The molecular evolution of the spiral-horned antelope (Mammalia: Tragelaphini)

Thesis (MSc)--Stellenbosch University, 2003.ENGLISH ABSTRACT: The evolutionary history of the African tribe Tragelaphini (spiral-horn antelope) is controversial. Past phylogenetic relationships among species were based on morphology or limited fossil evidence and are in conflict with mitochondrial DNA sequencing studies that have been conducted more recently. Although the group is distinguished from other African ungulates by the presence of spirally-twisted horns, the nine recognized extant species differ considerably in morphology, feeding habits and their habitat preference. The present study aims to resolve the phylogenetic uncertainties of the Tragelaphini using nuclear DNA sequence data derived from four independent DNA loci (MGF, PRKCl, SPTBN and THY). These data were combined with all previously published DNA sequences to produce a molecular supermatrix comprising approximately 6000 characters. Both parsimony and model based phylogenetic analyses of the nuclear DNA support the associations resulting from the analysis of mitochondrial genes. These findings suggest that the morphological characters previously used to delimit species within the group are subject to convergent evolution. The molecular phylogeny presented herein suggests that early members of Tragelaphini diverged from the other bovids during the mid-Miocene approximately 15.7 million years before present (MYBP). The common nyala (Tragelaphus enqest; and lesser kudu (Tragelaphus imberbis) representing the most basal species, separated from the other tragelaphids approximately 7.1 MYBP. This was subsequently followed by the radiation of those species adapted to a more tropical environment and they include the mountain nyala (Tragelaphus buxtom), bongo (Tragelaphus euryceros), sitatunga (Tragelaphus spekel) and bushbuck (Tragelaphus scriptus), and the arid adapted clade comprising the giant eland (Taurotragus derbianus), common eland (Taurotragus oryx) and greater kudu (Tragelaphus strepsiceros). It is thought that this split occurred at the Miocene-Pliocene boundary approximately 5.4 MYBP. The timing of evolutionary events within the tribe suggests climatic oscillations and subsequent biotic shifts as the major driving forces underpinning speciation in the tribe Tragalaphini.AFRIKAANSE OPSOMMING; Die evolusionêre geskiedenis van die ras Tragelaphini (spiraalhoringwildsbokke) is kontroversieël. Vorige filogenetiese verwantskappe tussen die spesies is gebaseer op morfologie of beperkte fossiel bewyse. Meer onlangse studies, gebaseer op mitochondriale ONS nukleotieddata, is in teenstryding met baie van die evolusionêre hypotese afkomstig van morfologiese studies. Alhoewel die groep van die ander hoefdiere uitgeken kan word deur die aanwesigheid van spiraalvormige horings, verskil die nege hedendaagse spesies grootliks ten opsigte van morfologie, voedingswyse en habitat. Die hoof doelwit van hierdie studie was om die filogenetise verwantskappe tussen die Tragelaphini spesies te ontleed deur gebruik te maak van nukluêre ONS nukleotieddata afkomstig van vier onafhanklike ONS merkers (MGF, PRKCl, SPTBN en THY). Die data verkry is saamgevoeg by vorige gepubliseerde ONS nukleotidedata om 'n "supermatris" van sowat 6000 karakters te produseer. Parsimonie en modelgebaseerde filogenetise analise van die nukluêre ONS nukleotieddata het ooreengestem met die resultate van vorige mitochondriale studies. Hierdie bevindings dui daarop dat die morfologiese karakters wat voorheen gebruik is om die evolusionêre verwantskappe tussen die Tragelaphini spesies te ontleed onderhewig is aan konvergente evolusie. Die molekulêre filogenie wat hierin beskryf word stel voor dat die ras Tragelaphini gedurende die mid- Miocene, omtrent 15.7 miljoen jaar (MJ) gelede van die ander lede van die subfamilie Bovinae geskei het. Tragelaphus angasi en Tragelaphus imberbis, die mees basale spesies in die filogenie, het omtrent 7.1 MJ gelede van die ander lede van die Tragelaphini geskei. Hierdie skeiding is gevolg deur 'n split tussen die spesies aangepas vir 'n meer tropiese habitat (Tragelaphus buxtoni, Tragelaphus euryceros, Tragelaphus spekei en Tragelaphus scriptus) en die spesies aangepas vir 'n droë habitat (Taurotragus derbianus, Taurotragus oryx en Tragelaphus strepsiceros) Hierdie finale skeiding het gedurende die Miocene-Pliocene oorgang plaasgevind. Die tydsberekening van die evolusionêre gebeurtenisse wat binne die Tragelaphini ras plaasgevind het, gekoppel aan paleoklimaatdata, dui aan dat veranderinge in klimaat en die geassosieerde habitatveranderinge verantwoordelik was vir die spesiasie patroon wat ons vandag in die Tragelaphini ras waarneem

Phylogeography and population genetics of the endemic Malagasy bat, Macronycteris commersoni s.s. (Chiroptera: Hipposideridae)

Macronycteris commersoni (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island and utilizes a range of habitat types including open woodland, degraded habitats, and forested areas from sea level to 1,325 m. Despite being widely distributed, there is evidence that M. commersoni exhibits morphological and bioacoustic variation across its geographical range. We investigated the fine-scale phylogeographic structure of populations in the western half of the island using extensive spatial sampling and sequence data from two mitochondrial DNA regions. Our results indicated several lineages within M. commersoni. Individuals collected from northern Madagascar formed a single monophyletic clade (clade C). A second clade (clade B) included individuals collected from the south-western portion of the island. This second clade displayed more phylogeographical partitioning with differences in mtDNA haplotypes frequency detected between populations collected in different bioclimatic regions. Lineage dispersal, genetic divergence, and timing of expansion events of M. commersoni were probably associated with Pleistocene climate fluctuations. Our data suggest that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene

Metabarcoding of zooplankton to derive indicators of pelagic ecosystem status

Zooplankton play a key role in marine food webs and carbon cycling and are useful indicators of climate-related changes and ocean health in pelagic ecosystems. Zooplankton are traditionally identified to species through microscopy, but new molecular techniques have enabled the identification of individual specimens (DNA barcoding) or multiple species in the same sample (DNA metabarcoding). Metabarcoding has been tested and refined using zooplankton collected in South African waters for the first time. Challenges to the implementation of DNA-based methods to measure zooplankton biodiversity easily and routinely include an incomplete DNA barcode reference library, logistical complexity and uptake of the new technology by environmental management agencies. These challenges call for a national effort to intensify zooplankton barcoding initiatives and to effectively engage stakeholders in developing a roadmap towards application of DNA-based methods in marine environmental management. Significance: Metabarcoding has been successfully applied to marine zooplankton for the first time in South Africa, demonstrating its potential as a tool to generate ecosystem indicators during routine ocean observations. National barcoding efforts must be intensified to provide a comprehensive reference library of zooplankton DNA. Effective engagement with stakeholders is required to overcome logistical and policy challenges, and to provide a roadmap towards application of DNA-based methods in marine environmental management

How to build science-action partnerships for local land-use planning and management: Lessons from Durban, South Africa

The gap between scientific knowledge and implementation in the fields of biodiversity conservation, environmental management, and climate change adaptation has resulted in many calls from practitioners and academics to provide practical solutions responding effectively to the risks and opportunities of global environmental change, e.g., Future Earth. We present a framework to guide the implementation of science-action partnerships based on a real-world case study of a partnership between a local municipality and an academic institution to bridge the science-action gap in the eThekwini Municipal Area, South Africa. This partnership aims to inform the implementation of sustainable land-use planning, biodiversity conservation, environmental management, and climate change adaptation practice and contributes to the development of human capacity in these areas of expertise. Using a transdisciplinary approach, implementation-driven research is being conducted to develop several decision-making products to better inform land-use planning and management. Lessons learned through this partnership are synthesized and presented as a framework of enabling actions operating at different levels, from the individual to the interorganizational. Enabling actions include putting in place enabling organizational preconditions, assembling a functional well-structured team, and actively building interpersonal and individual collaborative capacity. Lessons learned in the case study emphasize the importance of building collaborative capacity and social capital, and paying attention to the process of transdisciplinary research to achieve more tangible science, management, and policy objectives in science-action partnerships. By documenting and reflecting on the process, this case study provides conceptual and practical guidance on bridging the science-action gap through partnerships

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress

The molecular evolution of the spiral-horned antelope (Mammalia: Tragelaphini)

Thesis (MSc)--Stellenbosch University, 2003.ENGLISH ABSTRACT: The evolutionary history of the African tribe Tragelaphini (spiral-horn antelope) is controversial. Past phylogenetic relationships among species were based on morphology or limited fossil evidence and are in conflict with mitochondrial DNA sequencing studies that have been conducted more recently. Although the group is distinguished from other African ungulates by the presence of spirally-twisted horns, the nine recognized extant species differ considerably in morphology, feeding habits and their habitat preference. The present study aims to resolve the phylogenetic uncertainties of the Tragelaphini using nuclear DNA sequence data derived from four independent DNA loci (MGF, PRKCl, SPTBN and THY). These data were combined with all previously published DNA sequences to produce a molecular supermatrix comprising approximately 6000 characters. Both parsimony and model based phylogenetic analyses of the nuclear DNA support the associations resulting from the analysis of mitochondrial genes. These findings suggest that the morphological characters previously used to delimit species within the group are subject to convergent evolution. The molecular phylogeny presented herein suggests that early members of Tragelaphini diverged from the other bovids during the mid-Miocene approximately 15.7 million years before present (MYBP). The common nyala (Tragelaphus enqest; and lesser kudu (Tragelaphus imberbis) representing the most basal species, separated from the other tragelaphids approximately 7.1 MYBP. This was subsequently followed by the radiation of those species adapted to a more tropical environment and they include the mountain nyala (Tragelaphus buxtom), bongo (Tragelaphus euryceros), sitatunga (Tragelaphus spekel) and bushbuck (Tragelaphus scriptus), and the arid adapted clade comprising the giant eland (Taurotragus derbianus), common eland (Taurotragus oryx) and greater kudu (Tragelaphus strepsiceros). It is thought that this split occurred at the Miocene-Pliocene boundary approximately 5.4 MYBP. The timing of evolutionary events within the tribe suggests climatic oscillations and subsequent biotic shifts as the major driving forces underpinning speciation in the tribe Tragalaphini.AFRIKAANSE OPSOMMING; Die evolusionêre geskiedenis van die ras Tragelaphini (spiraalhoringwildsbokke) is kontroversieël. Vorige filogenetiese verwantskappe tussen die spesies is gebaseer op morfologie of beperkte fossiel bewyse. Meer onlangse studies, gebaseer op mitochondriale ONS nukleotieddata, is in teenstryding met baie van die evolusionêre hypotese afkomstig van morfologiese studies. Alhoewel die groep van die ander hoefdiere uitgeken kan word deur die aanwesigheid van spiraalvormige horings, verskil die nege hedendaagse spesies grootliks ten opsigte van morfologie, voedingswyse en habitat. Die hoof doelwit van hierdie studie was om die filogenetise verwantskappe tussen die Tragelaphini spesies te ontleed deur gebruik te maak van nukluêre ONS nukleotieddata afkomstig van vier onafhanklike ONS merkers (MGF, PRKCl, SPTBN en THY). Die data verkry is saamgevoeg by vorige gepubliseerde ONS nukleotidedata om 'n "supermatris" van sowat 6000 karakters te produseer. Parsimonie en modelgebaseerde filogenetise analise van die nukluêre ONS nukleotieddata het ooreengestem met die resultate van vorige mitochondriale studies. Hierdie bevindings dui daarop dat die morfologiese karakters wat voorheen gebruik is om die evolusionêre verwantskappe tussen die Tragelaphini spesies te ontleed onderhewig is aan konvergente evolusie. Die molekulêre filogenie wat hierin beskryf word stel voor dat die ras Tragelaphini gedurende die mid- Miocene, omtrent 15.7 miljoen jaar (MJ) gelede van die ander lede van die subfamilie Bovinae geskei het. Tragelaphus angasi en Tragelaphus imberbis, die mees basale spesies in die filogenie, het omtrent 7.1 MJ gelede van die ander lede van die Tragelaphini geskei. Hierdie skeiding is gevolg deur 'n split tussen die spesies aangepas vir 'n meer tropiese habitat (Tragelaphus buxtoni, Tragelaphus euryceros, Tragelaphus spekei en Tragelaphus scriptus) en die spesies aangepas vir 'n droë habitat (Taurotragus derbianus, Taurotragus oryx en Tragelaphus strepsiceros) Hierdie finale skeiding het gedurende die Miocene-Pliocene oorgang plaasgevind. Die tydsberekening van die evolusionêre gebeurtenisse wat binne die Tragelaphini ras plaasgevind het, gekoppel aan paleoklimaatdata, dui aan dat veranderinge in klimaat en die geassosieerde habitatveranderinge verantwoordelik was vir die spesiasie patroon wat ons vandag in die Tragelaphini ras waarneem

Microsatellite genotypes of South African Cape vulture (Gyps coprotheres)

Multilocus microsatellite genotypes of 605 Gyps coprotheres individuals. This first column contains the individual sample identity as provided in Supplementary Data 1 and subsequent columns are allele scores in single row format. Alleles are scored according to their molecular size (in base pairs); missing data is encoded as "0"