Archaeological evidence from the last 8,000 years indicates that early African food-producing societies relied predominantly on livestock, particularly cattle, rather than crops. Cattle have since remained central to economies ranging from sedentary farming to mobile pastoralism across diverse ecosystems. The widespread use and persistence of cattle across Africa likely reflects their admixed ancestry, combining African taurine (Bos taurus), indicine (Bos indicus), and European taurine lineages, which were introduced at different times over the last ~8,000 years. To determine how varied human livelihood patterns and environmental factors affected the geographic distribution of these ancestries, we generated whole-genome sequences from 1,392 African cattle within a combined dataset of ~4,900 genomes, including two ancient genomes, one from Great Zimbabwe (~750 years old) and one from the Western Cape (~280 years old). Using local ancestry inference, we show that taurine and indicine lineages, despite co-existing in the same genomes for over a millennium, have followed markedly different trajectories: taurine ancestry is strongly structured geographically, maintained by sedentary communities under local selection; indicine ancestry is poorly geographically structured which likely reflects dispersal through pastoralist movement; and European taurine heritage is highly localised in South Africa where it is associated with strong selection for beef cattle. Together, these results reframe African cattle as carriers of co-resident lineages, each preserving a distinct record of human subsistence strategy, ecological constraint, and adaptive evolution.

The transition to agriculture was a transformative process in human history with wide-ranging demographic and social consequences1. Across South America, agriculture was adopted at different times and through diverse pathways, resulting in a mosaic of regionally distinct farming histories2,3. The Uspallata Valley, at the southern frontier of Andean farming, offers a unique opportunity to examine a case of late adoption of agriculture. Here we show that agriculture in the Uspallata Valley was adopted by local hunter-gatherers, as evidenced by genetic continuity between pre-farming and farming populations inferred from 46 newly sequenced ancient human genomes. These groups carried a distinct genetic component in Indigenous American diversity, indicating a unique population history in the region. Palaeodietary isotopes (δ13C/δ15N) reveal fluctuating maize intake consistent with flexible farming. Strontium isotopes (87Sr/86Sr) indicate the arrival of migrants from nearby regions between around 810-700 cal years BP, shortly before the Inka expansion. Genomic and isotopic analyses show that these migrants belonged to the same regional metapopulation as local groups, relied heavily on maize, probably moved in matrilineally organized family groups, exhibited stress markers (including malnutrition and diseases, such as tuberculosis, as confirmed by pathogen genomics) and experienced a long-term demographic decline. Our results suggest that these groups used social organization and migration as resilience strategies in the face of a multidimensional crisis.

The isotopic composition of body tissues can provide information about diet and patterns of movement or migration during life. Here, we report δ13C, δ15N and 87Sr/86Sr analyses for a small sample of fauna and for the 12 humans buried at Faraoskop, and make inferences about how these people ranged across the landscape as they hunted and foraged. δ13C and δ15N values for collagen from cortical and cancellous bone and (for two individuals) desiccated muscle tissue are similar, reflecting consumption of isotopically similar, mostly terrestrial foods throughout life. Not all individuals had teeth preserved but for five we were able to measure 87Sr/86Sr in tooth enamel in an earlier- and a later-forming tooth. Where possible, teeth were analysed near the occlusal surface, half-way up the height of the crown and near the dentine/enamel junction, to assess variation during the period of crown formation. Only one of the five (UCT 394) showed significant intra-individual variation in 87Sr/86Sr, between 0.6 and 3.5 years of age. Two individuals yielded enamel 87Sr/86Sr like the geologically recent sediments of the coastal plain to the west of Faraoskop, while three individuals had values intermediate between the coastal plain and the more ancient shales and sandstones of the Table Mountain Group to the east. As young children, people buried at Faraoskop ranged over different areas of the local landscape, probably as part of different social groups.

Strontium isotopes (87Sr/86Sr) are increasingly used as a provenance tool in multiple disciplines. Application to biological materials requires knowledge of the variation in bioavailable 87Sr/86Sr across the landscape, potentially in the form of an isoscape (a quantitative model of spatial isotopic variability). This paper summarizes and provides advice on our current understanding of the main concerns in creating and interpreting isoscapes of bioavailable 87Sr/86Sr. Isoscape creation approaches include domain mapping, geostatistical contour mapping and machine learning, the last becoming more readily achievable with the availability of software packages. It is critically important to develop isoscapes at a resolution appropriate for addressing the research questions. Choice of sample materials depends on the research questions and availability: plants or fauna with small ranges are favoured, with some analytes (snails, soil leachates) posing challenges. Interpreting 87Sr/86Sr in biological tissues requires considering Sr metabolism and the timing of tissue formation, thus far underappreciated. The numerous sources of error involved in developing and applying isoscapes must be recognized to avoid over-interpreting data and spurious provenance precision. We hope this paper will help researchers investigating provenance, mobility, landscape use and migration to develop the most appropriate isoscapes for their purposes, and possible future use by others.

Study Region: Between 2015 and 2017, the Western Cape region of South Africa experienced its worst drought in over 100 years, culminating in a threat to cut off municipal water supply to over 4 million people in the Cape Town municipality. Study Focus: The oxygen and hydrogen isotope composition in groundwater from boreholes, natural springs, and rivers, with the Sr-isotope composition of selected samples. New Hydrological Insights for the Region: The mean and median EC of all groundwater samples are 1624 and 757 mu S/cm (n = 414), respectively. The delta D and delta 18O values of groundwater cluster around the local meteoric water line, which is consistent with aquifers being recharged by local, present-day rainfall. Low EC, and the lack of correlation between EC and isotope composition, is not consistent with seawater infiltration. Where EC is high, it is attributed to dissolution of salt from the sandy substrate. The range in 87Sr/86Sr ratios was 0.7094-0.7311; the lowest 87Sr/86Sr ratios appear dominated by strontium from sea spray or dissolved shells in the substrate, whereas higher 87Sr/86Sr ratios reflect strontium derived from bedrock. Seawater Sr dominates at low altitude in shallow boreholes whereas the component of bedrock Sr dominates at higher altitude and in deeper boreholes. Combined, these data are consistent with rapid recharge of groundwater by ambient rainfall, and groundwater use being sustainable at the current level of abstraction.

This study explores patterning in delta O-18 values of tooth enamel in contemporary African herbivores from mainly C-3-dominated ecosystems. Evapotranspiration causes plants to lose (H2O)-O-16 to a greater extent than (H2O)-O-18, leaving leaves enriched in 18O. In eastern Africa, ES species (evaporation-sensitive species: those obtaining water from food) tend to have more positive delta(18)(Oenamel) values than EI species (evaporation-insensitive species: those heavily dependent on drinking water); the magnitude of the difference increases with increasing aridity. We find the same pattern applies in the winter and year-round rainfall region of southern Africa, allowing us to use delta(18)(Oenamel) in fossil animals to examine paleo-aridity. We apply this approach to infer aridity at Quaternary fossil assemblages from present-day winter and year-round rainfall zones, including Elandsfontein (ca. 1-0.6 Ma), Hoedjiespunt (ca. 300-130 ka), and Nelson Bay Cave (23.5-3 ka). This analysis suggests that (1) at various times during the Pleistocene, Elandsfontein and Hoedjiespunt environments were wetter than last glacial maximum (LGM) to Holocene environments at Nelson Bay Cave (year-round rainfall zone); and (2) considered alongside other evidence from the year-round rainfall zone, wetter conditions across the Pleistocene-Holocene transition at Nelson Bay Cave suggests that climate changes at near-coastal sites may be out of phase with the adjacent interior.

Southern Africa has one of the longest records of fossil hominins and harbours the largest human genetic diversity in the world. Yet, despite its relevance for human origins and spread around the globe, the formation and processes of its gene pool in the past are still largely unknown. Here, we present a time transect of genome-wide sequences from nine individuals recovered from a single site in South Africa, Oakhurst Rockshelter. Spanning the whole Holocene, the ancient DNA of these individuals allows us to reconstruct the demographic trajectories of the indigenous San population and their ancestors during the last 10,000 years. We show that, in contrast to most regions around the world, the population history of southernmost Africa was not characterized by several waves of migration, replacement and admixture but by long-lasting genetic continuity from the early Holocene to the end of the Later Stone Age. Although the advent of pastoralism and farming substantially transformed the gene pool in most parts of southern Africa after 1,300 bp, we demonstrate using allele-frequency and identity-by-descent segment-based methods that the double dagger Khomani San and Karretjiemense from South Africa still show direct signs of relatedness to the Oakhurst hunter-gatherers, a pattern obscured by recent, extensive non-Southern African admixture. Yet, some southern San in South Africa still preserve this ancient, Pleistocene-derived genetic signature, extending the period of genetic continuity until today. Oakhurst rockshelter in South Africa documents marked cultural change during the Holocene, but genome-wide data from ancient human individuals at the site now demonstrate a remarkable degree of genetic continuity over the last 9,000 years: the contemporary double dagger Khomani San and Karretjiemense from South Africa still show direct signs of relatedness to the Oakhurst hunter-gatherers.

This study reports on the bioarchaeology and evidence of interpersonal violence in a group of archaeological skeletons found near Ladismith, Western Cape, South Africa. The co-mingled skeletal remains derive from at least ten individuals of varying ages and both sexes. Overlapping radiocarbon dates on three individuals place them in the first half of the 15th century CE, pre-dating first European contact at the end of that century. Three juvenile crania have perimortem perforations, the locations of which indicate violent deaths. The sizes and shapes of the lesions suggest impact by a blade at least 110mm long and 50mm wide but with edges only 2mm thick. Based on these dimensions, we hypothesise that this was a metal-tipped spear. The nearest metal-working communities at this time lived approximately 500 km away, implying long-distance trade or exchange. δ13C, δ15N and 87Sr/86Sr values indicate that this was a heterogenous group of individuals who had spent their early lives in different locations and consumed varied diets, who had come together and were living in or travelling through the Ladismith area at the time of their deaths. This finding extends the timeframe and location for the practice of communal burial in the Holocene of southern Africa and provides additional support for the hypothesis that communal burials in this region tend to be associated with violence.

This new project studies the diversity of socioecological niches across the agropastoral transition in the Andes, utilising a multi-isotope approach to track human territories and allocate subsistence tasks. During the agropastoral period, we discriminate different diachronic niches with varying extents of maize farming and altitudinal mobility.

In the archaeological quest towards better understanding the precolonial farming communities of South Africa, Bokoni settlements are doubly important. They represent the only 'island' of agricultural intensification in the region. They are also characterised by a wider use of stone in construction than any other such communities. This distinguishing attribute provides us with far greater potential for reconstructing the patterns according to which space was organised in Bokoni, than is possible with other precolonial farming societies. This applies particularly to the larger and more densely built settlements such as Moxomatsi, where intensive use was made of available space. Here we describe the various types of stone-built features and the spatial patterning we can derive from them. Networks of roads and footpaths, together with related features, give us insight into patterns of circulation by people and livestock within the settlement. Circulation routes together with walls, terraces and stone lines contribute to patterns on the ground, which indicate ways in which cultivated land was subdivided and allocated, both adjacent to homesteads and at some distance away. Ways in which groups of homesteads are linked seem to reflect clustering based on kinship, an organisational principle which resonates with ethnographic evidence. Local environmental issues of hydrology, topography, geology, and soils have also played a significant part in how the community made use of the landscape.

OBJECTIVE:To identify, critically analyse and describe severe bilateral skeletal pathology involving the ossa coxae of an individual from historic era Cape Town.MATERIALS:A single individual from the University of Cape Town's Human Skeletal Repository was analysed under research approval (HREC# 035/2021).METHODS:An osteobiography was constructed, radiocarbon dating and isotopic analyses were conducted. Pathological description and contextualised disability analyses followed, along with differential diagnosis. The pelvis and femora were visualised macroscopically and radiographically.RESULTS:This individual was a non-European middle-aged adult male who lived in the 17-18th centuries CE. Morphological changes showed hypoplastic hips with collapsed femoral heads and neoacetabulae. A diagnosis of developmental dysplasia of the hips (DDH) was made. Then a contextualised disability analysis including consideration of the clinical and functional impacts of the condition were applied. No signs of maltreatment, physiological stress or persistent infections were present. His bones were well developed, illustrating mobility and use.CONCLUSIONS:He developed DDH early in life and lived through adulthood, and his strong, healthy bones suggest resilience, some mobility and contribution to society through less physically demanding tasks.SIGNIFICANCE:Value for palaepathological analyses to inform and understand disability and culturally significant health mediation to offer a more objective interpretation and improve understanding of past people. It expands our understanding of the presence of DDH globally and in Africa and provides insight into disease impact for individuals with bilateral expression.SUGGESTIONS FOR FUTURE RESEARCH:Further contextual research is required.LIMITATIONS:Poor scene recovery hindered in-depth care analysis and interpretation of the condition.

We describe a process of restitution of nine unethically acquired human skeletons to their families, together with attempts at redress. Between 1925-1927 C.E., the skeletonised remains of nine San or Khoekhoe people, eight of them known-in-life, were removed from their graves on the farm Kruisrivier, near Sutherland in the Northern Cape Province of South Africa. They were donated to the Anatomy Department at the University of Cape Town. This was done without the knowledge or permission of their families. The donor was a medical student who removed the remains from the labourers' cemetery on his family farm. Nearly 100 years later, the remains are being returned to their community, accompanied by a range of community-driven interdisciplinary historical, archaeological and analytical (osteobiographic, craniofacial, ancient DNA, stable isotope) studies to document, as far as possible, their lives and deaths. The restitution process began by contacting families living in the same area with the same surnames as the deceased. The restitution and redress process prioritises the descendant families' memories, wishes and desire to understand the situation, and learn more about their ancestors. The descendant families have described the process as helping them to reconnect with their ancestors. A richer appreciation of their ancestors' lives, gained in part from scientific analyses, culminating with reburial, is hoped to aid the descendant families and wider community in [re-]connecting with their heritage and culture, and contribute to restorative justice, reconciliation and healing while confronting a traumatic historical moment. While these nine individuals were exhumed as specimens, they will be reburied as people.

The study explores the effects of environmental and climatic variables on the 813C, 815N and 818O values of carnivores from modern C3 dominated environments in South Africa. Stable isotope ratios of carnivores may reflect large-scale environmental patterns better than those of herbivores because carnivores integrate variation seen at lower trophic levels. To explore this further, we have analysed 813C and 815N in bone collagen and 813C and 818O in tooth enamel of 12 species of carnivores obtained mostly from game parks and nature reserves in the winter and year-round rainfall zones of southern Africa. Sampling localities span several vegetation types, with varying rainfall, temperature, etc. We developed regression models for carnivore 813C, 815N and 818O against nine meteorological variables: mean annual precipitation, mean annual temperature, mean annual soil moisture stress, mean annual potential evapotranspiration, relative humidity, summer aridity index, winter concentration of rainfall, moisture index and water deficit. There were significant correlations between 813Cenamel and 813Ccollagen and eight out of nine of the meteorological factors tested; the strongest correlations were with mean annual soil moisture stress (MASMS) (813Cenamel r2(adj) = 0.69 and 813Ccollagen r2(adj) = 0.66). 818Oenamel showed significant correlations with mean annual precipitation, mean annual potential evapotranspiration, summer aridity index, water deficit, relative humidity and the moisture index, but the r2 values were low. 815Ncollagen showed significant correlations with eight out of nine of the meteorological factors (r2 values up to 0.63); only summer aridity index was not significantly correlated). Correlations between consumer 813C values and mete-orological variables were stronger for carnivores than in a previously published study of herbivores from the same region; the opposite pattern was seen in 818O. Carnivore 813C and 815N are therefore effective integrators of environments. Where sample sizes permit, carnivores may be better proxies than herbivores for palae-oenvironmental reconstruction.

Accurate population-specific sex estimation standards do not exist for southern African Holocene San and Khoekhoe populations. Due to markedly small stature, skeletal gracility, and physically active lifestyle, this population exhibits reduced sexual dimorphism, complicating application of standards developed elsewhere. The effectiveness of common sex estimation approaches were assessed and optimized for San and Khoekhoe populations. One-hundred seventy-five adult archaeological San and Khoekhoe skeletons were studied. Sex estimates from seven morphological traits (cranial and mandibular) and six metrical parameters (mandibular, humeral, and femoral) were compared with pelvic (Phenice) sex estimates to assess agreement. Results were analyzed using chi-squared tests, univariate statistics, and cross-validated discriminant function analysis. The effectiveness of individual cranial and mandibular traits varied: The mastoid process and mandibular shape produced the highest agreement rates with pelvic sex estimates (73% and 72%, respectively), while mental eminence and nuchal crest produced the lowest (both 53%). The nuchal crest exhibited a strong sex bias. All mandibular and long-bone metrical parameters were sexually dimorphic; femoral and humeral vertical head diameter (FHD and HVHD) were the most discriminatory. The discriminant function equations showing the highest agreement with pelvic sex estimates were direct multivariate bicondylar breadth, FHD and HVHD (77%), univariate FHD (75%), and stepwise multivariate FHD and HVHD (73%). All variables were sexually dimorphic, but the reduced sexual dimorphism in this population necessitates careful choice of traits. Trait scores considered diagnostic of males and females may require adjustment to improve discriminating power. This study identified the most accurate areas to target for sex estimation and generated the first discriminant functions specific to archaeological San and Khoekhoe people.