Entwined African and Asian genetic roots of medieval peoples of the Swahili coast.

The urban peoples of the Swahili coast traded across eastern Africa and the Indian Ocean and were among the first practitioners of Islam among sub-Saharan people1,2. The extent to which these early interactions between Africans and non-Africans were accompanied by genetic exchange remains unknown. Here we report ancient DNA data for 80 individuals from 6 medieval and early modern (AD 1250-1800) coastal towns and an inland town after AD 1650. More than half of the DNA of many of the individuals from coastal towns originates from primarily female ancestors from Africa, with a large proportion-and occasionally more than half-of the DNA coming from Asian ancestors. The Asian ancestry includes components associated with Persia and India, with 80-90% of the Asian DNA originating from Persian men. Peoples of African and Asian origins began to mix by about AD 1000, coinciding with the large-scale adoption of Islam. Before about AD 1500, the Southwest Asian ancestry was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by people of the Swahili coast3. After this time, the sources of DNA became increasingly Arabian, consistent with evidence of growing interactions with southern Arabia4. Subsequent interactions with Asian and African people further changed the ancestry of present-day people of the Swahili coast in relation to the medieval individuals whose DNA we sequenced.

Ancient DNA and deep population structure in sub-Saharan African foragers.

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa1-4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations3,5. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80-20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.

Ethics of DNA research on human remains: five globally applicable guidelines.

We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3) researchers must minimize damage to human remains; (4) researchers must ensure that data are made available following publication to allow critical re-examination of scientific findings; and (5) researchers must engage with other stakeholders from the beginning of a study and ensure respect and sensitivity to stakeholder perspectives. We commit to adhering to these guidelines and expect they will promote a high ethical standard in DNA research on human remains going forward.

Human burials at the Kisese II rockshelter, Tanzania.

OBJECTIVES: The Late Pleistocene and early Holocene in eastern Africa are associated with complex evolutionary and demographic processes that contributed to the population variability observed in the region today. However, there are relatively few human skeletal remains from this time period. Here we describe six individuals from the Kisese II rockshelter in Tanzania that were excavated in 1956, present a radiocarbon date for one of the individuals, and compare craniodental morphological diversity among eastern African populations. MATERIALS AND METHODS: This study used standard biometric analyses to assess the age, sex, and stature of the Kisese II individuals. Eastern African craniodental morphological variation was assessed using measures of dental size and a subset of Howells' cranial measurements for the Kisese II individuals as well as early Holocene, early pastoralist, Pastoral Neolithic, and modern African individuals. RESULTS: Our results suggest a minimum of six individuals from the Kisese II collections with two adults and four juveniles. While the dating for most of the burials is uncertain, one individual is directly radiocarbon dated to ~7.1 ka indicating that at least one burial is early Holocene in age. Craniodental metric comparisons indicate that the Kisese II individuals extend the amount of human morphological diversity among Holocene eastern Africans. CONCLUSIONS: Our findings contribute to a growing body of evidence that Late Pleistocene and early Holocene eastern Africans exhibited relatively high amounts of morphological diversity. However, the Kisese II individuals suggest morphological similarity at localized sites potentially supporting increased regionalization during the early Holocene.

Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa.

Africa hosts the greatest human genetic diversity globally, but legacies of ancient population interactions and dispersals across the continent remain understudied. Here, we report genome-wide data from 20 ancient sub-Saharan African individuals, including the first reported ancient DNA from the DRC, Uganda, and Botswana. These data demonstrate the contraction of diverse, once contiguous hunter-gatherer populations, and suggest the resistance to interaction with incoming pastoralists of delayed-return foragers in aquatic environments. We refine models for the spread of food producers into eastern and southern Africa, demonstrating more complex trajectories of admixture than previously suggested. In Botswana, we show that Bantu ancestry post-dates admixture between pastoralists and foragers, suggesting an earlier spread of pastoralism than farming to southern Africa. Our findings demonstrate how processes of migration and admixture have markedly reshaped the genetic map of sub-Saharan Africa in the past few millennia and highlight the utility of combined archaeological and archaeogenetic approaches.

Ancient West African foragers in the context of African population history.

Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children-two of whom were buried approximately 8,000 years ago and two 3,000 years ago-from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group1-11. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region12,13. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today-as well as speakers of Bantu languages from across the continent-are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.

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.

Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.

How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.

The bioarchaeology of mid-Holocene pastoralist cemeteries west of Lake Turkana, Kenya.

Early herders in eastern Africa built elaborate megalithic cemeteries ~ 5000 BP overlooking what is now Lake Turkana in northwestern Kenya. At least six 'pillar sites' were constructed during a time of rapid change: cattle, sheep, and goats were introduced to the basin as the lake was shrinking at the end of the African Humid Period. Cultural changes at this time include new lithic and ceramic technologies and the earliest monumentality in eastern Africa. Isolated human remains previously excavated from pillar sites east of Lake Turkana seemed to indicate that pillar site platforms were ossuaries for secondary burials. Recent bioarchaeological excavations at four pillar sites west of the lake have now yielded ≥49 individuals, most from primary and some from secondary interments, challenging earlier interpretations. Here we describe the mortuary cavities, and burial contexts, and included items such as adornments from Lothagam North, Lothagam West, Manemanya, and Kalokol pillar sites. In doing so, we reassess previous hypotheses regarding pillar site construction, use, and inter-site variability. We also present the first osteological analyses of skeletons buried at these sites. Although the human remains are fragmentary, they are nevertheless informative about the sex, age, and body size of the deceased and give evidence for health and disease processes. Periosteal moulds of long bone midshafts (n = 34 elements) suggest patterns of terrestrial mobility. Pillar site deposits provide important new insights into early herder lifeways in eastern Africa and the impact of the transition to pastoralism on past human populations.

A monumental cemetery built by eastern Africa's first herders near Lake Turkana, Kenya.

Monumental architecture is a prime indicator of social complexity, because it requires many people to build a conspicuous structure commemorating shared beliefs. Examining monumentality in different environmental and economic settings can reveal diverse reasons for people to form larger social units and express unity through architectural display. In multiple areas of Africa, monumentality developed as mobile herders created large cemeteries and practiced other forms of commemoration. The motives for such behavior in sparsely populated, unpredictable landscapes may differ from well-studied cases of monumentality in predictable environments with sedentary populations. Here we report excavations and ground-penetrating radar surveys at the earliest and most massive monumental site in eastern Africa. Lothagam North Pillar Site was a communal cemetery near Lake Turkana (northwest Kenya) constructed 5,000 years ago by eastern Africa's earliest pastoralists. Inside a platform ringed by boulders, a 119.5-m2 mortuary cavity accommodated an estimated minimum of 580 individuals. People of diverse ages and both sexes were buried, and ornaments accompanied most individuals. There is no evidence for social stratification. The uncertainties of living on a "moving frontier" of early herding-exacerbated by dramatic environmental shifts-may have spurred people to strengthen social networks that could provide information and assistance. Lothagam North Pillar Site would have served as both an arena for interaction and a tangible reminder of shared identity.

Land Snail Shell Beads in the Sub-Saharan Archaeological Record: When, Where, and Why?

Shell beads are well established in the archaeological record of sub-Saharan Africa and appear as early as 75,000 BP; however, most research has focused on ostrich eggshell (OES) and various marine mollusc species. Beads made from various land snails shells (LSS), frequently described as Achatina, also appear to be widespread. Yet tracking their appearance and distribution is difficult because LSS beads are often intentionally or unintentionally lumped with OES beads, there are no directly dated examples, and bead reporting in general is highly variable in the archaeological literature. Nevertheless, Achatina and other potential cases of LSS beads are present at over 80 archaeological sites in at least eight countries, spanning the early Holocene to recent past. Here, we collate published cases and report on several more. We also present a new case from Magubike Rockshelter in southern Tanzania with the first directly dated LSS beads, which we use to illustrate methods for identifying LSS as a raw material. Despite the long history of OES bead production on the continent and the abundance of land snails available throughout the Pleistocene, LSS beads appear only in the late Holocene and are almost exclusively found in Iron Age contexts. We consider possible explanations for the late adoption of land snails as a raw material for beadmaking within the larger context of environmental, economic, and social processes in Holocene Africa. By highlighting the existence of these artifacts, we hope to facilitate more in-depth research on the timing, production, and distribution of LSS beads in African prehistory.

Les perles de coquillages sont bien établies dans les archives archéologiques de l'Afrique subsaharienne et apparaissent dès 75 000 BP, mais la plupart des recherches ont porté sur la coquille d'œuf d'autruche (OES) et diverses espèces de mollusques marins. Les perles fabriquées à partir de diverses coquilles d'escargots terrestres (LSS), souvent décrites comme Achatina, semblent également être répandues. Cependant, le suivi de leur apparence et de leur distribution est. difficile parce que les billes LSS sont souvent volontairement ou involontairement regroupées avec des billes OES, il n'y a pas d'exemples directement datés, et les rapports sur les perles en général sont très variables dans la littérature archéologique. Néanmoins, Achatina et d'autres cas potentiels de perles LSS sont présents sur plus de 80 sites archéologiques dans au moins huit pays, couvrant le début de l'Holocène à un passé récent. Ici, nous rassemblons les cas publiés et rapportons plusieurs autres cas. Nous présentons également un nouveau cas de Magubike Rockshelter dans le sud de la Tanzanie avec les premières perles LSS directement datées, que nous utilisons pour illustrer les méthodes d'identification du LSS comme matière première. Malgré la longue histoire de la production de perles d'OES sur le continent et l'abondance d'escargots terrestres disponibles tout au long du Pléistocène, les perles de LSS n'apparaissent qu'à la fin de l'Holocène et sont presque exclusivement trouvées dans des contextes de l'âge du fer. Nous considérons les explications possibles de l'adoption tardive des escargots terrestres en tant que matière première pour la fabrication de perles dans le contexte plus large des processus environnementaux, économiques et sociaux en Afrique de l'Holocène. En mettant en évidence l'existence de ces artefacts, nous espérons faciliter des recherches plus approfondies sur le calendrier, la production et la distribution des perles LSS dans la préhistoire africaine.