Mary E. Prendergast

Rice University · Department of Anthropology

Recent methodological advances have increased the pace and scale of African ancient DNA (aDNA) research, inciting a rush to sample broadly from museum collections, and raising ethical concerns over the destruction of human remains. In the absence of discipline-wide protocols, teams are often left to navigate aDNA sampling on an individual basis, co...

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 a...

The ecological adaptations that stimulated the dispersal and technological strategies of our species during the Late Pleistocene remain hotly disputed, with some influential theories focusing on grassland biomes or marine resources as key drivers behind the rapid expansion and material culture innovations of Homo sapiens within and beyond Africa. H...

Analysis of ancient human DNA from western Central Africa offers insights into African population history, including the origin of speakers of the Bantu languages. The findings are reported in this week’s Nature. Shum Laka in western Cameroon, Africa, is an important archaeological site for the study of Late Pleistocene and Holocene prehistory in...

The initial spread of food production in eastern Africa is associated with livestock herding during the Pastoral Neolithic. Recent excavation at Luxmanda, Tanzania, a site dating to c. 3000 BP, revealed circular installations of lower grinding stones and numerous handstones. This discovery, unprecedented for this era, challenges previous ideas abou...

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 Africa1,2,3,4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient pop...

Common assumptions about the ephemeral archaeological signature of pastoralist settlements have limited the application of geophysical techniques in the investigation of past herding societies. Here, the authors present a geophysical survey of Luxmanda, Tanzania, the largest-known settlement documented for the Pastoral Neolithic era in eastern Afri...

Archaeologists have various hypotheses for how populations changed in Africa about 50,000 years ago, during the Later Stone Age transition. Now, the earliest available ancient-DNA sequences from sub-Saharan Africa reveal a complex Late Pleistocene population structure, pointing to large shifts in human movement and in patterns of social interaction...

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 recommenda...

In eastern Africa, ecologists have found that when mobile pastoralists abandon their temporary encampments, the accumulation of burned animal dung, wood, and other organic waste enriches the concentration of nutrients (e.g., calcium, phosphorous, magnesium) essential to soil health, in comparison to other soils without prior human habitation. These...

Open Access Check for updates on crossmark Research articles Collagen fingerprinting traces the introduction of caprines to island Eastern Africa Courtney Culley, Anneke Janzen, Samantha Brown, Mary E. Prendergast, Jesse Wolfhagen, Bourhane Abderemane, Abdallah K. Ali, Othman Haji, Mark C. Horton, Ceri Shipton, Jillian Swift, Tabibou A. Tabibou, He...

The origin and evolution of hominin mortuary practices are topics of intense interest and debate1–3. Human burials dated to the Middle Stone Age (MSA) are exceedingly rare in Africa and unknown in East Africa1–6. Here we describe the partial skeleton of a roughly 2.5- to 3.0-year-old child dating to 78.3 ± 4.1 thousand years ago, which was recovere...

The morphological differentiation of African bovids in highly fragmented zooarchaeological assemblages is a major hindrance to reconstructing the nature and spread of pastoralism in sub-Saharan Africa. Here we employ collagen peptide mass fingerprinting, known as Zooarchaeology by Mass Spectrometry (ZooMS), coupled with recently published African Z...

The Middle to Later Stone Age transition is a critical period of human behavioral change that has been variously argued to pertain to the emergence of modern cognition, substantial population growth, and major dispersals of Homo sapiens within and beyond Africa. However, there is little consensus about when the transition occurred, the geographic p...

Bone surface modifications (BSMs) in faunal assemblages are frequently used to infer past agency and actions of hominins and carnivores, with implications for the emergence of key human behaviours. Patterning of BSMs has mostly been defined as a combination of the intensity of marks per bone portion and sometimes per element. Numerous variables inv...

The development of pastoralism transformed human diets and societies in grasslands worldwide. The long-term success of cattle herding in Africa has been sustained by dynamic food systems, consumption of a broad range of primary and secondary livestock products, and the evolution of lactase persistence (LP), which allows digestion of lactose into ad...

Large-scale reconstructions of the spread of food production systems require fine-scale analyses of dietary evidence. One current impediment to understanding early African pastoralism is a lack of high-resolution portraits of herd management, specifically with respect to sheep (Ovis aries) and goat (Capra hircus), osteologically similar but behavio...

The spread of early herders across Africa is a pivotal event in prehistory, but the context of this event remains poorly understood due to a lack of paleoenvironmental data. We present new radiocarbon dates and multi-proxy Holocene paleoecological records for two distinct settings on the pathways through which livestock herding spread across easter...

Hard animal materials were key components of prehistoric daily life, with many such raw materials shaped into diverse tool types and personal ornaments. With few exceptions, outside of the far south and north of Africa, osseous artefacts have been largely understudied on the continent, with this situation particularly applying to pastoralist contex...

The originally published version of this Article contained an error in Fig. 3, whereby an additional unrelated graph was overlaid on top of the magnetic susceptibility plot. Furthermore, the Article title contained an error in the capitalisation of 'Stone Age'. Both of these errors have now been corrected in both the PDF and HTML versions of the Ar...

The Middle to Later Stone Age transition in Africa has been debated as a significant shift in human technological, cultural, and cognitive evolution. However, the majority of research on this transition is currently focused on southern Africa due to a lack of long-term, stratified sites across much of the African continent. Here, we report a 78,000...

During the African Humid Period (AHP; c. 15–5.5 ka), the rivers and lakes of much of the continent swelled due to changes in monsoonal rainfall driven by Earth's orbital precession. This period witnessed the growth of diverse fisher-forager communities, whose members adapted their settlement patterns and created new technologies in order to take ad...

The later Holocene spread of pastoralism throughout eastern Africa profoundly changed socioeconomic and natural landscapes. During the Pastoral Neolithic (ca. 5000–1200 B.P.), herders spreadthrough southern Kenya and northern Tanzania — areas previously occupied only by huntergatherers — eventually developing the specialized forms of pastoralism th...

Past populations inhabiting the Swahili coast – an area stretching from southern Somalia to Mozambique and including offshore islands, the Comoros and Madagascar – encountered a rich and diverse set of animals, many of which were incorporated into their social realm in various forms and can be traced in the archaeological record. Early research on...

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 ance...

Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first...

Details of methods used in ancient DNA (aDNA) and Zooarchaeology by Mass Spectrometry (ZooMS) collagen fingerprinting analyses. (DOCX)

Total reads used in the BLAST analysis and results of Burrows-Wheeler Alignments (BWA). (DOCX)

Results of experimental study of false positives. Incorrect genus identifications resulting from 500 test "libraries" obtained from whole mtDNA genomes of the genus Gallus. See text for explanation of experimental method. (DOCX)

Reference specimens for ZooMS collagen fingerprinting. (DOCX)

Decision tree illustrating research protocols. Tree illustrates the selection of faunal samples, the order in which specific analyses were applied to each subsample, and result. (TIF)

Landmarks used in dental analysis. R. exulans tooth in occlusal view with simplified diagram to the right. The fixed landmarks are illustrated by large blue circles, sliding semi-landmarks by small red circles. The boundaries of the cusps and the stylids (small flat or saddle like surfaces joining cusps) are difficult to precisely identify, but hav...

Reference specimens for analysis of tooth morphology. (DOCX)

mapDamage analysis of deanimation patterns in bird specimens. For each of the sequenced specimens (specimen numbers indicated by JK0000), mapDamage analysis illustrates C to T (red) and G to A (blue) frequencies of mis-incorporation at 3’ and 5’ ends. (PDF)

Spectra from modern Rattus taxa. MALDI peptide mass fingerprint spectra of collagen tryptic digests from the reference bone material of Rattus rattus (top), Rattus norvegicus (middle) and Rattus exulans (bottom). (TIF)

Sites excavated by the Sealinks Project. (DOCX)

Previously excavated sites included in the present analysis. (DOCX)

Detailed results for bird specimens. Results of multiple ancient DNA analyses, with radiocarbon dates where available. Sites ordered from north to south. (DOCX)

Detailed results for rodent specimens. Results of ancient DNA analysis, ZooMS collagen fingerprinting, and tooth morphology, with radiocarbon dates where available. Sites ordered from north to south. (DOCX)

Spectra from modern rodent genera other than Rattus. A: MALDI peptide mass fingerprint spectra of collagen tryptic digests from the reference bone material of Aethomys kaiseri (top), Mastomys coucha (middle) and Mus minutoides (bottom). B: MALDI peptide mass fingerprint spectra of collagen tryptic digests from the reference bone material of Gerbill...

Example of MALDI peptide mass fingerprint spectra in archaeological samples. Example of MALDI peptide mass fingerprint spectra of collagen tryptic digests from the archaeological samples studied, showing the three most commonly identified types: Rattus rattus (bottom); Group 1 (middle), which most closely resembles Mastomys; and Group 2 (top), whic...

Spectra from unknown taxa in archaeological samples. MALDI peptide mass fingerprint spectra of collagen tryptic digests from archaeological specimens that form groups of unknown taxa. (TIF)

The cat has long been important to human societies as a pest-control agent, object of symbolic value and companion animal, but little is known about its domestication process and early anthropogenic dispersal. Here we show, using ancient DNA analysis of geographically and temporally widespread archaeological cat remains, that both the Near Eastern...

The Turkana Basin in northern Kenya is located in an environmentally sensitive region along the eastern African Rift system. Lake Turkana's sensitivity to fluctuations in precipitation makes this an ideal place to study prehistoric human adaptations during key climatic transitions. Here we present eleven radio-carbon dates from two recently excavat...

The spread of agriculture across sub-Saharan Africa has long been attributed to the large-scale migration of Bantu-speaking groups out of their west Central African homeland from about 4000 years ago. These groups are seen as having expanded rapidly across the sub-continent, carrying an ‘Iron Age’ package of farming, metal-working, and pottery, and...

Occupants of coastal and island eastern Africa – now known as the “Swahili coast” – were involved in long-distance trade with the Indian Ocean world during the later first millennium CE. Such exchanges may be traced via the appearance of non-native animals in the archaeofaunal record; additionally, this record reveals daily culinary practices of th...

Figure S1. Remains of scombrids from Unguja Ukuu: (a) left maxilla from context 1418 and (b) caudal vertebra from context 1412H. Figure S2. Size distributions of reconstructed total length (TL) of Lethrinus spp. individuals from early and late phases of occupation at Unguja Ukuu. The mean length is marked with a red dashed line (early = 32.4, late...

The origin and dispersal of the domestic cat remain elusive despite its importance to human societies around the world. Archaeological evidence for domestication centers in the Near East and in Egypt is contested, and genetic data on modern cats show that Felis silvestris lybica , the subspecies of wild cat inhabiting at present the Near East and N...

Recent archaeological research has firmly established eastern Africa's offshore islands as important localities for understanding the region's pre-Swahili maritime adaptations and early Indian Ocean trade connections. While the importance of the sea and small offshore islands to the development of urbanized and mercantile Swahili societies has long...

Most of our current knowledge of late Pleistocene African bone technology is drawn from southern African sites, with recent discoveries indicating that bone- and stone-tipped arrows (propelled by a bow) were in use prior to 60,000 years BP. Integration of archaeological with ethnographic data similarly suggests that hunting with poison-tipped arrow...

The late Pleistocene and Holocene history of eastern Africa is complex and major gaps remain in our understanding of human occupation during this period. Questions concerning the identities, geographical distributions and chronologies of foraging, herding and agricultural populations — often problematically equated with the chronological labels ‘La...

With rising sea levels at the end of the Pleistocene, land-bridge or continental islands were formed around the world. Many of these islands have been extensively studied from a biogeographical perspective, particularly in terms of impacts of island creation on terrestrial vertebrates. However, a majority of studies rely on contemporary faunal dist...

Radiometric dating for Trench 10, Kuumbi Cave. (DOCX)

Diversity indices at Kuumbi Cave. Diversity indices (Shannon’s E, Simpson’s Dominance; left axis), and richness (NTAXA; right axis), calculated by phase using both NISP and MNI. (TIF)

Taphonomic variables recorded in the Kuumbi Cave Trench 10 assemblage. (DOCX)

Taxonomic representation at Kuumbi Cave Trench 10. (XLSX)

Kuumbi Cave is one of a group of caves that underlie a flight of marine terraces in Pleistocene limestone in eastern Zanzibar (Indian Ocean). Drawing on the findings of geoarchaeological field survey and archaeological excavation, we discuss the formation and evolution of Kuumbi Cave and its wider littoral landscape. In the later part of the Quater...

While Africa has sometimes been peripheral to accounts of the early Indian Ocean world, studies of food globalisation necessarily place it centre stage. Africa has dispatched and received an extraordinary range of plants, animals and foodstuffs through Indian Ocean trade and other avenues. Here we explore these patterns of food globalisation vis-A...

This paper presents and contextualizes two radiocarbon dates directly obtained from Kansyore and Savanna Pastoral Neolithic (Narosura) ceramic sherds from sites near Lake Eyasi in Tanzania. The dates improve upon those obtained during prior research, which were compromised by problematic samples and stratigraphic disturbance. This underscores the i...