Plants, people, and place: complex, mutualistic, and co-evolving global patterns through time
- Authors: Van Wijk, Yvette Ethné
- Date: 2019
- Subjects: Ethnobotany -- South Africa -- Western Cape , Khoisan (African people) -- Ethnobotany , Human-plant relationships -- South Africa -- Western Cape , Plants -- Classification -- South Africa -- Western Cape , Plant remains (Archaeology) -- South Africa -- Western Cape , Ethnoscience -- South Africa -- Western Cape , Regression analysis
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/76575 , vital:30609
- Description: My thesis studies and analyses the suite of distinctive plant taxa which persist in small patches of vegetation growing in close association with archaeological habitation sites in the southern Cape, South Africa. The unexpected correlation and overlap between botanical taxa collected at 75 site complexes, and ethnobotanical data collected in collaboration with modern Khoi-San communities in the same area, is explored and interrogated. Although sparse, reports of the same suite of taxa recovered from archaeological excavations in the Cape provinces provides depth of time to the study, linking the past to the present. The three-way correlation of a suite of plants closely associated with humans and habitation sites through time, allows for triangulation of the data in order to validate and cross verify the results using more than one frame of reference. Both the plants and the knowledge about their uses have persisted in spite of historical attrition, and alienation of land and language, suffered by the Khoi-San over the past 300 years. Drawing on a large body of primary and secondary data, and using an interdisciplinary, abductive and pragmatic mixed methods approach, a pattern can be traced throughout Africa and globally. Regression analysis strongly indicates that the most ubiquitous taxa were selected for a purpose and are not randomly present in association with humans. Botanical, anthropological, and archaeological studies seldom focus on the inter-connectedness of people and plants at the sites they inhabited. Very little research into modern vegetation in close association with the sites has been undertaken, and vegetation mapping has not captured the occurrence of these site-specific small vegetation patches recorded during my surveys. The topographically, geologically, and vegetatively complex and varied southern Cape, and greater Cape area, is extremely rich in archaeological sites and history. This study suggests that the value of site-specific plant taxa to humans throughout the aeons of pre-agricultural history, persists into the present. Due to tolerance of a broad range of climatic and environmental variables, there is value in the study of these ancient and neglected useful plants in the face of climate change. That this vegetation is so closely associated with archaeological sites of cultural and historic importance confers an urgency to recognising the existence and significance of the distinctive and possibly anthropogenic vegetation surrounding the sites.
- Full Text:
- Authors: Van Wijk, Yvette Ethné
- Date: 2019
- Subjects: Ethnobotany -- South Africa -- Western Cape , Khoisan (African people) -- Ethnobotany , Human-plant relationships -- South Africa -- Western Cape , Plants -- Classification -- South Africa -- Western Cape , Plant remains (Archaeology) -- South Africa -- Western Cape , Ethnoscience -- South Africa -- Western Cape , Regression analysis
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/76575 , vital:30609
- Description: My thesis studies and analyses the suite of distinctive plant taxa which persist in small patches of vegetation growing in close association with archaeological habitation sites in the southern Cape, South Africa. The unexpected correlation and overlap between botanical taxa collected at 75 site complexes, and ethnobotanical data collected in collaboration with modern Khoi-San communities in the same area, is explored and interrogated. Although sparse, reports of the same suite of taxa recovered from archaeological excavations in the Cape provinces provides depth of time to the study, linking the past to the present. The three-way correlation of a suite of plants closely associated with humans and habitation sites through time, allows for triangulation of the data in order to validate and cross verify the results using more than one frame of reference. Both the plants and the knowledge about their uses have persisted in spite of historical attrition, and alienation of land and language, suffered by the Khoi-San over the past 300 years. Drawing on a large body of primary and secondary data, and using an interdisciplinary, abductive and pragmatic mixed methods approach, a pattern can be traced throughout Africa and globally. Regression analysis strongly indicates that the most ubiquitous taxa were selected for a purpose and are not randomly present in association with humans. Botanical, anthropological, and archaeological studies seldom focus on the inter-connectedness of people and plants at the sites they inhabited. Very little research into modern vegetation in close association with the sites has been undertaken, and vegetation mapping has not captured the occurrence of these site-specific small vegetation patches recorded during my surveys. The topographically, geologically, and vegetatively complex and varied southern Cape, and greater Cape area, is extremely rich in archaeological sites and history. This study suggests that the value of site-specific plant taxa to humans throughout the aeons of pre-agricultural history, persists into the present. Due to tolerance of a broad range of climatic and environmental variables, there is value in the study of these ancient and neglected useful plants in the face of climate change. That this vegetation is so closely associated with archaeological sites of cultural and historic importance confers an urgency to recognising the existence and significance of the distinctive and possibly anthropogenic vegetation surrounding the sites.
- Full Text:
The conservation, ecology, and distribution of the critically endangered Encephalartos latifrons Lehm
- Authors: Swart, Carin
- Date: 2019
- Subjects: Encephalartos , Cycadaceae , Cycads -- Conservation -- South Africa , Botany, Economic -- South Africa , Rare plants -- South Africa , Endangered plants -- South Africa , Wild plant trade -- Law and legislation -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/94483 , vital:31049
- Description: Cycads have attracted global attention both as horticulturally interesting and often valuable plants; but also as some of the most threatened organisms on the planet. In this thesis I investigate the conservation management, biology, reproductive ecology and distribution of Encephalartos latifrons populations in the wild and draw out conclusions on how best to conserve global cycad biodiversity. I also employ computer-modelling techniques in some of the chapters of this thesis to demonstrate how to improve conservation outcomes for E. latifrons and endangered species in general, where information on the distribution, biology and habitat requirements of such species are inherently limited, often precluding robust conservation decision-making. In Chapter 1 of this thesis I introduce the concept of extinction debt and elucidate the importance of in situ cycad conservation. I explain how the concept of extinction debt relates to single species, as well as give details on the mechanisms causing extinction debt in cycad populations. I introduce the six extinction trajectory threshold model and how this relates to extinction debt in cycads. I discuss the vulnerability of cycads to extinction and give an overview of biodiversity policy in South Africa. I expand on how national and global policies contribute to cycad conservation and present various global initiatives that support threatened species conservation. I conclude Chapter 1 by explaining how computer-based models can assist conservation decision-making for rare, threatened, and endangered species in the face of uncertainty. Chapter 2 of this thesis illustrates how a modelling approach, using limited available historical and present day locality information, is a feasible method to determine areas of suitable habitat for E. latifrons and other critically endangered cycad species where locality information is inherently uncommon. Results from this chapter show that conservation planning through structured decision-making may be improved by the use of computer models, even when locality data are limited. These results may be incorporated into biodiversity conservation plans or used to assist conservation-decision makers when undertaking recovery efforts for E. latifrons and may provide guidance to conservation planners and policy makers when undertaking conservation plans to improve cycad biodiversity both nationally and globally. There was limited information available in the biology and ecological requirements of E. latifrons. This information is important when making policy decisions such as the publication of non-detriment findings and compiling biodiversity management plans for this and other cycad species. Chapter 3 investigates the life-history, population structure, fire response and survival of an in situ E. latifrons population. A demographic census was undertaken between 2013 and 2017 on a previously undiscovered population. Population characteristics of the “new” population were compared to the demographics of a well-known and intensively managed population. Results of this chapter show that at least one in situ E. latifrons population is stable and increasing under current environmental conditions. Importantly, the population is naturally recruiting seedlings without the need for artificial pollination. Demographic information described in this chapter is a necessary precursor to undertaking a Population Viability Assessment for the species. This will assist conservation decision-makers when determining the best conservation management strategy for E. latifrons. It may also be useful to apply generalisatons to other cycad species (with similar life-histories and habitat requirements) where there is limited information available on the species biological and ecological requirements, restricting robust policy conservation decision-making. It was important for this study to determine the extent and variety of cone fauna within existing E. latifrons wild populations. Previous anecdotal evidence suggested that E. latifrons is functionally extinct as a species, but evidence to the contrary was found when a healthy, self-sustaining wild population was discovered to be naturally recruiting. It was important to establish the existence and diversity of male cone faunal species (an important breeding site for weevil pollinators) within wild populations. Chapter 4 set out to determine if potential pollinators exist in the wild and if so, how diverse are they and in what numbers. This is the first comprehensive analysis of cone fauna present in wild E. latifrons populations. Equally important was the need to determine if wild populations are capable of producing viable seeds under conditions conducive to natural pollination. Results of this chapter show that there is a relatively high diversity of insect fauna in the male cones of some wild E. latifrons populations. Furthermore, some wild populations are capable of producing viable seeds through natural pollination; even though they may not be naturally recruiting seedlings into the population. A staggered germination pattern displayed by one of the wild E. latifrons populations was studied, suggesting the evolution of an adaptive trait given the stochastic environment (climatically and disturbances such as fire) within which E. latifrons populations may be found. Species recovery (restoration and/or population augmentation) may be the only conservation solution remaining to save endangered species such as E. latifrons from extinction in the wild. Chapter 5 involves the return of 25 seedlings germinated as part of a seed viability experiment (see Chapter 4) back into a wild population from where they originated. The primary threat to seedling survival at the site was livestock activity (grazing/trampling). The population was subsequently fenced off to mitigate this threat and seedlings planted both inside and outside a fenced area to establish if there was a difference in seedling survival between the unprotected and protected sites. A high percentage (92%) of seedlings planted perished in total. None of the seedlings planted outside the fenced area survived over the monitoring period, while only two seedlings planted within the fenced area survived. Survival of the seedlings inside the fenced area was only after placing individual cages on the seedlings to prevent further losses. The primary causes of death for all seedlings included uprooting, and defoliation with some of the seedlings missing completely. This chapter found that the lack of natural seedling recruitment at the site was as a result of livestock activity. Grazing by livestock poses a significant threat to natural recruitment in some E. latifrons populations. Alternative restoration methods are suggested and protection of seedlings while undertaking a restoration/augmentation programme is emphasised. Developing conservation management plans for rare and/or endangered species is often met with high levels of uncertainty, particularly if there is limited information available on the biology and ecological requirements for the species concerned. Population viability analysis (PVA) is often suggested as a tool to determine conservation management scenarios that may enhance wild population persistence. The standard PVA approach is however problematic as it is a time-consuming process requiring the collection of demographic data over long time periods. In addition, the PVA approach does not take in to account non-biological factors which may impede the effective implementation of conservation plans. Chapter 6 of this thesis makes use of a Multi-Criteria Decision Making (MCDM) approach called the Analytical Hierarchy Process (AHP) to decide on the best conservation management strategy for an E. latifrons population. Sensitivity analysis was completed to test the robustness of the decision and to identify which criteria influenced the original results. In this study, the development of the decision tree and criteria judgements, were made solely by the researcher. It is emphasised that the decision outcome may be biased if not conducted as part of a multi-stakeholder workshop using the same approach. Nevertheless, it is recommended that a Population Viability Risk Management (PVRM) assessment be undertaken for E. latifrons using an MCDM approach such as AHP as a prestudy, before the revision of the Biodiversity Management Plan (BMP) for E. latifrons. This method is particularly useful when non-biological criteria are to be incorporated into the decision-making process. It is also a viable and holistic alternative to the standard PVA approach when developing conservation management plans for rare and endangered species. In Chapter 7 I review the concept of extinction debt in cycads using E. latifrons as an example. I assimilate historical information to understand mechanisms that may have impacted on E. latifrons populations in the past. This was done to understand the scale of extinction time lags on E. latifrons and to relate this to its present position on the exitinction trajectory. I recommend aligning South African policies and biodiversity assessments with international initiatives and draw out general conclusions for the conservation of global cycad biodiversity. I conclude by recommending further research for E. latifrons.
- Full Text:
- Authors: Swart, Carin
- Date: 2019
- Subjects: Encephalartos , Cycadaceae , Cycads -- Conservation -- South Africa , Botany, Economic -- South Africa , Rare plants -- South Africa , Endangered plants -- South Africa , Wild plant trade -- Law and legislation -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/94483 , vital:31049
- Description: Cycads have attracted global attention both as horticulturally interesting and often valuable plants; but also as some of the most threatened organisms on the planet. In this thesis I investigate the conservation management, biology, reproductive ecology and distribution of Encephalartos latifrons populations in the wild and draw out conclusions on how best to conserve global cycad biodiversity. I also employ computer-modelling techniques in some of the chapters of this thesis to demonstrate how to improve conservation outcomes for E. latifrons and endangered species in general, where information on the distribution, biology and habitat requirements of such species are inherently limited, often precluding robust conservation decision-making. In Chapter 1 of this thesis I introduce the concept of extinction debt and elucidate the importance of in situ cycad conservation. I explain how the concept of extinction debt relates to single species, as well as give details on the mechanisms causing extinction debt in cycad populations. I introduce the six extinction trajectory threshold model and how this relates to extinction debt in cycads. I discuss the vulnerability of cycads to extinction and give an overview of biodiversity policy in South Africa. I expand on how national and global policies contribute to cycad conservation and present various global initiatives that support threatened species conservation. I conclude Chapter 1 by explaining how computer-based models can assist conservation decision-making for rare, threatened, and endangered species in the face of uncertainty. Chapter 2 of this thesis illustrates how a modelling approach, using limited available historical and present day locality information, is a feasible method to determine areas of suitable habitat for E. latifrons and other critically endangered cycad species where locality information is inherently uncommon. Results from this chapter show that conservation planning through structured decision-making may be improved by the use of computer models, even when locality data are limited. These results may be incorporated into biodiversity conservation plans or used to assist conservation-decision makers when undertaking recovery efforts for E. latifrons and may provide guidance to conservation planners and policy makers when undertaking conservation plans to improve cycad biodiversity both nationally and globally. There was limited information available in the biology and ecological requirements of E. latifrons. This information is important when making policy decisions such as the publication of non-detriment findings and compiling biodiversity management plans for this and other cycad species. Chapter 3 investigates the life-history, population structure, fire response and survival of an in situ E. latifrons population. A demographic census was undertaken between 2013 and 2017 on a previously undiscovered population. Population characteristics of the “new” population were compared to the demographics of a well-known and intensively managed population. Results of this chapter show that at least one in situ E. latifrons population is stable and increasing under current environmental conditions. Importantly, the population is naturally recruiting seedlings without the need for artificial pollination. Demographic information described in this chapter is a necessary precursor to undertaking a Population Viability Assessment for the species. This will assist conservation decision-makers when determining the best conservation management strategy for E. latifrons. It may also be useful to apply generalisatons to other cycad species (with similar life-histories and habitat requirements) where there is limited information available on the species biological and ecological requirements, restricting robust policy conservation decision-making. It was important for this study to determine the extent and variety of cone fauna within existing E. latifrons wild populations. Previous anecdotal evidence suggested that E. latifrons is functionally extinct as a species, but evidence to the contrary was found when a healthy, self-sustaining wild population was discovered to be naturally recruiting. It was important to establish the existence and diversity of male cone faunal species (an important breeding site for weevil pollinators) within wild populations. Chapter 4 set out to determine if potential pollinators exist in the wild and if so, how diverse are they and in what numbers. This is the first comprehensive analysis of cone fauna present in wild E. latifrons populations. Equally important was the need to determine if wild populations are capable of producing viable seeds under conditions conducive to natural pollination. Results of this chapter show that there is a relatively high diversity of insect fauna in the male cones of some wild E. latifrons populations. Furthermore, some wild populations are capable of producing viable seeds through natural pollination; even though they may not be naturally recruiting seedlings into the population. A staggered germination pattern displayed by one of the wild E. latifrons populations was studied, suggesting the evolution of an adaptive trait given the stochastic environment (climatically and disturbances such as fire) within which E. latifrons populations may be found. Species recovery (restoration and/or population augmentation) may be the only conservation solution remaining to save endangered species such as E. latifrons from extinction in the wild. Chapter 5 involves the return of 25 seedlings germinated as part of a seed viability experiment (see Chapter 4) back into a wild population from where they originated. The primary threat to seedling survival at the site was livestock activity (grazing/trampling). The population was subsequently fenced off to mitigate this threat and seedlings planted both inside and outside a fenced area to establish if there was a difference in seedling survival between the unprotected and protected sites. A high percentage (92%) of seedlings planted perished in total. None of the seedlings planted outside the fenced area survived over the monitoring period, while only two seedlings planted within the fenced area survived. Survival of the seedlings inside the fenced area was only after placing individual cages on the seedlings to prevent further losses. The primary causes of death for all seedlings included uprooting, and defoliation with some of the seedlings missing completely. This chapter found that the lack of natural seedling recruitment at the site was as a result of livestock activity. Grazing by livestock poses a significant threat to natural recruitment in some E. latifrons populations. Alternative restoration methods are suggested and protection of seedlings while undertaking a restoration/augmentation programme is emphasised. Developing conservation management plans for rare and/or endangered species is often met with high levels of uncertainty, particularly if there is limited information available on the biology and ecological requirements for the species concerned. Population viability analysis (PVA) is often suggested as a tool to determine conservation management scenarios that may enhance wild population persistence. The standard PVA approach is however problematic as it is a time-consuming process requiring the collection of demographic data over long time periods. In addition, the PVA approach does not take in to account non-biological factors which may impede the effective implementation of conservation plans. Chapter 6 of this thesis makes use of a Multi-Criteria Decision Making (MCDM) approach called the Analytical Hierarchy Process (AHP) to decide on the best conservation management strategy for an E. latifrons population. Sensitivity analysis was completed to test the robustness of the decision and to identify which criteria influenced the original results. In this study, the development of the decision tree and criteria judgements, were made solely by the researcher. It is emphasised that the decision outcome may be biased if not conducted as part of a multi-stakeholder workshop using the same approach. Nevertheless, it is recommended that a Population Viability Risk Management (PVRM) assessment be undertaken for E. latifrons using an MCDM approach such as AHP as a prestudy, before the revision of the Biodiversity Management Plan (BMP) for E. latifrons. This method is particularly useful when non-biological criteria are to be incorporated into the decision-making process. It is also a viable and holistic alternative to the standard PVA approach when developing conservation management plans for rare and endangered species. In Chapter 7 I review the concept of extinction debt in cycads using E. latifrons as an example. I assimilate historical information to understand mechanisms that may have impacted on E. latifrons populations in the past. This was done to understand the scale of extinction time lags on E. latifrons and to relate this to its present position on the exitinction trajectory. I recommend aligning South African policies and biodiversity assessments with international initiatives and draw out general conclusions for the conservation of global cycad biodiversity. I conclude by recommending further research for E. latifrons.
- Full Text:
Systematics and biogeography of forest snails, chondrocyclus (mollusca: gastropoda: caenogastropoda: cyclophoridae) in Southern Africa
- Authors: Cole, Mary Louise
- Date: 2017
- Subjects: Chondrocyclus , Mollusks -- South Africa , Cyclophoridae -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/4356 , vital:20651
- Description: This study presents a molecular phylogeny and systematic revision of Chondrocyclus, the major South African group of the large family of operculate terrestrial molluscs, the Cyclophoridae. Chondrocyclus snails are small gastropods found in forest and moist thicket throughout South Africa. This is the first detailed systematic treatment of a group of Cyclophoridae in mainland Africa and the first to provide molecular data. This study complements regional studies on the systematics of the family in Asia and provides comparative data for studies of higher level relationships within the Cyclophoridae. Phylogenetic reconstruction by BI and ML methods of combined and single gene datasets of 16S and CO 1 all showed Chondrocyclus to be monophyletic and recovered five well-supported clades that corresponded to groups of populations identifiable on the basis of combinations of morphological characters. Species were diagnosed morphologically and were shown to be genetically distinct lineages. Informative morphological features include shell dimensions, protoconch, periostracum, operculum, radula and penis. Two species in Afromontane regions of Zimbabwe and Malawi respectively are excluded from Chondrocyclus based on morphology and tentatively placed in Cyathopoma. Diversity recognised within the genus more than doubled, from a previous seven South African species to seventeen. Re-descriptions of established species and descriptions of new species are provided, together with photographs of morphological characteristics. New taxon names and nomenclatural acts within it are disclaimed and are therefore not available in the sense of the International Code of Zoological Nomenclature until validly published elsewhere. Several cryptic species within previously widespread “species” and unrecorded narrowly endemic species were documented. The clade consisting of populations of “Chondrocyclus isipingoensis”, now considered to be a species complex, was sister to a group containing the other four clades. The “Isipingoensis” clade occurs widely in Afromontane regions, along the Great Escarpment, and on the south-east coast. The other four clades occur from Zululand to the Cape Peninsula with a pattern of east-west lineage turnover. The biogeography of Chondrocyclus is interpreted by comparison with concordant patterns in other terrestrial molluscs and unrelated taxa with poor dispersal ability. This study complements other research on composition, spatial distribution and phylogenetic diversity of low-vagility invertebrates and expands the data available for biodiversity conservation in South Africa.
- Full Text:
- Authors: Cole, Mary Louise
- Date: 2017
- Subjects: Chondrocyclus , Mollusks -- South Africa , Cyclophoridae -- South Africa
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/4356 , vital:20651
- Description: This study presents a molecular phylogeny and systematic revision of Chondrocyclus, the major South African group of the large family of operculate terrestrial molluscs, the Cyclophoridae. Chondrocyclus snails are small gastropods found in forest and moist thicket throughout South Africa. This is the first detailed systematic treatment of a group of Cyclophoridae in mainland Africa and the first to provide molecular data. This study complements regional studies on the systematics of the family in Asia and provides comparative data for studies of higher level relationships within the Cyclophoridae. Phylogenetic reconstruction by BI and ML methods of combined and single gene datasets of 16S and CO 1 all showed Chondrocyclus to be monophyletic and recovered five well-supported clades that corresponded to groups of populations identifiable on the basis of combinations of morphological characters. Species were diagnosed morphologically and were shown to be genetically distinct lineages. Informative morphological features include shell dimensions, protoconch, periostracum, operculum, radula and penis. Two species in Afromontane regions of Zimbabwe and Malawi respectively are excluded from Chondrocyclus based on morphology and tentatively placed in Cyathopoma. Diversity recognised within the genus more than doubled, from a previous seven South African species to seventeen. Re-descriptions of established species and descriptions of new species are provided, together with photographs of morphological characteristics. New taxon names and nomenclatural acts within it are disclaimed and are therefore not available in the sense of the International Code of Zoological Nomenclature until validly published elsewhere. Several cryptic species within previously widespread “species” and unrecorded narrowly endemic species were documented. The clade consisting of populations of “Chondrocyclus isipingoensis”, now considered to be a species complex, was sister to a group containing the other four clades. The “Isipingoensis” clade occurs widely in Afromontane regions, along the Great Escarpment, and on the south-east coast. The other four clades occur from Zululand to the Cape Peninsula with a pattern of east-west lineage turnover. The biogeography of Chondrocyclus is interpreted by comparison with concordant patterns in other terrestrial molluscs and unrelated taxa with poor dispersal ability. This study complements other research on composition, spatial distribution and phylogenetic diversity of low-vagility invertebrates and expands the data available for biodiversity conservation in South Africa.
- Full Text:
Genetics and thermal biology of littorinid snails of the genera Afrolittorina, Echinolittorina and Littoraria (Gastropoda: Littorinidae) from temperate, subtropical and tropical regions
- Authors: Matumba, Tshifhiwa Given
- Date: 2013
- Subjects: Littorinidae -- South Africa Littorinidae -- Brunei Littorinidae -- Adaptation -- South Africa Littorinidae -- Adaptation -- Brunei Littorinidae -- Effect of temperature on -- South Africa Littorinidae -- Effect of temperature on -- Brunei Littorinidae -- Physiology Snails -- South Africa Snails -- Brunei Gastropoda -- South Africa Gastropoda -- Brunei Intertidal animals -- South Africa Intertidal animals -- Brunei
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5588 , http://hdl.handle.net/10962/d1001953
- Description: With the anticipated effects of climate change due to global warming, there is concern over how animals, especially ectotherms, will respond to or tolerate extreme and fluctuating environmental temperature stress. Littorinid snails are intertidal ectotherms that live high on the shore where they experience both extreme and variable conditions of temperature and desiccation stress, and are believed to live close to their tolerance limits. This study investigated the thermal biology of littorinid snails of the genera Afrolittorina, Echinolittorina and Littoraria from temperate, subtropical and tropical regions in South Africa and Brunei Darussalam using thermal tolerance, heart function, and proteome approaches. The effects of conditions, such as rate of change in temperature, acclimation, heat shock, season and starvation were also tested. In addition, the evolutionary relationships and genetic diversity between and within the South African Afrolittorina spp. were investigated using mitochondrial and nuclear markers. Genetic results confirmed that these are two distinct species, with the brown to black A. knysnaensis predominant in the cool-temperate region of South Africa and the pale blue-grey A. africana in the subtropical region. There was low genetic variation and differentiation within each species, suggesting high gene flow among populations as a result of the effects of ocean currents on the dispersal of their planktotrophic larvae. Tests using exposure to high temperatures revealed differences in the thermal tolerances, heart performance and protein profiles of species from different latitudes, regions and zones on the shore. Thermal tolerance conformed to expectations, with clear, statistically significant trends from high tolerance in subtropical species to lower tolerance in temperate species. However, for Afrolittorina spp., there were no significant differences in the thermal tolerances of conspecifics from different regions, though there was a significant difference in thermal tolerance between juveniles and adults. Overall, adults of all species showed higher thermal tolerances than juveniles. Although lethal temperatures for these species were higher in summer than winter, laboratory acclimation had no effect on heat coma temperatures. All species showed some regulation of heart rate, with a degree of independence of heart rate from temperature across mid-range temperatures. The tropical species showed quick induction and good regulation of heart rate followed by the subtropical and temperate species, which displayed mixed responses including regulation, partial regulation and lack of regulation. Overall, tropical Echinolittorina spp. showed good regulation, while the subtropical E. natalensis and Littoraria glabrata exhibited a mixture of partial regulation and regulation. The subtropical/temperate Afrolittorina spp. showed high individual variability, some animals exhibiting regulation, while others did not. These effects seem to be largely phylogenetically determined as there were no differences in the heart rate responses of Afrolittorina spp. from different regions. The temperatures at which heart rate became independent of temperature (thermoneutral zone) were within the range experienced under natural conditions. In addition, there were differences in Arrhenius breakpoint and endpoint temperatures, showing a trend from higher in tropical animals to lower for temperate animals. Conditions such as acclimation, heat shock and starvation had little or no effect on heart performance. However, a slow increase in temperature induced good regulation of heart rate with noticeable shifts of breakpoints and endpoints for Afrolittorina spp. Lastly, there were differences in the proteome responses between and within Afrolittorina spp. as a function of species, size and treatment. Although both large and small A. knysnaensis had a greater number of protein spots in their proteome than A. africana (though the difference was not significant), the later showed significantly higher differential expression of certain proteins following heat stress. In addition, juveniles of both species displayed greater numbers of protein spots in their proteome than adults. The results indicate a difference in the physiological and biochemical responses (i.e. adaptations) of these snails to temperature, and this seems to relate to differences in biogeography, phylogeny, species identity and ecology. The ability to regulate heart rate is phylogenetically determined, while thresholds and lethal limits correspond to biogeography and species ecology. The proteome seems to correspond to species ecology. The results also indicate that these littorinids can tolerate high temperature stress and in this respect they are well suited to life in the intertidal zones or habitats where temperature and other stresses or conditions are extreme and can change abruptly. However, the limited ability of these snails to acclimate to different temperatures suggests that they are already living close to their tolerance limits with small safety margins or narrow thermal windows and so may be vulnerable to small rises in substratum temperature and/or solar radiation.
- Full Text:
- Authors: Matumba, Tshifhiwa Given
- Date: 2013
- Subjects: Littorinidae -- South Africa Littorinidae -- Brunei Littorinidae -- Adaptation -- South Africa Littorinidae -- Adaptation -- Brunei Littorinidae -- Effect of temperature on -- South Africa Littorinidae -- Effect of temperature on -- Brunei Littorinidae -- Physiology Snails -- South Africa Snails -- Brunei Gastropoda -- South Africa Gastropoda -- Brunei Intertidal animals -- South Africa Intertidal animals -- Brunei
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5588 , http://hdl.handle.net/10962/d1001953
- Description: With the anticipated effects of climate change due to global warming, there is concern over how animals, especially ectotherms, will respond to or tolerate extreme and fluctuating environmental temperature stress. Littorinid snails are intertidal ectotherms that live high on the shore where they experience both extreme and variable conditions of temperature and desiccation stress, and are believed to live close to their tolerance limits. This study investigated the thermal biology of littorinid snails of the genera Afrolittorina, Echinolittorina and Littoraria from temperate, subtropical and tropical regions in South Africa and Brunei Darussalam using thermal tolerance, heart function, and proteome approaches. The effects of conditions, such as rate of change in temperature, acclimation, heat shock, season and starvation were also tested. In addition, the evolutionary relationships and genetic diversity between and within the South African Afrolittorina spp. were investigated using mitochondrial and nuclear markers. Genetic results confirmed that these are two distinct species, with the brown to black A. knysnaensis predominant in the cool-temperate region of South Africa and the pale blue-grey A. africana in the subtropical region. There was low genetic variation and differentiation within each species, suggesting high gene flow among populations as a result of the effects of ocean currents on the dispersal of their planktotrophic larvae. Tests using exposure to high temperatures revealed differences in the thermal tolerances, heart performance and protein profiles of species from different latitudes, regions and zones on the shore. Thermal tolerance conformed to expectations, with clear, statistically significant trends from high tolerance in subtropical species to lower tolerance in temperate species. However, for Afrolittorina spp., there were no significant differences in the thermal tolerances of conspecifics from different regions, though there was a significant difference in thermal tolerance between juveniles and adults. Overall, adults of all species showed higher thermal tolerances than juveniles. Although lethal temperatures for these species were higher in summer than winter, laboratory acclimation had no effect on heat coma temperatures. All species showed some regulation of heart rate, with a degree of independence of heart rate from temperature across mid-range temperatures. The tropical species showed quick induction and good regulation of heart rate followed by the subtropical and temperate species, which displayed mixed responses including regulation, partial regulation and lack of regulation. Overall, tropical Echinolittorina spp. showed good regulation, while the subtropical E. natalensis and Littoraria glabrata exhibited a mixture of partial regulation and regulation. The subtropical/temperate Afrolittorina spp. showed high individual variability, some animals exhibiting regulation, while others did not. These effects seem to be largely phylogenetically determined as there were no differences in the heart rate responses of Afrolittorina spp. from different regions. The temperatures at which heart rate became independent of temperature (thermoneutral zone) were within the range experienced under natural conditions. In addition, there were differences in Arrhenius breakpoint and endpoint temperatures, showing a trend from higher in tropical animals to lower for temperate animals. Conditions such as acclimation, heat shock and starvation had little or no effect on heart performance. However, a slow increase in temperature induced good regulation of heart rate with noticeable shifts of breakpoints and endpoints for Afrolittorina spp. Lastly, there were differences in the proteome responses between and within Afrolittorina spp. as a function of species, size and treatment. Although both large and small A. knysnaensis had a greater number of protein spots in their proteome than A. africana (though the difference was not significant), the later showed significantly higher differential expression of certain proteins following heat stress. In addition, juveniles of both species displayed greater numbers of protein spots in their proteome than adults. The results indicate a difference in the physiological and biochemical responses (i.e. adaptations) of these snails to temperature, and this seems to relate to differences in biogeography, phylogeny, species identity and ecology. The ability to regulate heart rate is phylogenetically determined, while thresholds and lethal limits correspond to biogeography and species ecology. The proteome seems to correspond to species ecology. The results also indicate that these littorinids can tolerate high temperature stress and in this respect they are well suited to life in the intertidal zones or habitats where temperature and other stresses or conditions are extreme and can change abruptly. However, the limited ability of these snails to acclimate to different temperatures suggests that they are already living close to their tolerance limits with small safety margins or narrow thermal windows and so may be vulnerable to small rises in substratum temperature and/or solar radiation.
- Full Text:
Historical biogeography of the tribe Platypleurini Schmidt, 1918 (Hemiptera: Cicadidae) with a focus on Southern Africa
- Authors: Price, Benjamin Wills
- Date: 2010
- Subjects: Biogeography -- History -- Africa, Southern Cicadas -- Africa, Southern Cicada (Genus) -- Africa, Southern Biodiversity -- Africa, Southern Cicadas -- Variation -- Africa, Southern
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5708 , http://hdl.handle.net/10962/d1005394
- Description: With our contemporary biota under increasing threat of extinction, it is of interest to understand where, why and how biological diversity is generated. If focussed on appropriate taxa, phylogeographic and phylogenetic studies can assist in the identification of both places and processes central to the origin and maintenance of biological diversity. It is explained why southern Africa presents a perfect test-bed for exploring such mechanisms of diversification and why cicadas (Hemiptera: Cicadidae) have proved very suitable tools for studies of historical biogeography. This study then exemplifies these points by providing the first large-scale investigation of the historical biogeography of the tribe Platypleurini Schmidt, 1918, with emphasis on the genus Platypleura Amyot & Seville, 1843 in southern Africa. Standard methods of DNA sequencing provided data from portions of the mitochondrial small subunit ribosomal 16S RNA (16S) and cytochrome oxidase subunits I (COI) and II (COII); and the nuclear elongation factor 1 alpha (EF-1α) from 400 ethanol-preserved specimens. These data were analysed using standard phylogenetic methods and a time scale of diversification was estimated using a Bayesian framework and both fossil data and DNA substitution rates. The results showed that the tribe is too recent to be of Gondwanan origin. The lack of monophyly of the genera represented in both Asia and Africa showed that the tribe needs formal taxonomic revision. Diversification of the African platypleurine genera coincides with aridification in the early Oligocene. Dispersal of Asian platypleurine taxa coincides with the meeting of Africa and Eurasia in the mid-Oligocene. Two radiations within African Platypleura are hypothesised; one distributed over most of sub-Saharan Africa and the second restricted to southern Africa, with clades restricted within regional biomes. Within each of the three focal biomes, cryptic taxonomic diversity was confirmed, suggesting that, even in relatively well understood groups such as the southern African platypleurine cicadas, molecular data can identify further diversity. Although each focal taxon was restricted to non-overlapping biomes, comparison of the three biomes highlighted interactions between palaeoclimates and fixed landscape features (coastal topography, river catchments and escarpments) as causative agents of vicariance, dispersal, extinction and diversification of these volant insects. The results of using co-distributed species for comparative study cautions against making inferences based on single-taxon datasets and highlights the need to use many, evolutionarily independent taxa when identifying mechanisms of diversification. The dating analyses imply that within-species lineage diversification occurred overwhelmingly within the Pleistocene, a trend that is being increasingly recognised in print for other biota. Some caveats about using phylogenetic approaches to estimate ancestral areas are illustrated. Several recommendations are made regarding additional taxa and data sources for understanding the origin and maintenance of biological diversity.
- Full Text:
- Authors: Price, Benjamin Wills
- Date: 2010
- Subjects: Biogeography -- History -- Africa, Southern Cicadas -- Africa, Southern Cicada (Genus) -- Africa, Southern Biodiversity -- Africa, Southern Cicadas -- Variation -- Africa, Southern
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5708 , http://hdl.handle.net/10962/d1005394
- Description: With our contemporary biota under increasing threat of extinction, it is of interest to understand where, why and how biological diversity is generated. If focussed on appropriate taxa, phylogeographic and phylogenetic studies can assist in the identification of both places and processes central to the origin and maintenance of biological diversity. It is explained why southern Africa presents a perfect test-bed for exploring such mechanisms of diversification and why cicadas (Hemiptera: Cicadidae) have proved very suitable tools for studies of historical biogeography. This study then exemplifies these points by providing the first large-scale investigation of the historical biogeography of the tribe Platypleurini Schmidt, 1918, with emphasis on the genus Platypleura Amyot & Seville, 1843 in southern Africa. Standard methods of DNA sequencing provided data from portions of the mitochondrial small subunit ribosomal 16S RNA (16S) and cytochrome oxidase subunits I (COI) and II (COII); and the nuclear elongation factor 1 alpha (EF-1α) from 400 ethanol-preserved specimens. These data were analysed using standard phylogenetic methods and a time scale of diversification was estimated using a Bayesian framework and both fossil data and DNA substitution rates. The results showed that the tribe is too recent to be of Gondwanan origin. The lack of monophyly of the genera represented in both Asia and Africa showed that the tribe needs formal taxonomic revision. Diversification of the African platypleurine genera coincides with aridification in the early Oligocene. Dispersal of Asian platypleurine taxa coincides with the meeting of Africa and Eurasia in the mid-Oligocene. Two radiations within African Platypleura are hypothesised; one distributed over most of sub-Saharan Africa and the second restricted to southern Africa, with clades restricted within regional biomes. Within each of the three focal biomes, cryptic taxonomic diversity was confirmed, suggesting that, even in relatively well understood groups such as the southern African platypleurine cicadas, molecular data can identify further diversity. Although each focal taxon was restricted to non-overlapping biomes, comparison of the three biomes highlighted interactions between palaeoclimates and fixed landscape features (coastal topography, river catchments and escarpments) as causative agents of vicariance, dispersal, extinction and diversification of these volant insects. The results of using co-distributed species for comparative study cautions against making inferences based on single-taxon datasets and highlights the need to use many, evolutionarily independent taxa when identifying mechanisms of diversification. The dating analyses imply that within-species lineage diversification occurred overwhelmingly within the Pleistocene, a trend that is being increasingly recognised in print for other biota. Some caveats about using phylogenetic approaches to estimate ancestral areas are illustrated. Several recommendations are made regarding additional taxa and data sources for understanding the origin and maintenance of biological diversity.
- Full Text:
The phytogeography of the Sneeuberg, Nuweveldberge and Roggeveldberge (Great Escarpment): assessing migration routes and endemism
- Authors: Clark, Vincent Ralph
- Date: 2010
- Subjects: Phytogeography -- South Africa Endemic plants -- South Africa Plants -- Migration -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4187 , http://hdl.handle.net/10962/d1003756
- Description: The Great Escarpment forms a semi-continuous mountain system 5 000 km long, stretching from Angola in the north-west, south through Namibia, and into western, southern and eastern South Africa, including Lesotho and Swaziland. It is composed of a wide variety of geological suites but is unified in representing the edge of the African plateau and the passive Gondwanan continental margin. The Great Escarpment falls into all major climatic zones on the subcontinent, is a repository of palaeo- and neo-endemics, hosts more than half of southern Africa‟s centres of plant endemism, and has a rich suite of endemic fauna. In addition, the Great Escarpment is believed to be both a refugium and corridor for biological diversity. Despite the biological richness of the Great Escarpment, research to date has been fragmented and many sections of the Great Escarpment have not been studied. The aim of this study is to contribute to research on the Great Escarpment by undertaking a detailed floristic study of the southern Great Escarpment (the Sneeuberg, Nuweveldberge and Roggeveldberge). Together these mountains comprise approximately 1 000 km (one fifth) of the Great Escarpment, and occupy a transition zone between the summer rainfall zone in the east and the winter rainfall zone in the west. They are also the sections of Great Escarpment most closely situated to the Cape Floristic Region (CFR) and would thus be involved in hypothesised migration routes for lineages that also occur further north through the Drakensberg Alpine Centre (DAC) to the East African mountain chain. Detailed fieldwork of the southern Great Escarpment was undertaken over a period of four years in all seasons. Approximately 8 000 specimens were collected. Particular emphasis was placed on areas that may represent refugia, i.e. the highest plateaux and peaks, mesic areas and cliff-lines. An overview of each mountain range, together with their endemic plant species and phytogeography, is provided. Approximately ten new species have been discovered during this study, two of which have been described to date. Numerous endemics only known from their types have also been rediscovered. The Sneeuberg is defined as a new centre of plant endemism on the Great Escarpment (endemism of 2.3%), and the role of the Boschberg and Groot-Bruintjieshoogde (part of the Sneeuberg) as a nexus for floristic migration routes is discussed. The Nuweveldberge is shown to have low endemism despite a floristic tally similar to the Sneeuberg, while the Roggeveldberge are confirmed to be the most endemic-rich section of the southern Great Escarpment. The field data collected was augmented by available data in taxonomic revisions, and floras for the Sneeuberg, Nuweveldberge and Roggeveldberge were compiled. In order to floristically compare the southern Great Escarpment with other sections of the Great Escarpment and the CFR, a database of some 12 000 taxa was created using available floristic data for the CFR, DAC and Great WinterbergAmatolas, together with the data collated for the Sneeuberg, Nuweveldberge and Roggeveldberge. These data were analysed using phenetic methods and Parsimony Analysis of Endemicity (PAE). The results indicate stronger linkages in the east, particularly between the Sneeuberg and Nuweveldberge, and between the Sneeuberg and the Great WinterbergAmatolas. The relationship of the Roggeveldberge with the rest of the southern Great Escarpment remains ambiguous. In order to refine notions of connectivity and migration routes, 19 well-sampled phylogenies were assessed for sister-taxon disjunctions to explore CFRGreat Escarpment connections. Palaeo-connectivity between the CFR and southern Great Escarpment is most strongly supported for the south-eastern (SE) connection, and less so for the north-western (NW) and Matjiesfontein connections. There is support for the current (or recent) use of these three connections from numerous species that occur on both sides of the connections. Results of these analyses indicate that the southern Great Escarpment is a palaeo-corridor, the functioning of which has been broken by the aridification of the Nuweveldberge since the Last Glacial Maximum (LGM). Floristic connectivity is strongest in the east, from the Nuweveldberge to the DAC, and is less so in the west between the Nuweveldberge and the Roggeveldberge a finding attributed to the transition from a reliable winter rainfall regime on the Roggeveldberge to an unpredictable moisture regime on the Nuweveldberge. The mountains of the southern Great Escarpment are thus a series of refugia from a previous moister, cooler climate and are a corridor between the eastern and western components of the Great Escarpment. The SE connection is the primary link between the CFR and the eastern Great Escarpment Afromontane region in southern Africa. The implications of this research are that accurate conservation assessments and Red Data listings for many of the previously poorly-known endemics can now be made, and appropriate conservation measures implemented. Climate change remains the primary threat to these endemics and montane taxa in general, while degradation of wetlands is the primary threat to the water catchment service provided by the southern Great Escarpment. Future detailed research on the Great WinterbergAmatolas and Stormberg and a comprehensive flora of the HantamRoggeveldberge will further enhance our understanding of the floristics of the southern Great Escarpment, and provide the necessary data for comprehensive GIS-based models of proposed climate change scenarios for local, regional and national conservation planning.
- Full Text:
- Authors: Clark, Vincent Ralph
- Date: 2010
- Subjects: Phytogeography -- South Africa Endemic plants -- South Africa Plants -- Migration -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4187 , http://hdl.handle.net/10962/d1003756
- Description: The Great Escarpment forms a semi-continuous mountain system 5 000 km long, stretching from Angola in the north-west, south through Namibia, and into western, southern and eastern South Africa, including Lesotho and Swaziland. It is composed of a wide variety of geological suites but is unified in representing the edge of the African plateau and the passive Gondwanan continental margin. The Great Escarpment falls into all major climatic zones on the subcontinent, is a repository of palaeo- and neo-endemics, hosts more than half of southern Africa‟s centres of plant endemism, and has a rich suite of endemic fauna. In addition, the Great Escarpment is believed to be both a refugium and corridor for biological diversity. Despite the biological richness of the Great Escarpment, research to date has been fragmented and many sections of the Great Escarpment have not been studied. The aim of this study is to contribute to research on the Great Escarpment by undertaking a detailed floristic study of the southern Great Escarpment (the Sneeuberg, Nuweveldberge and Roggeveldberge). Together these mountains comprise approximately 1 000 km (one fifth) of the Great Escarpment, and occupy a transition zone between the summer rainfall zone in the east and the winter rainfall zone in the west. They are also the sections of Great Escarpment most closely situated to the Cape Floristic Region (CFR) and would thus be involved in hypothesised migration routes for lineages that also occur further north through the Drakensberg Alpine Centre (DAC) to the East African mountain chain. Detailed fieldwork of the southern Great Escarpment was undertaken over a period of four years in all seasons. Approximately 8 000 specimens were collected. Particular emphasis was placed on areas that may represent refugia, i.e. the highest plateaux and peaks, mesic areas and cliff-lines. An overview of each mountain range, together with their endemic plant species and phytogeography, is provided. Approximately ten new species have been discovered during this study, two of which have been described to date. Numerous endemics only known from their types have also been rediscovered. The Sneeuberg is defined as a new centre of plant endemism on the Great Escarpment (endemism of 2.3%), and the role of the Boschberg and Groot-Bruintjieshoogde (part of the Sneeuberg) as a nexus for floristic migration routes is discussed. The Nuweveldberge is shown to have low endemism despite a floristic tally similar to the Sneeuberg, while the Roggeveldberge are confirmed to be the most endemic-rich section of the southern Great Escarpment. The field data collected was augmented by available data in taxonomic revisions, and floras for the Sneeuberg, Nuweveldberge and Roggeveldberge were compiled. In order to floristically compare the southern Great Escarpment with other sections of the Great Escarpment and the CFR, a database of some 12 000 taxa was created using available floristic data for the CFR, DAC and Great WinterbergAmatolas, together with the data collated for the Sneeuberg, Nuweveldberge and Roggeveldberge. These data were analysed using phenetic methods and Parsimony Analysis of Endemicity (PAE). The results indicate stronger linkages in the east, particularly between the Sneeuberg and Nuweveldberge, and between the Sneeuberg and the Great WinterbergAmatolas. The relationship of the Roggeveldberge with the rest of the southern Great Escarpment remains ambiguous. In order to refine notions of connectivity and migration routes, 19 well-sampled phylogenies were assessed for sister-taxon disjunctions to explore CFRGreat Escarpment connections. Palaeo-connectivity between the CFR and southern Great Escarpment is most strongly supported for the south-eastern (SE) connection, and less so for the north-western (NW) and Matjiesfontein connections. There is support for the current (or recent) use of these three connections from numerous species that occur on both sides of the connections. Results of these analyses indicate that the southern Great Escarpment is a palaeo-corridor, the functioning of which has been broken by the aridification of the Nuweveldberge since the Last Glacial Maximum (LGM). Floristic connectivity is strongest in the east, from the Nuweveldberge to the DAC, and is less so in the west between the Nuweveldberge and the Roggeveldberge a finding attributed to the transition from a reliable winter rainfall regime on the Roggeveldberge to an unpredictable moisture regime on the Nuweveldberge. The mountains of the southern Great Escarpment are thus a series of refugia from a previous moister, cooler climate and are a corridor between the eastern and western components of the Great Escarpment. The SE connection is the primary link between the CFR and the eastern Great Escarpment Afromontane region in southern Africa. The implications of this research are that accurate conservation assessments and Red Data listings for many of the previously poorly-known endemics can now be made, and appropriate conservation measures implemented. Climate change remains the primary threat to these endemics and montane taxa in general, while degradation of wetlands is the primary threat to the water catchment service provided by the southern Great Escarpment. Future detailed research on the Great WinterbergAmatolas and Stormberg and a comprehensive flora of the HantamRoggeveldberge will further enhance our understanding of the floristics of the southern Great Escarpment, and provide the necessary data for comprehensive GIS-based models of proposed climate change scenarios for local, regional and national conservation planning.
- Full Text:
A taxonomic revision of the southern African endemic genus Gazania (Asteraceae) based on morphometric, genetic and phylogeographic data
- Authors: Howis, Seranne
- Date: 2007
- Subjects: Compositae Plant genetics DNA Endemic plants -- South Africa Plant ecology -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4200 , http://hdl.handle.net/10962/d1003769
- Description: Gazania is a small genus of the subtribe Gorteriinae, tribe Arctoteae, that is endemic to southern Africa. The genus was last revised in 1959 by Roessler, who noted that delimitation of the species of Gazania can be “extraordinarily difficult”. Morphometric data was collected to test the reality of the 16 species as delimited by Roessler, who based species boundaries on morphological characters. Only six taxa were found to be morphologically distinct, while the remaining samples showed no species cohesion. DNA sequence data from two nuclear spacer regions (ITS and ETS) and four chloroplast noncoding regions (the trnL and rpS16 introns, and the psbA-trnH and trnL-F spacers) of 43 samples were utilised to create a species level phylogeny and to investigate correlations between genetically delimited units and morphologically defined taxa. DNA sequence data reveal that seven species (as delimited by Roessler) are morphologically and genetically distinct. The remaining nine of Roessler’s species fall into a morphologically and genetically overlapping continuum that forms an ochlospecies. Phylogeographic methods (based on an expanded ITS and ETS DNA sequence data set from 169 samples) were employed to further resolve the limits of species, with special focus on the clades within the ochlospecies. These genetically defined clades were correlated with their geographical distributions, and in combination with molecular dating techniques, used to elucidate the recent climatic or environmental factors that may have shaped the phylogeographic structure of the genus. Phylogeographic patterns and molecular dating reveals that the genus Gazania is an example of a South African endemic clade that has undergone episodic cladogenesis in response to fluctuating climatic conditions over the last seven million years. The ochlospecies within Gazania is a result of repeated cycles of climate driven isolation in refugia and subsequent expansion and hybridization events during the Pliocene and Pleistocene. Comparisons with phylogeographic studies on other organisms reveal a common pattern indicative of the presence and evolutionary importance of an ancestral refugium in the arid Richtersveld / Namib region of southern Africa.
- Full Text:
- Authors: Howis, Seranne
- Date: 2007
- Subjects: Compositae Plant genetics DNA Endemic plants -- South Africa Plant ecology -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4200 , http://hdl.handle.net/10962/d1003769
- Description: Gazania is a small genus of the subtribe Gorteriinae, tribe Arctoteae, that is endemic to southern Africa. The genus was last revised in 1959 by Roessler, who noted that delimitation of the species of Gazania can be “extraordinarily difficult”. Morphometric data was collected to test the reality of the 16 species as delimited by Roessler, who based species boundaries on morphological characters. Only six taxa were found to be morphologically distinct, while the remaining samples showed no species cohesion. DNA sequence data from two nuclear spacer regions (ITS and ETS) and four chloroplast noncoding regions (the trnL and rpS16 introns, and the psbA-trnH and trnL-F spacers) of 43 samples were utilised to create a species level phylogeny and to investigate correlations between genetically delimited units and morphologically defined taxa. DNA sequence data reveal that seven species (as delimited by Roessler) are morphologically and genetically distinct. The remaining nine of Roessler’s species fall into a morphologically and genetically overlapping continuum that forms an ochlospecies. Phylogeographic methods (based on an expanded ITS and ETS DNA sequence data set from 169 samples) were employed to further resolve the limits of species, with special focus on the clades within the ochlospecies. These genetically defined clades were correlated with their geographical distributions, and in combination with molecular dating techniques, used to elucidate the recent climatic or environmental factors that may have shaped the phylogeographic structure of the genus. Phylogeographic patterns and molecular dating reveals that the genus Gazania is an example of a South African endemic clade that has undergone episodic cladogenesis in response to fluctuating climatic conditions over the last seven million years. The ochlospecies within Gazania is a result of repeated cycles of climate driven isolation in refugia and subsequent expansion and hybridization events during the Pliocene and Pleistocene. Comparisons with phylogeographic studies on other organisms reveal a common pattern indicative of the presence and evolutionary importance of an ancestral refugium in the arid Richtersveld / Namib region of southern Africa.
- Full Text:
Evolutionary and biogeographic studies in the genus Kniphofia moench (Asphodelaceae)
- Authors: Ramdhani, Syd
- Date: 2007
- Subjects: Asphodelaceae Asphodelaceae -- Genetics Cladistic analysis
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4220 , http://hdl.handle.net/10962/d1003789
- Description: Kniphofia, a genus of approximately 71 species, is almost entirely African with two species occurring in Madagascar and one in Yemen. Commonly known as ‘red hot pokers’ they are popular among horticulturists. The genus is also well known for its complex alpha taxonomy. To date, no studies have examined the phylogenetic relationships among species or the evolutionary history of the genus, and little work has been done on their biogeography. The main focus of this study was (i) to review the alpha taxonomy, (ii) to assess diversity and endemism in Kniphofia, (iii) to use DNA sequence data to reconstruct a specieslevel phylogeny to understand intra-generic species relationships and evolutionary processes (iv) to use phylogeographic approaches to study the biogeography and evaluate biogeographical patterns, and (v) to assess anatomical variation and determine if anatomical characters are useful for species delimitation. It was found that the genus has six centres of diversity, five of which are centres of endemism. The South African Centre is the most speciose and is also the largest centre of endemism. Kniphofia shows a strong Afromontane grassland affinity in Tropical and East Africa. In South Africa, it is found from high altitudes to coastal habitats, with the most speciose regions being Afromontane grasslands. It is thus not considered to be an Afromontane element, but rather an Afromontane associate. Five major evolutionary lineages were identified using cpDNA sequence data (trnT-L spacer), four of which are southern African. The fifth lineage is represented by material from Madagascar, East and Tropical Africa. The nuclear ITS region failed to provide resolution, as many sequences were identical. The five lineages recovered using cpDNA showed some congruence with geographic origin rather than the taxonomic arrangement based on morphology. All of the species with multiple samples were non-monophyletic. This could be due to hybridisation and/or incomplete lineage sorting. The nested clade analysis, although preliminary, did not completely agree with the phylogenetic analyses. One of the three third level nested clades appears to show fragmentation between the Cape Region, KwaZulu-Natal and northern parts of southern Africa. Furthermore, another nested clades recovered suggest a range expansion and radiation from the Drakensberg into the adjacent Drakensberg-Maputoland-Pondoland transition. Morphological species of Kniphofia exhibited substantial leaf anatomical variation and anatomical characters do not cluster samples into their morphological species. The anatomical results do not fit any geographic pattern, nor do they correspond to the lineages recovered using molecular markers or the nested clades. Leaf anatomical variation does not appear to be influenced by geographical or environmental factors. However, hybridisation may play a role but was not tested in this study. In light of the above findings it is proposed that the evolutionary and biogeographic history of Kniphofia is strongly linked to tectonic events, and Quaternary climatic cycles and vegetation changes. Tectonic events (viz. uplifts) may have resulted in vicariance events that may account for the five cpDNA lineages recovered in phylogenetic analyses, while Quaternary climatic cycles and vegetation changes may have had a more recent impact on evolution and biogeography. It is hypothesised that the ancestral area for Kniphofia was much more widespread when Afromontane grasslands were more extensive during cooler and drier glacial episodes. Kniphofia on the high mountains of Tropical and East Africa would have tracked Afromontane grasslands as they expanded their ranges in cooler periods. While during wetter and warmer interglacial periods Kniphofia would have retreated into refugia on the mountains of Tropical and East Africa, with no gene flow possible between these refugia. In South Africa, where latitude compensates for altitude, Kniphofia may have maintained a distribution that extended into the lowlands even during interglacials. A cyclic climate change hypothesis implies that populations of Kniphofia (at different phases of the climatic cycle) would have experienced periods of contractions and fragmentation followed by periods of range expansion and coalescence or secondary contact. Altitudinal shifting is proposed to be the most likely mechanism for fragmentation and range expansion, and would would possibly promoted hybridisation. Within the five lineages there is evidence for recent differentiation as the branch lengths are short, there are numerous nonmonophyletic species and numerous identical haplotypes (cpDNA and ITS) which collectively indicate a recent radiation in southern Africa. A recent radiation would also account for the taxonomic confusion and difficulty in differentiating morpho-species. These climatic events may also account for the substantial anatomical variation in southern African Kniphofia species.
- Full Text:
- Authors: Ramdhani, Syd
- Date: 2007
- Subjects: Asphodelaceae Asphodelaceae -- Genetics Cladistic analysis
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4220 , http://hdl.handle.net/10962/d1003789
- Description: Kniphofia, a genus of approximately 71 species, is almost entirely African with two species occurring in Madagascar and one in Yemen. Commonly known as ‘red hot pokers’ they are popular among horticulturists. The genus is also well known for its complex alpha taxonomy. To date, no studies have examined the phylogenetic relationships among species or the evolutionary history of the genus, and little work has been done on their biogeography. The main focus of this study was (i) to review the alpha taxonomy, (ii) to assess diversity and endemism in Kniphofia, (iii) to use DNA sequence data to reconstruct a specieslevel phylogeny to understand intra-generic species relationships and evolutionary processes (iv) to use phylogeographic approaches to study the biogeography and evaluate biogeographical patterns, and (v) to assess anatomical variation and determine if anatomical characters are useful for species delimitation. It was found that the genus has six centres of diversity, five of which are centres of endemism. The South African Centre is the most speciose and is also the largest centre of endemism. Kniphofia shows a strong Afromontane grassland affinity in Tropical and East Africa. In South Africa, it is found from high altitudes to coastal habitats, with the most speciose regions being Afromontane grasslands. It is thus not considered to be an Afromontane element, but rather an Afromontane associate. Five major evolutionary lineages were identified using cpDNA sequence data (trnT-L spacer), four of which are southern African. The fifth lineage is represented by material from Madagascar, East and Tropical Africa. The nuclear ITS region failed to provide resolution, as many sequences were identical. The five lineages recovered using cpDNA showed some congruence with geographic origin rather than the taxonomic arrangement based on morphology. All of the species with multiple samples were non-monophyletic. This could be due to hybridisation and/or incomplete lineage sorting. The nested clade analysis, although preliminary, did not completely agree with the phylogenetic analyses. One of the three third level nested clades appears to show fragmentation between the Cape Region, KwaZulu-Natal and northern parts of southern Africa. Furthermore, another nested clades recovered suggest a range expansion and radiation from the Drakensberg into the adjacent Drakensberg-Maputoland-Pondoland transition. Morphological species of Kniphofia exhibited substantial leaf anatomical variation and anatomical characters do not cluster samples into their morphological species. The anatomical results do not fit any geographic pattern, nor do they correspond to the lineages recovered using molecular markers or the nested clades. Leaf anatomical variation does not appear to be influenced by geographical or environmental factors. However, hybridisation may play a role but was not tested in this study. In light of the above findings it is proposed that the evolutionary and biogeographic history of Kniphofia is strongly linked to tectonic events, and Quaternary climatic cycles and vegetation changes. Tectonic events (viz. uplifts) may have resulted in vicariance events that may account for the five cpDNA lineages recovered in phylogenetic analyses, while Quaternary climatic cycles and vegetation changes may have had a more recent impact on evolution and biogeography. It is hypothesised that the ancestral area for Kniphofia was much more widespread when Afromontane grasslands were more extensive during cooler and drier glacial episodes. Kniphofia on the high mountains of Tropical and East Africa would have tracked Afromontane grasslands as they expanded their ranges in cooler periods. While during wetter and warmer interglacial periods Kniphofia would have retreated into refugia on the mountains of Tropical and East Africa, with no gene flow possible between these refugia. In South Africa, where latitude compensates for altitude, Kniphofia may have maintained a distribution that extended into the lowlands even during interglacials. A cyclic climate change hypothesis implies that populations of Kniphofia (at different phases of the climatic cycle) would have experienced periods of contractions and fragmentation followed by periods of range expansion and coalescence or secondary contact. Altitudinal shifting is proposed to be the most likely mechanism for fragmentation and range expansion, and would would possibly promoted hybridisation. Within the five lineages there is evidence for recent differentiation as the branch lengths are short, there are numerous nonmonophyletic species and numerous identical haplotypes (cpDNA and ITS) which collectively indicate a recent radiation in southern Africa. A recent radiation would also account for the taxonomic confusion and difficulty in differentiating morpho-species. These climatic events may also account for the substantial anatomical variation in southern African Kniphofia species.
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Habitat segregation in competing species of intertidal mussels in South Africa
- Authors: Bownes, Sarah
- Date: 2006
- Subjects: Mussels -- South Africa Mussels -- Growth Mussels -- Habitat -- South Africa Mussels -- Larvae Perna -- South Africa Mytilus galloprovincialis -- South Africa Choromytilus meridionalis -- South Africa Mytilidae -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5706 , http://hdl.handle.net/10962/d1005392
- Description: Mytilus galloprovincialis is invasive on rocky shores on the west coast of South Africa where it has become the dominant intertidal mussel. The success of this species on the west coast and its superior competitive abilities, have led to concern that it may become invasive on the south coast at the expense of the indigenous mussel Perna perna. On shores where these species co-occur, there appears to be habitat segregation among zones occupied by mussels. M.galloprovincialis dominates the high-shore and P.perna the low-shore, with a mixed zone at mid-shore level. This study examined the factors responsible for these differences in distribution and abundance. The study was conducted in Plettenberg Bay and Tsitsikamma (70km apart) on the south coast of South Africa. Each site included two randomly selected locations (300-400m apart). A third mussel species, Choromytilus meridionalis, is found in large numbers at the sand/rock interface at one location in Plettenberg Bay. Aspects of settlement, recruitment, growth and mortality of juvenile and adult mussels were examined at different tidal heights at each site. Quantitative analysis of mussel population structure at these sites supported the initial observation of vertical habitat segregation. Post-larvae were identified to species and this was confirmed using hinge morphology and mitochondrial DNA analysis. Size at settlement was determined for each species to differentiate between primary and secondary settlement. Adult distribution of C.meridionalis was primarily determined by settlement, which was highly selective in this species. Settlement, recruitment and growth of P.perna decreased with increasing tidal height, while post-settlement mortality and adult mortality increased higher upshore. Thus all aspects of P.perna’s life history contribute to the adult distribution of this species. Presumably, the abundance of P.perna on the high-shore is initially limited by recruitment while those that survive remain prone to elimination throughout adulthood. M.galloprovincialis displayed the same patterns of settlement and recruitment as P.perna. However, post-settlement mortality in this species was consistently low in the low and high zones. Juvenile growth also decreased upshore, suggesting that M.galloprovincialis may be able to maintain high densities on the high-shore through the persistence of successive settlements of slow-growing individuals. The low cover of M.galloprovincialis on the lowshore appeared to be determined by adult interactions. M.galloprovincialis experienced significantly higher adult mortality rates than P.perna in this zone. There were seasonal variations in the competitive advantages enjoyed by each species through growth, recruitment or mortality on the low-shore. In summer, P.perna had higher recruitment rates, faster growth and lower mortality rates, while M.galloprovincialis had slightly higher recruitment rates and faster growth rates in winter. P.perna is a warm water species while M.galloprovincialis thrives on the cold-temperate west coast of South Africa. Therefore both species appear to be at the edge of their optimal temperature regimes on the south coast, which may explain the seasonal advantages of each. Nevertheless, P.perna has maintained spatial dominance on the low-shore suggesting that it may ultimately be the winner in competition between these species. M.galloprovincialis appears to have a refuge from competition with P.perna on the high-shore due to its greater tolerance of desiccation stress, while being competitively excluded from the low-shore. Warm water temperatures coupled with poor recruitment rates at most sites may limit the success of M.galloprovincialis on this coast.
- Full Text:
- Authors: Bownes, Sarah
- Date: 2006
- Subjects: Mussels -- South Africa Mussels -- Growth Mussels -- Habitat -- South Africa Mussels -- Larvae Perna -- South Africa Mytilus galloprovincialis -- South Africa Choromytilus meridionalis -- South Africa Mytilidae -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:5706 , http://hdl.handle.net/10962/d1005392
- Description: Mytilus galloprovincialis is invasive on rocky shores on the west coast of South Africa where it has become the dominant intertidal mussel. The success of this species on the west coast and its superior competitive abilities, have led to concern that it may become invasive on the south coast at the expense of the indigenous mussel Perna perna. On shores where these species co-occur, there appears to be habitat segregation among zones occupied by mussels. M.galloprovincialis dominates the high-shore and P.perna the low-shore, with a mixed zone at mid-shore level. This study examined the factors responsible for these differences in distribution and abundance. The study was conducted in Plettenberg Bay and Tsitsikamma (70km apart) on the south coast of South Africa. Each site included two randomly selected locations (300-400m apart). A third mussel species, Choromytilus meridionalis, is found in large numbers at the sand/rock interface at one location in Plettenberg Bay. Aspects of settlement, recruitment, growth and mortality of juvenile and adult mussels were examined at different tidal heights at each site. Quantitative analysis of mussel population structure at these sites supported the initial observation of vertical habitat segregation. Post-larvae were identified to species and this was confirmed using hinge morphology and mitochondrial DNA analysis. Size at settlement was determined for each species to differentiate between primary and secondary settlement. Adult distribution of C.meridionalis was primarily determined by settlement, which was highly selective in this species. Settlement, recruitment and growth of P.perna decreased with increasing tidal height, while post-settlement mortality and adult mortality increased higher upshore. Thus all aspects of P.perna’s life history contribute to the adult distribution of this species. Presumably, the abundance of P.perna on the high-shore is initially limited by recruitment while those that survive remain prone to elimination throughout adulthood. M.galloprovincialis displayed the same patterns of settlement and recruitment as P.perna. However, post-settlement mortality in this species was consistently low in the low and high zones. Juvenile growth also decreased upshore, suggesting that M.galloprovincialis may be able to maintain high densities on the high-shore through the persistence of successive settlements of slow-growing individuals. The low cover of M.galloprovincialis on the lowshore appeared to be determined by adult interactions. M.galloprovincialis experienced significantly higher adult mortality rates than P.perna in this zone. There were seasonal variations in the competitive advantages enjoyed by each species through growth, recruitment or mortality on the low-shore. In summer, P.perna had higher recruitment rates, faster growth and lower mortality rates, while M.galloprovincialis had slightly higher recruitment rates and faster growth rates in winter. P.perna is a warm water species while M.galloprovincialis thrives on the cold-temperate west coast of South Africa. Therefore both species appear to be at the edge of their optimal temperature regimes on the south coast, which may explain the seasonal advantages of each. Nevertheless, P.perna has maintained spatial dominance on the low-shore suggesting that it may ultimately be the winner in competition between these species. M.galloprovincialis appears to have a refuge from competition with P.perna on the high-shore due to its greater tolerance of desiccation stress, while being competitively excluded from the low-shore. Warm water temperatures coupled with poor recruitment rates at most sites may limit the success of M.galloprovincialis on this coast.
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