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:
Progress in implementing the ecosystem approach to fisheries in South Africa in principle and in practice
- Duna, Elethu Zamandlane Lona
- Authors: Duna, Elethu Zamandlane Lona
- Date: 2017
- Subjects: Fisheries -- Environmental aspects -- South Africa , Sustainable fisheries -- South Africa , Fishery management -- South Africa , South African Sustainable Seafood Initiative
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/44879 , vital:25449
- Description: Over the last century, the population of the world has more than doubled, resulting in an increase in seafood consumption (FAO 2010), and placing strain on fisheries wild stocks, their habitats, and the coastal communities that rely on them for food and survival. The ecosystem approach to fisheries (EAF) differs from other management approaches by combining all aspects of ecosystem management, and strives to conserve ecosystem structure, maintain diversity, productivity, and integrity, and to meet human food and economic needs. This study aims to assess how South Africa is progressing in implementing EAF in principle and in practice, to identify challenges, and suggest solutions, where appropriate. The law sets precedence on governance. An assessment of the Marine Living Resources Act, (MLRA) and the South African Policy for Small-scale Fisheries (SSFP) revealed that, although these instruments recognise and contain elements of EAF, this management approach has not been adequately implemented. In practice, the status of implementation of EAF was assessed through the Southern African Sustainable Seafood Initiative (SASSI) and the Ecological Risk Assessments (ERA). The scores of 65 assessments, conducted in 2013 and 2014, were obtained from SASSI. Of the 65 species assessed; 18.4% were listed as Green, 50.8% were listed as Orange and 30.8% were listed as Red. Two methods were used to analyse the data; non-metric multidimensional scaling (NMDS), and cluster analysis in the statistical program R. Analysis of the SASSI assessments indicates that there has been progress in implementing EAF since the World Summit on Sustainable Development in 2002. The high number of Orange and Red listed species however, indicate that major sustainability issues still exist. Species in commercially important fisheries enjoy the bulk of research and management attention compared to other species, including bycatch species, as reflected by a high proportion of Green-rated commercially important species. Based on these results, four fisheries were chosen for further indepth analysis using additional information found in ecological risk assessments: offshore demersal trawl, inshore demersal trawl, West Coast rock lobster fishery and the line fishery. The documents and published literature of the Department of Agriculture, Forestry and Fisheries Internal Scientific Working Groups provided further information. A Wilcoxon signed rank test conducted in the programme R on the results of the ERAs showed that there was a decline in implementation of EAF and reinforced the earlier conclusion that large commercial fisheries, offshore and inshore demersal trawl, were progressing in implementing EAF faster than West Coast rock lobster and line fisheries, which are examples of smaller-scale fisheries that are more accessible to many resource users. Both progress and challenges appeared to be largely influenced by several common factors, which include the presence or absence of positive incentives, co-management, management plans, access, compliance, economic importance, capacity, and the interests of rights holders and other stakeholders.
- Full Text:
- Authors: Duna, Elethu Zamandlane Lona
- Date: 2017
- Subjects: Fisheries -- Environmental aspects -- South Africa , Sustainable fisheries -- South Africa , Fishery management -- South Africa , South African Sustainable Seafood Initiative
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/44879 , vital:25449
- Description: Over the last century, the population of the world has more than doubled, resulting in an increase in seafood consumption (FAO 2010), and placing strain on fisheries wild stocks, their habitats, and the coastal communities that rely on them for food and survival. The ecosystem approach to fisheries (EAF) differs from other management approaches by combining all aspects of ecosystem management, and strives to conserve ecosystem structure, maintain diversity, productivity, and integrity, and to meet human food and economic needs. This study aims to assess how South Africa is progressing in implementing EAF in principle and in practice, to identify challenges, and suggest solutions, where appropriate. The law sets precedence on governance. An assessment of the Marine Living Resources Act, (MLRA) and the South African Policy for Small-scale Fisheries (SSFP) revealed that, although these instruments recognise and contain elements of EAF, this management approach has not been adequately implemented. In practice, the status of implementation of EAF was assessed through the Southern African Sustainable Seafood Initiative (SASSI) and the Ecological Risk Assessments (ERA). The scores of 65 assessments, conducted in 2013 and 2014, were obtained from SASSI. Of the 65 species assessed; 18.4% were listed as Green, 50.8% were listed as Orange and 30.8% were listed as Red. Two methods were used to analyse the data; non-metric multidimensional scaling (NMDS), and cluster analysis in the statistical program R. Analysis of the SASSI assessments indicates that there has been progress in implementing EAF since the World Summit on Sustainable Development in 2002. The high number of Orange and Red listed species however, indicate that major sustainability issues still exist. Species in commercially important fisheries enjoy the bulk of research and management attention compared to other species, including bycatch species, as reflected by a high proportion of Green-rated commercially important species. Based on these results, four fisheries were chosen for further indepth analysis using additional information found in ecological risk assessments: offshore demersal trawl, inshore demersal trawl, West Coast rock lobster fishery and the line fishery. The documents and published literature of the Department of Agriculture, Forestry and Fisheries Internal Scientific Working Groups provided further information. A Wilcoxon signed rank test conducted in the programme R on the results of the ERAs showed that there was a decline in implementation of EAF and reinforced the earlier conclusion that large commercial fisheries, offshore and inshore demersal trawl, were progressing in implementing EAF faster than West Coast rock lobster and line fisheries, which are examples of smaller-scale fisheries that are more accessible to many resource users. Both progress and challenges appeared to be largely influenced by several common factors, which include the presence or absence of positive incentives, co-management, management plans, access, compliance, economic importance, capacity, and the interests of rights holders and other stakeholders.
- Full Text:
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