Research Outputs (School of Geosciences)

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3D techniques and fossil identification: An elephant shrew hemi-mandible from the Malapa site.
(Academy of Science of South Africa (ASSAf), 2011-11-07) Val, A.; Carlson, K.J; Kibii, J.M.; Steininger, C.; Churms, C.; Kuhn, B.F.; Berger, L.R.
Conventional methods for extracting fossilised bones from calcified clastic sediments, using air drills or chemical preparations, can damage specimens to the point of rendering them unidentifiable. As an alternative, we tested an in silico approach that extended preparation and identification possibilities beyond those realisable using physical methods, ultimately proving to be crucial in identifying a fragile fossil. Image data from a matrix-encased hemi-mandible of a micromammal that was collected from the Plio-Pleistocene site of Malapa, Cradle of Humankind, South Africa, were acquired using microtomography. From the resultant images, a 3D rendering of the fossil was digitally segmented. Diagnostic morphologies were evaluated on the rendering for comparison with extant comparative specimens, positively identifying the specimen as an elephant shrew (Elephantulus sp.). This specimen is the first positively identified micromammal in the Malapa faunal assemblage. Cutting-edge in silico preparation technology provides a novel tool for identifying fossils without endangering bone integrity, as is commonly risked with physical preparation.
An Acheulean handaxe from Gladysvale Cave site, Gauteng, South Africa.
(Academy of Science of South Africa (ASSAf), 2006-03) Hall, G.; Pickering, R.; Lacruz, R.; Hancox, J.; Berger, L.R.; Schmid, P.
WE DESCRIBE A SINGLE HANDAXE FROM fossiliferous breccias at Gladysvale Cave, South Africa. The artefact is the only known tool so far discovered during the controlled excavations conducted at this site over the last decade, and was recovered from decalcified sediments near the stratigraphic interface of two breccia units, making it difficult to assign it with confidence to either. The morphology of the handaxe indicates a middle-late Acheulean industry, and preliminary electron spin resonance and palaeomagnetic dating suggest an age of greater than 780 000 years.
Archaean zircons in Miocene oceanic hotspot rocks establish ancient continental crust beneath Mauritius
(Nature Publishing Group, 2017-01) Ashwal, L.D.; Wiedenbeck, M.; Torsvik, T.H.
A fragment of continental crust has been postulated to underlie the young plume-related lavas of the Indian Ocean island of Mauritius based on the recovery of Proterozoic zircons from basaltic beach sands. Here we document the first U-Pb zircon ages recovered directly from 5.7 Ma Mauritian trachytic rocks. We identified concordant Archaean xenocrystic zircons ranging in age between 2.5 and 3.0 Ga within a trachyte plug that crosscuts Older Series plume-related basalts of Mauritius. Our results demonstrate the existence of ancient continental crust beneath Mauritius; based on the entire spectrum of U-Pb ages for old Mauritian zircons, we demonstrate that this ancient crust is of central-east Madagascar affinity, which is presently located ∼700 km west of Mauritius. This makes possible a detailed reconstruction of Mauritius and other Mauritian continental fragments, which once formed part of the ancient nucleus of Madagascar and southern India.
Arrested development-A comparative analysis of multilayer corona textures in high-grade metamorphic rocks
(European Geosciences Union (EGU), 2017-02) Ogilvie, P.; Gibson, R.L.
Coronas, including symplectites, provide vital clues to the presence of arrested reaction and preservation of partial equilibrium in metamorphic and igneous rocks. Compositional zonation across such coronas is common, indicating the persistence of chemical potential gradients and incomplete equilibration. Major controls on corona mineralogy include prevailing pressure (P), temperature (T ) and water activity (aH2O) during formation, reaction duration (t ) single-stage or sequential corona layer growth; reactant bulk compositions (X) and the extent of metasomatic exchange with the surrounding rock; relative diffusion rates for major components; and/or contemporaneous deformation and strain. High-variance local equilibria in a corona and disequilibrium across the corona as a whole preclude the application of conventional thermobarometry when determining P-T conditions of corona formation, and zonation in phase composition across a corona should not be interpreted as a record of discrete P-T conditions during successive layer growth along the P-T path. Rather, the local equilibria between mineral pairs in corona layers more likely reflect compositional partitioning of the corona domain during steadystate growth at constant P and T . Corona formation in pelitic and mafic rocks requires relatively dry, residual bulk rock compositions. Since most melt is lost along the high-T prograde to peak segment of the P-T path, only a small fraction of melt is generally retained in the residual post-peak assemblage. Reduced melt volumes with cooling limit length scales of diffusion to the extent that diffusion-controlled corona growth occurs. On the prograde path, the low melt (or melt-absent) volumes required for diffusion-controlled corona growth are only commonly realized in mafic igneous rocks, owing to their intrinsic anhydrous bulk composition, and in dry, residual pelitic compositions that have lost melt in an earlier metamorphic event. Experimental work characterizing rate-limiting reaction mechanisms and their petrogenetic signatures in increasingly complex, higher-variance systems has facilitated the refinement of chemical fractionation and partial equilibration diffusion models necessary to more fully understand corona development. Through the application of quantitative physical diffusion models of coronas coupled with phase equilibria modelling utilizing calculated chemical potential gradients, it is possible to model the evolution of a corona through P-T-X-t space by continuous, steady-state and/or sequential, episodic reaction mechanisms. Most coronas in granulites form through a combination of these endmember reaction mechanisms, each characterized by distinct textural and chemical potential signatures with very different petrogenetic implications. An understanding of the inherent petrogenetic limitations of a reaction mechanism model is critical if an appropriate interpretation of P-T evolution is to be inferred from a corona. Since corona modelling employing calculated chemical potential gradients assumes nothing about the sequence in which the layers form and is directly constrained by phase compositional variation within a layer, it allows far more nuanced and robust understanding of corona evolution and its implications for the path of a rock in P-T-X space.
Comments on 'the age of fossil stw573 ('little foot'): An alternative interpretation of 26al/10be burial data'.
(Academy of Science of South Africa (ASSAf), 2017-05) Stratford, D.; Granger, D.E.; Bruxelles, L.; Clarke, R.J.; Kuman, K.; Gibbon, R.J.
No abstract available.
Comparison of Holocene temperature data (Boomplaas Cave) and oxygen isotope data (Cango Caves)
(Academy of Science of South Africa (ASSAf), 2016-05) Thackeray, J.F.
Cranial bosses of choerosaurus dejageri (therapsida, therocephalia): Earliest evidence of cranial display structures in eutheriodonts.
(Public Library of Science, 2016-08) Benoit, J.; Manger, P.R.; Fernandez, V.; Rubidge, B.S.
Choerosaurus dejageri, a non-mammalian eutheriodont therapsid from the South African late Permian (∼259 Ma), has conspicuous hemispheric cranial bosses on the maxilla and the mandible. These bosses, the earliest of this nature in a eutheriodont, potentially make C. dejageri a key species for understanding the evolutionary origins of sexually selective behaviours (intraspecific competition, ritualized sexual and intimidation displays) associated with cranial outgrowths at the root of the clade that eventually led to extant mammals. Comparison with the tapinocephalid dinocephalian Moschops capensis, a therapsid in which head butting is strongly supported, shows that the delicate structure of the cranial bosses and the gracile structure of the skull of Choerosaurus would be more suitable for display and low energy combat than vigorous head butting. Thus, despite the fact that Choerosaurus is represented by only one skull (which makes it impossible to address the question of sexual dimorphism), its cranial bosses are better interpreted as structures involved in intraspecific selection, i.e. low-energy fighting or display. Display structures, such as enlarged canines and cranial bosses, are widespread among basal therapsid clades and are also present in the putative basal therapsid Tetraceratops insignis. This suggests that sexual selection may have played a more important role in the distant origin and evolution of mammals earlier than previously thought. Sexual selection may explain the subsequent independent evolution of cranial outgrowths and pachyostosis in different therapsid lineages (Biarmosuchia, Dinocephalia, Gorgonopsia and Dicynodontia).
Developmental simulation of the adult cranial morphology of australopithecus sediba.
(Academy of Science of South Africa (ASSAf), 2016-07) Carlson, K.B.; De Ruiter, D.J.; Dewitt, T.J.; Mcnuity, K.P.; Tafforeau, P.; Berger, L.R.; Carlson, K.J.
The type specimen of Australopithecus sediba (MH1) is a late juvenile, prompting some commentators to suggest that had it lived to adulthood its morphology would have changed sufficiently so as to render hypotheses regarding its phylogenetic relations suspect. Considering the potentially critical position of this species with regard to the origins of the genus Homo, a deeper understanding of this change is especially vital. As an empirical response to this critique, a developmental simulation of the MH1 cranium was carried out using geometric morphometric techniques to extrapolate adult morphology using extant male and female chimpanzees, gorillas and humans by modelling remaining development. Multivariate comparisons of the simulated adult A. sediba crania with other early hominin taxa indicate that subsequent cranial development primarily reflects development of secondary sexual characteristics and would not likely be substantial enough to alter suggested morphological affinities of A. sediba. This study also illustrates the importance of separating developmental vectors by sex when estimating ontogenetic change. Results of the ontogenetic projections concur with those from mandible morphology, and jointly affirm the taxonomic validity of A. sediba.
Multimodal spatial mapping and visualisation of Dinaledi Chamber and Rising Star Cave.
(Academic of Science of South Africa (ASSAf), 2016-05) Kruger, A.; Randolph-Quinney, P.; Elliot, M.
The Dinaledi Chamber of the Rising Star Cave has yielded 1550 identifiable fossil elements - representing the largest single collection of fossil hominin material found on the African continent to date. The fossil chamber in which Homo naledi was found was accessible only through a near-vertical chute that presented immense practical and methodological limitations on the excavation and recording methods that could be used within the Cave. In response to practical challenges, a multimodal set of recording and survey methods was thus developed and employed: (1) recording of fossils and the excavation process was achieved through the use of white-light photogrammetry and laser scanning; (2) mapping of the Dinaledi Chamber was accomplished by means of high-resolution laser scanning, with scans running from the excavation site to the ground surface and the cave entrance; (3) at ground surface, the integration of conventional surveying techniques as well as photogrammetry with the use of an unmanned aerial vehicle was applied. Point cloud data were used to provide a centralised and common data structure for conversion and to corroborate the influx of different data collection methods and input formats. Data collected with these methods were applied to the excavations, mapping and surveying of the Dinaledi Chamber and the Rising Star Cave. This multimodal approach provides a comprehensive spatial framework from individual bones to landscape level.
A New Centrosaurine Ceratopsid, Machairoceratops cronusi gen et sp. nov., from the Upper Sand Member of the Wahweap Formation (Middle Campanian), Southern Utah
(Public Library of Science, 2016-05) Lund, E.K.; O'Connor, P.M.; Loewen, M.A.; Jinnah, Z.A.
The Upper Cretaceous (middle-late Campanian) Wahweap Formation of southern Utah contains the oldest diagnostic evidence of ceratopsids (to date, all centrosaurines) in North America, with a number of specimens recovered from throughout a unit that spans between 81 and 77 Ma. Only a single specimen has been formally named, Diabloceratops eatoni, from the lower middle member of the formation. Machairoceratops cronusi gen. et sp. nov., a new centrosaurine ceratopsid from the upper member of the Wahweap Formation, is here described based on cranial material representing a single individual recovered from a calcareous mudstone. The specimen consists of two curved and elongate orbital horncores, a left jugal, a nearly complete, slightly deformed braincase, the left squamosal, and a mostly complete parietal ornamented by posteriorly projected, anterodorsally curved, elongate spikes on either side of a midline embayment. The fan-shaped, stepped-squamosal is diagnostic of Centrosaurinae, however, this element differs from the rectangular squamosal in Diabloceratops. Machairoceratops also differs in the possession of two anterodorsally (rather than laterally) curved epiparietal ornamentations on either side of a midline embayment that are distinguished by a posteromedially-oriented sulcus along the entire length of the epiparietal. Additionally, the parietosquamosal frill is lacking any other epiossifications along its periphery. Machairoceratops shares a triangular (rather than round) frill and spikelike epiparietal loci (p1) ornamentation with the stratigraphically lower Diabloceratops. Both parsimony and Bayesian phylogenetic analyses place Machairoceratops as an earlybranching centrosaurine. However, the parsimony-based analysis provides little resolution for the position of the new taxon, placing it in an unresolved polytomy with Diabloceratops. The resultant Bayesian topology yielded better resolution, aligning Machairoceratops as the definitive sister taxon to a clade formed by Diabloceratops and Albertaceratops. Considered together, both phylogenetic methods unequivocally place Machairoceratops as an early-branching centrosaurine, and given the biostratigraphic position of Machairoceratops, these details increase the known ceratopsid diversity from both the Wahweap Formation and the southern portion of Laramidia. Finally, the unique morphology of the parietal ornamentation highlights the evolutionary disparity of frill ornamentation near the base of Centrosaurinae.
New fossil remains of Homo naledi from the Lesedi Chamber, South Africa
(eLife Sciences Publications Ltd, 2017-05) Hawks, J.; Elliott, M.; Schmid, P.; Churchill, S.E.; de Ruiter, D.J.; Roberts, E.M.; Hilbert-Wolf, H.; Garvin, H.M.; Williams, S.A.; Delezene, L.K.; Feuerriegel, E.M.; Randolph-Quinney, P.; Kivell, T.L.; Laird, M.F.; Tawane, G.; DeSilva, J.M.; Bailey, S.E.; Brophy, J.K.; Meyer, M.R.; Skinner, M.M.; Tocheri, M.W.; VanSickle, C.; Walker, C.S.; Campbell, T.L.; Kuhn, B.; Kruger, A.; Tucker, S.; Gurtov, A.; Hlophe, N.; Hunter, R.; Morris, H.; Peixotto, B.; Ramalepa, M.; van Rooyen, D.; Tsikoane, M.; Boshoff, P.; Dirks, P.H.G.M.; Berger, L.R.
The Rising Star cave system has produced abundant fossil hominin remains within the Dinaledi Chamber, representing a minimum of 15 individuals attributed to Homo naledi. Further exploration led to the discovery of hominin material, now comprising 131 hominin specimens, within a second chamber, the Lesedi Chamber. The Lesedi Chamber is far separated from the Dinaledi Chamber within the Rising Star cave system, and represents a second depositional context for hominin remains. In each of three collection areas within the Lesedi Chamber, diagnostic skeletal material allows a clear attribution to H. naledi. Both adult and immature material is present. The hominin remains represent at least three individuals based upon duplication of elements, but more individuals are likely present based upon the spatial context. The most significant specimen is the near-complete cranium of a large individual, designated LES1, with an endocranial volume of approximately 610 ml and associated postcranial remains. The Lesedi Chamber skeletal sample extends our knowledge of the morphology and variation of H. naledi, and evidence of H. naledi from both recovery localities shows a consistent pattern of differentiation from other hominin species.
On the Triggering Mechanisms of Upward Lightning
(Nature Research, 2019-12) Schumann, C.; Saba, M; Warner, T.; Ferro, M.; Helsdon Jr, J.H.; Thomas, R.; Orville, R.E.
Upward lightning studies took place in Rapid City, South Dakota, USA and S. Paulo, Brazil during the summer thunderstorm seasons from 2011 to 2016. One of the main objectives of these campaigns was to evaluate and characterize the triggering of upward positive leaders from tall objects due to preceding nearby flash activity. 110 upward flashes were observed with a combination of high- and standard-speed video and digital still cameras, electric field meters, fast electric-field antenna systems, and for two seasons, a Lightning Mapping Array. These data were analyzed, along with correlated lightning location system data, to determine the triggering flash type responsible for the initiation of upward leaders from towers. In this paper, we describe the various processes during flash activity that can trigger upward leaders from tall objects in the USA and in Brazil. We conclude that the most effective triggering component is the propagation of the in-cloud negative leader during the continuing current that follows a positive return stroke.
Osteopathology and insect traces in the Australopithecus africanus skeleton StW 431
(Academy of Science of South Africa (ASSAf), 2017-01) Zipfel, B.; Jakata, K.; Bonney, H.; Odes, E.J.; Parkinson, A.H.; Randolph-Quinney, P.S.; Berger, L.R.
We present the first application of high-resolution micro computed tomography in an analysis of both the internal and external morphology of the lumbar region of StW 431 - a hominin skeleton recovered from Member 4 infill of the Sterkfontein Caves (South Africa) in 1987. The lumbar vertebrae of the individual present a number of proliferative and erosive bony processes, which were investigated in this study. Investigations suggest a complex history of taphonomic alteration to pre-existing spinal degenerative joint disease (SDJD) as well as post-mortem modification by an unknown insect. This study is in agreement with previous pathological diagnoses of SDJD which affected StW 431 and is the first time insect traces on this hominin are described. The results of this analysis attest to the complex series of post-mortem processes affecting the Sterkfontein site and its fossil assemblages.
Oxygen isotopes suggest elevated thermometabolism within multiple permo-triassic therapsid clades
(eLife Sciences Publications Ltd, 2017-07) Rey, K.; Amiot, R.; Fourel, F.; Abdala, F.; Fluteau, F.; Jalil, N.-E.; Liu, J.; Rubidge, B.S.; Smith, R.M.H.; Steyer, J.S.; Viglietti, P.A.; Wang, X.; Lécuyer, C.
The only true living endothermic vertebrates are birds and mammals, which produce and regulate their internal temperature quite independently from their surroundings. For mammal ancestors, anatomical clues suggest that endothermy originated during the Permian or Triassic. Here we investigate the origin of mammalian thermoregulation by analysing apatite stable oxygen isotope compositions (d18Op) of some of their Permo-Triassic therapsid relatives. Comparing of the d18Op values of therapsid bone and tooth apatites to those of co-existing non-therapsid tetrapods, demonstrates different body temperatures and thermoregulatory strategies. It is proposed that cynodonts and dicynodonts independently acquired constant elevated thermometabolism, respectively within the Eucynodontia and Lystrosauridae + Kannemeyeriiformes clades. We conclude that mammalian endothermy originated in the Epicynodontia during the middle-late Permian. Major global climatic and environmental fluctuations were the most likely selective pressures on the success of such elevated thermometabolism.
Pacific plate motion change caused the Hawaiian-Emperor Bend
(Nature Publishing Group, 2017-06) Torsvik, T.H.; Doubrovine, P. V.; Steinberger, B.; Gaina, C.; Spakman, W.; Domeier, M.
A conspicuous 60° bend of the Hawaiian-Emperor Chain in the north-western Pacific Ocean has variously been interpreted as the result of an abrupt Pacific plate motion change in the Eocene (∼47 Ma), a rapid southward drift of the Hawaiian hotspot before the formation of the bend, or a combination of these two causes. Palaeomagnetic data from the Emperor Seamounts prove ambiguous for constraining the Hawaiian hotspot drift, but mantle flow modelling suggests that the hotspot drifted 4-9° south between 80 and 47 Ma. Here we demonstrate that southward hotspot drift cannot be a sole or dominant mechanism for formation of the Hawaiian-Emperor Bend (HEB). While southward hotspot drift has resulted in more northerly positions of the Emperor Seamounts as they are observed today, formation of the HEB cannot be explained without invoking a prominent change in the direction of Pacific plate motion around 47 Ma.
A partial skull of Paranthropus robustus from Cooper's Cave, South Africa.
(Academy of Science of South Africa (ASSAf), 2008-03) Berger, L.R.; Kuhn, B.F.; Steininger, C.
A partial hominin skull (COB 101) was identified in the fossil collections of the Transvaal Museum, Pretoria, attributed to the Cooper's Cave site in South Africa. The find represents the most complete hominin specimen recovered from localities at this site to date. COB 101 comprises the supraorbital, zygomatic, infraorbital and nasoalveolar regions of the right side, and the right upper third premolar. The specimen has undergone post-depositional distortion that resulted in the flattening of the facial structures. Here we describe and compare COB 101 with other hominin material from Africa and find that this specimen shares numerous diagnostic features with Paranthropus robustus. The discovery of COB 101 augments the number of specimens attributed to this species from other South African sites and other Cooper's Cave localities.
The Piltdown case: Further questions
(Academy of Science of South Africa (ASSAf), 2016-09) Thackeray, J.F.
The possibility of lichen growth on bones of Homo naledi: Were they exposed to light?
(Academy of Science of South Africa (ASSAf), 2016-08) Thackeray, J.F.
Potential for identifying plant-based toxins on San hunter-gatherer arrowheads
(Academy of Science of South Africa (ASSAf), 2017-03) Wooding, M.; Bradfield, J.; Maharaj, V.; Koot, D.; Wadley, L.; Prinsloo, L.; Lombard, M.
The antiquity of the use of hunting poisons has received much attention in recent years. In this paper we present the results of a pilot study designed to detect the presence of organic compounds, typically of less than 1200 Da, from poisonous plants that may have been used as hunting poisons in the past. We used ultra-performance liquid chromatography connected to a Synapt G2 high-resolution MS-QTOF mass spectrometer (UPLC-QTOF-MS) to provisionally identify plant-based toxins present in (1) extracts of fresh plant material, (2) a blind control recipe consisting of three plant ingredients and (3) a Hei||om arrow poison of unknown ingredients. Although not all expected toxic compounds were identified, those that were identified compared favourably with those reported in the literature and confirmed through databases, specifically the Dictionary of Natural Products and ChemSpider. MS/MS fragmentation patterns and accurate mass were used for tentative identification of compounds because archaeological residues usually contain insufficient material for unambiguous identification using nuclear magnetic resonance. We highlight the potential of this method for accurately identifying plant-based toxins present on archaeological artefacts and unique (albeit non-toxic) chemical markers that may allow one to infer the presence of toxic plant ingredients in arrow poisons. Any chemical study of archaeological material should consider the unique environmental degradative factors and be sensitive to the oxidative by-products of toxic compounds.
A probabilistic definition of a species, fuzzy boundaries and 'sigma taxonomy'
(Academy of Science of South Africa (ASSAF)., 2017-05) Schrein, C.M.; Thackeray, J.F.
No abstract available.

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