Juliet K. Brophy

Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa

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. DOI: http://dx.doi.org/10.7554/eLife.09560.001

Faunal assemblage composition and paleoenvironment of Plovers Lake, a Middle Stone Age locality in Gauteng Province, South Africa

Plovers Lake is a dolomitic cave infill located approximately 45km northwest of Johannesburg in the Bloubank Valley, Gauteng Province, South Africa. Excavations between 2002-2004 revealed a rich and diverse fauna, a moderate-sized stone tool assemblage of Middle Stone Age (MSA) character, and human skeletal remains. Two principal depositional units are recognized: 1) a disturbed ex situ component that was likely displaced from 2) an otherwise relatively undisturbed in situ component from which the human skeletal material was recovered. The in situ depositional unit is bracketed by 2 flowstone layers, with U-series dates of 62.9 (+/-1.3)ka for the capping flowstone and 88.7 (+/-1.6)ka for the underlying flowstone. A single isochron ESR date of 75.6 (+/-5.6)ka corroborates the U-series dates. This paper presents an analysis of the mammalian, bird, and reptile faunas recovered from these two units. The two faunal assemblages show close correspondence in taphonomic, taxonomic, and ecological composition, supporting a common origin for both the ex situ and in situ components. Although human skeletal material, cut-marked bone, and stone tools have been recovered, these indications are too rare to consider Plovers Lake a human occupation site. Instead, a high abundance of carnivores, coprolites, and carnivore damaged bones point to brown hyenas as the principal, though not exclusive, bone accumulating agent. In the absence of a significant taphonomic bias relating to accumulating agent, Plovers Lake allows us to document an environment occupied by MSA humans, even if the humans were not resident in the cave itself. We reconstruct the paleoenvironment of Plovers Lake as predominantly grassland, though it was colder, moister, and more wooded than at present. Paleoclimatic conditions appear to have been as different from historic norms as those seen in several fossil localities in the Western Cape, pointing to greater environmental heterogeneity than has previously been documented for the region in the later Pleistocene.

Mandibular Remains Support Taxonomic Validity of Australopithecus sediba

Since the announcement of the species Australopithecus sediba, questions have been raised over whether the Malapa fossils represent a valid taxon or whether inadequate allowance was made for intraspecific variation, in particular with reference to the temporally and geographically proximate species Au. africanus. The morphology of mandibular remains of Au. sediba, including newly recovered material discussed here, shows that it is not merely a late-surviving morph of Au. africanus. Rather—as is seen elsewhere in the cranium, dentition, and postcranial skeleton—these mandibular remains share similarities with other australopiths but can be differentiated from the hypodigm of Au. africanus in both size and shape as well as in their ontogenetic growth trajectory.

New fossil remains of Homo naledi from the Lesedi Chamber, South Africa

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. DOI: http://dx.doi.org/10.7554/eLife.24232.001

Pleistocene Bovidae (Mammalia) from Malapa, Gauteng Province, South Africa

This study presents an analysis of the collection of Bovidae (Mammalia: Artiodactyla) currently available from the Australopithecus sediba-bearing site of Malapa, Gauteng Province, South Africa. The assemblage consists of partially articulated and closely associated skeletal elements. Estimates of ontogenetic age and, when possible, body mass were made based on the postcrania. The bovids are represented by a minimum number of 13 individuals, four of which have been identified below the Tribe level including Makapania broomi, Tragelaphus scriptus, Megalotragus sp., and Antidorcas recki. The sample size of the bovids is small, therefore only a preliminary paleoenvironmental reconstruction is indicated. The paleoenvironment is consistent with reconstructions of nearby sites in the Cradle of Humankind, including a mosaic of grasslands and more extensive woodlands than historically recorded for the area. A permanent water source is also indicated. Taphonomic analysis of the bovid remains demonstrates bone breakage patterns indicative of dry, post depositional fractures. The bones do not exhibit marks particular to a bone accumulating agent. Despite the small sample size, the taphonomic analyses support the reconstruction of Malapa as a vertical death trap. These results suggest that the remains were buried and fossilized in a manner similar to the hominins, supporting a common origin for the hominin and non-hominin fauna ca. 1.977 million years ago. Over a relatively short span of time complete bovid individuals, alongside the individuals of A. sediba, entered the vertical death trap of Malapa, either accidentally or of their own volition, and ultimately became fossilized. Juliet K. Brophy. Department of Geography and Anthropology, Louisiana State University, Baton Rouge, Louisiana and Evolutionary Studies Institute, University of Witwatersrand, Johannesburg, South Africa. jbrophy@lsu.edu Darryl J. de Ruiter. Evolutionary Studies Institute, University of Witwatersrand, Johannesburg, South Africa and Department of Anthropology, Texas A&M University, College Station, Texas. deruiter@tamu.edu Mikael Fortelius. Department of Geosciences and Geography, Institute of Biotechnology; Finnish Museum of Natural History. mikael.fortelius@helsinki.fi Marion Bamford. Evolutionary Studies Institute, University of Witwatersrand, Johannesburg, South Africa. marion.bamford@wits.ac.za Brophy, Juliet K., de Ruiter, Darryl J., Fortelius, Mikael, Bamford, Marion, and Berger, Lee R. 2016. Pleistocene Bovidae (Mammalia) from Malapa, Gauteng Province, South Africa. Palaeontologia Electronica 19.2.16A: 1-22 palaeo-electronica.org/content/2016/1463-bovidae-from-malapa Copyright: Palaeontological Association June 2016 BROPHY: BOVIDAE FROM MALAPA Lee R. Berger. Evolutionary Studies Institute, University of Witwatersrand, Johannesburg, South Africa. profleeberger@yahoo.com

Metric and nonmetric features of the Homo naledi dentition

Leprosy is one of the few specific infectious diseases that can be studied in bioarchaeology due to its characteristic debilitating and disfiguring skeletal changes. Leprosy has been, and continues to be, one of the most socially stigmatising diseases in history, over-riding all other aspects of social identity for the sufferers and frequently resulting in social exclusion. This study examines the stable isotopic evidence of mobility patterns of children, adolescents, and young adult individuals with the lepromatous form of leprosy in Medieval England (10 th –12 th centuries AD) to assess whether the individuals buried with the disease were non-locals, possibly from further afield. Enamel samples from 19 individuals from the St. Mary Magdalen Leprosy Hospital, Winchester (UK) were selected for strontium ( 87 Sr/ 86 6U DQG R[\JHQ į 18 O) stable isotope analysis based on age at death (<30 years), the presence of bone changes associated with lepromatous leprosy, and the underlying geology of their burial locations. The results from these data indicate that the St. Mary Magdalen Leprosy Hospital received an almost equal mixture of local and non-local individuals from further afield, including early pilgrims. At present, the St. Mary Magdalen Leprosy Hospital is the earliest dedicated leprosaria found within Britain and mobility studies such as these can help elucidate and test some of the broader historical notions and identities associated with the movements of those infected with the disease in Medieval England.

A comparison of machine learning techniques for taxonomic classification of teeth from the Family Bovidae

Abstract This study explores the performance of machine learning algorithms on the classification of fossil teeth in the Family Bovidae. Isolated bovid teeth are typically the most common fossils found in southern Africa and they often constitute the basis for paleoenvironmental reconstructions. Taxonomic identification of fossil bovid teeth, however, is often imprecise and subjective. Using modern teeth with known taxons, machine learning algorithms can be trained to classify fossils. Previous work by Brophy et al. [Quantitative morphological analysis of bovid teeth and implications for paleoenvironmental reconstruction of plovers lake, Gauteng Province, South Africa, J. Archaeol. Sci. 41 (2014), pp. 376–388] uses elliptical Fourier analysis of the form (size and shape) of the outline of the occlusal surface of each tooth as features in a linear discriminant analysis (LDA) framework. This manuscript expands on that previous work by exploring how different machine learning approaches classify the teeth and testing which technique is best for classification. In addition to LDA, four other machine learning techniques were considered (neural networks, nuclear penalized multinomial regression,random forests, and support vector machines) with support vector machines and random forests performing the best in terms of log loss and classification rate.

Examining the use of Amazon’s Mechanical Turk for edge extraction of the occlusal surface of fossilized bovid teeth

In order to reconstruct environments associated with Plio-Pleistocene hominins in southern Africa, researchers frequently rely upon the animals associated with the hominins, in particular, animals in the Family Bovidae. Bovids in southern Africa are typically identified by their teeth. However, identifying the taxon of a bovid tooth is challenging due to various biasing factors. Furthermore, inaccurate identification of fossil bovids can have significant consequences on the reconstructed paleoenvironment. Recent research on the classification of bovid fossil teeth has relied on using elliptical Fourier analysis to summarize the shape of the outline of the occlusal surface of the tooth and the resulting harmonic amplitudes. Currently, an expert in the field must manually place landmarks around the edges of each tooth which is slow and time consuming. This study tests whether it is possible to crowdsource this task, while maintaining the necessary level of quality needed to perform a statistical analysis on each tooth. Amazon Mechanical Turk workers place landmarks on the edge of the tooth which is compared to the performance of an expert in the field. The results suggest that crowdsourcing the digitization process is reliable and replicable. With the technical aspects of digitization managed, researchers can concentrate on analyzing and interpreting the data.