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.

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.

Earliest known Oldowan artifacts at >2.58 Ma from Ledi-Geraru, Ethiopia, highlight early technological diversity.

The manufacture of flaked stone artifacts represents a major milestone in the technology of the human lineage. Although the earliest production of primitive stone tools, predating the genus Homo and emphasizing percussive activities, has been reported at 3.3 million years ago (Ma) from Lomekwi, Kenya, the systematic production of sharp-edged stone tools is unknown before the 2.58-2.55 Ma Oldowan assemblages from Gona, Ethiopia. The organized production of Oldowan stone artifacts is part of a suite of characteristics that is often associated with the adaptive grade shift linked to the genus Homo Recent discoveries from Ledi-Geraru (LG), Ethiopia, place the first occurrence of Homo ∼250 thousand years earlier than the Oldowan at Gona. Here, we describe a substantial assemblage of systematically flaked stone tools excavated in situ from a stratigraphically constrained context [Bokol Dora 1, (BD 1) hereafter] at LG bracketed between 2.61 and 2.58 Ma. Although perhaps more primitive in some respects, quantitative analysis suggests the BD 1 assemblage fits more closely with the variability previously described for the Oldowan than with the earlier Lomekwian or with stone tools produced by modern nonhuman primates. These differences suggest that hominin technology is distinctly different from generalized tool use that may be a shared feature of much of the primate lineage. The BD 1 assemblage, near the origin of our genus, provides a link between behavioral adaptations-in the form of flaked stone artifacts-and the biological evolution of our ancestors.

The emergence and intensification of early hunter-gatherer niche construction.

Hunter-gatherers, especially Pleistocene examples, are not well-represented in archeological studies of niche construction. However, as the role of humans in shaping environments over long time scales becomes increasingly apparent, it is critical to develop archeological proxies and testable hypotheses about early hunter-gatherer impacts. Modern foragers engage in niche constructive behaviors aimed at maintaining or increasing the productivity of their environments, and these may have had significant ecological consequences over later human evolution. In some cases, they may also represent behaviors unique to modern Homo sapiens. Archeological and paleoenvironmental data show that African hunter-gatherers were niche constructors in diverse environments, which have legacies in how ecosystems function today. These can be conceptualized as behaviorally mediated trophic cascades, and tested using archeological and paleoenvironmental proxies. Thus, large-scale niche construction behavior is possible to identify at deeper time scales, and may be key to understanding the emergence of modern humans.

The origins and early elaboration of projectile technology.

The ability of Homo sapiens to kill prey at a distance is arguably one of the catalysts for our current ecological dominance. Many researchers have suggested its origins lie in the African Middle Stone Age or the European Middle Palaeolithic (∼300-30 thousand years ago), but the perishable components of armatures rarely preserve. Most research on this subject therefore emphasises analysis of armature tip size, shape, and diagnostic impacts or residues. Other lines of evidence have included human skeletal anatomy or analyses of the species composition of faunal assemblages. Projectile Impact Marks (PIMs) on archaeofaunal remains offer an ideal complement to this work, but their potential has been restricted mainly to the later Eurasian zooarchaeological record. A review of current evidence and approaches shows that systematic PIM research could add much to our understanding of early projectile technology, especially in Africa.

Taphonomy of fossils from the hominin-bearing deposits at Dikika, Ethiopia.

Two fossil specimens from the DIK-55 locality in the Hadar Formation at Dikika, Ethiopia, are contemporaneous with the earliest documented stone tools, and they collectively bear twelve marks interpreted to be characteristic of stone tool butchery damage. An alternative interpretation of the marks has been that they were caused by trampling animals and do not provide evidence of stone tool use or large ungulate exploitation by Australopithecus-grade hominins. Thus, resolving which agents created marks on fossils in deposits from Dikika is an essential step in understanding the ecological and taphonomic contexts of the hominin-bearing deposits in this region and establishing their relevance for investigations of the earliest stone tool use. This paper presents results of microscopic scrutiny of all non-hominin fossils collected from the Hadar Formation at Dikika, including additional fossils from DIK-55, and describes in detail seven assemblages from sieved surface sediment samples. The study is the first taphonomic description of Pliocene fossil assemblages from open-air deposits in Africa that were collected without using only methods that emphasize the selective retention of taxonomically-informative specimens. The sieved assemblages show distinctive differences in faunal representation and taphonomic modifications that suggest they sample a range of depositional environments in the Pliocene Hadar Lake Basin, and have implications for how landscape-based taphonomy can be used to infer past microhabitats. The surface modification data show that no marks on any other fossils resemble in size or shape those on the two specimens from DIK-55 that were interpreted to bear stone tool inflicted damage. A large sample of marks from the sieved collections has characteristics that match modern trampling damage, but these marks are significantly smaller than those on the DIK-55 specimens and have different suites of characteristics. Most are not visible without magnification. The data show that the DIK-55 marks are outliers amongst bone surface damage in the Dikika area, and that trampling is not the most parsimonious interpretation of their origin.

Nutritional values of tortoises relative to ungulates from the Middle Stone Age levels at Blombos Cave, South Africa: implications for foraging and social behaviour.

The site of Blombos Cave (BBC), Western Cape, South Africa has been a strong contributor to establishing the antiquity of important aspects of modern human behaviour, such as early symbolism and technological complexity. However, many linkages between Middle Stone Age (MSA) behaviour and the subsistence record remain to be investigated. Understanding the contribution of small fauna such as tortoises to the human diet is necessary for identifying shifts in overall foraging strategies as well as the collecting and processing behaviour of individuals unable to participate in large-game hunting. This study uses published data to estimate the number of calories present in tortoises as well as ungulates of different body size classes common at South African sites. A single tortoise (Chersina angulata) provides approximately 3332 kJ (796 kcal) of calories in its edible tissues, which is between 20 and 30% of the daily energetic requirements for an active adult (estimated between 9360 kJ [3327 kcal] and 14,580 kJ [3485 kcal] per day). Because they are easy to process, this would have made tortoises a highly-ranked resource, but their slow growth and reproduction makes them susceptible to over-exploitation. Zooarchaeological abundance data show that during the ca. 75 ka (thousands of years) upper Still Bay M1 phase at BBC, tortoises contributed twice as many calories to the diet relative to ungulates than they did during the ca. 100 ka lower M3 phase. However, in spite of the abundance of their fossils, their absolute caloric contribution relative to ungulates remained modest in both phases. At the end of the site's MSA occupation history, human subsistence strategies shifted to emphasise high-return large hunted mammals, which likely precipitated changes in the social roles of hunters and gatherers during the Still Bay.

Taphonomic analysis of the Middle Stone Age larger mammal faunal assemblage from Blombos Cave, southern Cape, South Africa.

A detailed taphonomic analysis is reported for a sample of the larger mammalian faunal assemblage (>4.5 kg live body weight) from Blombos Cave. The analysis provides an assessment of human involvement in the accumulation and modification of the faunal assemblage, and precedes equally detailed analyses and separate reports of Middle Stone Age (MSA) butchery, transport, and hunting behaviour. At Blombos, there are clear differences in the relative abundances of ungulate body size classes, with the lower MSA phases (upper/lower M2 and M3) showing a high representation of size 1 ungulates relative to the most recent MSA phase (M1). The bones from the earliest MSA phase (M3) have not undergone much post-depositional fragmentation, in contrast to fragments from more recent phases (M1 and upper M2). Much of this variability can be attributed to more burning activity and trampling during M1 and upper M2, which could indicate more intensive occupation. Bone surfaces are variably preserved, with high levels of exfoliation in the most recent two phases. Surface modification analyses revealed high proportions of human modification throughout the sequence, indicating that MSA humans were responsible for accumulating most of the larger mammals. After discard, the bones were modified by scavenging carnivores, leading to a moderate amount of density-mediated destruction and tooth-marking. Carnivores independently accumulated some of the smaller ungulates, mainly in the form of partially-digested remains. Raptorial birds are not implicated as major faunal accumulators. The results from Blombos are directly comparable with analogous datasets from two other sites in the Western Cape (Pinnacle Point Cave 13B and Die Kelders Cave 1). Such comparisons demonstrate that MSA faunal assemblages from nearby coastal sites have complex and different taphonomic histories both within and between sites. Because the human occupants were a major part of these processes, MSA subsistence behaviour and site use was also quite variable over time and space.

Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia.

Relatively little is known about Nubia's genetic landscape prior to the influence of the Islamic migrations that began in the late 1st millennium CE. Here, we increase the number of ancient individuals with genome-level data from the Nile Valley from three to 69, reporting data for 66 individuals from two cemeteries at the Christian Period (~650-1000 CE) site of Kulubnarti, where multiple lines of evidence suggest social stratification. The Kulubnarti Nubians had ~43% Nilotic-related ancestry (individual variation between ~36-54%) with the remaining ancestry consistent with being  introduced through Egypt and ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The Kulubnarti gene pool - shaped over a millennium - harbors disproportionately female-associated West Eurasian-related ancestry. Genetic similarity among individuals from the two cemeteries supports a hypothesis of social division without genetic distinction. Seven pairs of inter-cemetery relatives suggest fluidity between cemetery groups. Present-day Nubians are not directly descended from the Kulubnarti Nubians, attesting to additional genetic input since the Christian Period.

Early human impacts and ecosystem reorganization in southern-central Africa.

Modern Homo sapiens engage in substantial ecosystem modification, but it is difficult to detect the origins or early consequences of these behaviors. Archaeological, geochronological, geomorphological, and paleoenvironmental data from northern Malawi document a changing relationship between forager presence, ecosystem organization, and alluvial fan formation in the Late Pleistocene. Dense concentrations of Middle Stone Age artifacts and alluvial fan systems formed after ca. 92 thousand years ago, within a paleoecological context with no analog in the preceding half-million-year record. Archaeological data and principal coordinates analysis indicate that early anthropogenic fire relaxed seasonal constraints on ignitions, influencing vegetation composition and erosion. This operated in tandem with climate-driven changes in precipitation to culminate in an ecological transition to an early, pre-agricultural anthropogenic landscape.

Taphonomic analysis of the Middle Stone Age faunal assemblage from Pinnacle Point Cave 13B, Western Cape, South Africa.

A detailed taphonomic analysis is provided for the mammalian and tortoise faunal assemblages from Pinnacle Point Cave 13B (PP13B). It is the first of several reports on the fauna from this site, and must necessarily precede analyses focused on higher level interpretations of Middle Stone Age (MSA) butchery, transport, and hunting behavior. The taphonomic work shows that the faunal assemblage is well preserved and there are discernable differences in the taphonomic pathways to which the fauna was subjected at PP13B between the Middle and Late Pleistocene, between the front and back of the cave, and between body size classes. The largest mammals (size classes 2-5, body weight >24 kg) were mainly accumulated by MSA hominins. Size class 1 ungulates also exhibit a degree of hominin modification consistent with some hominin accumulation of fresh carcasses, but this is more variable through time and includes an observable degree of independent carnivore contribution. Basic taxonomic comparisons reveal a low representation of small mammals, tortoises, and marine mammals at PP13B relative to larger (>4.5 kg) terrestrial mammals. This is a different pattern from other MSA sites along the southwestern coast of South Africa, where small mammals and tortoises are abundant. A microscopic study of the bone surfaces confirms that MSA hominins exploited these small faunal components opportunistically, while focusing most heavily on large terrestrial ungulates. All faunal components show evidence of carnivore scavenging of hominin food debris and a high degree of density mediated destruction. Raptors are at no point implicated as major accumulators of any fauna. The study demonstrates that the full spectrum of MSA faunal exploitation can only be understood when the large mammal, small mammal, and tortoise components of fossil assemblages have all been subjected to comprehensive taphonomic analyses.

Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?

We challenge the view that our species, Homo sapiens, evolved within a single population and/or region of Africa. The chronology and physical diversity of Pleistocene human fossils suggest that morphologically varied populations pertaining to the H. sapiens clade lived throughout Africa. Similarly, the African archaeological record demonstrates the polycentric origin and persistence of regionally distinct Pleistocene material culture in a variety of paleoecological settings. Genetic studies also indicate that present-day population structure within Africa extends to deep times, paralleling a paleoenvironmental record of shifting and fractured habitable zones. We argue that these fields support an emerging view of a highly structured African prehistory that should be considered in human evolutionary inferences, prompting new interpretations, questions, and interdisciplinary research directions.

New opportunities rising.

More fossil specimens and an eagerly awaited age for Homo naledi raise new questions and open fresh opportunities for paleoanthropologists.