A test of psbK-psbI and atpF-atpH as potential plant DNA barcodes using the flora of the Kruger National Park (South Africa) as a model system.
- Authors: Lahaye, Renaud R. Y. , Savolainen, Vincent , Duthoit, Sylvie , Maurin, Olivier , Van der Bank, Michelle
- Date: 2008-05-16
- Subjects: Plant DNA barcoding , DNA barcoding , Kruger National Park (South Africa)
- Type: Article
- Identifier: uj:5728 , http://hdl.handle.net/10210/5286
- Description: DNA barcoding is a new technique that uses short, standardized DNA sequences (400-800 bp) of an organism to determine its identity. Because this sequence has to be variable enough to identify individual species, but not too variable within the same species so that a clear threshold can be defined between intra- and inter-specific diversities, it is very challenging to apply this technique to all species on the planet . A DNA barcode has been identified for animals, i.e. the mitochondrial gene cox1 , which shows strong abilities in identifying cryptic species, accelerating biodiversity inventories and helping to identify species from degraded material (e.g. to control trade of threatened). For plants, the identification of a suitable DNA barcode is more problematic. Cho et al. showed that mitochondrial DNA evolves too slowly in plants to provide a region variable enough to discriminate between species. Then the quest for the best suitable barcode started and is still ongoing.
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A test of psbK-psbI and atpF-atpH as potential plant DNA barcodes using the flora of the Kruger National Park as a model system (South Africa)
- Authors: Lahaye, Renaud , Savolainen, Vincent , Duthoit, Sylvie , Maurin, Olivier , Van der Bank, Michelle
- Date: 2008
- Subjects: DNA barcoding , Kruger National Park Africa (South Africa)
- Type: Article
- Identifier: uj:6275 , http://hdl.handle.net/10210/8915
- Description: A DNA barcode consists of a standardized short sequence of DNA (400-800bp) used to identify the taxonomic species a small organic fragment belongs to. Even though it has been easy to discriminate animal species by using the mitochondrial gene cox1, this is still difficult for plants seeing that the mitochondrial genome is not variable enough on the species level. During the Second International Barcode of Life Conference in Tapei (September 2007), different plastid regions were proposed as potential plant DNA barcodes, such as atpF-atpH and psbK-psbI, but no consensus on which region to use was reached during the meeting. The largest plant DNA barcoding study to date proposed matK as the best candidate and suggested that in combination with trnH-psbA a slight increase in performance could be achieved. However, no study has tested the suitability of the newly proposed psbK-psbI and atpF-atpH for plant barcoding purposes. Four potential DNA barcodes, matK, trnH-psbA, atpF-atpH, and psbK-psbI, were amplified and sequenced for a selective sampling including mainly trees and shrubs of the flora of the Kruger National Park Africa (South Africa). The performance of each region and also each possible combination of these were tested by applying a battery of metrics and statistical tests. Our results confirm that the second half (5’ end) of matK is the best candidate in a single locus barcoding approach reaching 87.5% of species correctly identified. Combining matK with trnH-psbA and psbK-psbI increased only slightly the performance in discriminating species. The results from this study show that the use of a ‘three-region barcode’ does not significantly outperform matK in a single-locus barcoding approach. We therefore argue against the ‘multiple barcode approach’ proposed by the plant working group, and instead propose to keep barcoding plants in line with the approach taken for animals, i.e. using one barcode: cox1 for animals and matK for plants.
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Evidence of constant diversification punctuated by a mass extinction in the African cycads
- Authors: Yessoufou, Kowiyou , Bamigboye, Samuel O. , Daru, Barnabas H. , Van der Bank, Michelle
- Date: 2013
- Subjects: Encephalartos , Cycads - Africa , Extinction (Biology)
- Type: Article
- Identifier: uj:5410 , ISSN 2045-8827 , http://hdl.handle.net/10210/10051
- Description: The recent evidence that extant cycads are not living fossils triggered a renewed search for a better understanding of their evolutionary history. In this study, we investigated the evolutionary diversification history of the genus Encephalartos, a monophyletic cycad endemic to Africa. We found an antisigmoidal pattern with a plateau and punctual explosive radiation. This pattern is typical of a constant radiation with mass extinction. The rate shift that we found may therefore be a result of a rapid recolonization of niches that have been emptied owing to mass extinction. Because the explosive radiation occurred during the transition Pliocene–Pleistocene, we argued that the processes might have been climatically mediated.
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Genetic variation and phylogenetic relationships in the Podalyrieae and related tribes (Fabaceae)
- Authors: Van der Bank, Michelle
- Date: 2012-09-12
- Subjects: Plants - Phylogeny - Research - South Africa , Legumes - Phylogeny - Research - South Africa
- Type: Thesis
- Identifier: uj:10137 , http://hdl.handle.net/10210/7518
- Description: Ph.D. , Genetic variation estimates and phylogenetic studies (based on genetic differentiation) of the Podalyrieae and related tribes (family Fabaceae) are presented. The tribe is endemic to the Cape fynbos region of South Africa, except for Calpurnia. Although Podalyrieae have been the focus of many taxonomic studies no genetic variation studies have been done on this group of plants. Genetic variation in selected populations, species and genera was studied to evaluate the use of enzyme electrophoresis in systematic studies on these three levels. Eight case studies are presented. Allelic data proved to be extremely useful at the population and congeneric species level. However, at a higher level, it showed some potential when treated with caution. It is not possible to predict beforehand if meaningful results can be obtained at this higher (i.e. confamilial genus) level of divergence. A large number of plant genetic data sets from the literature was analysed to determine typical levels and ranges of genetic differentiation within families, genera and species. A graph of probability against taxonomic rank was constructed and compared with results published by Thorpe (1982, 1983). The results indicate that plant taxa have a reduced biochemical evolution (less diverse than animals at comparable taxonomic ranks) in contrast to Thorpe's (1982, 1983) reports (which were based on less data for plant taxa). Genetic identity values between 3041 pairs of taxa were used in the present study. The phylogenetic relationships among genera of the tribe Podalyrieae were estimated from sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA as well as morphological and chemical data. Morphological and. ITS sequence data produced cladograms with similar topologies, both supporting the exclusion of Hypocalyptus from Podalyrieae. A broadening of Podalyrieae, which includes Xiphothecinae, Podalyriinae and Cyclopia, is suggested. The multidisciplinary approach followed in this study provided a better understanding of taxonomic and evolutionary relationships in the Podalyrieae and some other Cape legumes.
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