A multidisciplinary study to assess the ecology of the Cape sea urchin, Parechinus angulosus, and its emerging use as a bioindicator to monitor coastal resiliency
- Authors: Redelinghuys, Suzanne
- Date: 2024-04-05
- Subjects: Intertidal ecology , Parechinus angulosus , Sea urchins Morphology , Sea urchins Climatic factors , Phylogeography , Morphometrics , Microbiomes , Marine invertebrates
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/435691 , vital:73179 , DOI 10.21504/10962/435692
- Description: The resilience of marine species in the face of unpredictable climate change stands as a paramount concern for the maintenance of ecological stability. Under such fluctuating conditions, it is critical to understand how organisms mitigate these effects in physiological, genetic, and morphological terms. To that end, this thesis focused on the Cape sea urchin, Parechinus angulosus, employing a multidisciplinary approach encompassing morphology, genomics, and gut microbial diversity to assess its potential as a bioindicator species and elucidate its adaptive strategies in response to varying environmental conditions along the South African coastline. This was achieved through studying their anatomy in order to link observed variation to prevailing local environmental conditions, aided by the species’ wide distribution range which allows insight into adaptations across broad geographic regions and ecological settings. The first empirical chapter, Chapter 3, focusing on eight key morphometric traits of test, Aristotle’s lantern and spines, revealed distinct variation in the Cape sea urchin's morphology between the east and west coasts of South Africa, suggesting the presence of some level of local adaptation to the prevailing environmental factors found on the east and west coasts of South Africa. This points to potential bioindicator capabilities of the species, reflecting adaptive divergence amidst contrasting environmental conditions. Further analysis is however necessary in order to isolate specific physiological trends that may be associated with these morphometric differences, thereby enhancing and tightening their ecological implications. The second experimental chapter, Chapter 4, delved into the genetic structure of the Cape urchin by investigating genome-wide diversity, the presence of cryptic population structure, and spatial patterns of genomic diversity. Moderate genomic differentiation was detected among populations along the eastern and western coasts of South Africa by outlier loci that may undergo natural selection, which could indicate local adaptation to environmental conditions. This pattern hints at adaptive differentiation and cryptic genetic structures within the Cape sea urchin populations and emphasises the species' potential adaptive responses to localised (in this case regional) environmental pressures. Assigning functional significance to these genetic variations will require a comprehensive annotated reference genome, a limitation acknowledged in the current study. Chapter 5 explored the gut microbial diversity and revealed significant compositional variations between the east and west coast populations of South Africa, confirming regional and inter-regional variation. This chapter also highlighted the essential biochemical pathways critical to the survival of the host which is crucial for assessing the health of the urchin host. Together, the functional content of the gut bacteria and microbial diversity showcases its potential as a bioindicator for coastal ecosystem health. Logistical challenges and confounding factors like host physiology will need to be fully considered for its effective application. Overall, the findings of this doctoral research suggest that the Cape sea urchin displays promising characteristics as a bioindicator species due to its morphological, genetic, and gut microbial variations in response to environmental differences, providing a diverse array of means in which urchins could be used as bioindicators, from their uses to assess water quality and detect pollution, to ecosystem health monitoring and biodiversity studies in which sea urchin abundance, distribution, and presence are monitored. Further research, integrating these multidisciplinary approaches is recommended to validate and refine its bioindicator potential. Additionally, the development of a comprehensive annotated reference genome is imperative to harness the species' genetic information effectively. This study underscores the significance of integrating multiple disciplines in understanding how species respond to environmental change and their potentials contributions to monitor ecological resilience. The original multidisciplinary approach, combined with high computational outputs presents a promising framework for a comprehensive ecological monitoring in marine ecosystems. , Thesis (PhD) -- Faculty of Science, Zoology and Entomology, 2024
- Full Text:
- Authors: Redelinghuys, Suzanne
- Date: 2024-04-05
- Subjects: Intertidal ecology , Parechinus angulosus , Sea urchins Morphology , Sea urchins Climatic factors , Phylogeography , Morphometrics , Microbiomes , Marine invertebrates
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/435691 , vital:73179 , DOI 10.21504/10962/435692
- Description: The resilience of marine species in the face of unpredictable climate change stands as a paramount concern for the maintenance of ecological stability. Under such fluctuating conditions, it is critical to understand how organisms mitigate these effects in physiological, genetic, and morphological terms. To that end, this thesis focused on the Cape sea urchin, Parechinus angulosus, employing a multidisciplinary approach encompassing morphology, genomics, and gut microbial diversity to assess its potential as a bioindicator species and elucidate its adaptive strategies in response to varying environmental conditions along the South African coastline. This was achieved through studying their anatomy in order to link observed variation to prevailing local environmental conditions, aided by the species’ wide distribution range which allows insight into adaptations across broad geographic regions and ecological settings. The first empirical chapter, Chapter 3, focusing on eight key morphometric traits of test, Aristotle’s lantern and spines, revealed distinct variation in the Cape sea urchin's morphology between the east and west coasts of South Africa, suggesting the presence of some level of local adaptation to the prevailing environmental factors found on the east and west coasts of South Africa. This points to potential bioindicator capabilities of the species, reflecting adaptive divergence amidst contrasting environmental conditions. Further analysis is however necessary in order to isolate specific physiological trends that may be associated with these morphometric differences, thereby enhancing and tightening their ecological implications. The second experimental chapter, Chapter 4, delved into the genetic structure of the Cape urchin by investigating genome-wide diversity, the presence of cryptic population structure, and spatial patterns of genomic diversity. Moderate genomic differentiation was detected among populations along the eastern and western coasts of South Africa by outlier loci that may undergo natural selection, which could indicate local adaptation to environmental conditions. This pattern hints at adaptive differentiation and cryptic genetic structures within the Cape sea urchin populations and emphasises the species' potential adaptive responses to localised (in this case regional) environmental pressures. Assigning functional significance to these genetic variations will require a comprehensive annotated reference genome, a limitation acknowledged in the current study. Chapter 5 explored the gut microbial diversity and revealed significant compositional variations between the east and west coast populations of South Africa, confirming regional and inter-regional variation. This chapter also highlighted the essential biochemical pathways critical to the survival of the host which is crucial for assessing the health of the urchin host. Together, the functional content of the gut bacteria and microbial diversity showcases its potential as a bioindicator for coastal ecosystem health. Logistical challenges and confounding factors like host physiology will need to be fully considered for its effective application. Overall, the findings of this doctoral research suggest that the Cape sea urchin displays promising characteristics as a bioindicator species due to its morphological, genetic, and gut microbial variations in response to environmental differences, providing a diverse array of means in which urchins could be used as bioindicators, from their uses to assess water quality and detect pollution, to ecosystem health monitoring and biodiversity studies in which sea urchin abundance, distribution, and presence are monitored. Further research, integrating these multidisciplinary approaches is recommended to validate and refine its bioindicator potential. Additionally, the development of a comprehensive annotated reference genome is imperative to harness the species' genetic information effectively. This study underscores the significance of integrating multiple disciplines in understanding how species respond to environmental change and their potentials contributions to monitor ecological resilience. The original multidisciplinary approach, combined with high computational outputs presents a promising framework for a comprehensive ecological monitoring in marine ecosystems. , Thesis (PhD) -- Faculty of Science, Zoology and Entomology, 2024
- Full Text:
Systematics and phylogeography of mormyrid fishes in South Africa
- Authors: Maake, Pholoshi Abram
- Date: 2015-04-09
- Subjects: Marcusenius , Fishes Morphology , Petrocephalus , Fishes Phylogeny , Phylogeography , Fishes Identification
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/480323 , vital:78431
- Description: Two genera of mormyrids have been reognised from South Africa. Marcuseniusis the largest genus of the Mormyridae, comprising 38 species distributed throughout tropical and sub-tropical Africa. In southern and eastern Africa eight species have been recognized, including M. pongolensis from South Africa. Petrocephalus has about 30 species distributed mainly in tropical Africa, and 15 of these were recently identified in southern and eastern Africa. This thesis integrated several techniques, through the collection of complementary, but separate data sets to investigate the phylogeography of M. pongolensis in South Africa, and the systematics, evolutionary history, biogeography of Marcusenius and Petrocephalus fishes in southern and eastern Africa. Mitochondrial and nuclear genetic markers consistently demonstrated strong population structuring and identified three divergent lineages within South Africa. The widespread Pongola Lineage occurs partly in the Limpopo River system, and is very common in the Incomati, Pongola (type locality) and Kosi river systems. The Limpopo Lineage endemic only in the Limpopo River system is monophyletic with the Mhlatuze-Nseleni Lineage which is only known from the Mhlatuze and Nseleni rivers in the south. There was strong indication of historical isolation, in the form of allopatric fragmentation between genetically divergent Limpopo and Mhlatuze-Nseleni lineages. High genetic diversity was observed in the Limpopo River system within the Limpopo Lineage and the Pongola Lineage. The occurrence of the Mhlatuze-Nseleni Lineage in the far south cannot be explained by the hypothesis of confluence of rivers, river capture or episodic drainage connections, as the Mhlatuze and Nseleni Rivers would not have had a common confluence or shared low relief terrain with the Limpopo, Incomati, Pongola or Kosi river systems. Morphological studies of these lineages revealed even more differentiations and were described as: Marcusenius krameri sp. nov. for the Limpopo Lineage, and M. caudisquamatus sp. nov. from the Mhlatuze and Nseleni river systems. The specimens from the Ruvuma River were also well differentiated from all southern and eastern African species of Marcusenius, and were therefore recognised as M. lucombesisp. nov. New diagnosis characters of M. pongolensis were re-described and a key to the southern and eastern African species of Marcusenius was also provided. The results of all phylogenetic approaches that included all known southern and eastern African Marcusenius species are highly congruent and provided very strong support for recognizing Marcusenius species from these regions as a monophyletic assemblage that evolved from a single common ancestor. The southern and eastern African Petrocephalus is divided into two deeply mitochondrial and nuclear divergent Western and Eastern groups that are separated by the Victoria Falls. The phylogenetic relationships within each group were not supported and future studies incorporating more molecular characters and species will likely help to resolve the relationships. Speciation within Marcusenius and Petrocephalus ranges in the focus of at least 0.8-5 Million years ago in agreement with geological data, which suggested that vicariant events associated with the formation of the major river systems played a major role in the evolution and distribution of both genera in southern and eastern Africa. The high degree of genetic differentiation and at least four previously undescribed lineages recovered in this study suggested that mormyrid diversity within southern and eastern Africa may be underestimated. Possible threats to the studied mormyrid species and lineages and other freshwater-dependent species were identified during the course of this study. When described, the unidentified lineages would further increase the species diversity of both Marcusenius and Petrocephalus, and, therefore, the southern and eastern African ichthyofauna. , Thesis (PhD) -- Faculty of Science, Ichthyology and Fisheries Science, 2025
- Full Text:
- Authors: Maake, Pholoshi Abram
- Date: 2015-04-09
- Subjects: Marcusenius , Fishes Morphology , Petrocephalus , Fishes Phylogeny , Phylogeography , Fishes Identification
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/480323 , vital:78431
- Description: Two genera of mormyrids have been reognised from South Africa. Marcuseniusis the largest genus of the Mormyridae, comprising 38 species distributed throughout tropical and sub-tropical Africa. In southern and eastern Africa eight species have been recognized, including M. pongolensis from South Africa. Petrocephalus has about 30 species distributed mainly in tropical Africa, and 15 of these were recently identified in southern and eastern Africa. This thesis integrated several techniques, through the collection of complementary, but separate data sets to investigate the phylogeography of M. pongolensis in South Africa, and the systematics, evolutionary history, biogeography of Marcusenius and Petrocephalus fishes in southern and eastern Africa. Mitochondrial and nuclear genetic markers consistently demonstrated strong population structuring and identified three divergent lineages within South Africa. The widespread Pongola Lineage occurs partly in the Limpopo River system, and is very common in the Incomati, Pongola (type locality) and Kosi river systems. The Limpopo Lineage endemic only in the Limpopo River system is monophyletic with the Mhlatuze-Nseleni Lineage which is only known from the Mhlatuze and Nseleni rivers in the south. There was strong indication of historical isolation, in the form of allopatric fragmentation between genetically divergent Limpopo and Mhlatuze-Nseleni lineages. High genetic diversity was observed in the Limpopo River system within the Limpopo Lineage and the Pongola Lineage. The occurrence of the Mhlatuze-Nseleni Lineage in the far south cannot be explained by the hypothesis of confluence of rivers, river capture or episodic drainage connections, as the Mhlatuze and Nseleni Rivers would not have had a common confluence or shared low relief terrain with the Limpopo, Incomati, Pongola or Kosi river systems. Morphological studies of these lineages revealed even more differentiations and were described as: Marcusenius krameri sp. nov. for the Limpopo Lineage, and M. caudisquamatus sp. nov. from the Mhlatuze and Nseleni river systems. The specimens from the Ruvuma River were also well differentiated from all southern and eastern African species of Marcusenius, and were therefore recognised as M. lucombesisp. nov. New diagnosis characters of M. pongolensis were re-described and a key to the southern and eastern African species of Marcusenius was also provided. The results of all phylogenetic approaches that included all known southern and eastern African Marcusenius species are highly congruent and provided very strong support for recognizing Marcusenius species from these regions as a monophyletic assemblage that evolved from a single common ancestor. The southern and eastern African Petrocephalus is divided into two deeply mitochondrial and nuclear divergent Western and Eastern groups that are separated by the Victoria Falls. The phylogenetic relationships within each group were not supported and future studies incorporating more molecular characters and species will likely help to resolve the relationships. Speciation within Marcusenius and Petrocephalus ranges in the focus of at least 0.8-5 Million years ago in agreement with geological data, which suggested that vicariant events associated with the formation of the major river systems played a major role in the evolution and distribution of both genera in southern and eastern Africa. The high degree of genetic differentiation and at least four previously undescribed lineages recovered in this study suggested that mormyrid diversity within southern and eastern Africa may be underestimated. Possible threats to the studied mormyrid species and lineages and other freshwater-dependent species were identified during the course of this study. When described, the unidentified lineages would further increase the species diversity of both Marcusenius and Petrocephalus, and, therefore, the southern and eastern African ichthyofauna. , Thesis (PhD) -- Faculty of Science, Ichthyology and Fisheries Science, 2025
- Full Text:
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