Cultural diffusion was the main driving mechanism of the Neolithic transition in southern Africa

9,000 years of genetic continuity in southernmost Africa demonstrated at Oakhurst rockshelter

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 ‡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.

Worldwide Assessment of the Root and Root Canal Characteristics of Maxillary Premolars - A Multi-center Cone-beam Computed Tomography Cross-sectional Study With Meta-analysis

INTRODUCTION

This worldwide study examined the root and root canal characteristics of maxillary premolars and explored how demographic factors impact the outcomes.

METHODS

Observers from 44 countries assessed 26,400 maxillary premolars using cone-beam computed tomography and employed a standardized screening method to gather data on multiple canal morphology and 3-rooted configuration (primary outcomes), as well as secondary outcomes related to root and root canal anatomies. Demographic factors such as ethnicity, sex, and age were collected for each participant. The intra- and inter-observer tests ensured observer reliability. Primary outcomes were represented as odds ratios and untransformed proportions accompanied by 95% confidence interval (CI) forest plots. Meta-analysis compared sub-groups and identified sources of heterogeneity (α = 5%).

RESULTS

The overall prevalence of multiple canal morphology in the first premolar was 93.5% (95% CI, 93.3%-94.7%), while in the second premolar, it was 49.7% (95% CI, 44.9%-54.6%). The proportion of 3-rooted configuration was 1.8% (95% CI, 1.4%-2.1%) in the first premolar and 0.4% (95% CI, 0.3%-0.5%) in the second. Asian countries generally displayed fewer roots and root canals, while European nations showed higher counts (P < .05). Males exhibited higher percentages and odds ratios for both outcomes in both premolars. Younger patients demonstrated lower percentages of multiple root canal morphologies (P < .05). Factors such as tooth side, voxel size and field-of-view did not influence the outcomes (P > .05).

CONCLUSIONS

The worldwide assessment of root and root canal characteristics of maxillary premolars has revealed a discernible influence of various factors such as tooth type, geographical region, ethnicity, sex, and age.

The name of the game: palaeoproteomics and radiocarbon dates further refine the presence and dispersal of caprines in eastern and southern Africa

We report the first large-scale palaeoproteomics research on eastern and southern African zooarchaeological samples, thereby refining our understanding of early caprine (sheep and goat) pastoralism in Africa. Assessing caprine introductions is a complicated task because of their skeletal similarity to endemic wild bovid species and the sparse and fragmentary state of relevant archaeological remains. Palaeoproteomics has previously proved effective in clarifying species attributions in African zooarchaeological materials, but few comparative protein sequences of wild bovid species have been available. Using newly generated type I collagen sequences for wild species, as well as previously published sequences, we assess species attributions for elements originally identified as caprine or 'unidentifiable bovid' from 17 eastern and southern African sites that span seven millennia. We identified over 70% of the archaeological remains and the direct radiocarbon dating of domesticate specimens allows refinement of the chronology of caprine presence in both African regions. These results thus confirm earlier occurrences in eastern Africa and the systematic association of domesticated caprines with wild bovids at all archaeological sites. The combined biomolecular approach highlights repeatability and accuracy of the methods for conclusive contribution in species attribution of archaeological remains in dry African environments.

Bayesian analyses of direct radiocarbon dates reveal geographic variations in the rate of rice farming dispersal in prehistoric Japan

The adoption of rice farming during the first millennium BC was a turning point in Japanese prehistory, defining the subsequent cultural, linguistic, and genetic variation in the archipelago. Here, we use a suite of novel Bayesian techniques to estimate the regional rates of dispersal and arrival time of rice farming using radiocarbon dates on charred rice remains. Our results indicate substantial variations in the rate of dispersal of rice within the Japanese islands, hinting at the presence of a mixture of demic and cultural diffusion, geographic variations in the suitability of its cultivation, and the possible role of existing social networks in facilitating or hindering the adoption of the new subsistence economy.

Human-Plant Coevolution: A modelling framework for theory-building on the origins of agriculture

The domestication of plants and the origin of agricultural societies has been the focus of much theoretical discussion on why, how, when, and where these happened. The ‘when’ and ‘where’ have been substantially addressed by different branches of archaeology, thanks to advances in methodology and the broadening of the geographical and chronological scope of evidence. However, the ‘why’ and ‘how’ have lagged behind, holding on to relatively old models with limited explanatory power. Armed with the evidence now available, we can return to theory by revisiting the mechanisms allegedly involved, disentangling their connection to the diversity of trajectories, and identifying the weight and role of the parameters involved. We present the Human-Plant Coevolution (HPC) model, which represents the dynamics of coevolution between a human and a plant population. The model consists of an ecological positive feedback system (mutualism), which can be reinforced by positive evolutionary feedback (coevolution). The model formulation is the result of wiring together relatively simple simulation models of population ecology and evolution, through a computational implementation in R. The HPC model captures a variety of potential scenarios, though which conditions are linked to the degree and timing of population change and the intensity of selective pressures. Our results confirm that the possible trajectories leading to neolithisation are diverse and involve multiple factors. However, simulations also show how some of those factors are entangled, what are their effects on human and plant populations under different conditions, and what might be the main causes fostering agriculture and domestication.

Male-biased migration from East Africa introduced pastoralism into southern Africa

BACKGROUND

Hunter-gatherer lifestyles dominated the southern African landscape up to ~ 2000 years ago, when herding and farming groups started to arrive in the area. First, herding and livestock, likely of East African origin, appeared in southern Africa, preceding the arrival of the large-scale Bantu-speaking agro-pastoralist expansion that introduced West African-related genetic ancestry into the area. Present-day Khoekhoe-speaking Namaqua (or Nama in short) pastoralists show high proportions of East African admixture, linking the East African ancestry with Khoekhoe herders. Most other historical Khoekhoe populations have, however, disappeared over the last few centuries and their contribution to the genetic structure of present-day populations is not well understood. In our study, we analyzed genome-wide autosomal and full mitochondrial data from a population who trace their ancestry to the Khoekhoe-speaking Hessequa herders from the southern Cape region of what is now South Africa.

RESULTS

We generated genome-wide data from 162 individuals and mitochondrial DNA data of a subset of 87 individuals, sampled in the Western Cape Province, South Africa, where the Hessequa population once lived. Using available comparative data from Khoe-speaking and related groups, we aligned genetic date estimates and admixture proportions to the archaeological proposed dates and routes for the arrival of the East African pastoralists in southern Africa. We identified several Afro-Asiatic-speaking pastoralist groups from Ethiopia and Tanzania who share high affinities with the East African ancestry present in southern Africa. We also found that the East African pastoralist expansion was heavily male-biased, akin to a pastoralist migration previously observed on the genetic level in ancient Europe, by which Pontic-Caspian Steppe pastoralist groups represented by the Yamnaya culture spread across the Eurasian continent during the late Neolithic/Bronze Age.

CONCLUSION

We propose that pastoralism in southern Africa arrived through male-biased migration of an East African Afro-Asiatic-related group(s) who introduced new subsistence and livestock practices to local southern African hunter-gatherers. Our results add to the understanding of historical human migration and mobility in Africa, connected to the spread of food-producing and livestock practices.

Evidence for early dispersal of domestic sheep into Central Asia

The development and dispersal of agropastoralism transformed the cultural and ecological landscapes of the Old World, but little is known about when or how this process first impacted Central Asia. Here, we present archaeological and biomolecular evidence from Obishir V in southern Kyrgyzstan, establishing the presence of domesticated sheep by ca. 6,000 BCE. Zooarchaeological and collagen peptide mass fingerprinting show exploitation of Ovis and Capra, while cementum analysis of intact teeth implicates possible pastoral slaughter during the fall season. Most significantly, ancient DNA reveals these directly dated specimens as the domestic O. aries, within the genetic diversity of domesticated sheep lineages. Together, these results provide the earliest evidence for the use of livestock in the mountains of the Ferghana Valley, predating previous evidence by 3,000 years and suggesting that domestic animal economies reached the mountains of interior Central Asia far earlier than previously recognized.

Middle Pleistocene fire use: The first signal of widespread cultural diffusion in human evolution

Control of fire is one of the most important technological innovations within the evolution of humankind. The archaeological signal of fire use becomes very visible from around 400,000 y ago onward. Interestingly, this occurs at a geologically similar time over major parts of the Old World, in Africa, as well as in western Eurasia, and in different subpopulations of the wider hominin metapopulation. We interpret this spatiotemporal pattern as the result of cultural diffusion, and as representing the earliest clear-cut case of widespread cultural change resulting from diffusion in human evolution. This fire-use pattern is followed slightly later by a similar spatiotemporal distribution of Levallois technology, at the beginning of the African Middle Stone Age and the western Eurasian Middle Paleolithic. These archaeological data, as well as studies of ancient genomes, lead us to hypothesize that at the latest by 400,000 y ago, hominin subpopulations encountered one another often enough and were sufficiently tolerant toward one another to transmit ideas and techniques over large regions within relatively short time periods. Furthermore, it is likely that the large-scale social networks necessary to transmit complicated skills were also in place. Most importantly, this suggests a form of cultural behavior significantly more similar to that of extant Homo sapiens than to our great ape relatives.

Palaeoproteomics confirm earliest domesticated sheep in southern Africa ca. 2000 BP

We used palaeoproteomics and peptide mass fingerprinting to obtain secure species identifications of key specimens of early domesticated fauna from South Africa, dating to ca. 2000 BP. It can be difficult to distinguish fragmentary remains of early domesticates (sheep) from similar-sized local wild bovids (grey duiker, grey rhebok, springbok-southern Africa lacks wild sheep) based on morphology alone. Our analysis revealed a Zooarchaeology by Mass Spectrometry (ZooMS) marker (m/z 1532) present in wild bovids and we demonstrate through LC-MS/MS that it is capable of discriminating between wild bovids and caprine domesticates. We confirm that the Spoegrivier specimen dated to 2105 ± 65 BP is indeed a sheep. This is the earliest directly dated evidence of domesticated animals in southern Africa. As well as the traditional method of analysing bone fragments, we show the utility of minimally destructive sampling methods such as PVC eraser and polishing films for successful ZooMS identification. We also show that collagen extracted more than 25 years ago for the purpose of radiocarbon dating can yield successful ZooMS identification. Our study demonstrates the importance of developing appropriate regional frameworks of comparison for future research using ZooMS as a method of biomolecular species identification.

A southern African archaeological database of organic containers and materials, 800 cal BC to cal AD 1500: Possible implications for the transition from foraging to livestock-keeping

Although evidence of organic materials has consistently been reported in the archaeology of southern Africa little attention has been given to how this evidence, so slight in comparison to pottery and lithics, might be used to understand the transition from foraging to livestock-keeping in southern African Archaeology. We have compiled a geo-referenced, radiocarbon database of these organic, material culture remains, with particular reference to containers made of ostrich eggshell, wood, gourd, tortoise shell, twine, and leather over a 2300-year period to capture the periods before and after the appearance of livestock. We have mapped the organic materials for the period 800 cal BC to cal AD 1500 and explored the subsistence base of those who used them. This distribution is compared to that of pottery and livestock remains–conventionally the two archaeological markers of pastoralists. The paper interrogates what this might add to the vexed question of how the practice of livestock-keeping and pottery-making spread into and through the region (the hunter-herder debate). Our analysis suggests that ostrich eggshell containers can be used as a proxy for hunter-gatherers. By comparing areas of bead manufacture with those that have evidence only of bead use, we show the areas to which items may have travelled, along already established hunter-gatherer exchange networks. Our results suggest that hunter-gatherers widely and quickly adopted pottery across southern Africa in a process of cultural diffusion and local innovation, and that this was possibly the main mechanism for the dispersal of livestock at 2100 years ago.

Biased dispersal can explain fast human range expansions

Some human fronts spread faster than expected by models based on dispersal and reproduction. The only explanation proposed so far assumes that some autochthonous individuals are incorporated by the expanding populations, leading to faster front speeds. Here we show that simple models without this effect are also consistent with the observed speeds of two fronts (a Khoi-khoi expansion of herders and a Bantu expansion of farmers), provided that the dispersal of individuals is biased (i.e., more probable) in directions closer to the front propagation direction. The physical models presented may also be applied to other kinds of social phenomena, including innovation diffusion, rumor propagation, linguistic fronts, epidemic spread, diffusion in economic space and the evolution of cooperation in spatial systems. They can be also adapted to non-human systems with biased dispersal, including biological invasions, cancer tumors and virus treatment of tumors.

Ostrich eggshell bead diameter in the Holocene: Regional variation with the spread of herding in eastern and southern Africa

Despite their ubiquity in Holocene African archaeological assemblages, ostrich eggshell (OES) beads are rarely studied in detail. An exception is in southern Africa, where there is a proposed relationship between OES bead diameter and the arrival of herding ~2000 years before present. In 1987, Leon Jacobson first observed that beads from forager sites in Namibia tended to be smaller than those associated with herder sites. Studies examining bead size around the Western Cape have generally confirmed Jacobson's findings, though the driving forces of the diameter change remain unknown. Since this time, diameter has become an informal way of distinguishing forager and herder assemblages in southern Africa, but no large-scale studies of OES bead variation have been undertaken. Here we present an expanded analysis of Holocene OES bead diameters from southern, and for the first time, eastern Africa. Results reveal distinct patterns in OES bead size over time, reflecting different local dynamics associated with the spread of herding. In southern Africa, OES diameters display low variability and smaller absolute size through time. While larger beads begin to appear <2000 years ago, most beads in our study remained smaller. In contrast, eastern African OES bead diameters are consistently larger over the last 10,000 years and show no appreciable size change with the introduction of herding. Notably, larger beads thought to be associated with herders in southern Africa fall within the range of eastern African beads, indicating a potential connection between these regions in the Late Holocene consistent with genetic findings. Regional differences in bead size are subtle, on the order of millimeters, yet offer a potentially important line of evidence for investigating the spread of herding in sub-Saharan Africa. In order to understand the meaning of these changes, we encourage additional studies of OES bead assemblages and urge researchers to report individual bead diameters, rather than averages by level.

Assessing the importance of cultural diffusion in the Bantu spread into southeastern Africa

The subsistence of Neolithic populations is based on agriculture, whereas that of previous populations was based on hunting and gathering. Neolithic spreads due to dispersal of populations are called demic, and those due to the incorporation of hunter-gatherers are called cultural. It is well-known that, after agriculture appeared in West Africa, it spread across most of subequatorial Africa. It has been proposed that this spread took place alongside with that of Bantu languages. In eastern and southeastern Africa, it is also linked to the Early Iron Age. From the beginning of the last millennium BC, cereal agriculture spread rapidly from the Great Lakes area eastwards to the East African coast, and southwards to northeastern South Africa. Here we show that the southwards spread took place substantially more rapidly (1.50–2.27 km/y) than the eastwards spread (0.59–1.27 km/y). Such a faster southwards spread could be the result of a stronger cultural effect. To assess this possibility, we compare these observed ranges to those obtained from a demic-cultural wave-of-advance model. We find that both spreads were driven by demic diffusion, in agreement with most archaeological, linguistic and genetic results. Nonetheless, the southwards spread seems to have indeed a stronger cultural component, which could lead support to the hypothesis that, at the southern areas, the interaction with pastoralist people may have played a significant role.

The archaeological evidence for the appearance of pastoralism and farming in southern Africa

This paper is a response to the growing reference to archaeological evidence by linguists and geneticists interested in the spread of early farmers and pastoralists in southern Africa. It presents two databases. The first contains the archaeological evidence for pastoralism and farming in southern Africa, for the period 550 BC to AD 1050. This is the first time that the seven different types of archaeological evidence that have traditionally been used to identify both spread events are presented together at this scale. This was stimulated by our interest in investigating the antiquity of an early 'Iron Age package' relative to the spread of single archaeological traits. The analysis shows that the package appears approximately 700 years after sites containing pottery, cattle and sheep, without agriculture, appear in the drier parts of the sub-continent. It post-dates the appearance of earlier sites with pottery associated with farmers, metal-working and cultivation in the eastern half of the sub-continent. While poor preservation undoubtedly explains the absence of some parts of the package, the analysis suggests that other explanations should be considered. The second database is a quantitative, spatial study of archaeological publications on southern African farming and pastoralism for the period 1950 to 2016, covering the same geographical area and archaeological timeframe. This is presented as a proxy for research-intensive areas in attempt to show the gaps in archaeological fieldwork and knowledge.

Early Upper Paleolithic colonization across Europe: Time and mode of the Gravettian diffusion

This study presents new models on the origin, speed and mode of the wave-of-advance leading to the definitive occupation of Europe's outskirts by Anatomically Modern Humans, during the Gravettian, between c. 37 and 30 ka ago. These models provide the estimation for possible demic dispersal routes for AMH at a stable spread rate of c. 0.7 km/year, with the likely origin in Central Europe at the site of Geissenklosterle in Germany and reaching all areas of the European landscape. The results imply that: 1. The arrival of the Gravettian populations into the far eastern European plains and to southern Iberia found regions with very low human occupation or even devoid of hominins; 2. Human demography was likely lower than previous estimates for the Upper Paleolithic; 3. The likely early AMH paths across Europe followed the European central plains and the Mediterranean coast to reach to the ends of the Italian and Iberian peninsulas.

Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries

Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.

Livestock First Reached Southern Africa in Two Separate Events

After several decades of research on the subject, we now know when the first livestock reached southern Africa but the question of how they got there remains a contentious topic. Debate centres on whether they were brought with a large migration of Khoe-speakers who originated from East Africa; or whether the livestock were traded down-the-line among hunter-gatherer communities; or indeed whether there was a long history of diverse small scale population movements in this part of the world, one or more of which 'infiltrated' livestock into southern Africa. A new analysis of the distribution of stone toolkits from a sizeable sample of sub-equatorial African Later Stone Age sites, coupled with existing knowledge of the distribution of the earliest livestock remains and ceramics vessels, has allowed us to isolate two separate infiltration events that brought the first livestock into southern Africa just over 2000 years ago; one infiltration was along the Atlantic seaboard and another entered the middle reaches of the Limpopo River Basin. These findings agree well with the latest results of genetic research which together indicate that multiple, small-scale infiltrations probably were responsible for bringing the first livestock into southern Africa.