DNA barcoding reveals micro-evolutionary changes and river system-level phylogeographic resolution of African silver catfish, Schilbe intermedius (Actinopterygii: Siluriformes: Schilbeidae) from seven populations across different African river systems
- Van der Bank, H.F, Greenfield, R., Daru, B.H., Yessoufou, K.
- Authors: Van der Bank, H.F , Greenfield, R. , Daru, B.H. , Yessoufou, K.
- Date: 2012
- Subjects: DNA barcode , Species delimitation , Population genetic differentiation , Schilbe intermedius , Silver catfish , Micro-evolutionary adaptation
- Type: Article
- Identifier: uj:5970 , ISSN 1734-1515 , http://hdl.handle.net/10210/8255
- Description: Background. Under the tropics, less than 40% of known fishes are identified to species-level. Further, the ongoing global change poses unprecedented threat to biodiversity, and several taxa are likely to go extinct even before they could be described. Traditional ecological theory suggests that species would escape extinction risk posed by global threats (e.g., climate change) only by migrating to new environments. In this study, we hypothesise that micro-evolutionary changes (evolution within species and populations) are also important mechanisms for the survival of Schilbe intermedius in Africa, a continent subjected to uneven distribution of climate severity. Materials and methods. Using the mitochondrial cytochrome c oxidase subunit I (COI) gene, known as animal DNA barcode, we tested this hypothesis by analysing the genetic diversity and phylogenetic relations between seven populations of S. intermedius across different African river systems. Results. We reveal a clear geographical patterning in genetic variations, with three clear clusters (southern Africa, eastern Africa, and western Africa). In southern Africa, the South African population is distinct from that of Namibia and Botswana. In addition, within Nigerian populations of silver catfish, two sub-clusters emerged from two isolated river systems. We suggest that the phylogeographic pattern within African silver catfish populations mirror the past effects of selection and gene flow, and that the split within Nigerian silver catfish populations might be the result of micro-evolutionary adaptive responses to local selection pressures. Conclusion. We suggest that the strong genetic difference in African silver catfish among geographically isolated river systems might be the result of in situ micro-evolutionary adaptive responses to changing environments, and that DNA barcode has potential beyond species delimitation.
- Full Text:
- Authors: Van der Bank, H.F , Greenfield, R. , Daru, B.H. , Yessoufou, K.
- Date: 2012
- Subjects: DNA barcode , Species delimitation , Population genetic differentiation , Schilbe intermedius , Silver catfish , Micro-evolutionary adaptation
- Type: Article
- Identifier: uj:5970 , ISSN 1734-1515 , http://hdl.handle.net/10210/8255
- Description: Background. Under the tropics, less than 40% of known fishes are identified to species-level. Further, the ongoing global change poses unprecedented threat to biodiversity, and several taxa are likely to go extinct even before they could be described. Traditional ecological theory suggests that species would escape extinction risk posed by global threats (e.g., climate change) only by migrating to new environments. In this study, we hypothesise that micro-evolutionary changes (evolution within species and populations) are also important mechanisms for the survival of Schilbe intermedius in Africa, a continent subjected to uneven distribution of climate severity. Materials and methods. Using the mitochondrial cytochrome c oxidase subunit I (COI) gene, known as animal DNA barcode, we tested this hypothesis by analysing the genetic diversity and phylogenetic relations between seven populations of S. intermedius across different African river systems. Results. We reveal a clear geographical patterning in genetic variations, with three clear clusters (southern Africa, eastern Africa, and western Africa). In southern Africa, the South African population is distinct from that of Namibia and Botswana. In addition, within Nigerian populations of silver catfish, two sub-clusters emerged from two isolated river systems. We suggest that the phylogeographic pattern within African silver catfish populations mirror the past effects of selection and gene flow, and that the split within Nigerian silver catfish populations might be the result of micro-evolutionary adaptive responses to local selection pressures. Conclusion. We suggest that the strong genetic difference in African silver catfish among geographically isolated river systems might be the result of in situ micro-evolutionary adaptive responses to changing environments, and that DNA barcode has potential beyond species delimitation.
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Wetland assessment using Unmanned Aerial Vehicle (UAV) photogrammetry
- Boon, M.A., Greenfield, R., Tesfamichael, S.
- Authors: Boon, M.A. , Greenfield, R. , Tesfamichael, S.
- Date: 2016
- Subjects: Unmanned Arial Vehicle Photogrammetry , Remote sensing , 3D point clouds and surface models
- Language: English
- Type: Article
- Identifier: http://hdl.handle.net/10210/214778 , uj:21324 , Citation: Boon, M.A., Greenfield, R. & Tesfamichael, S. 2016. Wetland assessment using Unmanned Aerial Vehicle (UAV) photogrammetry.
- Description: Abstract: The use of Unmanned Arial Vehicle (UAV) photogrammetry is a valuable tool to enhance our understanding of wetlands. Accurate planning derived from this technological advancement allows for more effective management and conservation of wetland areas. This paper presents results of a study that aimed at investigating the use of UAV photogrammetry as a tool to enhance the assessment of wetland ecosystems. The UAV images were collected during a single flight within 2½ hours over a 100 ha area at the Kameelzynkraal farm, Gauteng Province, South Africa. An AKS Y-6 MKII multi-rotor UAV and a digital camera on a motion compensated gimbal mount were utilised for the survey. Twenty ground control points (GCPs) were surveyed using a Trimble GPS to achieve geometrical precision and georeferencing accuracy. Structure-from-Motion (SfM) computer vision techniques were used to derive ultra-high resolution point clouds, orthophotos and 3D models from the multi-view photos. The geometric accuracy of the data based on the 20 GCP’s were 0.018 m for the overall, 0.0025 m for the vertical root mean squared error (RMSE) and an over all root mean square reprojection error of 0.18 pixel. The UAV products were then edited and subsequently analysed, interpreted and key attributes extracted using a selection of tools/ software applications to enhance the wetland assessment. The results exceeded our expectations and provided a valuable and accurate enhancement to the wetland delineation, classification and health assessment which even with detailed field studies would have been difficult to achieve.
- Full Text:
- Authors: Boon, M.A. , Greenfield, R. , Tesfamichael, S.
- Date: 2016
- Subjects: Unmanned Arial Vehicle Photogrammetry , Remote sensing , 3D point clouds and surface models
- Language: English
- Type: Article
- Identifier: http://hdl.handle.net/10210/214778 , uj:21324 , Citation: Boon, M.A., Greenfield, R. & Tesfamichael, S. 2016. Wetland assessment using Unmanned Aerial Vehicle (UAV) photogrammetry.
- Description: Abstract: The use of Unmanned Arial Vehicle (UAV) photogrammetry is a valuable tool to enhance our understanding of wetlands. Accurate planning derived from this technological advancement allows for more effective management and conservation of wetland areas. This paper presents results of a study that aimed at investigating the use of UAV photogrammetry as a tool to enhance the assessment of wetland ecosystems. The UAV images were collected during a single flight within 2½ hours over a 100 ha area at the Kameelzynkraal farm, Gauteng Province, South Africa. An AKS Y-6 MKII multi-rotor UAV and a digital camera on a motion compensated gimbal mount were utilised for the survey. Twenty ground control points (GCPs) were surveyed using a Trimble GPS to achieve geometrical precision and georeferencing accuracy. Structure-from-Motion (SfM) computer vision techniques were used to derive ultra-high resolution point clouds, orthophotos and 3D models from the multi-view photos. The geometric accuracy of the data based on the 20 GCP’s were 0.018 m for the overall, 0.0025 m for the vertical root mean squared error (RMSE) and an over all root mean square reprojection error of 0.18 pixel. The UAV products were then edited and subsequently analysed, interpreted and key attributes extracted using a selection of tools/ software applications to enhance the wetland assessment. The results exceeded our expectations and provided a valuable and accurate enhancement to the wetland delineation, classification and health assessment which even with detailed field studies would have been difficult to achieve.
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Determination of sediment quality in the Nyl River system, Limpopo Province, South Africa
- Greenfield, R., van Vuren, J.H.J., Wepener, V.
- Authors: Greenfield, R. , van Vuren, J.H.J. , Wepener, V.
- Date: 2007
- Subjects: Nylsvley (South Africa) , Wetland management - South Africa - Nylsvley , Sediment quality - Souh Africa - Nyl River , Nyl River (Limpopo Province, South Africa)
- Type: Article
- Identifier: uj:5438 , ISSN 0378-4738 , http://hdl.handle.net/10210/12992
- Description: The importance of wetland management and conservation is becoming more and more prevalent in the world today. It is thus important to determine baseline contamination values for wetlands to assist in making informed management decisions. Sediment from the Nyl River flood plain in the dry Limpopo Province was analysed using sequential extraction and ICP-MS to determine baseline metal concentrations, and bioavailability thereof. Eight heavy metal (Cu, Cd, Cr, Al, As, Zn, Mn, Pb) concentrations were determined and compared to sediment quality guideline values to assess sediment quality. Fractionation of the elements was also noted to assess the bioavailability of the metals. The results indicated that the sediment is of a fair quality in comparison to the sediment quality guideline values. They also indicate that the metals will only become available in the presence of strong reducing agents as most of the metal concentrations were recorded in the 4th and 5th fractions obtained from the Tessier sequential extraction of the sediment samples. The study concluded that the sediment is of a fair quality and that it poses little potential threat to the system.
- Full Text:
- Authors: Greenfield, R. , van Vuren, J.H.J. , Wepener, V.
- Date: 2007
- Subjects: Nylsvley (South Africa) , Wetland management - South Africa - Nylsvley , Sediment quality - Souh Africa - Nyl River , Nyl River (Limpopo Province, South Africa)
- Type: Article
- Identifier: uj:5438 , ISSN 0378-4738 , http://hdl.handle.net/10210/12992
- Description: The importance of wetland management and conservation is becoming more and more prevalent in the world today. It is thus important to determine baseline contamination values for wetlands to assist in making informed management decisions. Sediment from the Nyl River flood plain in the dry Limpopo Province was analysed using sequential extraction and ICP-MS to determine baseline metal concentrations, and bioavailability thereof. Eight heavy metal (Cu, Cd, Cr, Al, As, Zn, Mn, Pb) concentrations were determined and compared to sediment quality guideline values to assess sediment quality. Fractionation of the elements was also noted to assess the bioavailability of the metals. The results indicated that the sediment is of a fair quality in comparison to the sediment quality guideline values. They also indicate that the metals will only become available in the presence of strong reducing agents as most of the metal concentrations were recorded in the 4th and 5th fractions obtained from the Tessier sequential extraction of the sediment samples. The study concluded that the sediment is of a fair quality and that it poses little potential threat to the system.
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A baseline study of metal contamination along the Namibian coastline for Perna perna and Choromytilus meridionalis.
- Dahms, S., van der Bank, F.H., Greenfield, R.
- Authors: Dahms, S. , van der Bank, F.H. , Greenfield, R.
- Date: 2014
- Subjects: Mussels - Effect of heavy metals on , Perna perna - Effect of heavy metals on , Choromytilus meridionalis - Effect of heavy metals on
- Type: Article
- Identifier: uj:5446 , http://hdl.handle.net/10210/13137
- Description: The use of bivalves such as the brown mussel (Perna perna) and the black mussel (Choromytilus meridionalis) is common in the study of marine pollution and the effect of these pollutants on ecosystems and are important in both economic and ecological roles. Namibian marine ecosystems are threatened by pollution from mining, commercial fishing and population growth. The aims of this study were to determine baseline metal concentrations, spatial variation and variation between species. Metal levels in C. meridionalis from Guano Platform (GP) are the lowest of all the sites. The most polluted sites are Rocky Point (RP), Halifax Island (HIL) and between Walvis Bay and Swakopmund (WS). The bioaccumulation of metals between P. perna and C. meridionalis were not uniform for all metals. Overall the study indicates the condition of the coastline to be mostly normal, with Cd and Pb levels being of concern.
- Full Text:
- Authors: Dahms, S. , van der Bank, F.H. , Greenfield, R.
- Date: 2014
- Subjects: Mussels - Effect of heavy metals on , Perna perna - Effect of heavy metals on , Choromytilus meridionalis - Effect of heavy metals on
- Type: Article
- Identifier: uj:5446 , http://hdl.handle.net/10210/13137
- Description: The use of bivalves such as the brown mussel (Perna perna) and the black mussel (Choromytilus meridionalis) is common in the study of marine pollution and the effect of these pollutants on ecosystems and are important in both economic and ecological roles. Namibian marine ecosystems are threatened by pollution from mining, commercial fishing and population growth. The aims of this study were to determine baseline metal concentrations, spatial variation and variation between species. Metal levels in C. meridionalis from Guano Platform (GP) are the lowest of all the sites. The most polluted sites are Rocky Point (RP), Halifax Island (HIL) and between Walvis Bay and Swakopmund (WS). The bioaccumulation of metals between P. perna and C. meridionalis were not uniform for all metals. Overall the study indicates the condition of the coastline to be mostly normal, with Cd and Pb levels being of concern.
- Full Text:
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