UCT Human Skeletal Repository: Its stewardship, history, composition and educational use.

The University of Cape Town (UCT) Human Skeletal Repository began in 1913 and its composition a century later reflects the history of biological anthropology at the University, in South Africa and internationally. It consists of 1059 skeletons from archaeological (472; 44%), cadaveric (372; 36%) and forensic contexts (160; 14%). They are used for educational and research purposes to provide engaged scholarship and experiential learning for undergraduate and postgraduate students from a variety of disciplines including health professionals. The cadaveric remains help build population specific standards, forensic cases assist to address social and criminal justice, and the archaeological discoveries to preserve African culture and heritage. Overall, the repository provides a distinct contribution to knowledge locally and globally. The new management approach of the repository is presented. Ethical considerations and management policies are discussed. Stewardship of these individuals is facing several challenges and there are areas that continue to require attention. UCT is committed to address past unethical procurement of remains through engaging with the relevant interested and affected parties in restitution and repatriation.

Reconstructing Prehistoric African Population Structure.

We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations. PAPERCLIP.

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.

Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.

Dynamics of Indian Ocean Slavery Revealed through Isotopic Data from the Colonial Era Cobern Street Burial Site, Cape Town, South Africa (1750-1827).

The Dutch East India Company (VOC) intended the Cape of Good Hope to be a refreshment stop for ships travelling between the Netherlands and its eastern colonies. The indigenous Khoisan, however, did not constitute an adequate workforce, therefore the VOC imported slaves from East Africa, Madagascar and Asia to expand the workforce. Cape Town became a cosmopolitan settlement with different categories of people, amongst them a non-European underclass that consisted of slaves, exiles, convicts and free-blacks. This study integrated new strontium isotope data with carbon and nitrogen isotope results from an 18th-19th century burial ground at Cobern Street, Cape Town, to identify non-European forced migrants to the Cape. The aim of the study was to elucidate individual mobility patterns, the age at which the forced migration took place and, if possible, geographical provenance. Using three proxies, 87Sr/86Sr, δ13Cdentine and the presence of dental modifications, a majority (54.5%) of the individuals were found to be born non-locally. In addition, the 87Sr/86Sr data suggested that the non-locally born men came from more diverse geographic origins than the migrant women. Possible provenances were suggested for two individuals. These results contribute to an improved understanding of the dynamics of slave trading in the Indian Ocean world.

First ancient mitochondrial human genome from a prepastoralist southern African.

The oldest contemporary human mitochondrial lineages arose in Africa. The earliest divergent extant maternal offshoot, namely haplogroup L0d, is represented by click-speaking forager peoples of southern Africa. Broadly defined as Khoesan, contemporary Khoesan are today largely restricted to the semidesert regions of Namibia and Botswana, whereas archeological, historical, and genetic evidence promotes a once broader southerly dispersal of click-speaking peoples including southward migrating pastoralists and indigenous marine-foragers. No genetic data have been recovered from the indigenous peoples that once sustained life along the southern coastal waters of Africa prepastoral arrival. In this study we generate a complete mitochondrial genome from a 2,330-year-old male skeleton, confirmed through osteological and archeological analysis as practicing a marine-based forager existence. The ancient mtDNA represents a new L0d2c lineage (L0d2c1c) that is today, unlike its Khoe-language based sister-clades (L0d2c1a and L0d2c1b) most closely related to contemporary indigenous San-speakers (specifically Ju). Providing the first genomic evidence that prepastoral Southern African marine foragers carried the earliest diverged maternal modern human lineages, this study emphasizes the significance of Southern African archeological remains in defining early modern human origins.

Trauma and violence in the Later Stone Age of southern Africa.

BACKGROUND: Antemortem and perimortem fractures in skeletons recovered from Later Stone Age burials in southern Africa demonstrate that people were, on occasion, the victims of severe trauma attributable to interpersonal violence. METHODS: Case studies are presented of cranial vault depression fractures on 4 different individuals and a young adult female who had 2 bone arrowheads embedded in the lower vertebrae. These are compared with other cases from the literature. RESULTS: The evidence from the archaeological skeletons suggests that interpersonal violence was a regular occurrence among prehistoric foragers. Additional cases show healed fractures of other bones, but these probably represent injuries from day-to-day activities rather than violent conflict. DISCUSSION: The ethnographic depiction of the San as 'harmless people' is probably inaccurate, or, at best, only representative of the situation in northern Botswana in the 1960s. Damage to the bones indicates that the cause of the trauma was intentional violence. Explanatory models that suggest intense competition between hunter-gatherer groups are probably more accurate than ones that suggest that the groups were non-aggressive. CONCLUSION: Historical references to the San as aggressive and dangerous adversaries may be more accurate than revisionist historians have argued.

Reconstruction of the late Pleistocene human skull from Hofmeyr, South Africa.

Human skeletal remains from sub-Saharan Africa are virtually non-existent for the period when genetic models indicate the first modern human emigration from this region. The skull from Hofmeyr, South Africa, which has been dated to c. 36ka, is one of the only specimens known from this critical part of the late Pleistocene. The Hofmeyr skull was largely intact at the time of its discovery but has suffered post-recovery mishandling, with the resultant loss of most of the lower facial skeleton, the mandibular angle, the right mastoid process, and much of the occipital. Given the potential significance of this specimen, we have undertaken its restoration and reconstruction so as to provide a more complete picture of the cranial morphology of the late Pleistocene population from which it derived. On the basis of photographs, measurements, and morphological description recorded prior to its having been damaged, we reconstructed some of the missing bone in modeling clay on a high resolution plastic cast of the cranium. The original specimen was CT scanned, as was the cast with the reconstructed maxilla and mastoid; these scans were employed in the final computer reconstruction of the skull. Virtual reconstruction of the remainder of the cranium was accomplished using mirror-imaging and reference-based methods, employing 3D geometric morphometrics from a sample of recent human crania to compute coordinate-based estimates of the missing parts. This reconstruction provides a more complete picture of the Hofmeyr cranium and serves as a basis for more comprehensive morphometric comparisons.

Prognostic value of measurements of angiogenesis in serous carcinoma of the ovary.

The study objective was to determine whether tumor vascularity correlates with patient survival, to compare newer semiautomated methods of angiogenesis assessment to older methods, and to determine if advanced image analysis methods can offer useful patient outcome data in serous ovarian cancer. Using the specific endothelial marker CD34, microvessel determinations were quantified in 132 serous ovarian tumors by manual counting at final magnifications of x 200 and x 400 in the most highly vascular areas. Computer-assisted image analysis microvessel counts, endothelial area estimates, and minimum spanning tree (MST) analysis of capillary architecture, which involves assessment of intercapillary distances, were correlated with traditional manual techniques.Manual, semiautomated, and advanced image analysis methods were found to be highly reproducible and express strong correlation with one another. Univariate cyclooxygenase analysis revealed angiogenesis parameters to be highly significant predictors for overall survival (OS) and disease-free survival. Multivariate cyclooxygenase analysis revealed maximum MST (P = 0.009), length MST (P = 0.005), 1 nearest neighbor (P

Morphometric cranial identity of prehistoric Malawians in the light of sub-Saharan African diversity.

Little has been described of the Holocene populations of South-Central Africa, despite the region demonstrating major subsistence shifts relating to dispersals of agriculturalists at least 2,000 years ago. Seven sites with associated human skeletal remains were selected. Hora, Chencherere, Fingura, and Mtuzi represent the Middle Holocene (2,000-5,000 years ago), and Phwadze, Mtemankhokwe, and Nkudzi Bay represent the Late Holocene and the arrival of agriculturalists between 500-2,000 years ago. Focusing on the identity of Hora and Chencherere specimens, two questions were addressed: are the various Holocene Malawians similar to each other, or do they suggest morphological change over time? What modern populations are closest to the prehistoric specimens? The archaeological sample was compared to modern sub-Saharan Africans from four regions, plus a historic Khoi-San foraging group. Factor analyses were performed in order to identify complex patterns of variation in metric traits of the skull. According to the results, prehistoric Malawians showed only slight differences between the Late and Middle Holocene, suggesting a population change without any major discontinuity. Later Stone Age skulls did not exclusively show similarities with the Khoi-San, as they frequently fit well within the variation of modern Bantu-speaking groups, especially West-Central Africa. Therefore, we reject the hypothesis that Middle Holocene South-Central Africans have an exclusively Khoi-San ancestry, and support an alternative hypothesis that both Middle and Late Holocene groups share a common biological heritage originating in West-Central Africa in earlier times.