic group and a major systematic revision is required. Furthermore, unidentified individuals from South Africa were found to group with species from Indo-West Pacific Oceans and were therefore considered to have been translocated through ballast water from Asia. While the molecular analysis indicated a significant northern-southern Benguela structure results from the principle component analysis (PCA) and discriminate function analysis (DFA) were unable to distinguish between O. vulgaris from different sampling localities throughout the Benguela Current region based on soft-parts, hard-parts and meristic characters. The lack of phenotypic variation, despite significant genetic divergence, highlights the importance of multi-method approaches in gaining a holistic understanding of the taxonomy and biogeography of species.
- Full Text:
- Date Issued: 2014
Modelling the spatial and genetic response of the endemic sparid: Polysteganus praeorbitalis (Pisces: Sparidae) to climate change in the Agulhas Current system
- Authors: Isemonger, Devin Neil
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54509 , vital:26576
- Description: The Scotsman Seabream, Polysteganus praeorbitalis, is one of several large, slow-growing members of the Sparidae family of fishes endemic to the Agulhas Current system in the Western Indian Ocean (WIO). Relatively little research has been conducted on this species despite its importance to both recreational and commercial line fisheries in South Africa and the drastic decline in catch per unit effort (CPUE) that has been recorded since the 1940s. Changing sea temperatures as a result of global climate change are further expected to affect the distribution and abundance of many fish species based on their thermal tolerances, life histories and population structures. The ability of these species to shift their distribution and adapt to new environments and thermal conditions will depend to some degree on the levels of genetic variation and gene flow, within and between populations. A combined approach using species distribution modelling and genetic analyses may prove to be a useful tool in investigating the potential effects of climate change on the distribution and genetic diversity of species. An ensemble species distribution model (SDM) based on 205 occurrence records and 30 years of Reynolds Optimum Interpolated (OI) sea surface temperature data was constructed to predict the distributional response of P. praeorbitalis to climate change in the Agulhas Current system. The ensemble SDM displayed a true skill statistic (TSS) of 0.975 and an area under the receiver operating curve (ROC) of 0.999, indicating good model fit. Autumn and winter minimum temperatures, as well as bathymetry, were the most important predictor variables in the majority of models, indicating that these variables may directly constrain the distribution of P. praeorbitalis. In particular, the southern range edge of this species appeared to be constrained by autumn and winter minima, with high model agreement on this range edge. Conversely, the northern range limit showed poor model agreement leading to a gradual reduction in occurrence. This indicates that this range edge may be constrained by other factors not included in the models such as species interactions. The ensemble SDM projected the current range of P. praeorbitalis to be 1500 km², smaller than the published range for this species. The model underestimated the northern range edge of this species by approximately 5° latitude when binary transformed. This is probably due to the rarity of this species in the landings of the Mozambican linefishery, which was assumed to be an indication of low abundance of P. praeorbitalis in these waters. The absence of a specimen to verify the published northern range edge of this species indicates that the northern range edge produced by this model is likely to be closer to the actual range limit of the species. A range contraction of 30% occurring at both the northern and southern edge of P. praeorbitalis’ range and range fragmentation occurring, towards its northern range edge by 2030, was predicted. These changes are modelled to be the results of cooling related to the intensification of the Port Alfred upwelling cell and of warming predicted north of the Natal Bight and in southern Mozambique. Genetic analyses of the nuclear DNA (nDNA) S7 intron 1 and mitochondrial DNA (mtDNA) control region genes were carried out using 118 tissue samples of P. praeorbitalis collected at four main localities: the Eastern Cape, Transkei, southern KwaZulu-Natal and northern KwaZulu-Natal. Analyses of genetic diversity levels revealed relatively low diversity in the mtDNA dataset (Hd = 0.488; π = 0.004) and moderate levels of diversity in the nDNA dataset (Ad = 0.922; π = 0.005). The low levels of diversity observed in the mtDNA dataset might be explained by a number of factors, including high variation in spawning success, the negative effects of over-harvesting, or a recent population bottleneck. The last explanation is supported by characteristic star-shaped haplotype networks and unimodal mismatch distributions displayed by both datasets. These results, in conjunction with a significant (p = 0.005) negative Tajimas D value (-2.029) in the mtDNA dataset and significant (p = 0.0005) negative Fu’s F statistic in both the nDNA (F = -26.5) and mtDNA (F = -11.9) datasets, provide strong evidence for a recent population expansion after a bottleneck event in this species. Spatially, mtDNA diversity was highest in the Eastern Cape and lowest in the middle localities, while nDNA diversity showed the opposite pattern. These results may be indicative of differences in the sex ratio between localities, possibly as a result of the protogynous hermaphroditism that has been postulated for this species. Although pairwise comparisons and exact tests of population differentiation revealed no significant geneticdifferentiation between populations in the mtDNA dataset, there was some evidence of low levels of differentiation in the nDNA dataset. This occurred for comparisons between the Eastern Cape and Transkei (Fst = 0.039; p <0.05), and the northern KwaZulu-Natal (Fst = 0.045; p < 0.05).. This might be the result of one or a combination of factors including the effects of the Port Alfred upwelling cell on dispersal and gene flow, or the possibility of more than one spawning ground for this species promoting sub-structuring. A SAMOVA analyses run on the nDNA dataset maximised variance by grouping the Eastern Cape and southern KwaZulu-Natal together and Transkei and northern KwaZulu-Natal together in two groups. This revealed no evidence of spatial structure (p = 0.36), with only 3.30% of variation explained by this grouping. The removal of individuals below the estimated length at 50% maturity in the nDNA dataset, in order to test for temporal structure, resulted in stronger evidence of differentiation between the Eastern Cape and all other localities: Transkei (Fst = 0.081; p< 0.05), southern KwaZulu-Natal (Fst = 0.031; p<0.05), and northern KwaZulu-Natal (Fst = 0.078; p< 0.05). This indicates that some temporal genetic structure may exist between age classes within this species. The differentiation observed between the Eastern Cape and other localities, coupled with the high percentage of private haplotypes in the mtDNA dataset in this locality, indicates that this area is where P. praeorbitalis is most vulnerable to the potential negative effects of climate change on its genetic diversity. However, the vast majority of this species genetic diversity appears to reside towards the centre of its range where it is most abundant and the lack of strong genetic structure indicates high levels of gene flow. In conclusion, while P. praeorbitalis is vulnerable to range loss as a result of climate change, its genetic diversity is unlikely to be greatly affected.
- Full Text:
- Date Issued: 2014
- Authors: Isemonger, Devin Neil
- Date: 2014
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54509 , vital:26576
- Description: The Scotsman Seabream, Polysteganus praeorbitalis, is one of several large, slow-growing members of the Sparidae family of fishes endemic to the Agulhas Current system in the Western Indian Ocean (WIO). Relatively little research has been conducted on this species despite its importance to both recreational and commercial line fisheries in South Africa and the drastic decline in catch per unit effort (CPUE) that has been recorded since the 1940s. Changing sea temperatures as a result of global climate change are further expected to affect the distribution and abundance of many fish species based on their thermal tolerances, life histories and population structures. The ability of these species to shift their distribution and adapt to new environments and thermal conditions will depend to some degree on the levels of genetic variation and gene flow, within and between populations. A combined approach using species distribution modelling and genetic analyses may prove to be a useful tool in investigating the potential effects of climate change on the distribution and genetic diversity of species. An ensemble species distribution model (SDM) based on 205 occurrence records and 30 years of Reynolds Optimum Interpolated (OI) sea surface temperature data was constructed to predict the distributional response of P. praeorbitalis to climate change in the Agulhas Current system. The ensemble SDM displayed a true skill statistic (TSS) of 0.975 and an area under the receiver operating curve (ROC) of 0.999, indicating good model fit. Autumn and winter minimum temperatures, as well as bathymetry, were the most important predictor variables in the majority of models, indicating that these variables may directly constrain the distribution of P. praeorbitalis. In particular, the southern range edge of this species appeared to be constrained by autumn and winter minima, with high model agreement on this range edge. Conversely, the northern range limit showed poor model agreement leading to a gradual reduction in occurrence. This indicates that this range edge may be constrained by other factors not included in the models such as species interactions. The ensemble SDM projected the current range of P. praeorbitalis to be 1500 km², smaller than the published range for this species. The model underestimated the northern range edge of this species by approximately 5° latitude when binary transformed. This is probably due to the rarity of this species in the landings of the Mozambican linefishery, which was assumed to be an indication of low abundance of P. praeorbitalis in these waters. The absence of a specimen to verify the published northern range edge of this species indicates that the northern range edge produced by this model is likely to be closer to the actual range limit of the species. A range contraction of 30% occurring at both the northern and southern edge of P. praeorbitalis’ range and range fragmentation occurring, towards its northern range edge by 2030, was predicted. These changes are modelled to be the results of cooling related to the intensification of the Port Alfred upwelling cell and of warming predicted north of the Natal Bight and in southern Mozambique. Genetic analyses of the nuclear DNA (nDNA) S7 intron 1 and mitochondrial DNA (mtDNA) control region genes were carried out using 118 tissue samples of P. praeorbitalis collected at four main localities: the Eastern Cape, Transkei, southern KwaZulu-Natal and northern KwaZulu-Natal. Analyses of genetic diversity levels revealed relatively low diversity in the mtDNA dataset (Hd = 0.488; π = 0.004) and moderate levels of diversity in the nDNA dataset (Ad = 0.922; π = 0.005). The low levels of diversity observed in the mtDNA dataset might be explained by a number of factors, including high variation in spawning success, the negative effects of over-harvesting, or a recent population bottleneck. The last explanation is supported by characteristic star-shaped haplotype networks and unimodal mismatch distributions displayed by both datasets. These results, in conjunction with a significant (p = 0.005) negative Tajimas D value (-2.029) in the mtDNA dataset and significant (p = 0.0005) negative Fu’s F statistic in both the nDNA (F = -26.5) and mtDNA (F = -11.9) datasets, provide strong evidence for a recent population expansion after a bottleneck event in this species. Spatially, mtDNA diversity was highest in the Eastern Cape and lowest in the middle localities, while nDNA diversity showed the opposite pattern. These results may be indicative of differences in the sex ratio between localities, possibly as a result of the protogynous hermaphroditism that has been postulated for this species. Although pairwise comparisons and exact tests of population differentiation revealed no significant geneticdifferentiation between populations in the mtDNA dataset, there was some evidence of low levels of differentiation in the nDNA dataset. This occurred for comparisons between the Eastern Cape and Transkei (Fst = 0.039; p <0.05), and the northern KwaZulu-Natal (Fst = 0.045; p < 0.05).. This might be the result of one or a combination of factors including the effects of the Port Alfred upwelling cell on dispersal and gene flow, or the possibility of more than one spawning ground for this species promoting sub-structuring. A SAMOVA analyses run on the nDNA dataset maximised variance by grouping the Eastern Cape and southern KwaZulu-Natal together and Transkei and northern KwaZulu-Natal together in two groups. This revealed no evidence of spatial structure (p = 0.36), with only 3.30% of variation explained by this grouping. The removal of individuals below the estimated length at 50% maturity in the nDNA dataset, in order to test for temporal structure, resulted in stronger evidence of differentiation between the Eastern Cape and all other localities: Transkei (Fst = 0.081; p< 0.05), southern KwaZulu-Natal (Fst = 0.031; p<0.05), and northern KwaZulu-Natal (Fst = 0.078; p< 0.05). This indicates that some temporal genetic structure may exist between age classes within this species. The differentiation observed between the Eastern Cape and other localities, coupled with the high percentage of private haplotypes in the mtDNA dataset in this locality, indicates that this area is where P. praeorbitalis is most vulnerable to the potential negative effects of climate change on its genetic diversity. However, the vast majority of this species genetic diversity appears to reside towards the centre of its range where it is most abundant and the lack of strong genetic structure indicates high levels of gene flow. In conclusion, while P. praeorbitalis is vulnerable to range loss as a result of climate change, its genetic diversity is unlikely to be greatly affected.
- Full Text:
- Date Issued: 2014
Molecular systematics and antifreeze biology of sub-Antarctic notothenioid fishes
- Authors: Miya, Tshoanelo Portia
- Date: 2014
- Subjects: Nototheniidae , Antifreeze proteins , Nototheniidae -- Classification -- Molecular aspects , Polyacrylamide gel electrophoresis
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5388 , http://hdl.handle.net/10962/d1020938
- Description: Fishes of the perciform suborder Notothenioidei are found in Antarctic and sub-Antarctic waters that are separated by the Antarctic Polar Front (APF), with some species being distributed on both sides of this front. In this wide latitudinal range, these fishes are exposed to different temperatures ranging from -2 °C in the High Antarctic regions to 12 °C in the sub-Antarctic regions. To survive in icy Antarctic waters, the Antarctic notothenioid species have evolved antifreeze glycoproteins (AFGPs) that prevent their body fluids from freezing. The findings of past research on the AFGP attributes of several notothenioid species inhabiting ice-free sub-Antarctic environments have presented a complex picture. Furthermore, previous taxonomic studies split widely distributed notothenioids into different species and/or subspecies, with other studies disagreeing with these splits. To understand the response of the sub-Antarctic notothenioids to warmer, ice-free environments, it is necessary to have a good understanding of their antifreeze biology and systematics. Therefore, this study aimed to determine the association, if any, between the antifreeze attributes of sub-Antarctic notothenioid fishes and their taxonomic status. And more...
- Full Text:
- Date Issued: 2014
- Authors: Miya, Tshoanelo Portia
- Date: 2014
- Subjects: Nototheniidae , Antifreeze proteins , Nototheniidae -- Classification -- Molecular aspects , Polyacrylamide gel electrophoresis
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5388 , http://hdl.handle.net/10962/d1020938
- Description: Fishes of the perciform suborder Notothenioidei are found in Antarctic and sub-Antarctic waters that are separated by the Antarctic Polar Front (APF), with some species being distributed on both sides of this front. In this wide latitudinal range, these fishes are exposed to different temperatures ranging from -2 °C in the High Antarctic regions to 12 °C in the sub-Antarctic regions. To survive in icy Antarctic waters, the Antarctic notothenioid species have evolved antifreeze glycoproteins (AFGPs) that prevent their body fluids from freezing. The findings of past research on the AFGP attributes of several notothenioid species inhabiting ice-free sub-Antarctic environments have presented a complex picture. Furthermore, previous taxonomic studies split widely distributed notothenioids into different species and/or subspecies, with other studies disagreeing with these splits. To understand the response of the sub-Antarctic notothenioids to warmer, ice-free environments, it is necessary to have a good understanding of their antifreeze biology and systematics. Therefore, this study aimed to determine the association, if any, between the antifreeze attributes of sub-Antarctic notothenioid fishes and their taxonomic status. And more...
- Full Text:
- Date Issued: 2014
Prioritising native fish populations for conservation using genetics in the Groot Marico catchment, North West Province, South Africa
- Authors: Van der Walt, Kerry-Ann
- Date: 2014
- Subjects: Native fishes Fishery management -- South Africa -- North West Fish populations Fishes -- Conservation -- South Africa -- Western Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/69102 , vital:29390
- Description: The Groot Marico catchment in the North West Province is a National Freshwater Ecosystem Priority Area (NFEPA) because it represents unique landscape features with unique biodiversity that are considered to be of special ecological significance. Three native freshwater species Amphilius uranoscopus, Chiloglanis pretoriae and Barbus motebensis, have high local conservation importance and B. motebensis is endemic to the catchment and is IUCN-listed as vulnerable. The main objective of this study is to contribute towards the effective conservation of these three species in the Groot Marico River system by assessing their genetic structure to determine whether tributary populations of the three species comprise of one genetic population or whether they are divided into genetically distinct subpopulations, in order to prioritise areas for conservation. The central null hypothesis was that there is no genetic differentiation between tributary populations (i.e., panmixia) of B. motebensis, A. uranoscopus and C. pretoriae in the Groot Marico catchment, North West Province. In total, 80 individuals per species were collected, targeting at least 10 individuals per population from a total of eight populations (seven tributaries and the Groot Marico main stem) and across the study area. Samples were collected by electrofishing and specimens were euthanized using an overdose of clove oil. A sample of muscle tissue was removed for genetic evaluation and the remainder of the specimens served as voucher specimens. For the genetic evaluation, mitochondrial (ND2, cyt b) and nuclear (S7) genes were used. Genetic techniques used were DNA extraction, polymerase chain reaction (PCR), purification and sequencing. From the 240 individuals collected, 123 sequences for B. motebensis, 111 sequences for A. uranoscopus and 103 sequences for C. pretoriae were analysed across all three genes. Statistical analysis included looking at cleaned sequences in order to obtain models using MODELTEST (version 3.06). Population structuring and phylogeographic analysis was performed in Arlequin (version 2000), TCS (version 1.2.1) and PAUP*. Results indicated that for B. motebensis the null hypothesis could be rejected as there were two distinct lineages (the Draai and Eastern lineages) that demonstrated significant divergence in both the ND2 and S7 genes, suggesting historical isolation. The low divergence in the mitochondrial cytochrome b gene (0% < D < 0.8%) suggests that this isolation is not very old and is probably not comparable to species level differentiation. The null hypothesis was also rejected for A. uranoscopus as there were also significant levels of differentiation between tributary populations resulting in the identification of two lineages (the Ribbok and Western lineages). However, for C. pretoriae, the null hypothesis could not be rejected as there was no genetic differentiation between tributary populations i.e., one panmictic population. Therefore, due to each species showing different genetic structuring within the tributary populations, more than one priority area for conservation needs to be implemented. These priority areas of conservation where therefore evaluated based on the current conservation status of the species (B. motebensis being vulnerable on the IUCN Red List), the number of Evolutionary Significant Units for each species and the overall genetic diversity of all three species in the Groot Marico catchment. In total, four tributary populations were conservation priorities areas, these were the Draai, Vanstraatens, Ribbok and Kaaloog tributaries. The Draai, Vanstraatens and Kaaloog tributaries were selected as priority areas for B. motebensis (B. motebensis is considered to be the most vulnerable of all three species). The Draai tributary was selected due to the B. motebensis population within the tributary showing isolation from the rest of the tributary populations. In order to conserve B. motebensis from the Southern lineage, the Vanstraatens and Kaaloog tributaries were selected. Reasons for selecting these two specific tributaries within the Southern lineage were that the Vanstraatens tributary had unique alleles (three Evolutionary Significant Units) for B. motebensis and the Kaaloog tributary had high genetic diversity (HD = 0.889, ND2 gene) when compared to the other tributary populations. The Ribbok and Vanstraatens tributaries were selected as priority areas for the conservation of A. uranoscopus. The Ribbok tributary was selected as it showed isolation from the rest of the tributary populations, as seen with the Draai tributary (B. motebensis) and the Vanstraatens tributary was selected to represent the Western lineage as it had the highest diversity for both genes (ND2 and S7). The Ribbok tributary has the highest prioritisation when compared to the Vanstraatens tributary. Chiloglanis pretoriae occurs within the Draai, Vanstraatens, Ribbok and Kaaloog tributaries, therefore by prioritising these tributaries for conservation, C. pretoriae will in turn be conserved.
- Full Text:
- Date Issued: 2014
- Authors: Van der Walt, Kerry-Ann
- Date: 2014
- Subjects: Native fishes Fishery management -- South Africa -- North West Fish populations Fishes -- Conservation -- South Africa -- Western Cape
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/69102 , vital:29390
- Description: The Groot Marico catchment in the North West Province is a National Freshwater Ecosystem Priority Area (NFEPA) because it represents unique landscape features with unique biodiversity that are considered to be of special ecological significance. Three native freshwater species Amphilius uranoscopus, Chiloglanis pretoriae and Barbus motebensis, have high local conservation importance and B. motebensis is endemic to the catchment and is IUCN-listed as vulnerable. The main objective of this study is to contribute towards the effective conservation of these three species in the Groot Marico River system by assessing their genetic structure to determine whether tributary populations of the three species comprise of one genetic population or whether they are divided into genetically distinct subpopulations, in order to prioritise areas for conservation. The central null hypothesis was that there is no genetic differentiation between tributary populations (i.e., panmixia) of B. motebensis, A. uranoscopus and C. pretoriae in the Groot Marico catchment, North West Province. In total, 80 individuals per species were collected, targeting at least 10 individuals per population from a total of eight populations (seven tributaries and the Groot Marico main stem) and across the study area. Samples were collected by electrofishing and specimens were euthanized using an overdose of clove oil. A sample of muscle tissue was removed for genetic evaluation and the remainder of the specimens served as voucher specimens. For the genetic evaluation, mitochondrial (ND2, cyt b) and nuclear (S7) genes were used. Genetic techniques used were DNA extraction, polymerase chain reaction (PCR), purification and sequencing. From the 240 individuals collected, 123 sequences for B. motebensis, 111 sequences for A. uranoscopus and 103 sequences for C. pretoriae were analysed across all three genes. Statistical analysis included looking at cleaned sequences in order to obtain models using MODELTEST (version 3.06). Population structuring and phylogeographic analysis was performed in Arlequin (version 2000), TCS (version 1.2.1) and PAUP*. Results indicated that for B. motebensis the null hypothesis could be rejected as there were two distinct lineages (the Draai and Eastern lineages) that demonstrated significant divergence in both the ND2 and S7 genes, suggesting historical isolation. The low divergence in the mitochondrial cytochrome b gene (0% < D < 0.8%) suggests that this isolation is not very old and is probably not comparable to species level differentiation. The null hypothesis was also rejected for A. uranoscopus as there were also significant levels of differentiation between tributary populations resulting in the identification of two lineages (the Ribbok and Western lineages). However, for C. pretoriae, the null hypothesis could not be rejected as there was no genetic differentiation between tributary populations i.e., one panmictic population. Therefore, due to each species showing different genetic structuring within the tributary populations, more than one priority area for conservation needs to be implemented. These priority areas of conservation where therefore evaluated based on the current conservation status of the species (B. motebensis being vulnerable on the IUCN Red List), the number of Evolutionary Significant Units for each species and the overall genetic diversity of all three species in the Groot Marico catchment. In total, four tributary populations were conservation priorities areas, these were the Draai, Vanstraatens, Ribbok and Kaaloog tributaries. The Draai, Vanstraatens and Kaaloog tributaries were selected as priority areas for B. motebensis (B. motebensis is considered to be the most vulnerable of all three species). The Draai tributary was selected due to the B. motebensis population within the tributary showing isolation from the rest of the tributary populations. In order to conserve B. motebensis from the Southern lineage, the Vanstraatens and Kaaloog tributaries were selected. Reasons for selecting these two specific tributaries within the Southern lineage were that the Vanstraatens tributary had unique alleles (three Evolutionary Significant Units) for B. motebensis and the Kaaloog tributary had high genetic diversity (HD = 0.889, ND2 gene) when compared to the other tributary populations. The Ribbok and Vanstraatens tributaries were selected as priority areas for the conservation of A. uranoscopus. The Ribbok tributary was selected as it showed isolation from the rest of the tributary populations, as seen with the Draai tributary (B. motebensis) and the Vanstraatens tributary was selected to represent the Western lineage as it had the highest diversity for both genes (ND2 and S7). The Ribbok tributary has the highest prioritisation when compared to the Vanstraatens tributary. Chiloglanis pretoriae occurs within the Draai, Vanstraatens, Ribbok and Kaaloog tributaries, therefore by prioritising these tributaries for conservation, C. pretoriae will in turn be conserved.
- Full Text:
- Date Issued: 2014
Regional connectivity, differentiation and biogeography of three species of the genus Lutjanus in the western Indian Ocean
- Authors: Morallana, Jonas Moqebelo
- Date: 2014
- Subjects: Lutjanus -- Indian Ocean , Biogeography -- Indian Ocean , Phylogeography -- Indian Ocean , Lutjanus -- Geographical distribution , Lutjanus -- Variation , Mitochondrial DNA , Animal genetics , Variation (Biology)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5369 , http://hdl.handle.net/10962/d1013293
- Description: Snappers of the genus Lutjanus are small to large predatory fishes occurring in inshore circumtropical and subtropical waters throughout the world. These fishes support fisheries across their distribution range. Within the Western Indian Ocean (WIO), previous studies on Lutjanus kasmira revealed limited spatial genetic differentiation, whereas Lutjanus fulviflamma showed high genetic connectivity. The phylogenetic relationships among WIO snappers are unknown. Previous studies in the Indo-Pacific (IP) did not include any WIO representatives. This study examined (1) the phylogeographic patterns in Lutjanus bohar, L. fulviflamma and L. lutjanus to understand the origins and factors influencing the distribution of diversity in the region, (2) how the physical environment, biological, and ecological factors influence genetic diversity, (3) the placement of WIO snappers in context to those from the IP, as well as the placement of taxa not included previously, (4) extent of differentiation among conspecifics from the two regions, and (5) the relationship of the Caesionidae to the Lutjanidae. Samples were sourced from across the WIO and from peripheral localities, where possible. DNA sequence data were generated from two mitochondrial gene regions (cyt-b and NADH-2) and a nuclear gene region (S7 intron 1). Data were analysed under a phylogeographic framework to examine genetic structure, diversity and differentiation among identified regions for each of the three species. Other sequence data were generated from two mitochondrial gene regions (COII and 16S rDNA) to examine the phylogenetic placement of WIO snappers in context of the IP snappers and the relationship of the Caesionidae to the Lutjanidae. Lutjanus bohar and L. fulviflamma displayed high genetic diversity, but lower diversities were observed for L. lutjanus. Genetic differentiation was observed between Mozambique and Maldives in L. bohar. Lutjanus fulviflamma was differentiated in South Africa, Mozambique, Mauritius and Thailand, while differentiation was observed between Kenya and Tanzania in Lutjanus lutjanus. Overall, low genetic differentiation and high connectivity were observed for each of the three species. This differentiation may result from intrinsic features of the species and extrinsic features of the environment, whereas the connectivity is mainly influenced by the pelagic larval duration. These patterns of differentiation are in accordance with a proposed vicariant biogeographic hypothesis for the origins of regional faunas of the IP. Phylogenies were similar to those published, with additional taxa not altering the previous groupings found. Conspecifics from the two regions clustered together, with varying degrees of differentiation among the WIO and IP, depending on the species. Members of the Caesionidae were nested within Lutjanidae, suggesting that morphological characters separating the two families are taxonomically insignificant. This affirms previous notions that the Caesionidae should be a subfamily within the Lutjanidae. This is the first multi-gene study, examining differentiation in multiple species of snapper over a wide geographic area in the WIO, and the results of this study could have potential implications for fisheries management and conservation.
- Full Text:
- Date Issued: 2014
- Authors: Morallana, Jonas Moqebelo
- Date: 2014
- Subjects: Lutjanus -- Indian Ocean , Biogeography -- Indian Ocean , Phylogeography -- Indian Ocean , Lutjanus -- Geographical distribution , Lutjanus -- Variation , Mitochondrial DNA , Animal genetics , Variation (Biology)
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5369 , http://hdl.handle.net/10962/d1013293
- Description: Snappers of the genus Lutjanus are small to large predatory fishes occurring in inshore circumtropical and subtropical waters throughout the world. These fishes support fisheries across their distribution range. Within the Western Indian Ocean (WIO), previous studies on Lutjanus kasmira revealed limited spatial genetic differentiation, whereas Lutjanus fulviflamma showed high genetic connectivity. The phylogenetic relationships among WIO snappers are unknown. Previous studies in the Indo-Pacific (IP) did not include any WIO representatives. This study examined (1) the phylogeographic patterns in Lutjanus bohar, L. fulviflamma and L. lutjanus to understand the origins and factors influencing the distribution of diversity in the region, (2) how the physical environment, biological, and ecological factors influence genetic diversity, (3) the placement of WIO snappers in context to those from the IP, as well as the placement of taxa not included previously, (4) extent of differentiation among conspecifics from the two regions, and (5) the relationship of the Caesionidae to the Lutjanidae. Samples were sourced from across the WIO and from peripheral localities, where possible. DNA sequence data were generated from two mitochondrial gene regions (cyt-b and NADH-2) and a nuclear gene region (S7 intron 1). Data were analysed under a phylogeographic framework to examine genetic structure, diversity and differentiation among identified regions for each of the three species. Other sequence data were generated from two mitochondrial gene regions (COII and 16S rDNA) to examine the phylogenetic placement of WIO snappers in context of the IP snappers and the relationship of the Caesionidae to the Lutjanidae. Lutjanus bohar and L. fulviflamma displayed high genetic diversity, but lower diversities were observed for L. lutjanus. Genetic differentiation was observed between Mozambique and Maldives in L. bohar. Lutjanus fulviflamma was differentiated in South Africa, Mozambique, Mauritius and Thailand, while differentiation was observed between Kenya and Tanzania in Lutjanus lutjanus. Overall, low genetic differentiation and high connectivity were observed for each of the three species. This differentiation may result from intrinsic features of the species and extrinsic features of the environment, whereas the connectivity is mainly influenced by the pelagic larval duration. These patterns of differentiation are in accordance with a proposed vicariant biogeographic hypothesis for the origins of regional faunas of the IP. Phylogenies were similar to those published, with additional taxa not altering the previous groupings found. Conspecifics from the two regions clustered together, with varying degrees of differentiation among the WIO and IP, depending on the species. Members of the Caesionidae were nested within Lutjanidae, suggesting that morphological characters separating the two families are taxonomically insignificant. This affirms previous notions that the Caesionidae should be a subfamily within the Lutjanidae. This is the first multi-gene study, examining differentiation in multiple species of snapper over a wide geographic area in the WIO, and the results of this study could have potential implications for fisheries management and conservation.
- Full Text:
- Date Issued: 2014
Taxonomy and life history of the zebra seabream, Diplodus cervinus (Perciformes: Sparidae), in southern Angola
- Authors: Winkler, Alexander Claus
- Date: 2014
- Subjects: Diplodus -- Classification Fish populations -- Angola Diplodus -- Angola Diplodus -- South Africa Diplodus -- Morphology Fisheries -- Angola Sparidae
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:5361 , http://hdl.handle.net/10962/d1012062
- Description: The zebra sea bream, Diplodus cervinus (Sparidae) is an inshore fish comprised of two boreal subspecies from the Gulf of Oman and the Mediterranean / north eastern Atlantic and one austral subspecies from South Africa and southern Angola. The assumption of a single austral subspecies has, however, been questioned due to mounting molecular and morphological evidence suggesting that the cool Benguela current is a vicariant barrier that has separated many synonymous inshore fish species between South Africa and southern Angola. The aims of this thesis are to conduct a comparative morphological analysis of Diplodus cervinus in southern Angola and South Africa in order to classify the southern Angolan population and then to conduct a life history assessment to assess the life history impact of allopatry on this species between the two regions. Results of the morphological findings of the present study (ANOSIM, p < 0.05, Rmeristic = 0.42) and (Rmorphometric = 0.30) along with a concurrent molecular study (FST = 0.4 – 0.6), identified significant divergence between specimens from South Africa (n = 25) and southern Angola (n = 37) and supported stock separation and possibly sub-speciation, depending on the classification criteria utilised. While samples from the two boreal subspecies were not available for the comparative morphological or molecular analysis, comparisons of the colouration patterns between the three subspecies, suggested similarity between the southern Angola and the northern Atlantic / Mediterranean populations. In contrast, the colouration patterns between the southern Angolan and South African specimens differed substantially, further supporting the morphological and molecular results. The distinct morphological divergence between the southern Angolan and South African populations was not reflected within the life history traits of both populations. A combination of methods, including length/age frequency analyses, adult sex ratios and histological analysis was used to determine that this species is a rudimentary hermaphrodite in southern Angola. Peak spawning season was observed between June and July. The overall sex ratio (M: F) was 1:1.52 with females dominating smaller younger size classes and 50% maturity was attained at 210 mm FL and 4.6 years. Females [L(t) = 287.5(1-e⁻°·¹⁸⁽t⁻²·⁸⁴⁾)] grew significantly faster (LRT, p < 0.05) than males [L(t) = 380.19(1-e⁻°·°⁶⁽t⁻⁷·¹²⁾)]. The higher maximum age of the southern Angolan population of D. cervinus (43 years) was older than that of South African individuals sampled in the tsitsikamma national park. The similarities in the life history of the two austral populations are probably a consequence of similar selective pressures in the similar warmtemperate habitats. Evidence to support the above comments was found in the feeding study which showed that the South African and Angolan populations were almost identical, with both populations feeding primarily on amphipods and polychaete worms throughout ontogeny. In contrast, the diet of their boreal conspecifics from the Mediterranean was different, where larger individuals tended to select larger, and more robust, prey items. The life history differences observed between the boreal and austral populations can be attributed to either sampling bias or environmental factors. Sampling biases included the use of different age and growth estimation techniques, while the environmental factors would include differential selective pressures most likely driven by different resource availability and exploitation. The present study provides crucial baseline life history information of a potentially exploitable species off southern Angola as well as information on the life history plasticity of the species. Unfortunately, the current lack of uniformity in the methods used to estimate life history parameters between studies conducted on the boreal and austral populations have complicated our understanding of the evolution of various life history trends in sparid fish. From a management perspective however, the results from the present study can be used to propose management strategies for an emerging trap fishery in southern Angola. Using a balanced exploitation fishery approach (harvesting up to the size-at-100% maturity), the size of the fish traps entrance was calculated based the morphological information from this and other small sparid species that are targeted and was estimated to be 62 mm.
- Full Text:
- Date Issued: 2014
- Authors: Winkler, Alexander Claus
- Date: 2014
- Subjects: Diplodus -- Classification Fish populations -- Angola Diplodus -- Angola Diplodus -- South Africa Diplodus -- Morphology Fisheries -- Angola Sparidae
- Language: English
- Type: Thesis , Masters , MA
- Identifier: vital:5361 , http://hdl.handle.net/10962/d1012062
- Description: The zebra sea bream, Diplodus cervinus (Sparidae) is an inshore fish comprised of two boreal subspecies from the Gulf of Oman and the Mediterranean / north eastern Atlantic and one austral subspecies from South Africa and southern Angola. The assumption of a single austral subspecies has, however, been questioned due to mounting molecular and morphological evidence suggesting that the cool Benguela current is a vicariant barrier that has separated many synonymous inshore fish species between South Africa and southern Angola. The aims of this thesis are to conduct a comparative morphological analysis of Diplodus cervinus in southern Angola and South Africa in order to classify the southern Angolan population and then to conduct a life history assessment to assess the life history impact of allopatry on this species between the two regions. Results of the morphological findings of the present study (ANOSIM, p < 0.05, Rmeristic = 0.42) and (Rmorphometric = 0.30) along with a concurrent molecular study (FST = 0.4 – 0.6), identified significant divergence between specimens from South Africa (n = 25) and southern Angola (n = 37) and supported stock separation and possibly sub-speciation, depending on the classification criteria utilised. While samples from the two boreal subspecies were not available for the comparative morphological or molecular analysis, comparisons of the colouration patterns between the three subspecies, suggested similarity between the southern Angola and the northern Atlantic / Mediterranean populations. In contrast, the colouration patterns between the southern Angolan and South African specimens differed substantially, further supporting the morphological and molecular results. The distinct morphological divergence between the southern Angolan and South African populations was not reflected within the life history traits of both populations. A combination of methods, including length/age frequency analyses, adult sex ratios and histological analysis was used to determine that this species is a rudimentary hermaphrodite in southern Angola. Peak spawning season was observed between June and July. The overall sex ratio (M: F) was 1:1.52 with females dominating smaller younger size classes and 50% maturity was attained at 210 mm FL and 4.6 years. Females [L(t) = 287.5(1-e⁻°·¹⁸⁽t⁻²·⁸⁴⁾)] grew significantly faster (LRT, p < 0.05) than males [L(t) = 380.19(1-e⁻°·°⁶⁽t⁻⁷·¹²⁾)]. The higher maximum age of the southern Angolan population of D. cervinus (43 years) was older than that of South African individuals sampled in the tsitsikamma national park. The similarities in the life history of the two austral populations are probably a consequence of similar selective pressures in the similar warmtemperate habitats. Evidence to support the above comments was found in the feeding study which showed that the South African and Angolan populations were almost identical, with both populations feeding primarily on amphipods and polychaete worms throughout ontogeny. In contrast, the diet of their boreal conspecifics from the Mediterranean was different, where larger individuals tended to select larger, and more robust, prey items. The life history differences observed between the boreal and austral populations can be attributed to either sampling bias or environmental factors. Sampling biases included the use of different age and growth estimation techniques, while the environmental factors would include differential selective pressures most likely driven by different resource availability and exploitation. The present study provides crucial baseline life history information of a potentially exploitable species off southern Angola as well as information on the life history plasticity of the species. Unfortunately, the current lack of uniformity in the methods used to estimate life history parameters between studies conducted on the boreal and austral populations have complicated our understanding of the evolution of various life history trends in sparid fish. From a management perspective however, the results from the present study can be used to propose management strategies for an emerging trap fishery in southern Angola. Using a balanced exploitation fishery approach (harvesting up to the size-at-100% maturity), the size of the fish traps entrance was calculated based the morphological information from this and other small sparid species that are targeted and was estimated to be 62 mm.
- Full Text:
- Date Issued: 2014
The genetic stock structure and distribution of Chrysoblephus Puniceus, a commercially important transboundary linefish species, endemic to the South West Indian Ocean
- Authors: Duncan, Murray Ian
- Date: 2014
- Subjects: Sparidae , Fishes -- Indian Ocean , Fish populations , Fishery management , Fish stock assessment -- South Africa , Fish stock assessment -- Mozambique , Overfishing , Habitat conservation , Fishes -- Genetics , Fishes -- Climatic factors , Fishes -- Variation , Fishes -- Migration
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5360 , http://hdl.handle.net/10962/d1011868 , Sparidae , Fishes -- Indian Ocean , Fish populations , Fishery management , Fish stock assessment -- South Africa , Fish stock assessment -- Mozambique , Overfishing , Habitat conservation , Fishes -- Genetics , Fishes -- Climatic factors , Fishes -- Variation , Fishes -- Migration
- Description: Chrysoblephus puniceus is an over-exploited linefish species, endemic to the coastlines off southern Mozambique and eastern South Africa. Over-exploitation and habitat loss are two of the biggest threats to the sustainability of fisheries globally. Assessing the genetic stock structure (a prerequisite for effective management) and predicting climate related range changes will provide a better understanding of these threats to C. puniceus which can be used to improve the sustainability of the fishery. Two hundred and eighty four genetic samples were collected from eight sampling sites between Ponta da Barra in Mozambique and Coffee Bay in South Africa. The mitochondrial control region and ten microsatellite loci were amplified to analyse the stock structure of C. puniceus. The majority of microsatellite and mtDNA pairwise population comparisons were not significant (P > 0.05) although Xai Xai and Inhaca populations had some significant population comparisons for mtDNA (P < 0.05). AMOVA did not explain any significant variation at the between groups hierarchical level for any pre-defined groupings except for a mtDNA grouping which separated out Xai Xai and Inhaca from other sampling sites. SAMOVA, isolation by distance tests, structure analysis, principle component analysis and spatial autocorrelation analysis all indicated a single population of C. puniceus as being most likely. The migrate-n analysis provided evidence of current driven larval transport, with net migration rates influenced by current dynamics.Two hundred and thirty six unique presence points of C. puniceus were correlated with seasonal maximum and minimum temperature data and bathymetry to model the current distribution and predict future distribution changes of the species up until 2030. Eight individual species distribution models were developed and combined into a mean ensemble model using the Biomod2 package. Winter minimum temperature was the most important variable in determining models outputs. Overall the ensemble model was accurate with a true skills statistic score of 0.962. Binary transformed mean ensemble models predicted a northern and southern range contraction of C. puniceus' distribution of 15 percent; by 2030. The mean ensemble probability of occurrence models indicated that C. puniceus' abundance is likely to decrease off the southern Mozambique coastline but remain high off KwaZulu-Natal. The results of the genetic analysis support the theory of external recruitment sustaining the KwaZulu Natal fishery for C. puniceus. While the high genetic diversity and connectivity may make C. puniceus more resilient to disturbances, the loss of 15 percent; distribution and 11 percent; genetic diversity by 2030 will increase the species vulnerability. The decrease in abundance of C. puniceus off southern Mozambique together with current widespread exploitation levels could result in the collapse of the fishery. A single transboundary stock of C. puniceus highlights the need for co-management of the species. A combined stock assessment between South Africa and Mozambique and the development of further Marine Protected Areas off southern Mozambique are suggested as management options to minimise the vulnerability of this species.
- Full Text:
- Date Issued: 2014
- Authors: Duncan, Murray Ian
- Date: 2014
- Subjects: Sparidae , Fishes -- Indian Ocean , Fish populations , Fishery management , Fish stock assessment -- South Africa , Fish stock assessment -- Mozambique , Overfishing , Habitat conservation , Fishes -- Genetics , Fishes -- Climatic factors , Fishes -- Variation , Fishes -- Migration
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5360 , http://hdl.handle.net/10962/d1011868 , Sparidae , Fishes -- Indian Ocean , Fish populations , Fishery management , Fish stock assessment -- South Africa , Fish stock assessment -- Mozambique , Overfishing , Habitat conservation , Fishes -- Genetics , Fishes -- Climatic factors , Fishes -- Variation , Fishes -- Migration
- Description: Chrysoblephus puniceus is an over-exploited linefish species, endemic to the coastlines off southern Mozambique and eastern South Africa. Over-exploitation and habitat loss are two of the biggest threats to the sustainability of fisheries globally. Assessing the genetic stock structure (a prerequisite for effective management) and predicting climate related range changes will provide a better understanding of these threats to C. puniceus which can be used to improve the sustainability of the fishery. Two hundred and eighty four genetic samples were collected from eight sampling sites between Ponta da Barra in Mozambique and Coffee Bay in South Africa. The mitochondrial control region and ten microsatellite loci were amplified to analyse the stock structure of C. puniceus. The majority of microsatellite and mtDNA pairwise population comparisons were not significant (P > 0.05) although Xai Xai and Inhaca populations had some significant population comparisons for mtDNA (P < 0.05). AMOVA did not explain any significant variation at the between groups hierarchical level for any pre-defined groupings except for a mtDNA grouping which separated out Xai Xai and Inhaca from other sampling sites. SAMOVA, isolation by distance tests, structure analysis, principle component analysis and spatial autocorrelation analysis all indicated a single population of C. puniceus as being most likely. The migrate-n analysis provided evidence of current driven larval transport, with net migration rates influenced by current dynamics.Two hundred and thirty six unique presence points of C. puniceus were correlated with seasonal maximum and minimum temperature data and bathymetry to model the current distribution and predict future distribution changes of the species up until 2030. Eight individual species distribution models were developed and combined into a mean ensemble model using the Biomod2 package. Winter minimum temperature was the most important variable in determining models outputs. Overall the ensemble model was accurate with a true skills statistic score of 0.962. Binary transformed mean ensemble models predicted a northern and southern range contraction of C. puniceus' distribution of 15 percent; by 2030. The mean ensemble probability of occurrence models indicated that C. puniceus' abundance is likely to decrease off the southern Mozambique coastline but remain high off KwaZulu-Natal. The results of the genetic analysis support the theory of external recruitment sustaining the KwaZulu Natal fishery for C. puniceus. While the high genetic diversity and connectivity may make C. puniceus more resilient to disturbances, the loss of 15 percent; distribution and 11 percent; genetic diversity by 2030 will increase the species vulnerability. The decrease in abundance of C. puniceus off southern Mozambique together with current widespread exploitation levels could result in the collapse of the fishery. A single transboundary stock of C. puniceus highlights the need for co-management of the species. A combined stock assessment between South Africa and Mozambique and the development of further Marine Protected Areas off southern Mozambique are suggested as management options to minimise the vulnerability of this species.
- Full Text:
- Date Issued: 2014
The geographic stock structure of chokka squid, Loligo Reynaudi, and its implications for management of the fishery
- Van der Vyver, Johan Samuel Frederik
- Authors: Van der Vyver, Johan Samuel Frederik
- Date: 2014
- Subjects: Squids -- Geographical distribution , Loligo fisheries -- Africa, Southern , Fishery management -- Africa, Southern , Squids -- Africa, Southern , Squid fisheries -- Africa, Southern , Loliginidae -- Africa, Southern , Fish stock assessment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5363 , http://hdl.handle.net/10962/d1012973
- Description: It is currently hypothesised that the chokka squid (Loligo reynaudi) consist of a single stock. This was tested through a spatial comparison of the morphology of this species. Forty three morphometric characters were measured from 1079 chokka squid collected from three regions: the south coast of South Africa, the west coast of South Africa, and southern Angola. While no significant differences were found for the hard body parts, results from discriminant function analyses showed the soft body morphometric characters from each of the three regions differed, with an overall correct classification rate of 100% for males and 99% for females in all three regions. Due to the existing model being used to assess the resource currently being updated it was not feasible to apply this model to the area-disaggregated data from this study. Rather, the CPUE trends and catches from the area-disaggregated data were compared against those of the area-aggregated data, as a first attempt to discern any appreciable differences which would suggest the use of disaggregated data in future assessments. Both the trawl and jig CPUE trends from the area-disaggregated analysis differed only slightly from those of the area-aggregated data. Similarly, the spring and autumn biomass trends for the main spawning area (east of 22°E) followed the same trends as for the full area. It is therefore concluded that there is currently no need to assess the resource on an area-disaggregated basis.
- Full Text:
- Date Issued: 2014
- Authors: Van der Vyver, Johan Samuel Frederik
- Date: 2014
- Subjects: Squids -- Geographical distribution , Loligo fisheries -- Africa, Southern , Fishery management -- Africa, Southern , Squids -- Africa, Southern , Squid fisheries -- Africa, Southern , Loliginidae -- Africa, Southern , Fish stock assessment
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5363 , http://hdl.handle.net/10962/d1012973
- Description: It is currently hypothesised that the chokka squid (Loligo reynaudi) consist of a single stock. This was tested through a spatial comparison of the morphology of this species. Forty three morphometric characters were measured from 1079 chokka squid collected from three regions: the south coast of South Africa, the west coast of South Africa, and southern Angola. While no significant differences were found for the hard body parts, results from discriminant function analyses showed the soft body morphometric characters from each of the three regions differed, with an overall correct classification rate of 100% for males and 99% for females in all three regions. Due to the existing model being used to assess the resource currently being updated it was not feasible to apply this model to the area-disaggregated data from this study. Rather, the CPUE trends and catches from the area-disaggregated data were compared against those of the area-aggregated data, as a first attempt to discern any appreciable differences which would suggest the use of disaggregated data in future assessments. Both the trawl and jig CPUE trends from the area-disaggregated analysis differed only slightly from those of the area-aggregated data. Similarly, the spring and autumn biomass trends for the main spawning area (east of 22°E) followed the same trends as for the full area. It is therefore concluded that there is currently no need to assess the resource on an area-disaggregated basis.
- Full Text:
- Date Issued: 2014
The role of the deep spawning grounds in chokka squid (Loligo reynaudi d'orbigny, 1845) recruitment
- Authors: Downey, Nicola Jean
- Date: 2014
- Subjects: Squids -- Spawning -- South Africa Squids -- Effect of temperature on -- South Africa Squids -- Embryos -- South Africa Squids -- South Africa -- Geographical distribution Loligo -- Research -- South Africa Loligo fisheries -- South Africa Recruitment (Population biology) -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5359 , http://hdl.handle.net/10962/d1011867
- Description: It was previously thought that the South African chokka squid Loligo reynaudi is exclusively an inshore, shallow water spawner. Although spawning mostly within shallow bays (<60 m) the presence of squid eggs in trawls at depths up to 130 m indicates this species frequently makes use of deeper spawning areas on the mid-shelf. The extent of mid-shelf spawning (referred to as deep spawning) and the contribution to recruitment has yet to be assessed. Studies have shown mid-shelf bottom temperature to vary considerably from those inshore, suggesting chokka squid spawn in two very different oceanographic environments. Considering these apparent environmental differences, what leads to the mid-shelf environment becoming a suitable spawning habitat? Does a suitable benthic habitat, required for the attachment of egg pods, occur on the mid-shelf? These questions are not only important for determining the extent of deep spawning, but also to the understanding of factors “driving” deep spawning. The fate of deep spawned hatchlings is another unknown. It has been proposed that the main chokka squid inshore spawning grounds are positioned to exploit the net westward currents on the Eastern Agulhas Bank, i.e. paralarvae would be transported west from the hatching site to the cold ridge, an area of high primary and secondary productivity on the Central Agulhas Bank. This concept has come to be known as the Western Transport Hypothesis. Lagrangian ROMS-IBMs (regional ocean model system – individual-based model) predict the net westward transport of paralarvae from both the inshore and deep spawning grounds, to the cold ridge. These simulations were used to investigate the transport of hatchlings to the cold ridge feeding grounds before the exhaustion of yolk reserves. The fate of paralarvae on reaching the feeding grounds has not yet been investigated. This work has contributed new knowledge to our understanding of deep spawning and its role in recruitment. Specific aims of this study were to (1) determine the extent, range and importance of the deep spawning grounds relative to those inshore; (2) investigate the deep spawning ground habitat (Agulhas Bank mid-shelf) morphology and oceanographic environment; (3) determine the transport and survival of deep spawned hatchlings; and (4) investigate the origin and distribution of chokka squid paralarvae on the Agulhas Bank. The extent, depth range and importance of the deep spawning grounds, relative to those inshore was assessed using 23 years of demersal trawl survey data. Data for both the west and south coasts of South Africa were examined for egg capsules. No spawning was found on the west coast. Data showed that chokka squid preferred the Eastern Agulhas Bank for spawning. Spawning occurred not only inshore but also on the mid-shelf extending to depths of 270 m near the shelf edge. The majority of deep spawned eggs however, were found in the depth range 71-130 m. Squid egg density markedly decreased beyond 70 m, suggesting delineation between the inshore and deep spawning grounds. Total egg biomass calculations for depths shallower and deeper than 70 m indicated the coastal area to be strongly favoured, i.e. 82 vs. 18%. These results contest the commonly accepted notion that chokka squid is an inshore spawner and redefine the spawning grounds to extend across the shelf. Apart from an initial study investigating bottom temperature on the mid-shelf, very little is known about the deep spawning habitat. St Francis Bay, a commonly used spawning location, was chosen as a demonstration area for further study. The deep spawning grounds (71-130 m) were mapped and benthic habitat described from underwater video footage. A study investigating cross-shelf bottom conditions was undertaken off Thys Bay. CTD data were used to compare seasonal bottom temperature and oxygen on the St Francis Bay inshore and deep spawning grounds. Squid movement between the two spawning habitats was assessed using filament tagging. Predation and fishing pressure across the spawning grounds was reviewed. The mid-shelf benthic habitat was found to be similar to that inshore and available for spawning. Despite the generally colder bottom temperatures on the mid-shelf, this study showed that bottom temperature in deeper waters can at times be warmer than inshore. Although mid-shelf warming events lasted from a few hours to a number of days, they resulted in similar conditions to those on the inshore spawning grounds. It is likely these events act to expand or shift spawning habitat. The movement of squid between the two spawning habitats makes it possible for them to seek patches of warm bottom water with appropiate substrate. This suggests they are spawning habitat opportunists. Predation and fishing pressure appear to be higher on the inshore spawning grounds. It is feasible that this also forces spawners to seek out more favourable habitat offshore. An individual-based model was used to predict the fate of mid-shelf and inshore hatched paralarvae. Within the model, both the highly productive cold ridge and inshore spawning grounds were considered feeding or nursery areas. Paralarvae were released from six inshore and six deep spawning sites, spanning the coast between Port Alfred and Knysna. All paralarvae not reaching the feeding areas before the exhaustion of yolk-reserves (≤5 days), not retained within the feeding grounds (≥14 days), and not retained on the Agulhas Bank after exiting the feeding grounds were considered lost. This work illustrated the dependence of paralarval transport success on both spawning location and time of hatching, as established in earlier studies. The current IBM has expanded on initial work, emphasizing the importance of the cold ridge and inshore spawning grounds as nursery areas for deep and inshore spawned paralarvae, respectively. This work has highlighted the complex interactions between processes influencing recruitment variability for chokka squid. Possible relationships between periods of highest recruitment success and spawning peaks were identified for both spawning habitats. Based on the likely autumn increase in deep spawning off Tsitsikamma, and the beneficial currents during this period, it can be concluded deep spawning may at times contribute significantly to recruitment. This is particularly true for years where the cold ridge persists into winter. Data on chokka squid paralarval distribution are scarce. Paralarval distribution and abundance, in relation to Agulhas Bank oceanography, was investigated using bongo caught paralarvae and corresponding oceanographic data. Individual-based models (IBMs) were used to predict the origin or spawning site of the wild caught paralarvae, with reference to inshore versus deep spawning. Although failing to predict realistic points of origin, this study provided evidence to support a number of scenarios previously assumed to influence chokka squid recruitment. First is the possible influence of coastal upwelling on the retention, and hence spatial distribution, of paralarvae on the inshore spawning grounds. The second factor thought to impact recruitment is the loss of paralarvae from the Agulhas Bank ecosystem. This study confirmed the removal of paralarvae from the Eastern Agulhas Bank due to Agulhas Current boundary phenomena and resultant offshelf leakage. In addition, data suggested that the formation of the cold ridge could enhance retention on the Central Agulhas Bank, and so prevent offshelf leakage from the Central and Western Agulhas Bank. A synthesis of the main conclusions is presented. Implications of the findings and directions for future research are discussed.
- Full Text:
- Date Issued: 2014
- Authors: Downey, Nicola Jean
- Date: 2014
- Subjects: Squids -- Spawning -- South Africa Squids -- Effect of temperature on -- South Africa Squids -- Embryos -- South Africa Squids -- South Africa -- Geographical distribution Loligo -- Research -- South Africa Loligo fisheries -- South Africa Recruitment (Population biology) -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5359 , http://hdl.handle.net/10962/d1011867
- Description: It was previously thought that the South African chokka squid Loligo reynaudi is exclusively an inshore, shallow water spawner. Although spawning mostly within shallow bays (<60 m) the presence of squid eggs in trawls at depths up to 130 m indicates this species frequently makes use of deeper spawning areas on the mid-shelf. The extent of mid-shelf spawning (referred to as deep spawning) and the contribution to recruitment has yet to be assessed. Studies have shown mid-shelf bottom temperature to vary considerably from those inshore, suggesting chokka squid spawn in two very different oceanographic environments. Considering these apparent environmental differences, what leads to the mid-shelf environment becoming a suitable spawning habitat? Does a suitable benthic habitat, required for the attachment of egg pods, occur on the mid-shelf? These questions are not only important for determining the extent of deep spawning, but also to the understanding of factors “driving” deep spawning. The fate of deep spawned hatchlings is another unknown. It has been proposed that the main chokka squid inshore spawning grounds are positioned to exploit the net westward currents on the Eastern Agulhas Bank, i.e. paralarvae would be transported west from the hatching site to the cold ridge, an area of high primary and secondary productivity on the Central Agulhas Bank. This concept has come to be known as the Western Transport Hypothesis. Lagrangian ROMS-IBMs (regional ocean model system – individual-based model) predict the net westward transport of paralarvae from both the inshore and deep spawning grounds, to the cold ridge. These simulations were used to investigate the transport of hatchlings to the cold ridge feeding grounds before the exhaustion of yolk reserves. The fate of paralarvae on reaching the feeding grounds has not yet been investigated. This work has contributed new knowledge to our understanding of deep spawning and its role in recruitment. Specific aims of this study were to (1) determine the extent, range and importance of the deep spawning grounds relative to those inshore; (2) investigate the deep spawning ground habitat (Agulhas Bank mid-shelf) morphology and oceanographic environment; (3) determine the transport and survival of deep spawned hatchlings; and (4) investigate the origin and distribution of chokka squid paralarvae on the Agulhas Bank. The extent, depth range and importance of the deep spawning grounds, relative to those inshore was assessed using 23 years of demersal trawl survey data. Data for both the west and south coasts of South Africa were examined for egg capsules. No spawning was found on the west coast. Data showed that chokka squid preferred the Eastern Agulhas Bank for spawning. Spawning occurred not only inshore but also on the mid-shelf extending to depths of 270 m near the shelf edge. The majority of deep spawned eggs however, were found in the depth range 71-130 m. Squid egg density markedly decreased beyond 70 m, suggesting delineation between the inshore and deep spawning grounds. Total egg biomass calculations for depths shallower and deeper than 70 m indicated the coastal area to be strongly favoured, i.e. 82 vs. 18%. These results contest the commonly accepted notion that chokka squid is an inshore spawner and redefine the spawning grounds to extend across the shelf. Apart from an initial study investigating bottom temperature on the mid-shelf, very little is known about the deep spawning habitat. St Francis Bay, a commonly used spawning location, was chosen as a demonstration area for further study. The deep spawning grounds (71-130 m) were mapped and benthic habitat described from underwater video footage. A study investigating cross-shelf bottom conditions was undertaken off Thys Bay. CTD data were used to compare seasonal bottom temperature and oxygen on the St Francis Bay inshore and deep spawning grounds. Squid movement between the two spawning habitats was assessed using filament tagging. Predation and fishing pressure across the spawning grounds was reviewed. The mid-shelf benthic habitat was found to be similar to that inshore and available for spawning. Despite the generally colder bottom temperatures on the mid-shelf, this study showed that bottom temperature in deeper waters can at times be warmer than inshore. Although mid-shelf warming events lasted from a few hours to a number of days, they resulted in similar conditions to those on the inshore spawning grounds. It is likely these events act to expand or shift spawning habitat. The movement of squid between the two spawning habitats makes it possible for them to seek patches of warm bottom water with appropiate substrate. This suggests they are spawning habitat opportunists. Predation and fishing pressure appear to be higher on the inshore spawning grounds. It is feasible that this also forces spawners to seek out more favourable habitat offshore. An individual-based model was used to predict the fate of mid-shelf and inshore hatched paralarvae. Within the model, both the highly productive cold ridge and inshore spawning grounds were considered feeding or nursery areas. Paralarvae were released from six inshore and six deep spawning sites, spanning the coast between Port Alfred and Knysna. All paralarvae not reaching the feeding areas before the exhaustion of yolk-reserves (≤5 days), not retained within the feeding grounds (≥14 days), and not retained on the Agulhas Bank after exiting the feeding grounds were considered lost. This work illustrated the dependence of paralarval transport success on both spawning location and time of hatching, as established in earlier studies. The current IBM has expanded on initial work, emphasizing the importance of the cold ridge and inshore spawning grounds as nursery areas for deep and inshore spawned paralarvae, respectively. This work has highlighted the complex interactions between processes influencing recruitment variability for chokka squid. Possible relationships between periods of highest recruitment success and spawning peaks were identified for both spawning habitats. Based on the likely autumn increase in deep spawning off Tsitsikamma, and the beneficial currents during this period, it can be concluded deep spawning may at times contribute significantly to recruitment. This is particularly true for years where the cold ridge persists into winter. Data on chokka squid paralarval distribution are scarce. Paralarval distribution and abundance, in relation to Agulhas Bank oceanography, was investigated using bongo caught paralarvae and corresponding oceanographic data. Individual-based models (IBMs) were used to predict the origin or spawning site of the wild caught paralarvae, with reference to inshore versus deep spawning. Although failing to predict realistic points of origin, this study provided evidence to support a number of scenarios previously assumed to influence chokka squid recruitment. First is the possible influence of coastal upwelling on the retention, and hence spatial distribution, of paralarvae on the inshore spawning grounds. The second factor thought to impact recruitment is the loss of paralarvae from the Agulhas Bank ecosystem. This study confirmed the removal of paralarvae from the Eastern Agulhas Bank due to Agulhas Current boundary phenomena and resultant offshelf leakage. In addition, data suggested that the formation of the cold ridge could enhance retention on the Central Agulhas Bank, and so prevent offshelf leakage from the Central and Western Agulhas Bank. A synthesis of the main conclusions is presented. Implications of the findings and directions for future research are discussed.
- Full Text:
- Date Issued: 2014
The water and nutrient potential of brewery effluent for hydroponic tomato production
- Authors: Power, Sean Duncan
- Date: 2014
- Subjects: Hydroponics , Tomatoes -- Breeding , Brewery waste , Water -- Purification , Algae culture , Algae -- Biotechnology , Nitric acid , Phosphoric acid
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5358 , http://hdl.handle.net/10962/d1011604 , Hydroponics , Tomatoes -- Breeding , Brewery waste , Water -- Purification , Algae culture , Algae -- Biotechnology , Nitric acid , Phosphoric acid
- Description: Brewery effluent that had undergone treatment in an anaerobic digester (AD) was used as an alternative water and nutrient source for hydroponic crop production. Brewery effluent was demonstrated to contain sufficient nutrients to support the growth, flowering and fruiting of Lycopersicum escolentum "Moneymaker" tomato crops. The adjustment of the effluent pH with phosphoric acid to between pH 6.0 and 6.5 increased the development of the crops by around 100% compared to crops grown in unaltered effluent. The pH adjusted effluent-grown plants grew to a mean height of 831.4 ± 21.1 mm and a dry biomass weight of 42.34 ± 2.76 g compared to the unaltered pH effluent plants which grew to a height of 410.6 ± 20.5 mm and a weight of 7.65 ± 0.68 g after 49 days. Effluent treatment in high-rate algal ponds (HRAP) was determined to have no positive effect on the nutritional potential of the effluent for Moneymaker production. The effluent-grown plants did not perform as well as plants grown in inorganic-fertilizer and municipal water. Plants grown in effluent grew taller but did not produce significantly more fruit when phosphoric acid (height: 1573.3 ± 50.4 mm, 19.4 ± 1.4 fruit per plant) was compared to nitric acid (height: 1254.1 ± 25.4 mm, 15.6 ± 1.5 fruit per plant) as the pH adjustment over 72 days. Direct and secondary plant stresses from effluent alkalinity, ammonium nutrition, nitrogen limitation, sodium concentrations and heat stress among other factors were probably confounding variables in these trials and require further investigation. Considering the raw effluent composition and manipulating the AD operation is a potential opportunity to improve overall AD performance, reduce chemical inputs in the effluent treatment process, reduce the final effluent alkalinity, and increase available nitrogen content in the final effluent. The anaerobic digester discharging >1000 m³ of nutrient enriched effluent every day is a resource with considerable potential. The benefits of developing this resource can contribute to cost-reduction at the brewery, more efficient water, nutrient and energy management at the brewery, and offer opportunities for job creation and potentially benefit local food security.
- Full Text:
- Date Issued: 2014
- Authors: Power, Sean Duncan
- Date: 2014
- Subjects: Hydroponics , Tomatoes -- Breeding , Brewery waste , Water -- Purification , Algae culture , Algae -- Biotechnology , Nitric acid , Phosphoric acid
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5358 , http://hdl.handle.net/10962/d1011604 , Hydroponics , Tomatoes -- Breeding , Brewery waste , Water -- Purification , Algae culture , Algae -- Biotechnology , Nitric acid , Phosphoric acid
- Description: Brewery effluent that had undergone treatment in an anaerobic digester (AD) was used as an alternative water and nutrient source for hydroponic crop production. Brewery effluent was demonstrated to contain sufficient nutrients to support the growth, flowering and fruiting of Lycopersicum escolentum "Moneymaker" tomato crops. The adjustment of the effluent pH with phosphoric acid to between pH 6.0 and 6.5 increased the development of the crops by around 100% compared to crops grown in unaltered effluent. The pH adjusted effluent-grown plants grew to a mean height of 831.4 ± 21.1 mm and a dry biomass weight of 42.34 ± 2.76 g compared to the unaltered pH effluent plants which grew to a height of 410.6 ± 20.5 mm and a weight of 7.65 ± 0.68 g after 49 days. Effluent treatment in high-rate algal ponds (HRAP) was determined to have no positive effect on the nutritional potential of the effluent for Moneymaker production. The effluent-grown plants did not perform as well as plants grown in inorganic-fertilizer and municipal water. Plants grown in effluent grew taller but did not produce significantly more fruit when phosphoric acid (height: 1573.3 ± 50.4 mm, 19.4 ± 1.4 fruit per plant) was compared to nitric acid (height: 1254.1 ± 25.4 mm, 15.6 ± 1.5 fruit per plant) as the pH adjustment over 72 days. Direct and secondary plant stresses from effluent alkalinity, ammonium nutrition, nitrogen limitation, sodium concentrations and heat stress among other factors were probably confounding variables in these trials and require further investigation. Considering the raw effluent composition and manipulating the AD operation is a potential opportunity to improve overall AD performance, reduce chemical inputs in the effluent treatment process, reduce the final effluent alkalinity, and increase available nitrogen content in the final effluent. The anaerobic digester discharging >1000 m³ of nutrient enriched effluent every day is a resource with considerable potential. The benefits of developing this resource can contribute to cost-reduction at the brewery, more efficient water, nutrient and energy management at the brewery, and offer opportunities for job creation and potentially benefit local food security.
- Full Text:
- Date Issued: 2014
Towards the development of a larval feeding strategy for the white-margined sole (Dagetichthys marginatus)
- Authors: Thompson, Ernst Frederick
- Date: 2014
- Subjects: Flatfishes -- South Africa , Soleidae -- South Africa , Soleidae -- Larvae , Soleidae -- Larvae -- Feeding and feeds , Soleidae -- Larvae -- Physiology , Artemia
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5364 , http://hdl.handle.net/10962/d1012982
- Description: The major bottleneck during the domestication of the white-margined sole Dagetichthys marginatus in South Africa has been low larval survival. The cause of this is not clear but considering current literature on flatfish culture and more specifically soleid culture, nutritional deficiencies are hypothesized to be the main possible cause. Following the importance of nutrition, the first aim of the research was to use an ontogenetic developmental approach to develop a species specific larval feeding strategy. Ontogenetic development of D. marginatus showed that weaning will take place at much later ages than other soleids currently being farmed. This makes the partial replacement of Artemia with a suitable inert diet in co-feeding strategies very important to cut the cost associated of live food production. This leads on to the second aim, in which an 'in vitro' approach was used to model the digestibility of Artemia, which could ultimately contribute towards designing inert feeds with similar digestibility characteristics to Artemia in the future. Obtaining nutrients from food is closely linked to the functional status of the digestive tract, the support organs and the external morphological characteristics required for the ingestion of live or inert feeds. Considering both morphological and physiological ontogenetic development, it is clear that D. marginatus follow a similar pattern to other soleids. Larvae can successfully feed on Artemia as early as 3 days after hatching but exhibit a slow metamorphosis into the juvenile stage when compared to other soleids. The absence of any detectable acidic protease activity during the first 45 days of development and the importance of exogenous enzymes from Artemia all points to limited capacity to digest artificial diets. Prior to modelling the 'in vitro' digestion of Artemia, digestive enzyme activity at different pH's were modelled using functional forms from the normal distributive category of functions. , As there is no substantiated information for the general effects of pH on enzyme activity in the literature for finfish larvae, three species occurring in the same bio-geographical region of Dagetichthys marginatus, namely Sarpa salpa, Diplodus sargus capensis and Argyrosomus japonicus were used to investigate this effect. The fitted parameters, namely the optimal pH and sigma (the slope around the optimal pH) showed two interesting results. When using a negative log likelihood ratio test to test for differences between species for a particular enzyme, the optimal pH for alkaline proteases (7.67), lipase (8.03), amylase (7.69) and phosphatase (9.84) activity was the same for all three species. Furthermore, the study illustrated the potential to detect dietary shifts during ontogenetic development based on changes in enzyme activity around the optimal pH using the sigma parameter. Sarpa salpa showed increased amylase activity and a decrease in protease activity around the optimal pH with increased size, corresponding to a change in diet from zooplankton to algae. The 'in vitro' modelling approach taken in this study was based on known enzyme interactions and dynamics which makes the results very interpretable. from Artemia is achieved based on gut evacuation time and enzyme levels. This 'in vitro' study furthermore clearly indicates the importance of exogenous enzymes from Artemia, contributing as much as 54 percent to protein digestion and 64 – 72 percent to carbohydrate digestion. This was however, only an initial investigation, and further expansion of the model is required to achieve a complete understanding of Artemia digestion and ultimately partial replacement with artificial diets. A feeding strategy for D. marginatus should therefore follow those of other farmed soleids, although there will be a general delay in implementation due to slower development. Problems can thus be solved and improvements made by transferring technology from other soleids to D. marginatus.
- Full Text:
- Date Issued: 2014
- Authors: Thompson, Ernst Frederick
- Date: 2014
- Subjects: Flatfishes -- South Africa , Soleidae -- South Africa , Soleidae -- Larvae , Soleidae -- Larvae -- Feeding and feeds , Soleidae -- Larvae -- Physiology , Artemia
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5364 , http://hdl.handle.net/10962/d1012982
- Description: The major bottleneck during the domestication of the white-margined sole Dagetichthys marginatus in South Africa has been low larval survival. The cause of this is not clear but considering current literature on flatfish culture and more specifically soleid culture, nutritional deficiencies are hypothesized to be the main possible cause. Following the importance of nutrition, the first aim of the research was to use an ontogenetic developmental approach to develop a species specific larval feeding strategy. Ontogenetic development of D. marginatus showed that weaning will take place at much later ages than other soleids currently being farmed. This makes the partial replacement of Artemia with a suitable inert diet in co-feeding strategies very important to cut the cost associated of live food production. This leads on to the second aim, in which an 'in vitro' approach was used to model the digestibility of Artemia, which could ultimately contribute towards designing inert feeds with similar digestibility characteristics to Artemia in the future. Obtaining nutrients from food is closely linked to the functional status of the digestive tract, the support organs and the external morphological characteristics required for the ingestion of live or inert feeds. Considering both morphological and physiological ontogenetic development, it is clear that D. marginatus follow a similar pattern to other soleids. Larvae can successfully feed on Artemia as early as 3 days after hatching but exhibit a slow metamorphosis into the juvenile stage when compared to other soleids. The absence of any detectable acidic protease activity during the first 45 days of development and the importance of exogenous enzymes from Artemia all points to limited capacity to digest artificial diets. Prior to modelling the 'in vitro' digestion of Artemia, digestive enzyme activity at different pH's were modelled using functional forms from the normal distributive category of functions. , As there is no substantiated information for the general effects of pH on enzyme activity in the literature for finfish larvae, three species occurring in the same bio-geographical region of Dagetichthys marginatus, namely Sarpa salpa, Diplodus sargus capensis and Argyrosomus japonicus were used to investigate this effect. The fitted parameters, namely the optimal pH and sigma (the slope around the optimal pH) showed two interesting results. When using a negative log likelihood ratio test to test for differences between species for a particular enzyme, the optimal pH for alkaline proteases (7.67), lipase (8.03), amylase (7.69) and phosphatase (9.84) activity was the same for all three species. Furthermore, the study illustrated the potential to detect dietary shifts during ontogenetic development based on changes in enzyme activity around the optimal pH using the sigma parameter. Sarpa salpa showed increased amylase activity and a decrease in protease activity around the optimal pH with increased size, corresponding to a change in diet from zooplankton to algae. The 'in vitro' modelling approach taken in this study was based on known enzyme interactions and dynamics which makes the results very interpretable. from Artemia is achieved based on gut evacuation time and enzyme levels. This 'in vitro' study furthermore clearly indicates the importance of exogenous enzymes from Artemia, contributing as much as 54 percent to protein digestion and 64 – 72 percent to carbohydrate digestion. This was however, only an initial investigation, and further expansion of the model is required to achieve a complete understanding of Artemia digestion and ultimately partial replacement with artificial diets. A feeding strategy for D. marginatus should therefore follow those of other farmed soleids, although there will be a general delay in implementation due to slower development. Problems can thus be solved and improvements made by transferring technology from other soleids to D. marginatus.
- Full Text:
- Date Issued: 2014
Towards understanding the effects of stocking density on farmed South African abalone, Haliotis Midae
- Authors: Nicholson, Gareth Hurst
- Date: 2014
- Subjects: Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalones -- South Africa , Fish stocking -- South Africa , Abalone populations -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5371 , http://hdl.handle.net/10962/d1015646
- Description: The profitability of abalone farms is heavily influenced by their production per unit of grow-out space. With farms having physically expanded to the maximum, and with increasing production costs, one of the most realistic ways for farms to increase their production is through optimizing stocking densities. The effect of stocking density on Haliotis midae performance is undocumented and optimal stocking densities for this species have not been determined. Experiments were conducted under farm conditions to investigate the effects of four different stocking densities (16 %, 20 %, 22 % and 24 % of available surface area) on growth, production and health of three different size classes of abalone (15-35 g, 45-65 g, and 70-90 g start weight). Each treatment was replicated four times and trials ran over a period of eight months with measurements being made at four month intervals. Abalone behaviour was observed during the trials in the experimental tanks. Weight gain per abalone decreased with an increase in density for all tested size classes (5.04 ± 0.18 to 2.38 ± 0.17; 5.35 ± 0.21 to 4.62 ± 0.29; 7.97 ± 0.37 to 6.53 ± 0.28 g.abalone-1.month-1 for the 15-35, 45-65 and 70-90 g classes respectively, with an increased density of 16 to 24 %). Individual weight gain of 15-35 g abalone was similar at stocking densities of 16 % and 20 % while weight gain of 45-65 g and 70-90 g abalone decreased when density was increased above 16 %. Biomass gain (kg.basket-1.month-1) was not affected by stocking density in the 15-35 g and 45-65 g size classes (1.29 ± 0.02 and 0.97 ± 0.02 kg.basket-1.month-1 respectively). However, the biomass gained by baskets stocked with 70-90 g abalone increased with stocking density (1.08 ± 0.02 to 1.33 ± 0.02 kg.basket-1.month-1) with an increased density of 16 to 24 %) and did not appear to plateau within the tested density range (16 to 24 %). Food conversion ratio did not differ significantly between densities across all size classes. Stocking density did not have a significant effect on abalone condition factor or health indices. The proportion of abalone above the level of the feeder plate increased with density (7.26 ± 1.33 to 16.44 ± 1.33 with an increased density of 16 to 24 %). As a proportion of abalone situated in the area of the basket, the same proportions were situated on the walls above the feeder plate and on the feeder plate itself irrespective of stocking density (p > 0.05). Higher proportions of animals had restricted access to feed at higher stocking densities (p = 0.03). The amount of formulated feed available on the feeder plate did not differ between stocking densities throughout the night (p = 0.19). Individual abalone spent more time above the feeder plate at higher stocking densities (p < 0.05). The percentage of time above the feeder plate, spent on the walls of the basket and on the feeding surface was not significantly different at densities of 20 %, 22 % and 24 % (p > 0.05) but abalone stocked at 16 % spent a greater percentage of time above the feeder plate on the feeding surface (83.99 ± 6.26 %) than on the basket walls (16.01 ± 6.26 %). Stocking density did not affect the positioning of abalone within a basket during the day or at night. Different size H. midae are affected differently by increases in stocking density in terms of growth performance. Findings from this research may be implemented into farm management strategies to best suit production goals, whether in terms of biomass production or individual weight gain. The fundamental mechanisms resulting in reduced growth at higher densities are not well understood, however results from behaviour observations suggest that competition for preferred attachment space and feed availability are contributing to decreased growth rates. With knowledge of abalone behaviour at different densities, innovative tank designs may be established in order to counter the reduction in growth at higher densities.
- Full Text:
- Date Issued: 2014
- Authors: Nicholson, Gareth Hurst
- Date: 2014
- Subjects: Haliotis midae -- South Africa , Haliotis midae fisheries -- South Africa , Abalones -- South Africa , Fish stocking -- South Africa , Abalone populations -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5371 , http://hdl.handle.net/10962/d1015646
- Description: The profitability of abalone farms is heavily influenced by their production per unit of grow-out space. With farms having physically expanded to the maximum, and with increasing production costs, one of the most realistic ways for farms to increase their production is through optimizing stocking densities. The effect of stocking density on Haliotis midae performance is undocumented and optimal stocking densities for this species have not been determined. Experiments were conducted under farm conditions to investigate the effects of four different stocking densities (16 %, 20 %, 22 % and 24 % of available surface area) on growth, production and health of three different size classes of abalone (15-35 g, 45-65 g, and 70-90 g start weight). Each treatment was replicated four times and trials ran over a period of eight months with measurements being made at four month intervals. Abalone behaviour was observed during the trials in the experimental tanks. Weight gain per abalone decreased with an increase in density for all tested size classes (5.04 ± 0.18 to 2.38 ± 0.17; 5.35 ± 0.21 to 4.62 ± 0.29; 7.97 ± 0.37 to 6.53 ± 0.28 g.abalone-1.month-1 for the 15-35, 45-65 and 70-90 g classes respectively, with an increased density of 16 to 24 %). Individual weight gain of 15-35 g abalone was similar at stocking densities of 16 % and 20 % while weight gain of 45-65 g and 70-90 g abalone decreased when density was increased above 16 %. Biomass gain (kg.basket-1.month-1) was not affected by stocking density in the 15-35 g and 45-65 g size classes (1.29 ± 0.02 and 0.97 ± 0.02 kg.basket-1.month-1 respectively). However, the biomass gained by baskets stocked with 70-90 g abalone increased with stocking density (1.08 ± 0.02 to 1.33 ± 0.02 kg.basket-1.month-1) with an increased density of 16 to 24 %) and did not appear to plateau within the tested density range (16 to 24 %). Food conversion ratio did not differ significantly between densities across all size classes. Stocking density did not have a significant effect on abalone condition factor or health indices. The proportion of abalone above the level of the feeder plate increased with density (7.26 ± 1.33 to 16.44 ± 1.33 with an increased density of 16 to 24 %). As a proportion of abalone situated in the area of the basket, the same proportions were situated on the walls above the feeder plate and on the feeder plate itself irrespective of stocking density (p > 0.05). Higher proportions of animals had restricted access to feed at higher stocking densities (p = 0.03). The amount of formulated feed available on the feeder plate did not differ between stocking densities throughout the night (p = 0.19). Individual abalone spent more time above the feeder plate at higher stocking densities (p < 0.05). The percentage of time above the feeder plate, spent on the walls of the basket and on the feeding surface was not significantly different at densities of 20 %, 22 % and 24 % (p > 0.05) but abalone stocked at 16 % spent a greater percentage of time above the feeder plate on the feeding surface (83.99 ± 6.26 %) than on the basket walls (16.01 ± 6.26 %). Stocking density did not affect the positioning of abalone within a basket during the day or at night. Different size H. midae are affected differently by increases in stocking density in terms of growth performance. Findings from this research may be implemented into farm management strategies to best suit production goals, whether in terms of biomass production or individual weight gain. The fundamental mechanisms resulting in reduced growth at higher densities are not well understood, however results from behaviour observations suggest that competition for preferred attachment space and feed availability are contributing to decreased growth rates. With knowledge of abalone behaviour at different densities, innovative tank designs may be established in order to counter the reduction in growth at higher densities.
- Full Text:
- Date Issued: 2014
Trends in the fish assemblage structure of two South African transition-zone estuaries : can these trends be linked to climate change?
- Authors: Midgley, Craig
- Date: 2014
- Subjects: Estuarine fishes -- South Africa -- Climatic factors , Fish communities -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5368 , http://hdl.handle.net/10962/d1013173
- Description: Changes in the fish communities of the Breede and Mbashe estuaries were investigated in relation to the environmental variables that influence the fish assemblages in these systems. The Breede Estuary (34° 24’21.6”S, 20° 51’ 08.2”E) occurs within the warm-temperate/cool-temperate transition-zone, while the Mbashe Estuary (32o 14' 55.4"S, 28o 54' 03.7"E) falls within the subtropical/warm-temperate transition-zone along the South African coastline. The Breede Estuary was sampled (seine and gill nets) during summer (January-March) over a period of 10 years (2002-2012), while the Mbashe Estuary was sampled (seine net) during spring (October) over a period of three years (2010-2012). The proportion of tropical fish species was higher in the Mbashe Estuary compared to the Breede Estuary, while the Breede Estuary contained a higher proportion of temperate species than the Mbashe Estuary. Although the abundance of individual species in both estuaries varied, the ranking of species in the Breede Estuary was stable over the 10 year period. Multivariate analysis showed that the fish communities within each reach (upper, middle, lower) of the Breede Estuary remained similar, regardless of year. In contrast, species composition in the Mbashe Estuary differed significantly between years mainly due to differences in the river flow regime during the study period. Environmental variables responsible for structuring the fish assemblage in each estuary differed. Salinity significantly impacted the spatial fish assemblage structure of the Breede Estuary, with most of the species recorded being associated with the more saline lower reaches. The abundance of tropical species near their distributional limit in the Breede Estuary appeared to be impacted by sea surface temperature (SST) as peak total abundance of these species coincided with the warmest SST, while the lowest total abundance coincided with the coldest annual SST during the study period. The fish assemblage structure in the Mbashe Estuary was impacted by differing freshwater input prior to sampling, with flooding negatively impacting the mean total abundance, species composition and diversity in this system. The variables that influenced the fish assemblage structure of both transition-zone estuaries will be affected by climate change in the future. These variables will, in turn, determine the composition, abundance and diversity of species within these important estuarine systems. In order to measure these impacts with any degree of understanding, long-term studies on the abiotic and biotic (including the ichthyofauna) features of these estuaries are required to interpret climate change trends.
- Full Text:
- Date Issued: 2014
- Authors: Midgley, Craig
- Date: 2014
- Subjects: Estuarine fishes -- South Africa -- Climatic factors , Fish communities -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5368 , http://hdl.handle.net/10962/d1013173
- Description: Changes in the fish communities of the Breede and Mbashe estuaries were investigated in relation to the environmental variables that influence the fish assemblages in these systems. The Breede Estuary (34° 24’21.6”S, 20° 51’ 08.2”E) occurs within the warm-temperate/cool-temperate transition-zone, while the Mbashe Estuary (32o 14' 55.4"S, 28o 54' 03.7"E) falls within the subtropical/warm-temperate transition-zone along the South African coastline. The Breede Estuary was sampled (seine and gill nets) during summer (January-March) over a period of 10 years (2002-2012), while the Mbashe Estuary was sampled (seine net) during spring (October) over a period of three years (2010-2012). The proportion of tropical fish species was higher in the Mbashe Estuary compared to the Breede Estuary, while the Breede Estuary contained a higher proportion of temperate species than the Mbashe Estuary. Although the abundance of individual species in both estuaries varied, the ranking of species in the Breede Estuary was stable over the 10 year period. Multivariate analysis showed that the fish communities within each reach (upper, middle, lower) of the Breede Estuary remained similar, regardless of year. In contrast, species composition in the Mbashe Estuary differed significantly between years mainly due to differences in the river flow regime during the study period. Environmental variables responsible for structuring the fish assemblage in each estuary differed. Salinity significantly impacted the spatial fish assemblage structure of the Breede Estuary, with most of the species recorded being associated with the more saline lower reaches. The abundance of tropical species near their distributional limit in the Breede Estuary appeared to be impacted by sea surface temperature (SST) as peak total abundance of these species coincided with the warmest SST, while the lowest total abundance coincided with the coldest annual SST during the study period. The fish assemblage structure in the Mbashe Estuary was impacted by differing freshwater input prior to sampling, with flooding negatively impacting the mean total abundance, species composition and diversity in this system. The variables that influenced the fish assemblage structure of both transition-zone estuaries will be affected by climate change in the future. These variables will, in turn, determine the composition, abundance and diversity of species within these important estuarine systems. In order to measure these impacts with any degree of understanding, long-term studies on the abiotic and biotic (including the ichthyofauna) features of these estuaries are required to interpret climate change trends.
- Full Text:
- Date Issued: 2014
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