63 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
Evidence of constant diversification punctuated by a mass extinction in the African cycads
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 PlioceneâPleistocene, we argued that the processes might have been climatically mediated
Phylogeny of Iridaceae Subfamily Crocoideae Based on a Combined Multigene Plastid DNA Analysis
The phylogeny of Crocoideae, the largest of four subfamilies currently recognized in Tridaceae, has eluded resolution until sequences of two more plastid DNA regions were added here to a previously published matrix containing sequences from four DNA plastid regions. Sister to the core Nivenioideae, the woody Klattia, Nivenia, and Witsenia, Crocoideae are a climax group in lridaceae, comprising some 995 species, slightly more than half of the total in the family. Synapomorphies of Crocoideae include pollen exine perforate, pollen aperture operculate, ovule campylotropous (or hypotropous), root xylem vessels with simple perforations, cormous rootstock, inflorescence a spike, and plants deciduous. The six DNA region analysis here that includes examples of 27 of the 28 genera of the subfamily shows the southern African Tritoniopsis sister to the remaining genera, which resolve into four well-supported clusters (bootstrap support \u3e85%). Each of these major clades is treated as a tribe, the synapomorphies of which are discussed in light of the molecular phylogenetic analyses. Original embryological and seed developmental studies largely support the tribal classification. Tritoniopsideae alone has the inner floral bracts not forked apically, and a hypotropous ovule, while this tribe and Watsonieae have axillary corm development. The remaining three tribes have apical corm development, and together with Watsonieae have a campylotropous ovule, and the inner layer of the inner integument crushed at maturity
Unveiling South African insect diversity: DNA barcodingâs contribution to biodiversity data
Insects are one of the most species-rich groups on Earth. They comprise much of animal diversity and play vital roles in ecosystems, including pollination, pest control, and decomposition. However, only a fraction of this diversity has been formally described. South Africa is recognised as one of the most biologically diverse countries globally, with an estimated 44 000 insect species. Many crops rely on insect pollinators, including canola, apples, oranges, and sunflowers. A shortage of wild pollinators currently threatens crop yields, yet our knowledge of insect diversity within South Africa is sparse. There are few taxonomic specialists relative to South Africaâs biodiversity, and the methods used for insect identification can be time-consuming and expensive. DNA barcoding provides an important research tool to accelerate insect biodiversity research. In this review, we queried the public DNA barcoding BOLD (Barcode of Life Data System) database for records of âInsectaâ within South Africa, and 416 211 published records assigned to 28 239 unique BINs (Barcode Index Numbers) were returned. We identified five taxonomic orders with more BINs than known species in southern Africa (Hymenoptera, Diptera, Thysanoptera, Plecoptera, and Strepsiptera). Most of the barcoded records were derived from Malaise trap sampling in Gauteng, Mpumalanga and Limpopo, while the rest of South Africa remains poorly sampled. We suggest that there is a need for a comprehensive national sampling effort alongside increased investment in taxonomic expertise to generate critical baseline data on insect biodiversity before species are lost to extinction.
Significance:
Insects provide critical ecosystem services, but our knowledge of insect biodiversity is limited. DNA barcoding can help fill biodiversity knowledge gaps; however, within South Africa, sampling has been uneven. Well-sampled provinces include Gauteng, Mpumalanga and Limpopo, while the Eastern Cape, Free State, KwaZulu-Natal, Northern Cape, North-West and Western Cape remain under-sampled. We argue for a broad national Malaise trapping effort to generate crucial baseline data on insect biodiversity. Without urgent investment in taxonomic expertise and biomonitoring, we risk losing much of our biodiversity before it is even described
Unravelling the evolutionary origins of biogeographic assemblages
AIM : Floristic and faunal diversity fall within species assemblages that can be grouped into distinct biomes or ecoregions. Understanding the origins of such biogeographic assemblages helps illuminate the processes shaping presentâday diversity patterns and identifies regions with unique or distinct histories. While the fossil record is often sparse, dated phylogenies can provide a window into the evolutionary past of these regions. Here, we present a novel phylogenetic approach to investigate the evolutionary origins of presentâday biogeographic assemblages and highlight their conservation value.
LOCATION : Southern Africa.
METHODS : We evaluate the evolutionary turnover separating species clusters in space at different time slices to determine the phylogenetic depth at which the signal for their presentâday structure emerges. We suggest presentâday assemblages with distinct evolutionary histories might represent important units for conservation. We apply our method to the vegetation of southern Africa using a dated phylogeny of the woody flora of the region and explore how the evolutionary history of vegetation types compares to common conservation currencies, including species richness, endemism and threat.
RESULTS : We show the differentiation of most presentâday vegetation types can be traced back to evolutionary splits in the Miocene. The woody flora of the Fynbos is the most evolutionarily distinct, and thus has deeper evolutionary roots, whereas the Savanna and Miombo Woodland show close phylogenetic affinities and likely represent a more recent separation. However, evolutionarily distinct phyloregions do not necessarily capture the most unique phylogenetic diversity, nor are they the most speciesârich or threatened.
MAIN CONCLUSIONS : Our approach complements analyses of the fossil record and serves as a link to the history of diversification, migration and extinction of lineages within biogeographic assemblages that is separate from patterns of species richness and endemism. Our analysis reveals how phyloregions capture conservation value not represented by traditional biodiversity metrics.The Government of Canada through Genome Canada and Ontario Genomics Institute (2008âOGIâICIâ03), International Development Research Centre (IDRC) and University of Johannesburg.http://wileyonlinelibrary.com/journal/ddi2019-03-01hj2018Plant Production and Soil Scienc
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
Bacterial diversity in the waterholes of the Kruger National Park : an eDNA metabarcoding approach
Bacteria are essential components of natural environments. They contribute to ecosystem functioning through roles as mutualists and pathogens for larger species, and as key components of food webs and nutrient cycles. Bacterial communities respond to environmental disturbances, and the tracking of these communities across space and time may serve as indicators of ecosystem health in areas of conservation concern. Recent advances in DNA sequencing of environmental samples allow for rapid and culture-free characterization of bacterial communities. Here we conduct the first metabarcoding survey of bacterial diversity in the waterholes of the Kruger National Park, South Africa. We show that eDNA can be amplified from waterholes and find strongly structured microbial communities, likely reflecting local abiotic conditions, animal ecology, and anthropogenic disturbance. Over timescales from days to weeks we find increased turnover in community composition, indicating bacteria may represent host-associated taxa of large vertebrates visiting the waterholes. Through taxonomic annotation we also identify pathogenic taxa, demonstrating the utility of eDNA metabarcoding for surveillance of infectious diseases. These samples serve as a baseline survey of bacterial diversity in the Kruger National Park, and in the future, spatially distinct microbial communities may be used as markers of ecosystem disturbance, or biotic homogenization across the park.This paper is part of a special issue entitled âTrends in DNA Barcoding and Metabarcodingâ.M.J.F. was supported by a Vanier NSERC CGS and the CIHR Systems Biology Training Program, with project funding supported by the Quebec Centre for Biodiversity Science, the McGill Biology Department, and an NSERC Discovery Grant awarded to T.J.D.http://www.nrcresearchpress.com/journal/genhj2019Paraclinical Science
Biodiversity baselines : tracking insects in Kruger National Park with DNA barcodes
Reflecting their species richness and ecological diversification, insects play a central role in terrestrial ecosystems
but difficulties in species-level assignments have restricted large-scale analysis of their community structure.
Employing South Africaâs largest national park as a model system, we demonstrate that DNA barcoding can break
this barrier. A year-long deployment of Malaise traps at 25 sites in Kruger National Park (KNP) generated 1000+
weekly collections containing about 800,000 specimens. Insect biomass averaged 1.05 g per trap-day but varied
by up to 2-fold between months, being lower in the dry than wet season. Nearly 370,000 specimens were
individually analyzed to reveal 19,730 Barcode Index Numbers (BINs; species proxy), a count equal to 43% of the
known insect fauna of southern Africa. There was clear differentiation in insect richness and composition between KNPâs two ecoregions, but little among the vegetation types comprising them. The spatial gradient in
annual rainfall explained more than half of the variation in compositional similarity among sites with less
similarity among samples in the wet season, particularly among those in high rainfall areas. These results suggest
that the factors organising insect communities in KNP are not fine-scale vegetation differences, but larger-scale
processes associated with ecoregions and rainfall. Estimates of sample coverage indicate that the species not
collected are rare, comprising only 4% of the individuals in the community. With a well-parameterized DNA
barcode reference library in place, metabarcoding can be used to assess future shifts in the insect fauna of KNP
rapidly and inexpensively.http://www.elsevier.com/locate/bioconpm2021Paraclinical Science
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
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