Isolation of filamentous species of two Aspergillum genera from compound feeds produced in South ... more Isolation of filamentous species of two Aspergillum genera from compound feeds produced in South Africa, and subsequent extraction of their individual DNA in this study, presents a simple but rapid molecular procedure for high through-put analysis of the individual morphological forms. DNA was successfully isolated from the Aspergillus spp. from agar cultures by use of a commercial kit. Agarose gel electrophoresis fractionation of the fungi DNA, showed distinct bands. The DNA extracted by this procedure appears to be relatively pure with a ratio absorbance at 260 and 280 nm. However, the overall morphological and molecular data indicated that 67.5 and 51.1% of feed samples were found to be contaminated with A. flavus and A. parasiticus, respectively, with poultry feed having the highest contamination mean level of 5.7×105 CFU/g when compared to cattle (mean: 4.0 × 106 CFU/g), pig (mean: 2.7 x 104 CFU/g) and horse (1.0 x102 CFU) feed. This technique presents a readily achievable, easy to use method in the extraction of filamentous fungal DNA and it’s identification. Hence serves as an important tool towards molecular study of these organisms for routine analysis check in monitoring and improving compound feed quality against fungal contamination.
The recent evidence that extant cycads are not living fossils triggered a renewed search for a be... more 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.
Phylogenetic analysis of plastid (rbcLa, matK, trnH-psbA and the trnL intron) and nuclear (ITS1) ... more Phylogenetic analysis of plastid (rbcLa, matK, trnH-psbA and the trnL intron) and nuclear (ITS1) sequence datasets in a wide sampling of species of Asphodelaceae: Alooideae provides a generally well-resolved phylogeny. Among traditionally accepted genera only Astroloba and Gasteria are supported as monophyletic. Species of Haworthia are distributed among three clades corresponding to the current subgenera. Aloe s. l. (including Chortolirion) segregates into six, well-supported clades corresponding respectively to sections Dracoaloe (= Aloidendron), Kumara + Haemanthifoliae, Macrifoliae, Aristatae, Serrulatae, and the remainder of the genus. The first three clades are retrieved as early branching lineages, whereas A. sects. Aristatae and Serrulatae are strongly supported as members of a clade including Astroloba + Haworthia subg. Robustipedunculatae. We examine possible options for recircumscribing the genera of Alooideae as reciprocally monophyletic entities. Although morphological and molecular data are consistent with expansion of Aloe to include all members of Alooideae, we accept and implement an alternative option maintaining historical usage in the group as far as possible. Astroloba and Gasteria are retained as currently circumscribed; Haworthia is restricted to H. subg. Haworthia; the genus Tulista is accepted for members of H. subg. Robustipedunculatae, with the new combination T. minima ; and H. subg. Hexangulares is treated as the genus Haworthiopsis with the new combinations H. koelmaniorum , H. pungens , and H. tessellata . The genus Aloe is restricted to the clade comprising the ‘true aloes’, with Aloidendron, Aloiampelos, and Kumara accepted as segregates, the latter broadened to include A. haemanthifolia as K. haemanthifolia . Aloe aristata is segregated in the monotypic genus Aristaloe as A. aristata and Aloe sect. Serrulatae is treated as the new genus Gonialoe with the species G. dinteri , G. sladeniana , and G. variegata.
The mangrove biome stands out as a distinct forest type at the interface between terrestrial, est... more The mangrove biome stands out as a distinct forest type at the interface between terrestrial, estuarine, and near-shore marine ecosystems. However, mangrove species are increasingly threatened and experiencing range contraction across the globe that requires urgent conservation action. Here, we assess the spatial distribution of mangrove species richness and evolutionary diversity, and evaluate potential predictors of global declines and risk of extinction. We found that human pressure, measured as the number of different uses associated with mangroves, correlated strongly, but negatively, with extinction probability, whereas species ages were the best predictor of global decline, explaining 15% of variation in extinction risk. Although the majority of mangrove species are categorised by the IUCN as Least Concern, our finding that the more threatened species also tend to be those that are more evolutionarily unique is of concern because their extinction would result in a greater loss of phylogenetic diversity. Finally, we identified biogeographic regions that are relatively species-poor but rich in evolutionary history, and suggest these regions deserve greater conservation priority. Our study provides phylogenetic information that is important for developing a unified management plan for mangrove ecosystems worldwide.
Asphodelaceae subfam. Alooideae (Asparagales) currently comprises five genera, four of which are ... more 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.
Previous phylogenetic studies have indicated that Acacia Miller s.l. is polyphyletic and in need ... more Previous phylogenetic studies have indicated that Acacia Miller s.l. is polyphyletic and in need of reclassification. A proposal to conserve the name Acacia for the larger Australian contingent of the genus (formerly subgenus Phyllodineae) resulted in the retypification of the genus with the Australian A. penninervis. However, Acacia s.l. comprises at least four additional distinct clades or genera, some still requiring formal taxonomic transfer of species. These include Vachellia (formerly subgenus Acacia), Senegalia (formerly subgenus Aculeiferum), Acaciella (formerly subgenus Aculeiferum section Filicinae) and Mariosousa (formerly the A. coulteri group). In light of this fragmentation of Acacia s.l., there is a need to assess relationships of the non-Australian taxa. A molecular phylogenetic study of Acacia s.l and close relatives occurring in Africa was conducted using sequence data from matK/trnK, trnL-trnF and psbA-trnH with the aim of determining the placement of the African species in the new generic system. The results reinforce the inevitability of recognizing segregate genera for Acacia s.l. and new combinations for the African species in Senegalia and Vachellia are formalized.
Background. Under the tropics, less than 40% of known fishes are identified to species-level. Fur... more 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 (eg, climate change) only by migrating to new environments.
There is an urgent need to reduce drastically the rate at which biodiversity is declining worldwi... more There is an urgent need to reduce drastically the rate at which biodiversity is declining worldwide. Phylogenetic methods are increasingly being recognised as providing a useful framework for predicting future losses, and guiding efforts for pre-emptive conservation actions. In this study, we used a reconstructed phylogenetic tree of angiosperm species of the Eastern Arc Mountains - an important African biodiversity hotspot - and described the distribution of extinction risk across taxonomic ranks and phylogeny. We provide evidence for both taxonomic and phylogenetic selectivity in extinction risk. However, we found that selectivity varies with IUCN extinction risk category. Vulnerable species are more closely related than expected by chance, whereas endangered and critically endangered species are not significantly clustered on the phylogeny. We suggest that the general observation for taxonomic and phylogenetic selectivity (i.e. phylogenetic signal, the tendency of closely related species to share similar traits) in extinction risks is therefore largely driven by vulnerable species, and not necessarily the most highly threatened. We also used information on altitudinal distribution and climate to generate a predictive model of at-risk species richness, and found that greater threatened species richness is found at higher altitude, allowing for more informed conservation decision making. Our results indicate that evolutionary history can help predict plant susceptibility to extinction threats in the hyper-diverse but woefully-understudied Eastern Arc Mountains, and illustrate the contribution of phylogenetic approaches in conserving African floristic biodiversity where detailed ecological and evolutionary data are often lacking.
Understanding how ecosystems function is critical to shed light on processes that lead to species... more Understanding how ecosystems function is critical to shed light on processes that lead to species coexistence. Ficus species provide highly specialized niches for frugivores in tropical forests, but little is known about how Ficus-frugivore interactions evolve over time. Here we applied three approaches to investigate these interactions based on key parameters. We tested for model of evolution that could explain interaction patterns, evaluated the phylogenetic signal, and assessed the evolutionary rate of niches generated by Ficus species. We showed that interactions are best explained by Brownian motion model, indicating a random walk. However, the signal observed is lower than expected under this model, and at the same time the evolutionary rate provides evidence for niche conservatism. Such findings are incompatible with an unbounded Brownian process. We therefore proposed that a random walk constrained by ecological forces towards a stabilizing selection could better explain fig-frugivore interactions in tropical forests.
Large-scale DNA barcoding provides a new technique for species identification and evaluation of r... more Large-scale DNA barcoding provides a new technique for species identification and evaluation of relationships across various levels (populations and species) and may reveal fundamental processes in recently diverged species. Here, we analysed DNA sequence variation in the recently diverged legumes from the Psoraleeae (Fabaceae) occurring in the Cape Floristic Region (CFR) of southern Africa to test the utility of DNA barcodes in species identification and discrimination. We further explored the phylogenetic signal on fire response trait (reseeding and resprouting) at species and generic levels. We showed that Psoraleoid legumes of the CFR exhibit a barcoding gap yielding the combination of matK and rbcLa (matK+rbcLa) dataset as a better barcode than single regions. We found a high score (100%) of correct identification of individuals to their respective genera but very low score (<50%) in identifying them to species. We found a considerable match (54%) between genetic species and...
While fig trees (Ficus: Moraceae) are acknowledged as keystone resources for frugivore communitie... more While fig trees (Ficus: Moraceae) are acknowledged as keystone resources for frugivore communities in tropical forests, their detailed use by frugivores is often poorly understood. In this study, we found over 400 fig trees of 12 species in Amurum Forest Reserve, Nigeria. We analyse bird visits to 12 individual trees of eight Ficus species, observed over a two-year period (2007–9), during which we recorded 3234 visits by 48 bird species. Different fig trees received between 23 and 826 visits during our observations; the diurnal pattern of visits was similar for all fig species, with clear morning (8h00–9h30, larger) and late afternoon (16h00, lesser) peaks, with a lull in visits around mid-day. Mean visit duration varied between 2.9 ± 1.8 min. and 20.5 ± 19.2 min. (mean ± SD) at different fig species. Birds ate between 1.7 ± 1.1 and 5.2 ± 4.4 figs per visit at different fig species. Our study provides preliminary information on Ficus–bird associations and confirms that figs are impo...
Isolation of filamentous species of two Aspergillum genera from compound feeds produced in South ... more Isolation of filamentous species of two Aspergillum genera from compound feeds produced in South Africa, and subsequent extraction of their individual DNA in this study, presents a simple but rapid molecular procedure for high through-put analysis of the individual morphological forms. DNA was successfully isolated from the Aspergillus spp. from agar cultures by use of a commercial kit. Agarose gel electrophoresis fractionation of the fungi DNA, showed distinct bands. The DNA extracted by this procedure appears to be relatively pure with a ratio absorbance at 260 and 280 nm. However, the overall morphological and molecular data indicated that 67.5 and 51.1% of feed samples were found to be contaminated with A. flavus and A. parasiticus, respectively, with poultry feed having the highest contamination mean level of 5.7×105 CFU/g when compared to cattle (mean: 4.0 × 106 CFU/g), pig (mean: 2.7 x 104 CFU/g) and horse (1.0 x102 CFU) feed. This technique presents a readily achievable, easy to use method in the extraction of filamentous fungal DNA and it’s identification. Hence serves as an important tool towards molecular study of these organisms for routine analysis check in monitoring and improving compound feed quality against fungal contamination.
The recent evidence that extant cycads are not living fossils triggered a renewed search for a be... more 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.
Phylogenetic analysis of plastid (rbcLa, matK, trnH-psbA and the trnL intron) and nuclear (ITS1) ... more Phylogenetic analysis of plastid (rbcLa, matK, trnH-psbA and the trnL intron) and nuclear (ITS1) sequence datasets in a wide sampling of species of Asphodelaceae: Alooideae provides a generally well-resolved phylogeny. Among traditionally accepted genera only Astroloba and Gasteria are supported as monophyletic. Species of Haworthia are distributed among three clades corresponding to the current subgenera. Aloe s. l. (including Chortolirion) segregates into six, well-supported clades corresponding respectively to sections Dracoaloe (= Aloidendron), Kumara + Haemanthifoliae, Macrifoliae, Aristatae, Serrulatae, and the remainder of the genus. The first three clades are retrieved as early branching lineages, whereas A. sects. Aristatae and Serrulatae are strongly supported as members of a clade including Astroloba + Haworthia subg. Robustipedunculatae. We examine possible options for recircumscribing the genera of Alooideae as reciprocally monophyletic entities. Although morphological and molecular data are consistent with expansion of Aloe to include all members of Alooideae, we accept and implement an alternative option maintaining historical usage in the group as far as possible. Astroloba and Gasteria are retained as currently circumscribed; Haworthia is restricted to H. subg. Haworthia; the genus Tulista is accepted for members of H. subg. Robustipedunculatae, with the new combination T. minima ; and H. subg. Hexangulares is treated as the genus Haworthiopsis with the new combinations H. koelmaniorum , H. pungens , and H. tessellata . The genus Aloe is restricted to the clade comprising the ‘true aloes’, with Aloidendron, Aloiampelos, and Kumara accepted as segregates, the latter broadened to include A. haemanthifolia as K. haemanthifolia . Aloe aristata is segregated in the monotypic genus Aristaloe as A. aristata and Aloe sect. Serrulatae is treated as the new genus Gonialoe with the species G. dinteri , G. sladeniana , and G. variegata.
The mangrove biome stands out as a distinct forest type at the interface between terrestrial, est... more The mangrove biome stands out as a distinct forest type at the interface between terrestrial, estuarine, and near-shore marine ecosystems. However, mangrove species are increasingly threatened and experiencing range contraction across the globe that requires urgent conservation action. Here, we assess the spatial distribution of mangrove species richness and evolutionary diversity, and evaluate potential predictors of global declines and risk of extinction. We found that human pressure, measured as the number of different uses associated with mangroves, correlated strongly, but negatively, with extinction probability, whereas species ages were the best predictor of global decline, explaining 15% of variation in extinction risk. Although the majority of mangrove species are categorised by the IUCN as Least Concern, our finding that the more threatened species also tend to be those that are more evolutionarily unique is of concern because their extinction would result in a greater loss of phylogenetic diversity. Finally, we identified biogeographic regions that are relatively species-poor but rich in evolutionary history, and suggest these regions deserve greater conservation priority. Our study provides phylogenetic information that is important for developing a unified management plan for mangrove ecosystems worldwide.
Asphodelaceae subfam. Alooideae (Asparagales) currently comprises five genera, four of which are ... more 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.
Previous phylogenetic studies have indicated that Acacia Miller s.l. is polyphyletic and in need ... more Previous phylogenetic studies have indicated that Acacia Miller s.l. is polyphyletic and in need of reclassification. A proposal to conserve the name Acacia for the larger Australian contingent of the genus (formerly subgenus Phyllodineae) resulted in the retypification of the genus with the Australian A. penninervis. However, Acacia s.l. comprises at least four additional distinct clades or genera, some still requiring formal taxonomic transfer of species. These include Vachellia (formerly subgenus Acacia), Senegalia (formerly subgenus Aculeiferum), Acaciella (formerly subgenus Aculeiferum section Filicinae) and Mariosousa (formerly the A. coulteri group). In light of this fragmentation of Acacia s.l., there is a need to assess relationships of the non-Australian taxa. A molecular phylogenetic study of Acacia s.l and close relatives occurring in Africa was conducted using sequence data from matK/trnK, trnL-trnF and psbA-trnH with the aim of determining the placement of the African species in the new generic system. The results reinforce the inevitability of recognizing segregate genera for Acacia s.l. and new combinations for the African species in Senegalia and Vachellia are formalized.
Background. Under the tropics, less than 40% of known fishes are identified to species-level. Fur... more 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 (eg, climate change) only by migrating to new environments.
There is an urgent need to reduce drastically the rate at which biodiversity is declining worldwi... more There is an urgent need to reduce drastically the rate at which biodiversity is declining worldwide. Phylogenetic methods are increasingly being recognised as providing a useful framework for predicting future losses, and guiding efforts for pre-emptive conservation actions. In this study, we used a reconstructed phylogenetic tree of angiosperm species of the Eastern Arc Mountains - an important African biodiversity hotspot - and described the distribution of extinction risk across taxonomic ranks and phylogeny. We provide evidence for both taxonomic and phylogenetic selectivity in extinction risk. However, we found that selectivity varies with IUCN extinction risk category. Vulnerable species are more closely related than expected by chance, whereas endangered and critically endangered species are not significantly clustered on the phylogeny. We suggest that the general observation for taxonomic and phylogenetic selectivity (i.e. phylogenetic signal, the tendency of closely related species to share similar traits) in extinction risks is therefore largely driven by vulnerable species, and not necessarily the most highly threatened. We also used information on altitudinal distribution and climate to generate a predictive model of at-risk species richness, and found that greater threatened species richness is found at higher altitude, allowing for more informed conservation decision making. Our results indicate that evolutionary history can help predict plant susceptibility to extinction threats in the hyper-diverse but woefully-understudied Eastern Arc Mountains, and illustrate the contribution of phylogenetic approaches in conserving African floristic biodiversity where detailed ecological and evolutionary data are often lacking.
Understanding how ecosystems function is critical to shed light on processes that lead to species... more Understanding how ecosystems function is critical to shed light on processes that lead to species coexistence. Ficus species provide highly specialized niches for frugivores in tropical forests, but little is known about how Ficus-frugivore interactions evolve over time. Here we applied three approaches to investigate these interactions based on key parameters. We tested for model of evolution that could explain interaction patterns, evaluated the phylogenetic signal, and assessed the evolutionary rate of niches generated by Ficus species. We showed that interactions are best explained by Brownian motion model, indicating a random walk. However, the signal observed is lower than expected under this model, and at the same time the evolutionary rate provides evidence for niche conservatism. Such findings are incompatible with an unbounded Brownian process. We therefore proposed that a random walk constrained by ecological forces towards a stabilizing selection could better explain fig-frugivore interactions in tropical forests.
Large-scale DNA barcoding provides a new technique for species identification and evaluation of r... more Large-scale DNA barcoding provides a new technique for species identification and evaluation of relationships across various levels (populations and species) and may reveal fundamental processes in recently diverged species. Here, we analysed DNA sequence variation in the recently diverged legumes from the Psoraleeae (Fabaceae) occurring in the Cape Floristic Region (CFR) of southern Africa to test the utility of DNA barcodes in species identification and discrimination. We further explored the phylogenetic signal on fire response trait (reseeding and resprouting) at species and generic levels. We showed that Psoraleoid legumes of the CFR exhibit a barcoding gap yielding the combination of matK and rbcLa (matK+rbcLa) dataset as a better barcode than single regions. We found a high score (100%) of correct identification of individuals to their respective genera but very low score (<50%) in identifying them to species. We found a considerable match (54%) between genetic species and...
While fig trees (Ficus: Moraceae) are acknowledged as keystone resources for frugivore communitie... more While fig trees (Ficus: Moraceae) are acknowledged as keystone resources for frugivore communities in tropical forests, their detailed use by frugivores is often poorly understood. In this study, we found over 400 fig trees of 12 species in Amurum Forest Reserve, Nigeria. We analyse bird visits to 12 individual trees of eight Ficus species, observed over a two-year period (2007–9), during which we recorded 3234 visits by 48 bird species. Different fig trees received between 23 and 826 visits during our observations; the diurnal pattern of visits was similar for all fig species, with clear morning (8h00–9h30, larger) and late afternoon (16h00, lesser) peaks, with a lull in visits around mid-day. Mean visit duration varied between 2.9 ± 1.8 min. and 20.5 ± 19.2 min. (mean ± SD) at different fig species. Birds ate between 1.7 ± 1.1 and 5.2 ± 4.4 figs per visit at different fig species. Our study provides preliminary information on Ficus–bird associations and confirms that figs are impo...
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Publications by Barnabas Daru
Papers by Barnabas Daru