78 research outputs found
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)
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 (5â 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 âthree-region barcodeâ does not significantly outperform matK in a single-locus barcoding approach. We therefore argue against the âmultiple barcode approachâ 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
Molecular and morphological analysis of subfamily Alooideae (Asphodelaceae) and the inclusion of chortolirion in aloe
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
A novel phylogenetic regionalization of phytogeographical zones of southern Africa reveals their hidden evolutionary affinities
AIM : Although existing bioregional classification schemes often consider the
compositional affinities within regional biotas, they do not typically incorporate
phylogenetic information explicitly. Because phylogeny captures information
on the evolutionary history of taxa, it provides a powerful tool for
delineating biogeographical boundaries and for establishing relationships
among them. Here, we present the first vegetation delineation of the woody
flora of southern Africa based upon evolutionary relationships.
LOCATION : Southern Africa.
METHODS : We used a published time-calibrated phylogenetic tree for 1400
woody plant species along with their geographical distributions and a metric of
phylogenetic beta diversity to generate a phylogenetic delineation of the woody
vegetation of southern Africa. We then explored environmental correlates of
phylogenetic turnover between them, and the evolutionary distinctiveness of
the taxa within them.
RESULTS : We identified 15 phylogenetically distinct biogeographical units, here
referred to as phyloregions. The largest phyloregion broadly overlaps with
Savanna vegetation, while the phyloregion overlapping with the south-western
portion of the Fynbos biome is the most evolutionarily distinct. Potential evapotranspiration
and mean annual temperature differ significantly among phyloregions
and correlate with patterns of phylogenetic beta diversity between
them. Our phylogeny-based delimitation of southern Africaâs woody vegetation
broadly matches currently recognized phytogeographical classifications, but also
highlights parts of the Namib Karoo and Greater Limpopo Transfrontier Park
as distinct, but previously under-recognized biogeographical units.
MAIN CONCLUSIONS : Our analysis provides new insights into the structure and
phylogenetic relationships among the woody flora of southern Africa. We show
that evolutionary affinities differentiate phyloregions closely resembling existing
vegetation classifications, yet also identify âcrypticâ phyloregions that are as evolutionarily
distinct as some of the recognized African vegetation types.Government of Canada through Genome Canada and the Ontario Genomics Institute
(2008-OGI-ICI-03), the International Development Research Centre (IDRC) Canada, the University of Johannesburg and the South African National Research Foundation (NRF).http://onlinelibrary.wiley.com/doi/10.1111/jbi.126192017-01-31hb201
DNA barcodes reveal microevolutionary signals in fire response trait in two legume genera
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 morphologicallydelimited
species. We also found that different lineages showed a weak but
significant phylogenetic conservatism in their response to fire as reseeders or
resprouters, with more clustering of resprouters than would be expected by
chance. These novel microevolutionary patterns might be acting continuously
over time to produce multi-scale regularities of biodiversity. This study
provides the first insight into the DNA barcoding campaign of land plants in
species identification and detection of phylogenetic signal in recently diverged
lineages of the CFR.The South African National
Research Foundation (NRF; AMM); Nigeria Tertiary Education Trust Fund
(NTETF) / Umaru Musa Yarâadua University Katsina, Nigeria (Fellowship
Grant; A. Bello); and University of Cape Town, J. W. Jagger Centenary Gift
Scholarship (to A. Bello).http://aobpla.oxfordjournals.orgam2016Physiotherap
Phylogenetic position and revised classification of Acacia s.l. (Fabaceae: Mimosoideae) in Africa, including new combinations in Vachellia and Senegalia
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.Web of Scienc
A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses.
Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly 1/8th of all angiosperm species, based on two plastid barcoding genes, matK (incl. trnK) and rbcL. Novel sequences were generated for several species, while the rest of the data were mined from GenBank. The resulting tree was dated using 56 angiosperm fossils as calibration points. The resulting megaphylogeny is one of the largest dated phylogenetic tree of angiosperms yet, consisting of 36,101 sampled species, representing 8,399 genera, 426 families and all orders. This novel framework will be useful for investigating different broad scale research questions in ecological and evolutionary biology
Savanna fire and the origins of the 'underground forests' of Africa
1. The origin of fire-adapted lineages is a long-standing question in ecology.
Although phylogeny can provide a significant contribution to the ongoing debate,
its use has been precluded by the lack of comprehensive DNA data. Here we focus
on the âunderground treesâ (= geoxyles) of southern Africa, one of the most
distinctive growth forms characteristic of fire-prone savannas.
2. We placed geoxyles within the most comprehensive dated phylogeny for the
regional flora comprising over 1400 woody species. Using this phylogeny, we
tested whether African geoxyles evolved concomitantly with those of the South
American cerrado and used their phylogenetic position to date the appearance of
humid savannas.
3. We found multiple independent origins of the geoxyle life-form mostly from the
Pliocene, a period consistent with the origin of cerrado, with the majority of
divergences occurring within the last 2 Ma. When contrasted with their tree
relatives, geoxyles occur in regions characterized by higher rainfall and greater fire
frequency.
4. Our results indicate that the geoxylic growth form may have evolved in response to
the interactive effects of frequent fires and high precipitation. As such, geoxyles
may be regarded as markers of fire-maintained savannas occurring in climates
suitable for forests.Government of Canada through Genome Canada and the Ontario Genomics Institute (2008-OGI-ICI-03), the International Development Research Centre (IDRC), Canada and the University of Johannesburg.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1469-81372015-10-31hb201
The Astropy Problem
The Astropy Project (http://astropy.org) is, in its own words, "a community
effort to develop a single core package for Astronomy in Python and foster
interoperability between Python astronomy packages." For five years this
project has been managed, written, and operated as a grassroots,
self-organized, almost entirely volunteer effort while the software is used by
the majority of the astronomical community. Despite this, the project has
always been and remains to this day effectively unfunded. Further, contributors
receive little or no formal recognition for creating and supporting what is now
critical software. This paper explores the problem in detail, outlines possible
solutions to correct this, and presents a few suggestions on how to address the
sustainability of general purpose astronomical software
Diversification into novel habitats in the Africa clade of Dioscorea (Dioscoreaceae): erect habit and elephantâs foot tubers
Background: Dioscorea is a widely distributed and highly diversified genus in tropical regions where it is represented
by ten main clades, one of which diversified exclusively in Africa. In southern Africa it is characterised by a distinct
group of species with a pachycaul or âelephantâs footâ structure that is partially to fully exposed above the substrate.
In contrast to African representatives of the genus from other clades, occurring mainly in forest or woodland, the
pachycaul taxa and their southern African relatives occur in diverse habitats ranging from woodland to open
vegetation. Here we investigate patterns of diversification in the African clade, time of transition from forest to
more open habitat, and morphological traits associated with each habitat and evaluate if such transitions have
led to modification of reproductive organs and mode of dispersal.
Results: The Africa clade originated in the Oligocene and comprises four subclades. The Dioscorea buchananii
subclade (southeastern tropical Africa and South Africa) is sister to the East African subclade, which is respectively
sister to the recently evolved sister South African (e. g., Cape and Pachycaul) subclades. The Cape and Pachycaul
subclades diversified in the east of the Cape Peninsula in the mid Miocene, in an area with complex geomorphology
and climate, where the fynbos, thicket, succulent karoo and forest biomes meet.
Conclusions: Diversification out of forest is associated with major shifts in morphology of the perennial tuber
(specifically an increase in size and orientation which presumably led them to become pachycaul) and rotation of
stem (from twining to non-twining). The iconic elephant's foot morphology, observed in grasslands and thicket
biomes, where its corky bark may offer protection against fire and herbivory, evolved since mid Miocene. A shift
in pollination trait is observed within the forest, but entry into open habitat does not show association with
reproductive morphology, except in the seed wing, which has switched from winged all round the seed margin
to just at the base or at the apex of it, or has been even replaced by an elaiosome
Angular analysis of the B-0 -> K*(0) e(+) e(-) decay in the low-q(2) region
An angular analysis of the decay is performed using a data sample, corresponding to an integrated luminosity of 3.0 {\mbox{fb}^{-1}}, collected by the LHCb experiment in collisions at centre-of-mass energies of 7 and 8 TeV during 2011 and 2012. For the first time several observables are measured in the dielectron mass squared () interval between 0.002 and 1.120. The angular observables and which are related to the polarisation and to the lepton forward-backward asymmetry, are measured to be and , where the first uncertainty is statistical and the second systematic. The angular observables and which are sensitive to the photon polarisation in this range, are found to be and . The results are consistent with Standard Model predictions.An angular analysis of the B â K^{*}^{0} e e decay is performed using a data sample, corresponding to an integrated luminosity of 3.0 fb, collected by the LHCb experiment in pp collisions at centre-of-mass energies of 7 and 8 TeV during 2011 and 2012. For the first time several observables are measured in the dielectron mass squared (q) interval between 0.002 and 1.120 GeV /c. The angular observables F and A which are related to the K^{*}^{0} polarisation and to the lepton forward-backward asymmetry, are measured to be F = 0.16 ± 0.06 ± 0.03 and A â=â0.10â±â0.18â±â0.05, where the first uncertainty is statistical and the second systematic. The angular observables A and A which are sensitive to the photon polarisation in this q range, are found to be A â=âââ0.23â±â0.23â±â0.05 and A â=â0.14â±â0.22â±â0.05. The results are consistent with Standard Model predictions.An angular analysis of the decay is performed using a data sample, corresponding to an integrated luminosity of 3.0 {\mbox{fb}^{-1}}, collected by the LHCb experiment in collisions at centre-of-mass energies of 7 and 8 TeV during 2011 and 2012. For the first time several observables are measured in the dielectron mass squared () interval between 0.002 and 1.120. The angular observables and which are related to the polarisation and to the lepton forward-backward asymmetry, are measured to be and , where the first uncertainty is statistical and the second systematic. The angular observables and which are sensitive to the photon polarisation in this range, are found to be and . The results are consistent with Standard Model predictions
- âŠ