Population genomics analysis of yellowfin tuna Thunnus albacares off South Africa reveals need for a shifted management boundary
- Authors: Mullins, Rachel Brenna
- Date: 2017
- Subjects: Yellowfin tuna fisheries -- South Africa -- Western Cape , Genomics , Tuna fisheries -- South Africa , Fishery management -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/57819 , vital:26992
- Description: Yellowfin tuna Thunnus albacares is a commercially and economically important fisheries species, which comprises the second largest component of South Africa’s catch of tuna and tuna-like species. Catches of the species off South Africa are treated as two discrete stocks by the two tuna Regional Fisheries Management Organisations (tRFMOs) under whose jurisdictions they fall. Individuals caught off the Western Cape, west of the boundary between the tRFMOs at 20°E, are included in assessment and management of the Atlantic Ocean yellowfin tuna stock by the International Commission for the Conservation of Atlantic Tunas (ICCAT), and those caught east of this boundary are assessed and managed as part of the Indian Ocean stock by the Indian Ocean Tuna Commission (IOTC). The boundary between these stocks is based on the confluence of the two oceans in this region and does not incorporate the population structure of species. For sustainable exploitation of fisheries resources, it is important that the definition of management stocks reflects species’ biological population structure; the fine-scale stock structure of yellowfin tuna off South Africa is therefore a research priority which this study aimed to address by means of population genomics analyses. Yellowfin tuna exhibit shallow genetic differentiation over wide geographic areas, and as such traditional population genetic approaches have limited power in resolving fishery significant population structure in the species. Herein, a population genomic approach was employed, specifically, genome-wide analysis of single nucleotide polymorphisms (SNPs) discovered using a next-generation DNA sequencing approach, to confer (i) increased statistical power to detect neutral structuring reflecting population connectivity patterns and (ii) signatures of local adaptation. The mitochondrial Control Region (mtDNA CR) was also sequenced to compare the resolving power of different approaches and to permit coalescent based analyses of the species evolutionary history in the region. Neutral SNP loci revealed significant structure within the dataset (Fst=0.0043; P<0.0001); partitioning of this differentiation within the dataset indicated significant differentiation between yellowfin tuna from the Western Cape and the Gulf of Guinea in the eastern Atlantic Ocean, with no significant differentiation between individuals from the Western Cape and Western Indian Ocean regions. This indicates two population units wherein there is a separation of the Gulf of Guinea from the remaining samples (Indian Ocean including Western Cape) that are largely derived from a single genetic population. This pattern was also supported by assignment tests. Positive outlier SNPs, exhibiting signatures of diversifying selection, suggest that individuals from these regions may be locally adapted, as well as demographically isolated. The mtDNA CR did not reveal any significant genetic structure among samples (Fst=0.0030; P=0.309), demonstrating the increased resolving power provided by population genomics approaches, but revealed signatures of historical demographic fluctuations associated with glacial cycles. Based on the findings of this study, it is suggested that yellowfin tuna caught off the Western Cape of South Africa are migrants from the Indian Ocean population, exhibiting significant genetic differentiation from the Atlantic Ocean Gulf of Guinea individuals, and should thus be included in the assessment and management of the Indian Ocean stock. It is therefore recommended that the boundary between the Atlantic and Indian Ocean yellowfin tuna stocks, under the mandates of ICCAT and the IOTC respectively, should be shifted to approximately 13.35°E to include all individuals caught in South African waters in the Indian Ocean stock.
- Full Text:
- Authors: Mullins, Rachel Brenna
- Date: 2017
- Subjects: Yellowfin tuna fisheries -- South Africa -- Western Cape , Genomics , Tuna fisheries -- South Africa , Fishery management -- South Africa
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/57819 , vital:26992
- Description: Yellowfin tuna Thunnus albacares is a commercially and economically important fisheries species, which comprises the second largest component of South Africa’s catch of tuna and tuna-like species. Catches of the species off South Africa are treated as two discrete stocks by the two tuna Regional Fisheries Management Organisations (tRFMOs) under whose jurisdictions they fall. Individuals caught off the Western Cape, west of the boundary between the tRFMOs at 20°E, are included in assessment and management of the Atlantic Ocean yellowfin tuna stock by the International Commission for the Conservation of Atlantic Tunas (ICCAT), and those caught east of this boundary are assessed and managed as part of the Indian Ocean stock by the Indian Ocean Tuna Commission (IOTC). The boundary between these stocks is based on the confluence of the two oceans in this region and does not incorporate the population structure of species. For sustainable exploitation of fisheries resources, it is important that the definition of management stocks reflects species’ biological population structure; the fine-scale stock structure of yellowfin tuna off South Africa is therefore a research priority which this study aimed to address by means of population genomics analyses. Yellowfin tuna exhibit shallow genetic differentiation over wide geographic areas, and as such traditional population genetic approaches have limited power in resolving fishery significant population structure in the species. Herein, a population genomic approach was employed, specifically, genome-wide analysis of single nucleotide polymorphisms (SNPs) discovered using a next-generation DNA sequencing approach, to confer (i) increased statistical power to detect neutral structuring reflecting population connectivity patterns and (ii) signatures of local adaptation. The mitochondrial Control Region (mtDNA CR) was also sequenced to compare the resolving power of different approaches and to permit coalescent based analyses of the species evolutionary history in the region. Neutral SNP loci revealed significant structure within the dataset (Fst=0.0043; P<0.0001); partitioning of this differentiation within the dataset indicated significant differentiation between yellowfin tuna from the Western Cape and the Gulf of Guinea in the eastern Atlantic Ocean, with no significant differentiation between individuals from the Western Cape and Western Indian Ocean regions. This indicates two population units wherein there is a separation of the Gulf of Guinea from the remaining samples (Indian Ocean including Western Cape) that are largely derived from a single genetic population. This pattern was also supported by assignment tests. Positive outlier SNPs, exhibiting signatures of diversifying selection, suggest that individuals from these regions may be locally adapted, as well as demographically isolated. The mtDNA CR did not reveal any significant genetic structure among samples (Fst=0.0030; P=0.309), demonstrating the increased resolving power provided by population genomics approaches, but revealed signatures of historical demographic fluctuations associated with glacial cycles. Based on the findings of this study, it is suggested that yellowfin tuna caught off the Western Cape of South Africa are migrants from the Indian Ocean population, exhibiting significant genetic differentiation from the Atlantic Ocean Gulf of Guinea individuals, and should thus be included in the assessment and management of the Indian Ocean stock. It is therefore recommended that the boundary between the Atlantic and Indian Ocean yellowfin tuna stocks, under the mandates of ICCAT and the IOTC respectively, should be shifted to approximately 13.35°E to include all individuals caught in South African waters in the Indian Ocean stock.
- Full Text:
The identification of key vulnerability components within Solomon Islands coastal communities
- Authors: Malherbe, Willem Stefanus
- Date: 2017
- Subjects: Solomon Islands -- Environmental conditions , Coastal ecology -- Solomon Islands , Island ecology -- Solomon Islands , Climatic changes -- Solomon Islands , Sociology, Urban -- Solomon Islands , Sociology, Rural -- Solomon Islands
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:21184 , http://hdl.handle.net/10962/6827
- Description: The impacts of climate change are disproportionally felt across the planet, with small island developing states some of the countries most at risk. Furthermore, climate change may compound existing problems such as over harvested resources, leading to knock-on effects on national economies. Both direct and indirect stressors may impact communities differently based on their level of exposure to stressors, their intrinsic sensitivity to these stressors, and their ability to adapt to stressors. This study aims to answer the primary research question: Why are some communities more vulnerable than others? A vulnerability assessment is used to identify both vulnerable and non-vulnerable attributes of Solomon Islands’ communities. Surveys comprised a comprehensive questionnaire to draw inference on each vulnerability category; sensitivity, exposure and adaptive capacity, along with their various components and subcomponents. An analysis of household and community livelihood strategies was conducted to compliment vulnerability scores and provide a deeper understanding of livelihood practises. As is expected of small island states, exposure presents the biggest threat to coastal communities. Within this category, environmental changes and personal exposure from shoreline erosion and safety at sea provide evidence of high vulnerability. Within the sensitivity category, the cultural importance of fishing, as well as attachment to place and fishing, renders communities more vulnerable. Simultaneously, local ecological knowledge and economic dependence on resources other than fishing proved to be resilient attributes by decreasing vulnerability. Low vulnerability scores for the adaptive capacity category were achieved by communities where physical capital, such as community infrastructure, was evident. A lack of both institutional support and bridging of social capital were attributes which contributed to community vulnerability. This study has identified key attributes that have both positive and negative effects on the vulnerability of Solomon Islands communities. Having done this, I have also attempted to determine the drivers that render some attributes more vulnerable than others. It is acknowledged that the drivers of all key attributes of vulnerability is required to determine areas where adaptation plans will be most effective. Importantly, drivers of high vulnerability should not be considered as the primary focus of adaptation planning, but also the drivers of low vulnerability, such as community cohesion, which provide resilience within communities.
- Full Text:
- Authors: Malherbe, Willem Stefanus
- Date: 2017
- Subjects: Solomon Islands -- Environmental conditions , Coastal ecology -- Solomon Islands , Island ecology -- Solomon Islands , Climatic changes -- Solomon Islands , Sociology, Urban -- Solomon Islands , Sociology, Rural -- Solomon Islands
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:21184 , http://hdl.handle.net/10962/6827
- Description: The impacts of climate change are disproportionally felt across the planet, with small island developing states some of the countries most at risk. Furthermore, climate change may compound existing problems such as over harvested resources, leading to knock-on effects on national economies. Both direct and indirect stressors may impact communities differently based on their level of exposure to stressors, their intrinsic sensitivity to these stressors, and their ability to adapt to stressors. This study aims to answer the primary research question: Why are some communities more vulnerable than others? A vulnerability assessment is used to identify both vulnerable and non-vulnerable attributes of Solomon Islands’ communities. Surveys comprised a comprehensive questionnaire to draw inference on each vulnerability category; sensitivity, exposure and adaptive capacity, along with their various components and subcomponents. An analysis of household and community livelihood strategies was conducted to compliment vulnerability scores and provide a deeper understanding of livelihood practises. As is expected of small island states, exposure presents the biggest threat to coastal communities. Within this category, environmental changes and personal exposure from shoreline erosion and safety at sea provide evidence of high vulnerability. Within the sensitivity category, the cultural importance of fishing, as well as attachment to place and fishing, renders communities more vulnerable. Simultaneously, local ecological knowledge and economic dependence on resources other than fishing proved to be resilient attributes by decreasing vulnerability. Low vulnerability scores for the adaptive capacity category were achieved by communities where physical capital, such as community infrastructure, was evident. A lack of both institutional support and bridging of social capital were attributes which contributed to community vulnerability. This study has identified key attributes that have both positive and negative effects on the vulnerability of Solomon Islands communities. Having done this, I have also attempted to determine the drivers that render some attributes more vulnerable than others. It is acknowledged that the drivers of all key attributes of vulnerability is required to determine areas where adaptation plans will be most effective. Importantly, drivers of high vulnerability should not be considered as the primary focus of adaptation planning, but also the drivers of low vulnerability, such as community cohesion, which provide resilience within communities.
- Full Text:
The influence of environmental variability on the catch of chokka, Loligo reynaudii, off the coast of South Africa
- Authors: Joyner, Jessica Mary
- Date: 2017
- Subjects: Loligo reynaudii , Loligo fisheries -- South Africa , Squid fisheries -- South Africa , Loligo fisheries -- Environmental aspects -- South Africa , Squid fisheries -- Environmental aspects - South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/32130 , vital:24013
- Description: Globally, cephalopod fisheries are being relied on more heavily due to the depletion of longer-lived teleost species. The South African chokka squid (Loligo reynaudii) fishery is a case in point. Although previously numerous squid were often caught as bycatch, the fishery has officially been in place since 1985. Since the inception of the chokka fishery in South Africa, several studies have investigated the relationship between environmental drivers and annual chokka squid catch, with varying degrees of success. Recently, in 2013, chokka squid catches hit a record low, prompting resurgence in the topic of the squid environment-catch relationship. This study was initiated in an attempt to provide a quantitative relationship between the chokka squid catch and environmental variability, and to build a predictive model that could be used in fisheries management strategies. Historical data were obtained from various sources and included the mean and standard deviation in ocean bottom temperature; the mean and standard deviation in sea surface temperature; the maximum and minimum as well as the variation in wind speed; the mean, predominant and standard deviation in wind direction; the mean and standard deviation in atmospheric pressure; the mean chlorophyll concentration; the number of upwelling events; the hours of easterly winds blowing per day; and two large variation-in-climate indices, namely, the oceanic Nino index and the Antarctic Oscillation index. The monthly catch data were also provided. These data were initially analysed for inter-annual and intra-annual cyclic trends and followed by analysis of the delay in response of catch to the environmental variables, anticipating some impact on the different stages of the chokka life cycle. These lagged data were incorporated into a negative binomial generalised linear model, as well as a generalised additive model, which revealed a strong relationship (r²=0.707) between the catch and environmental variability. The inclusion of all the parameters was necessary; however, the mean bottom temperature and the standard deviation in sea surface temperature were the only parameters that had a significant effect on the catch. These results were used to build a predictive model that indicated that, although the relationship was strong, the ability of the model to predict catch was weak, particularly from the year 2005 onwards.
- Full Text:
- Authors: Joyner, Jessica Mary
- Date: 2017
- Subjects: Loligo reynaudii , Loligo fisheries -- South Africa , Squid fisheries -- South Africa , Loligo fisheries -- Environmental aspects -- South Africa , Squid fisheries -- Environmental aspects - South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/32130 , vital:24013
- Description: Globally, cephalopod fisheries are being relied on more heavily due to the depletion of longer-lived teleost species. The South African chokka squid (Loligo reynaudii) fishery is a case in point. Although previously numerous squid were often caught as bycatch, the fishery has officially been in place since 1985. Since the inception of the chokka fishery in South Africa, several studies have investigated the relationship between environmental drivers and annual chokka squid catch, with varying degrees of success. Recently, in 2013, chokka squid catches hit a record low, prompting resurgence in the topic of the squid environment-catch relationship. This study was initiated in an attempt to provide a quantitative relationship between the chokka squid catch and environmental variability, and to build a predictive model that could be used in fisheries management strategies. Historical data were obtained from various sources and included the mean and standard deviation in ocean bottom temperature; the mean and standard deviation in sea surface temperature; the maximum and minimum as well as the variation in wind speed; the mean, predominant and standard deviation in wind direction; the mean and standard deviation in atmospheric pressure; the mean chlorophyll concentration; the number of upwelling events; the hours of easterly winds blowing per day; and two large variation-in-climate indices, namely, the oceanic Nino index and the Antarctic Oscillation index. The monthly catch data were also provided. These data were initially analysed for inter-annual and intra-annual cyclic trends and followed by analysis of the delay in response of catch to the environmental variables, anticipating some impact on the different stages of the chokka life cycle. These lagged data were incorporated into a negative binomial generalised linear model, as well as a generalised additive model, which revealed a strong relationship (r²=0.707) between the catch and environmental variability. The inclusion of all the parameters was necessary; however, the mean bottom temperature and the standard deviation in sea surface temperature were the only parameters that had a significant effect on the catch. These results were used to build a predictive model that indicated that, although the relationship was strong, the ability of the model to predict catch was weak, particularly from the year 2005 onwards.
- Full Text:
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