Phylogeny and phylogeography of the Chacma Baboon (Papio ursinus): the role of landscape in shaping contemporary genetic structure in the southern African baboon

Includes abstract.Includes bibliographical references (leaves 146-175).This thesis contributes to our understanding of the role of climate and landscape change in structuring diversity within chacma baboons (Papio ursinus). The data set comprises molecular sequences from two mitochondrial DNA markers: the Brown region and the hypervariable D-loop. DNA was extracted from faecal samples of 261 free living chacma baboons across southern Africa. Phylogenetic and phylogeographic techniques, including coalescent modeling, were used to examine past and present population dynamics of chacma baboon populations. Bayesian tree constructions provide a timeline of diversification for the sample. Although the ecological drivers of ongoing differentiation remain unclear, it was shown that population contractions and expansions have also played a significant role in driving regional genetic structure within the species

Applying systems principles to achieve greater integration of student support at a decentralised institution

The role of student support in enabling successful student outcomes is widely acknowledged. However, student support functions and the structures within which they reside often emerge independently at universities, and are seldom designed with integration in mind, leading to systemic inefficiencies. This paper draws on systems thinking to develop a framework to guide the assessment and improvement of student support. Following an exploratory case study design, we collected data on staff and student perceptions of student support by conducting semi-structured interviews and a focus group in a single faculty within a South African university. These data are analyzed alongside several documents produced by the faculty that refer to, and are part of, student support. We map four student support functions used by students within the faculty. These are: orientation, student advising, peer mentoring, and career advising. The analyses reveal that student support in the faculty does not constitute an integrated system and that this creates challenges in communication, continuity and efficiency of student support within the faculty. This paper argues that by adapting existing support structures to closer approximate an integrated system we can increase the efficiency of student support without the need for complete redesign or a significant increase in resources or staff capacity

Student sense of belonging and its impacts on help seeking behaviour

Entering higher education can be an alienating experience leading to institutional and systemic drop out. Academic help-seeking behaviour as a self-regulated learning strategy is one way to counteract this. But help-seeking can be enabled or hindered by several factors including a student’s sense of belonging. In this study we attempted to understand how issues of belonging impact on student help-seeking behaviour and, if they are positively related, how institutions of higher education might promote a greater sense of belonging. We collected a total of 818 student submissions from students in an academic recovery programme. Our thematic analysis of these submissions revealed that students did feel a lack of belonging leading to help-seeking hesitancy. We also captured students’ voices to understand what conditions would enable a greater sense of belonging and we make recommendations on how institutions may work to create these conditions for students and thereby empower their help-seeking behaviour

Pleistocene aridification cycles shaped the contemporary genetic architecture of southern african baboons

Plio-Pleistocene environmental change influenced the evolutionary history of many animal lineages in Africa, highlighting key roles for both climate and tectonics in the evolution of Africa’s faunal diversity. Here, we explore diversification in the southern African chacma baboon Papio ursinus sensu lato and reveal a dominant role for increasingly arid landscapes during past glacial cycles in shaping contemporary genetic structure. Recent work on baboons ( Papio spp.) supports complex lineage structuring with a dominant pulse of diversification occurring 1-2Ma, and yet the link to palaeoenvironmental change remains largely untested. Phylogeographic reconstruction based on mitochondrial DNA sequence data supports a scenario where chacma baboon populations were likely restricted to refugia during periods of regional cooling and drying through the Late Pleistocene. The two lineages of chacma baboon, ursinus and griseipes , are strongly geographically structured, and demographic reconstruction together with spatial analysis of genetic variation point to possible climate-driven isolating events where baboons may have retreated to more optimum conditions during cooler, drier periods. Our analysis highlights a period of continuous population growth beginning in the Middle to Late Pleistocene in both the ursinus and the PG2 griseipes lineages. All three clades identified in the study then enter a state of declining population size (Ne f ) through to the Holocene; this is particularly marked in the last 20,000 years, most likely coincident with the Last Glacial Maximum. The pattern recovered here conforms to expectations based on the dynamic regional climate trends in southern Africa through the Pleistocene and provides further support for complex patterns of diversification in the region’s biodiversity

Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

The use of fossil evidence to calibrate divergence time estimation has a long history. More recently Bayesian MCMC has become the dominant method of divergence time estimation and fossil evidence has been re-interpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called "soft calibrations" have become widely used but the statistical properties of calibrated tree priors in a Bayesian setting has not been carefully investigated. Here we clarify that calibration densities, such as those defined in BEAST 1.5, do not represent the marginal prior distribution of the calibration node. We illustrate this with a number of analytical results on small trees. We also describe an alternative construction for a calibrated Yule prior on trees that allows direct specification of the marginal prior distribution of the calibrated divergence time, with or without the restriction of monophyly. This method requires the computation of the Yule prior conditional on the height of the divergence being calibrated. Unfortunately, a practical solution for multiple calibrations remains elusive. Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis

Conceptualisation and Early Implementation of an Academic Advising System at the University of Cape Town

AbstractAcademic advising is a High-Impact Practice that supports better outcomes for all students, particularly those encountering structural barriers to success. This paper presents a case study of processes followed in a three-year project (2018–20) at the University of Cape Town (UCT) to conceptualise, design, and start implementing an academic advising system. Three goals were formulated:1. to develop conceptual capacity and a theory of academic advising;2. to develop an academic advising model responsive to institutional context and student need; and3. to develop structures, relationships, tools, and resources to implement a coherent system.An informed grounded theory approach was used to analyse baseline data of existing support and advising at the institution. Data was collected through document and desktop research, interviews with stakeholders, and student focus groups. A monitoring and evaluation framework was developed to track and reflect on progress against the goals. Iterative cycles of data collection, analysis, and reflection took place as implementation started. A key finding was that UCT’s advising structures incline towards a decentralised faculty-based model, complemented by centralised support services that encompass advising functions. Low levels of integration were found, as well as inefficient duplication of services. To address these challenges, the conceptual and operational capacity of the academic advising team needed to be advanced. This was done by assembling a multidisciplinary team, undergoing professional training, and by running a journal club. A promising theoretical approach that emerged was a capability approach to academic advising. A shared model of academic advising was found to be best suited to the institutional context and a three-tiered model operationalised by faculty, professional, and peer advisers, as well as by automated advising tools, was designed. Implementation started through pilot projects. During Covid-19, innovative concept and centralised systems development that connected students to institutional resources, enabling them to practise agency and supporting their ability to achieve despite unprecedented structural barriers, demonstrated the viability of the capability approach adopted for steering further development of the system

Extreme Food-Plant Specialisation in Megabombus Bumblebees as a Product of Long Tongues Combined with Short Nesting Seasons

© 2015 Huang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. http://creativecommons.org/licenses/by/4.0/ The attached file is the published version of the article

SIVagm Infection in Wild African Green Monkeys from South Africa: Epidemiology, Natural History, and Evolutionary Considerations

Pathogenesis studies of SIV infection have not been performed to date in wild monkeys due to difficulty in collecting and storing samples on site and the lack of analytical reagents covering the extensive SIV diversity. We performed a large scale study of molecular epidemiology and natural history of SIVagm infection in 225 free-ranging AGMs from multiple locations in South Africa. SIV prevalence (established by sequencing pol, env, and gag) varied dramatically between infant/juvenile (7%) and adult animals (68%) (p<0.0001), and between adult females (78%) and males (57%). Phylogenetic analyses revealed an extensive genetic diversity, including frequent recombination events. Some AGMs harbored epidemiologically linked viruses. Viruses infecting AGMs in the Free State, which are separated from those on the coastal side by the Drakensberg Mountains, formed a separate cluster in the phylogenetic trees; this observation supports a long standing presence of SIV in AGMs, at least from the time of their speciation to their Plio-Pleistocene migration. Specific primers/probes were synthesized based on the pol sequence data and viral loads (VLs) were quantified. VLs were of 104-106 RNA copies/ml, in the range of those observed in experimentally-infected monkeys, validating the experimental approaches in natural hosts. VLs were significantly higher (107-108 RNA copies/ml) in 10 AGMs diagnosed as acutely infected based on SIV seronegativity (Fiebig II), which suggests a very active transmission of SIVagm in the wild. Neither cytokine levels (as biomarkers of immune activation) nor sCD14 levels (a biomarker of microbial translocation) were different between SIV-infected and SIV-uninfected monkeys. This complex algorithm combining sequencing and phylogeny, VL quantification, serology, and testing of surrogate markers of microbial translocation and immune activation permits a systematic investigation of the epidemiology, viral diversity and natural history of SIV infection in wild African natural hosts. © 2013 Ma et al

Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa

Background: Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa. Results: We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensifcation of the cold Benguela current, which caused western aridifcation and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fuctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by diferent climatic parameters, and that the niches difered substantially among the clades of the northern group but were similar among clades of the southern group. Conclusion: Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-

Seeing our world through science

We live in a time of exciting discoveries and developments in the field of science, allowing us to 'see' more than ever before, including 'seeing' into the past, the present and the future. For anyone who wants to learn more about seeing our world through science