Research Articles (Lee Berger Collection)

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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.
The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa
(eLife Sciences Publications Ltd, 2017-05) Dirks, P.H.G.M.; Roberts, E.M.; Hilbert-Wolf, H.; Kramers, J.D.; Hawks, J.; Dosseto, A.; Duval, M.; Elliott, M.; Evans, M.; Grün, R.; Hellstrom, J.; Herries, A.I.R.; Joannes-Boyau, R.; Makhubela, T.V.; Placzek, C.J.; Robbins, J.; Spandler, C.; Wiersma, J.; Woodhead, J.; Berger, L.R.
New ages for flowstone, sediments and fossil bones from the Dinaledi Chamber are presented. We combined optically stimulated luminescence dating of sediments with U-Th and palaeomagnetic analyses of flowstones to establish that all sediments containing Homo naledi fossils can be allocated to a single stratigraphic entity (sub-unit 3b), interpreted to be deposited between 236 ka and 414 ka. This result has been confirmed independently by dating three H. naledi teeth with combined U-series and electron spin resonance (US-ESR) dating. Two dating scenarios for the fossils were tested by varying the assumed levels of 222Rn loss in the encasing sediments: a maximum age scenario provides an average age for the two least altered fossil teeth of 253 +82/–70 ka, whilst a minimum age scenario yields an average age of 200 +70/–61 ka. We consider the maximum age scenario to more closely reflect conditions in the cave, and therefore, the true age of the fossils. By combining the US-ESR maximum age estimate obtained from the teeth, with the U-Th age for the oldest flowstone overlying Homo naledi fossils, we have constrained the depositional age of Homo naledi to a period between 236 ka and 335 ka. These age results demonstrate that a morphologically primitive hominin, Homo naledi, survived into the later parts of the Pleistocene in Africa, and indicate a much younger age for the Homo naledi fossils than have previously been hypothesized based on their morphology.
Botanical remains from a coprolite from the Pleistocene hominin site of Malapa, Sterkfontein Valley, South Africa
(Bernard Price Institute for Palaeontological Research, University of the Witwatersrand, 2010-12) Bamford, M.K.; Neumann, F.H.; Pereira, L.M.; Scott, L.; Dirks, P.H.G.M.; Berger, L.R.
A coprolite probably from a carnivore described in this paper was recovered from the decalcified sediments of Facies D, close to the cranium of a hominid child, Australopithecus sediba, at Malapa, and is dated at 1.95–1.78 Ma based on a combination of faunal, U-Pb and palaeomagnetic dating techniques. Maceration of the coprolite yielded wood fragments and pollen of Podocarpus sp. as well as phytolith morphotypes that occur in leaves of Podocarpus and many other woody taxa. The Malapa site today is in the Grassland Biome, close to the transition to the Savanna Biome. Podocarpus/Afrocarpus occurs about 30km distance in the Northern Afromontane Forest Biome and is restricted to small patches in the mountain kloofs or small canyons (altitude: 1500–1900 m). The occurrence of this vegetation at Malapa in the past implies that the cooler, moister forest vegetation was more widespread.
Carnivoran remains from the Malapa hominin site, South Africa.
(Public Library of Science, 2011-11-03) Kuhn, B.F.; Werdelin, L.; Hartstone-Rose, A.; Lacruz, R.S.; Berger, L.R.
Recent discoveries at the new hominin-bearing deposits of Malapa, South Africa, have yielded a rich faunal assemblage associated with the newly described hominin taxon Australopithecus sediba. Dating of this deposit using U-Pb and palaeomagnetic methods has provided an age of 1.977 Ma, being one of the most accurately dated, time constrained deposits in the Plio-Pleistocene of southern Africa. To date, 81 carnivoran specimens have been identified at this site including members of the families Canidae, Viverridae, Herpestidae, Hyaenidae and Felidae. Of note is the presence of the extinct taxon Dinofelis cf. D. barlowi that may represent the last appearance date for this species. Extant large carnivores are represented by specimens of leopard (Panthera pardus) and brown hyaena (Parahyaena brunnea). Smaller carnivores are also represented, and include the genera Atilax and Genetta, as well as Vulpes cf. V. chama. Malapa may also represent the first appearance date for Felis nigripes (Black-footed cat). The geochronological age of Malapa and the associated hominin taxa and carnivoran remains provide a window of research into mammalian evolution during a relatively unknown period in South Africa and elsewhere. In particular, the fauna represented at Malapa has the potential to elucidate aspects of the evolution of Dinofelis and may help resolve competing hypotheses about faunal exchange between East and Southern Africa during the late Pliocene or early Pleistocene.
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.
Discovering Hominins - Application of Medical Computed Tomography (CT) to Fossil-Bearing Rocks from the Site of Malapa, South Africa.
(Public Library of Science, 2015-12-18) Smilg, J.S.; Berger, L.R.; Smilg, Jacqueline S.
In the South African context, computed tomography (CT) has been used applied to individually prepared fossils and small rocks containing fossils, but has not been utilized on large breccia blocks as a means of discovering fossils, and particularly fossil hominins. Previous attempts at CT imaging of rocks from other South African sites for this purpose yielded disappointing results. For this study, 109 fossil- bearing rocks from the site of Malapa, South Africa were scanned with medical CT prior to manual preparation. The resultant images were assessed for accuracy of fossil identification and characterization against the standard of manual preparation. The accurate identification of fossils, including those of early hominins, that were not visible on the surface of individual blocks, is shown to be possible. The discovery of unexpected fossils is reduced, thus lowering the potential that fossils could be damaged through accidental encounter during routine preparation, or even entirely missed. This study should significantly change the way fossil discovery, recovery and preparation is done in the South African context and has potential for application in other palaeontological situations. Medical CT imaging is shown to be reliable, readily available, cost effective and accurate in finding fossils within matrix conglomerates. Improvements in CT equipment and in CT image quality are such that medical CT is now a viable imaging modality for this palaeontological application.
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.
Further evidence for eagle predation of, and feeding damage on, the Taung child.
(ASSAf, 2007-11) Berger, L.R.; McGraw, W.S.
We present new evidence supporting the hypothesis that a large raptor was responsible for the death of the c. 2.0-Myr-old Taung child, holotype of the early hominin species Australopithecus africanus. We compare the Taung child's skull with those of monkeys killed and eaten by modern crowned eagles, Stephanoaetus coronatus, in the Ivory Coast's Tai Forest. Close inspection of primate feeding remains from these large, powerful raptors reveals scratch marks in the orbital, frontal, temporal, parietal and occipital regions. Scratches similar in size and distribution are also present on the Taung child's skull. The new taphonomic evidence, combined with previously recognized similarities in breakage patterns and other assemblage characteristics, bolsters the case that a large bird of prey was responsible for the death of the juvenile hominin from Taung.
Geological and taphonomic context for the new hominin species Homo naledi from the Dinaledi Chamber, South Africa.
(eLife Sciences Publications Ltd, 2015-09) Dirks, P.H.G.M.; Berger, L.R.; Roberts, E.M.; Peixotto, B.; Tucker, S.; Kramers, J.D.; Hawks, J.; Randolph-Quinney, P.S.; Elliott, M.; Musiba, C.M.; Churchill, S.; de Ruiter, D.J.; Schmid, P.; Backwell, L.R.; Belyanin, G.A.; Boshoff, P.; Hunter, K.L.; Feuerriegel, E.M.; Gurtov, A.; Harrison, J.G.; Hunter, R.; Kruger, A.; Morris, H.; Makhubela, T.V.
We describe the physical context of the Dinaledi Chamber within the Rising Star cave, South Africa, which contains the fossils of Homo naledi. Approximately 1550 specimens of hominin remains have been recovered from at least 15 individuals, representing a small portion of the total fossil content. Macro-vertebrate fossils are exclusively H. naledi, and occur within clay-rich sediments derived from in situ weathering, and exogenous clay and silt, which entered the chamber through fractures that prevented passage of coarser-grained material. The chamber was always in the dark zone, and not accessible to non-hominins. Bone taphonomy indicates that hominin individuals reached the chamber complete, with disarticulation occurring during/after deposition. Hominins accumulated over time as older laminated mudstone units and sediment along the cave floor were eroded. Preliminary evidence is consistent with deliberate body disposal in a single location, by a hominin species other than Homo sapiens, at an as-yet unknown date.
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.
Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa.
(eLife Sciences Publications Ltd, 2015-09) Berger, L.R.; Hawks, J; de Ruiter, D.J; Wei, P.; Zipfel, B.; Churchill, S.E.; Schmid, P.; Delezene, L.K.; Kivell, T.L.; Garvin, H.M.; Williams, S.A.; DeSilva, J.M.; Skinner, M.M.; Musiba, C.M.; Cameron, N.; Holliday, T.W.; Harcourt-Smith, W.; Ackermann, R.R.; Bastir, M.; Bogin, B.; Bolter, D.; Brophy, J.; Cofran, Z.D.; Congdon, K.A.; Deane, A.S.; Dembo, M.; Drapeau, M.; Elliott, M.C.; Feuerriegel, E.M.; Garcia-Martinez, D.; Green, D.J.; Gurtov, A.; Irish, J.D.; Kruger, A.; Laird, M.F.; Marchi, D.; Meyer, M.R.; Nalla, S.; Negash, E.W.; Orr, C.M.; Radovcic, D.; Schroeder, L.; Scott, J.E.; Throckmorton, Z.; Tocheri, M.W.; VanSickle, C.; Walker, C.S.
Homo naledi is a previously-unknown species of extinct hominin discovered within the Dinaledi Chamber of the Rising Star cave system, Cradle of Humankind, South Africa. This species is characterized by body mass and stature similar to small-bodied human populations but a small endocranial volume similar to australopiths. Cranial morphology of H. naledi is unique, but most similar to early Homo species including Homo erectus, Homo habilis or Homo rudolfensis. While primitive, the dentition is generally small and simple in occlusal morphology. H. naledi has humanlike manipulatory adaptations of the hand and wrist. It also exhibits a humanlike foot and lower limb. These humanlike aspects are contrasted in the postcrania with a more primitive or australopith-like trunk, shoulder, pelvis and proximal femur. Representing at least 15 individuals with most skeletal elements repeated multiple times, this is the largest assemblage of a single species of hominins yet discovered in Africa.
Investigations of a credible report by a US Marine on the missing Peking Fossils.
(Academy of Science of South Africa (ASSAf), 2012-03) Berger, L.R.; Liu, W.; Wu, X.
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.
Papio cranium from the hominin-bearing site of Malapa: Implications for the evolution of modern baboon cranial morphology and South African Plio-Pleistocene biochronology.
(Public Library of Science, 2015-08-19) Gilbert, C.C.; Steininger, C.M.; Kibii, J.M.; Berger, L.R.
A new partial cranium (UW 88-886) of the Plio-Pleistocene baboon Papio angusticeps from Malapa is identified, described and discussed. UW 88-886 represents the only non-hominin primate yet recovered from Malapa and is important both in the context of baboon evolution as well as South African hominin site biochronology. The new specimen may represent the first appearance of modern baboon anatomy and coincides almost perfectly with molecular divergence date estimates for the origin of the modern P. hamadryas radiation. The fact that the Malapa specimen is dated between ~2.026–2.36 million years ago (Ma) also has implications for the biochronology of other South African Plio-Pleistocene sites where P. angusticeps is found.
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.
Response to Thackeray (2016) - the possibility of lichen growth on bones of Homo naledi: Were they exposed to light?
(Academy of Science of South Africa (ASSAf), 2016-09) Randolph-Quinney, P.S.; Backwell, L.R.; Berger, L.R.; Hawks, J.; Dirks, P.H.G.M.; Roberts, E.M.; Nhauro, G.; Kramers, J.
Small-bodied humans from Palau, Micronesia.
(Public Library of Science, 2008-03-12) Berger, L.R.; De Klerk, B.; Quinn, R.L.; Churchill, S.E.
Newly discovered fossil assemblages of small bodied Homo sapiens from Palau, Micronesia possess characters thought to be taxonomically primitive for the genus Homo. Background: Recent surface collection and test excavation in limestone caves in the the rock islands of Palau, Micronesia, has produced a sizeable sample of human skeletal remains dating roughly between 940-2890 cal ybp. Principle Findings: Preliminary analysis indicates that this material is important for two reasons. First, Individuals from the older time horizons are small in body size even relative to "pygmoid" populations from Southeast Asia and Indonesia, and thus may represent a marked case of human insular dwarfism. Second, while possessing a number of derived features that align them with Homo sapiens, the human remains from Palau also exhibit several skeletal traits that are considered to be primitive for the genus Homo. Significance. These features may be previously unrecognized developmental correlates of small body size and, if soo, they may have important implications for interpreting the taxonomic affinities of fossil specimens of Homo.

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