Research Articles (Evolutionary Studies Institute)

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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.
A comparison of hominin teeth from Lincoln Cave Sterkfontein L63 and Dinaledi Chamber South Africa
(Academy of Science of South Africa, 2019-05) Brophy, J.K.; Irish, J.; Churchill, S.E.; de Ruiter, D.J.; Hawks, J.; Berger, L.
Prior to the recovery of Homo naledi from the Dinaledi Chamber of the Rising Star Cave system, the Middle Pleistocene fossil record in Africa was particularly sparse. With the large sample size now available from Dinaledi, the opportunity exists to reassess taxonomically ambiguous teeth unearthed at the nearby site of Sterkfontein. Teeth recovered from Lincoln Cave South and area L/63 at Sterkfontein have been considered ‘most probably Homo ergaster’ and ‘perhaps Archaic Homo sapiens’, respectively. Given the similarities shared between Lincoln Cave, area L/63, and the Dinaledi Chamber with regard to climatic/geologic depositional context and age, two teeth from the former sites, StW 592 and StW 585 respectively, were compared with corresponding tooth types of H. naledi from the Dinaledi Chamber. The results of our study indicate that the Lincoln Cave and area L/63 teeth are morphologically inconsistent with the variation recognised in the H. naledi teeth. Significance: • The similar age and climatic/geologic depositional and post-depositional circumstances at Lincoln Cave South, area L/63 at Sterkfontein and the Dinaledi Chamber, Rising Star raise the possibility that these fossils might represent the same species. • The teeth StW 592 and StW 585 are not consistent with the variation evident in the known H. naledisample. • The results of the study do not add to the question of the existence of at least two species of the genus Homo living in close proximity to each other in South Africa at approximately the same time.
Cortical Structure of Hallucal Metatarsals and Locomotor Adaptations in Hominoids
(Public Library of Science, 2015-01-30) Jashashvili, T.; Dowdeswell, M.R.; Lebrun, R.; Carlson, K.J.
Diaphyseal morphology of long bones, in part, reflects in vivo loads experienced during the lifetime of an individual. The first metatarsal, as a cornerstone structure of the foot, presumably expresses diaphyseal morphology that reflects loading history of the foot during stance phase of gait. Human feet differ substantially from those of other apes in terms of loading histories when comparing the path of the center of pressure during stance phase, which reflects different weight transfer mechanisms. Here we use a novel approach for quantifying continuous thickness and cross-sectional geometric properties of long bones in order to test explicit hypotheses about loading histories and diaphyseal structure of adult chimpanzee, gorilla, and human first metatarsals. For each hallucal metatarsal, 17 cross sections were extracted at regularly-spaced intervals (2.5% length) between 25% and 65% length. Cortical thickness in cross sections was measured in one degree radially-arranged increments, while second moments of area were measured about neutral axes also in one degree radially-arranged increments. Standardized thicknesses and second moments of area were visualized using false color maps, while penalized discriminant analyses were used to evaluate quantitative species differences. Humans systematically exhibit the thinnest diaphyseal cortices, yet the greatest diaphyseal rigidities, particularly in dorsoplantar regions. Shifts in orientation of maximum second moments of area along the diaphysis also distinguish human hallucal metatarsals from those of chimpanzees and gorillas. Diaphyseal structure reflects different loading regimes, often in predictable ways, with human versus non-human differences probably resulting both from the use of arboreal substrates by non-human apes and by differing spatial relationships between hallux position and orientation of the substrate reaction resultant during stance. The novel morphological approach employed in this study offers the potential for transformative insights into form-function relationships in additional long bones, including those of extinct organisms (e.g., fossils).
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).
A decorated raven bone from the Zaskalnaya VI (Kolosovskaya) Neanderthal site, Crimea
(Public Library of Science, 2017-03) Majkic, A.; Evans, S.; Stepanchuk, V.; Tsvelykh, A.; D'Errico, F.
We analyze a radius bone fragment of a raven (Corvus corax) from Zaskalnaya VI rock shelter, Crimea. The object bears seven notches and comes from an archaeological level attributed to a Micoquian industry dated to between 38 and 43 cal kyr BP. Our study aims to examine the degree of regularity and intentionality of this set of notches through their technological and morphometric analysis, complemented by comparative experimental work. Microscopic analysis of the notches indicate that they were produced by the to-and-fro movement of a lithic cutting edge and that two notches were added to fill in the gap left between previously cut notches, probably to increase the visual consistency of the pattern. Multivariate analysis of morphometric data recorded on the archaeological notches and sets of notches cut by nine modern experimenters on radii of domestic turkeys shows that the variations recorded on the Zaskalnaya set are comparable to experimental sets made with the aim of producing similar, parallel, equidistant notches. Identification of the Weber Fraction, the constant that accounts for error in human perception, for equidistant notches cut on bone rods and its application to the Zaskalnaya set of notches and thirty-six sets of notches incised on seventeen Upper Palaeolithic bone objects from seven sites indicate that the Zaskalnaya set falls within the range of variation of regularly spaced experimental and Upper Palaeolithic sets of notches. This suggests that even if the production of the notches may have had a utilitarian reason the notches were made with the goal of producing a visually consistent pattern. This object represents the first instance of a bird bone from a Neanderthal site bearing modifications that cannot be explained as the result of butchery activities and for which a symbolic argument can be built on direct rather than circumstantial evidence.
Dental microwear differences between eastern and southern African fossil bovids and hominins.
(Academy of Science of South Africa (ASSAf), 2016-03) Ungar, P.S.; Scott, J.R.; Steininger, C.M.
Dental microwear has proven to be a valuable tool for reconstructing diets of fossil vertebrates. However, recent studies have suggested that the pattern of microscopic scratches and pits on teeth may be more reflective of environmental grit than of food preferences. Could differences in dental microwear between early hominins, for example, therefore be a result of dust level rather than of diet? We investigated this possibility using a palaeocommunity approach. We compared microwear texture differences between eastern and southern African Hominini, along with Plio-Pleistocene specimens representing two tribes of bovids, Alcelaphini and Antilopini, from the same deposits as the early hominins. If exogenous grit swamps diet signals, we would expect community-wide microwear patterns separating samples by region. Results indicate that each of the three tribes shows a different pattern of variation of microwear textures between eastern and southern Africa. These results imply that differences in microwear reflect diet rather than grit load, and that microwear can provide valuable information not just about environmental dust level, but about food preferences of fossil vertebrates.
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.
Earliest hominin cancer: 1.7-million-year- old osteosarcoma from Swartkrans Cave, South Africa
(Academy of Science of South Africa (ASSAf), 2016-07) Odes, E.J.; Randolph-Quinney, P.S.; Steyn, M.; Thockmorton, Z.; Smilg, J.S.; Zipfel, B.; Augustine, T.N.; de Beer, F.; Hoffman, J.W.; Franklin, R.D.; Berger, L.R.
The reported incidence of neoplasia in the extinct human lineage is rare, with only a few confirmed cases of Middle or Later Pleistocene dates reported. It has generally been assumed that premodern incidence of neoplastic disease of any kind is rare and limited to benign conditions, but new fossil evidence suggests otherwise. We here present the earliest identifiable case of malignant neoplastic disease from an early human ancestor dated to 1.8–1.6 million years old. The diagnosis has been made possible only by advances in 3D imaging methods as diagnostic aids. We present a case report based on re-analysis of a hominin metatarsal specimen (SK 7923) from the cave site of Swartkrans in the Cradle of Humankind, South Africa. The expression of malignant osteosarcoma in the Swartkrans specimen indicates that whilst the upsurge in malignancy incidence is correlated with modern lifestyles, there is no reason to suspect that primary bone tumours would have been any less frequent in ancient specimens. Such tumours are not related to lifestyle and often occur in younger individuals. As such, malignancy has a considerable antiquity in the fossil record, as evidenced by this specimen.
An early instance of upper palaeolithic personal ornamentation from China: The freshwater shell bead from Shuidonggou 2.
(Public Library of Science, 2016-05) Wei, Y.; D'Errico, F.; Vanhaeren, M.; Li, F.; Gao, X.
We report the discovery and present a detailed analysis of a freshwater bivalve from Shuidonggou Locality 2, layer CL3. This layer is located c. 40 cm below layer CL2, which has yielded numerous ostrich eggshell beads. The shell is identified as the valve of a Corbicula fluminea. Data on the occurrence of this species in the Shuidonggou region during Marine Isotope Stage 3 and taphonomic analysis, conducted in the framework of this study, of a modern biocoenosis and thanatocoenosis suggest that the archeological specimen was collected at one of the numerous fossil or sub-fossil outcrops where valves of this species were available at the time of occupation of level CL3. Experimental grinding and microscopic analysis of modern shells of the same species indicate that the Shuidonggou shell was most probably ground on coarse sandstone to open a hole on its umbo, attach a thread, and use the valve as a personal ornament. Experimental engraving of freshwater shells and microscopic analysis identify an incision crossing the archaeological valve outer surface as possible deliberate engraving. Reappraisal of the site chronology in the light of available radiocarbon evidence suggests an age of at least 34-33 cal kyr BP for layer CL3. Such estimate makes the C. fluminea recovered from CL3 one of the earliest instances of personal ornamentation and the earliest example of a shell bead from China.
A hominin first rib discovered at the Sterkfontein Caves, South Africa.
(Academy of Science of South Africa (ASSAf), 2016-05) Tawane, G.; Garcia-Martinez, D.; Eyre, J.; Bastir, M.; Berger, L.R.; Schmid, P.; Nalla, S.; Williams, S.A.
First ribs - the first or most superior ribs in the thorax - are rare in the hominin fossil record, and when found, have the potential to provide information regarding the upper thorax shape of extinct hominins. Here, we describe a partial first rib from Member 4 of the Sterkfontein Caves, South Africa. The rib shaft is broken away, so only the head and neck are preserved. The rib is small, falling closest to small-bodied Australopithecus first ribs (AL 288-1 and MH1). Given that it was recovered near the StW 318 femur excavation, which also represents a small individual, we suggest that the two may be associated. Three-dimensional geometric morphometric analyses were used to quantify the rib fragment morphology and compare it to extant hominoid and other fossil hominin ribs. While only the proximal end is preserved, our analyses show that South African Australopithecus share derived features of the proximal first rib more closely resembling A. afarensis and later hominins than great apes.
Homo naledi and Pleistocene hominin evolution in subequatorial Africa
(eLife Sciences Publications Ltd, 2017-05) Berger, L.R.; Hawks, J.; Dirks, P.H.G.M.; Elliott, M.; Roberts, E.M.
New discoveries and dating of fossil remains from the Rising Star cave system, Cradle of Humankind, South Africa, have strong implications for our understanding of Pleistocene human evolution in Africa. Direct dating of Homo naledi fossils from the Dinaledi Chamber (Berger et al., 2015) shows that they were deposited between about 236 ka and 335 ka (Dirks et al., 2017), placing H. naledi in the later Middle Pleistocene. Hawks and colleagues (Hawks et al., 2017) report the discovery of a second chamber within the Rising Star system (Dirks et al., 2015) that contains H. naledi remains. Previously, only large-brained modern humans or their close relatives had been demonstrated to exist at this late time in Africa, but the fossil evidence for any hominins in subequatorial Africa was very sparse. It is now evident that a diversity of hominin lineages existed in this region, with some divergent lineages contributing DNA to living humans and at least H. naledi representing a survivor from the earliest stages of diversification within Homo. The existence of a diverse array of hominins in subequatorial comports with our present knowledge of diversity across other savanna-adapted species, as well as with palaeoclimate and paleoenvironmental data. H. naledi casts the fossil and archaeological records into a new light, as we cannot exclude that this lineage was responsible for the production of Acheulean or Middle Stone Age tool industries.
A multi-disciplinary review of late Quaternary palaeoclimates and environments for Lesotho
(2016-07) Fitchett, J.M.; Grab, S.W; Bamford, M.K.; Mackay, A.W.
Lesotho provides a unique context for palaeoclimatic research. The small country is entirely landlocked by South Africa, yet has considerable variation in topography, climate, and associated vegetation over an approximate east–west transect. The region has been of archaeological interest for over a century, and hosts many Early to Late Stone Age sites with occupation preceding 80 000 years before present. The eastern Lesotho highlands are of interest to periglacial and glacial geomorphologists because of their well-preserved relict landforms and contentious evidence for permafrost and niche glaciation during the late Quaternary. However, continuous proxy records for palaeoenvironmental reconstructions for Lesotho are scarce and hampered by a range of methodological shortfalls. These challenges include uncertain ages, poor sampling resolution, and proxies extracted from archaeological excavations for which there may be bias in selection. Inferences on palaeoclimates are thus based predominantly on archaeological and palaeogeomorphological evidence for discrete periods during the late Quaternary. This review paper presents a more detailed multidisciplinary synthesis of late Quaternary conditions in Lesotho. We simultaneously considered the varying data that contribute to the under-studied palaeoenvironmental record for southern Africa. The collective palaeoenvironmental data for eastern Lesotho were shown to be relatively contradictory, with considerable variations in contemporaneous palaeoclimatic conditions within the study area. We argue that although methodological challenges may contribute to this variation, the marked changes in topography result in contrasting late Quaternary palaeoenvironments. Such environments are characterised by similar contrasting microclimates and niche ecologies as are witnessed in the contemporary landscape. These spatial variations within a relatively small landlocked country are of importance in understanding broader southern African palaeoenvironmental change.
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.
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.
Osteogenic tumour in Australopithecus sediba: Earliest hominin evidence for neoplastic disease
(Academy of Science of South Africa (ASSAf)., 2016-07) Randolph-Quinney, P.S.; Williams, S.A.; Steyn, M.; Meyer, M.R.; Smilg, J.S.; Churchill, S.E.; Odes, E.J.; Augustine, T.; Tafforeau, P.; Berger, L.R.
We describe the earliest evidence for neoplastic disease in the hominin lineage. This is reported from the type specimen of the extinct hominin Australopithecus sediba from Malapa, South Africa, dated to 1.98 million years ago. The affected individual was male and developmentally equivalent to a human child of 12 to 13 years of age. A penetrating lytic lesion affected the sixth thoracic vertebra. The lesion was macroscopically evaluated and internally imaged through phase-contrast X-ray synchrotron microtomography. A comprehensive differential diagnosis was undertaken based on gross- and micro-morphology of the lesion, leading to a probable diagnosis of osteoid osteoma. These neoplasms are solitary, benign, osteoid and bone-forming tumours, formed from well-vascularised connective tissue within which there is active production of osteoid and woven bone. Tumours of any kind are rare in archaeological populations, and are all but unknown in the hominin record, highlighting the importance of this discovery. The presence of this disease at Malapa predates the earliest evidence of malignant neoplasia in the hominin fossil record by perhaps 200 000 years.
Patterns of change and continuity in ochre use during the late Middle Stone Age of the Horn of Africa: The Porc-Epic Cave record
(Public Library of Science, 2017-05) Rosso, D. E.; D'Errico, F.; Queffelec, A.
Ochre is found at numerous Middle Stone Age (MSA) sites and plays a key role in early modern human archaeology. Here we analyse the largest known East African MSA ochre assemblage, comprising 40 kg of ochre, found at Porc-Epic Cave, Ethiopia, spanning a period of at least 4,500 years. Visual characterisation of ochre types, microscopic identification of traces of modification, morphological and morphometric analysis of ochre pieces and modified areas, experimental reproduction of grinding processes, surface texture analysis of archaeological and experimentally ground ochre facets, laser granulometry of ochre powder produced experimentally on different grindstones and by Hamar and Ovahimba women from Ethiopia and Namibia respectively, were, for the first time, combined to explore diachronic shifts in ochre processing technology. Our results identify patterns of continuity in ochre acquisition, treatment and use reflecting both persistent use of the same geological resources and similar uses of iron-rich rocks by late MSA Porc-Epic inhabitants. Considering the large amount of ochre processed at the site, this continuity can be interpreted as the expression of a cohesive cultural adaptation, largely shared by all community members and consistently transmitted through time. A gradual shift in preferred processing techniques and motions is interpreted as reflecting cultural drift within this practice. Evidence for the grinding of ochre to produce small quantities of powder throughout the sequence is consistent with a use in symbolic activities for at least part of the ochre assemblage from Porc-Epic Cave.
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.
Putting fossils on the map: Applying a geographical information system to heritage resources
(Academic of Science of South Africa (ASSAf)., 2015-12) Van ver Walt, M.; Cooper, A.K.; Netterberg, I.; Rubidge, B.S.
A geographical information system (GIS) database was compiled of Permo-Triassic tetrapod fossils from the Karoo Supergoup in South African museum collections. This database is the first of its kind and has great time applicability for understanding tetrapod biodiversity change though time more than 200 million years ago. Because the museum catalogues all differed in recorded information and were not compliant with field capture requirements, this information had to be standardised to a format that could be utilised for archival and research application. Our paper focuses on the processes involved in building the GIS project, capturing metadata on fossil collections and formulating future best practices. The result is a multi-layered GIS database of the tetrapod fossil record of the Beaufort Group of South Africa for use as an accurate research tool in palaeo- and geoscience research with applications for ecology, ecosystems, stratigraphy and basin development.
The stable isotope setting of Australopithecus sediba at Malapa, South Africa.
(Academic of Science of South Africa (ASSAf), 2016-07) Holt, E.; Dirks, P.; PLaczek, C.; Berger, L.R.
We report delta C-13 and delta O-18 results from carbonate-cemented cave sediments at Malapa in South Africa. The sediments were deposited during a short-period magnetic reversal at 1.977±0.003 Ma, immediately preceding deposition of Facies D sediments that contain the type fossils of Australopithecus sediba. Values of delta C-13 range between -5.65 and -2.09 with an average of -4.58±0.54% (Vienna Pee Dee Belemnite, VPDB) and values of delta O-18 range between -6.14 and -3.84 with an average of -4.93±0.44% (VPDB). Despite signs of diagenetic alteration from metastable aragonite to calcite, the Malapa isotope values are similar to those obtained in two previous studies in South Africa for the same relative time period. Broadly, the Malapa delta C-13 values provide constraints on the palaeovegetation at Malapa. Because of the complex nature of the carbonate cements and mixed mineralogy in the samples, our estimates of vegetation type (C4-dominant) must be regarded as preliminary only. However, the indication of a mainly C4 landscape is in contrast to the reported diet of A. sediba, and suggests a diverse environment involving both grassland and riparian woodland.

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