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

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

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

Seeing our world through science

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Spatial genetic diversity and population structure in chacma baboons across southern Africa.

<p>(a) Rooted NeighbourNet network for <i>ursinus</i> and <i>griseipes</i> chacma lineages together with <i>Papio cynacephalus</i> and <i>P</i>. <i>kindae</i>. Numerous recent studies based on mtDNA reveal <i>griseipes</i> as sister to these two more northerly species. (b) Bayesian analysis of spatial genetic structure reveals distinct geographic clustering in both lineages. PG1—blue; PG2—green; PU1—red; PU2—yellow; PU3—orange. (c) Landscape plots of genetic diversity across the sampling distributions of the PG (left) and PU (right) clades in southern Africa; the plots are oriented north-south.</p

Map of sampling localities across southern Africa.

<p>Circles indicate the sampling localities used in this study. Orange circles indicate the <i>ursinus</i> mitochondrial lineage, while blue circles indicate the <i>griseipes</i> mitochondrial lineage, following [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123207#pone.0123207.ref033" target="_blank">33</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123207#pone.0123207.ref043" target="_blank">43</a>]. Areas where both lineages were sampled are indicated with both colours. The extent of the Kalahari sand geologic formation is denoted by the yellow line. The Great Escarpment of southern Africa is denoted by the white dashed line. The escarpment edges the central southern African plateau and is a major geological formation in Africa. Digital elevation model (DEM) created with data from the NASA Shuttle Radar Topography Mission; all data are available from public domain sources. Sample details, collection site co-ordinates and clade associations are reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123207#pone.0123207.s002" target="_blank">S1 Table</a>. Numbers on the map follow <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123207#pone.0123207.s002" target="_blank">S1 Table</a>.</p

Diversity descriptors and estimators of demographic change for chacma baboons sampled across southern Africa, based on mtDNA D-loop sequence data.

<p>PU—<i>Papio ursinus</i> clade; PG—<i>Papio griseipes</i> clade.</p><p>Diversity descriptors and estimators of demographic change for chacma baboons sampled across southern Africa, based on mtDNA D-loop sequence data.</p

Bayesian Skyline Plots displaying changes in female effective population size (Ne<i>f</i>) through time in chacma baboons.

<p>Present day is on the left of the x-axis; 95% C.I. are indicated by the dashed lines. Increasing Ne<i>f</i> is observed in both PG2 and PU over the mid to late-Pleistocene, while all three clades reveal declining Ne<i>f</i> through the Holocene to the present day.</p

Chacma baboons photographed across the sampling range of this study.

<p><u>Top left</u>: Adult <i>ursinus</i> male, Augrabies National Park, South Africa (Photo. R. Sithaldeen). <u>Top right</u>: Adult <i>ursinus</i> male, Cape Point, South Africa (Photo. M. Lewis). <u>Bottom left</u>: Adult <i>ursinus</i> female and infant, Cape Point, South Africa (Photo. M. Lewis). <u>Bottom right</u>: Adult <i>griseipes</i> female and infant, Okavango Delta, South Africa (Photo. R. Ackermann).</p