A phylogenetic study of the family Combretaceae with emphasis on the genus Combretum in Africa
- Authors: Maurin, Olivier
- Date: 2011-05-16T07:41:51Z
- Subjects: Combretaceae phylogeny , Combretaceae in Africa , Combretaceae classification
- Type: Thesis
- Identifier: uj:7071 , http://hdl.handle.net/10210/3634
- Description: Ph.D. , The complexity of Combretaceae and lack of information on phylogenetic relationships within the family led me to explore relationships between and within genera of Combretaceae by means of combined analyses of plastid (rbcL, psaA-ycf3 spacer, and psbA-trnH spacer) and nuclear ribosomal ITS sequences for all but three of the 17 genera in Combretaceae. The current classification of the family into two subfamilies, Strephonematoideae and Combretoideae, is corroborated. Within Combretoideae, division into two tribes, Laguncularieae and Combreteae, is strongly supported. Within Combreteae subtribe Terminaliinae relationships between genera are largely unresolved. Terminalia is not supported as monophyletic, and two groups were identified, one containing mainly African species and another of mostly Asian species. Pteleopsis, Buchenavia and Anogeissus are embedded within Terminalia, and I suggest that all genera of Terminialiinae with the exception of Conocarpus should be included into an expanded Terminalia. Within subtribe Combretinae, a clade formed by the two monotypic genera Guiera and Calycopteris is sister to the rest of the subtribe. Within Combretinae, groupings are consistent with recent results based on morphological data. Combretum is currently divided into three subgenera: Apethalanthum, Cacoucia and Combretum. The two last were included in this study and supported as monophyletic. Meiostemon is sister to subgenus Combretum, and Quisqualis is embedded within subgenus Cacoucia. I recommend that subgenus Combretum should be expanded to include Meiostemon and subgenus Cacoucia to include Quisqualis. The sectional classification within Combretum proposed in earlier morphological studies is confirmed except for the exclusion of Combretum imberbe from section Hypocrateropsis into a separate and monotypic section and the inclusion of Combretum zeyheri (section Spathulipetala) within section Macrostigmatea. In order to accommodate Combretum imberbe a new section is suggested which is formally described in Maurin et al. (2010). The reinstatement of previously recognised sections Grandiflora and Trichopetala, both of which had been sunk into subgenus Cacoucia section Poivrea, is also suggested. In this study two new species from South Africa are presented: Combretum nwambiyana O.Maurin, M.Jordaan & A.E.van Wyk and Combretum stylesii Maurin, Jordaan & A.E.van Wyk. The formal description of these two new species will be done in regular journals. Divergence time estimates using a Bayesian MCMC approach implemented in BEAST suggested a crown date for Combretaceae around 82.6 mya with the two subtribes Combretinae and Terminaliinae splitting at the end of the Late Cretaceous during a period marked by a number of mass extinctions both in plants and animals. The Miocene and Pliocene are characterised by constant speciation with many clades within Combretaceae succesfully adapting to savanna vegetation and diversifying within it.
- Full Text:
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.
- Full Text:
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.
- Full Text:
Molecular and morphological analysis of subfamily Alooideae (Asphodelaceae) and the inclusion of chortolirion in aloe
- Authors: Daru, Barnabas H. , Manning, John C. , Boatwright, James S. , Maurin, Olivier , Maclean, Norman , Schaefer, Hanno , Kuzmina, Maria , van der Bank, Michelle
- Date: 2013
- Subjects: Asphodelaceae , Alooideae , Asparagales , Aloe , Chortolirion
- Type: Article
- Identifier: uj:5985 , http://hdl.handle.net/10210/8605
- Description: Asphodelaceae subfam. Alooideae (Asparagales) currently comprises five genera, four of which are endemic to southern Africa. Despite their importance in commercial horticulture the evolutionary relationships among the genera are still incompletely understood. This study examines phylogenetic relationships in the subfamily using an expanded molecular sequence dataset from three plastid regions (matK, rbcLa, trnH-psbA) and the first subunit of the nuclear ribosomal internal transcribed spacer (ITS1). Sequence data were analysed using maximum parsimony and Bayesian statistics, and selected morphological traits were mapped onto the molecular phylogeny. Haworthia is confirmed as being polyphyletic, comprising three main clades that largely correlate with current subgeneric circumscriptions. Astroloba and Gasteria are evidently each monophyletic and sister respectively to Astroloba and H. subg. Robustipedunculares. Chortolirion is shown to be deeply nested within Aloe and is formally included in that genus. Aloe itself is clearly polyphyletic, with the dwarf species A. aristata allied to Haworthia subg. Robustipedunculares. The taxonomic implications of these findings are examined but branch support at critical lower nodes is insufficient at this stage to justify implementing major taxonomic changes.
- Full Text: