Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments.

Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.

An abstract drawing from the 73,000-year-old levels at Blombos Cave, South Africa.

Depictive and abstract representations produced by drawing-known from Europe, Africa and Southeast Asia after 40,000 years ago-are a prime indicator of modern cognition and behaviour1. Here we report a cross-hatched pattern drawn with an ochre crayon on a ground silcrete flake recovered from approximately 73,000-year-old Middle Stone Age levels at Blombos Cave, South Africa. Our microscopic and chemical analyses of the pattern confirm that red ochre pigment was intentionally applied to the flake with an ochre crayon. The object comes from a level associated with stone tools of the Still Bay techno-complex that has previously yielded shell beads, cross-hatched engravings on ochre pieces and a variety of innovative technologies2-5. This notable discovery pre-dates the earliest previously known abstract and figurative drawings by at least 30,000 years. This drawing demonstrates the ability of early Homo sapiens in southern Africa to produce graphic designs on various media using different techniques.

Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups.

Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investigated the genetic make-up of an individual who lived there about 200 years ago. We further contextualize the genetic ancestry of this individual among prehistoric and current groups. From a hair sample excavated at the shelter, which was indirectly dated to about 200 years old, we sequenced the genome (1.01 times coverage) of a Later Stone Age individual. We analyzed the Vaalkrans genome together with genetic data from 10 ancient (pre-colonial) individuals from southern Africa spanning the last 2000 years. We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter-gatherers and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man's descendants have likely been assimilated into mixed-ancestry "Coloured" groups. The Vaalkrans man's genome reveals that Khoekhoe pastoralist groups/individuals lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. Our findings are also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations.

Subsistence strategies during the Late Pleistocene in the southern Cape of South Africa: Comparing the Still Bay of Blombos Cave with the Howiesons Poort of Klipdrift Shelter.

The Still Bay (SB) and Howiesons Poort (HP) were two significant techno-complexes in the Middle Stone Age and key periods in the expression of behavioral complexity. In this study, we compare the recently excavated fauna from the SB layers at Blombos Cave (BBC) with that from the HP levels at Klipdrift Shelter (KDS) in the southern Cape of South Africa. We consider our findings in the framework of recent models for early human subsistence behavior. In particular, we link our study with models involving resource intensification to examine whether foraging strategies in the HP were more or less intensive than those in the SB. Based on our criteria used to assess intensification-the exploitation of low-ranked prey, the processing of low-utility elements, transport decisions, and occupational intensity-intensive subsistence strategies are more evident at KDS than BBC. Our results suggest that low-ranked elements were processed more heavily and diet breath was broader at KDS than at BBC. However, foraging ranges may have been more extensive at BBC than at KDS. Taphonomic data also suggests that the SB at BBC was a low-intensity, sporadically occupied period in contrast to the high-intensity occupations during the HP at KDS. We argue that this may be related to differences in mobility and residential patterns between these techno-complexes.

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.

Thinking strings: additional evidence for personal ornament use in the Middle Stone Age at Blombos Cave, South Africa.

Here we report on newly identified beads recovered from four Middle Stone Age levels at Blombos Cave and, in particular, on a cluster of 24 perforated Nassarius kraussianus shells that probably originate from a single beadwork. Contextual information, morphometric, technological and use-wear analysis of the 68 published beads and those recently found, coupled with experimental reproduction of wear patterns, allow us to reconstruct the most probable way in which the N. kraussianus shells were strung. The results reveal unexpected regularities but also variability through the various levels that we interpret as resulting from changes in beadwork manufacture and design over time. The Blombos Cave beads may document one of the first examples of changes in social norms affecting the production and design of symbolic material culture.

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.

Engraved ochres from the Middle Stone Age levels at Blombos Cave, South Africa.

Powerful categories of evidence for symbolically mediated behaviour, variously described as 'modern' or 'cognitively modern' human behaviour, are geometric or iconographic representations. After 40,000 years ago such evidence is well documented in much of the Old World and is widely considered as typifying 'modern human culture,' but earlier evidence is rare. In Africa, this includes two deliberately engraved ochre pieces from c. 75,000 year old levels at Blombos Cave, Western Cape, South Africa and the greater than 55,000 year old incised ostrich egg shell from the Diepkloof shelter, located in the same province. Here we report on thirteen additional pieces of incised ochre recovered from c. 75,000-100,000 year old levels at Blombos Cave. These finds, taken together with other engraved objects reported from other southern African sites, suggest that symbolic intent and tradition were present in this region at an earlier date than previously thought.

Early Evidence for the Extensive Heat Treatment of Silcrete in the Howiesons Poort at Klipdrift Shelter (Layer PBD, 65 ka), South Africa.

Heating stone to enhance its flaking qualities is among the multiple innovative adaptations introduced by early modern human groups in southern Africa, in particular during the Middle Stone Age Still Bay and Howiesons Poort traditions. Comparatively little is known about the role and impact of this technology on early modern human behaviors and cultural expressions, due, in part, to the lack of comprehensive studies of archaeological assemblages documenting the heat treatment of stone. We address this issue through an analysis of the procedure used for heating and a technological analysis of a lithic assemblage recovered from one Howiesons Poort assemblage at Klipdrift Shelter (southern Cape, South Africa). The resulting data show extensive silcrete heat treatment, which adds a new dimension to our understanding of fire-related behaviors during the Howiesons Poort, highlighting the important role played by a heat treatment stage in the production of silcrete blades. These results are made possible by our new analytical procedure that relies on the analysis of all silcrete artifacts. It provides direct evidence of a controlled use of fire which took place during an early stage of core exploitation, thereby impacting on all subsequent stages of the lithic chaîne opératoire, which, to date, has no known equivalent in the Middle Stone Age or Middle Paleolithic record outside of southern Africa.

Climate, Environment and Early Human Innovation: Stable Isotope and Faunal Proxy Evidence from Archaeological Sites (98-59ka) in the Southern Cape, South Africa.

The Middle Stone Age (MSA) of southern Africa, and in particular its Still Bay and Howiesons Poort lithic traditions, represents a period of dramatic subsistence, cultural, and technological innovation by our species, Homo sapiens. Climate change has frequently been postulated as a primary driver of the appearance of these innovative behaviours, with researchers invoking either climate instability as a reason for the development of buffering mechanisms, or environmentally stable refugia as providing a stable setting for experimentation. Testing these alternative models has proved intractable, however, as existing regional palaeoclimatic and palaeoenvironmental records remain spatially, stratigraphically, and chronologically disconnected from the archaeological record. Here we report high-resolution records of environmental shifts based on stable carbon and oxygen isotopes in ostrich eggshell (OES) fragments, faunal remains, and shellfish assemblages excavated from two key MSA archaeological sequences, Blombos Cave and Klipdrift Shelter. We compare these records with archaeological material remains in the same strata. The results from both sites, spanning the periods 98-73 ka and 72-59 ka, respectively, show significant changes in vegetation, aridity, rainfall seasonality, and sea temperature in the vicinity of the sites during periods of human occupation. While these changes clearly influenced human subsistence strategies, we find that the remarkable cultural and technological innovations seen in the sites cannot be linked directly to climate shifts. Our results demonstrate the need for scale-appropriate, on-site testing of behavioural-environmental links, rather than broader, regional comparisons.

Diachronic Change within the Still Bay at Blombos Cave, South Africa.

Characteristically shaped bifacial points are stone artefacts with which the Middle Stone Age Still Bay techno-complex in Southern Africa is identified. Traditional approaches such as chaîne opératoire and two-dimensional metrics in combination with attribute analyses have been used to analyse variability within Still Bay point assemblages. Here we develop a protocol to extract and analyse high resolution 3-dimensional geometric morphometric information about Still Bay point morphology. We also investigate ways in which the independent variables of time, raw-material and tool size may be driving patterns of shape variation in the Blombos Cave point assemblage. We demonstrate that at a single, stratified Still Bay site points undergo significant modal changes in tool morphology and standardization. Our results caution against (1) treatment of the Still Bay as a static technological entity and (2) drawing demographic inferences stemming from grouping Still Bay point collections within the same cultural label.

A 100,000-year-old ochre-processing workshop at Blombos Cave, South Africa.

The conceptual ability to source, combine, and store substances that enhance technology or social practices represents a benchmark in the evolution of complex human cognition. Excavations in 2008 at Blombos Cave, South Africa, revealed a processing workshop where a liquefied ochre-rich mixture was produced and stored in two Haliotis midae (abalone) shells 100,000 years ago. Ochre, bone, charcoal, grindstones, and hammerstones form a composite part of this production toolkit. The application of the mixture is unknown, but possibilities include decoration and skin protection.

Early use of pressure flaking on lithic artifacts at Blombos Cave, South Africa.

Pressure flaking has been considered to be an Upper Paleolithic innovation dating to ~20,000 years ago (20 ka). Replication experiments show that pressure flaking best explains the morphology of lithic artifacts recovered from the ~75-ka Middle Stone Age levels at Blombos Cave, South Africa. The technique was used during the final shaping of Still Bay bifacial points made on heat-treated silcrete. Application of this innovative technique allowed for a high degree of control during the detachment of individual flakes, resulting in thinner, narrower, and sharper tips on bifacial points. This technology may have been first invented and used sporadically in Africa before its later widespread adoption.

Additional evidence for bone technology in the southern African Middle Stone Age.

Few Middle Stone Age sites have yielded convincing evidence for a complex bone technology, a behavior often associated with the emergence of modern cultures. Here, we review the published evidence for Middle Stone Age bone tools from southern Africa, analyze an additional nine bone artifacts recently recovered from Middle Stone Age levels at Blombos Cave, describe an unpublished bone tool from probable Middle Stone Age levels at Peers Cave, examine a single bone awl found at Blombosch Sands (an open site near Blombos Cave), and reappraise marked bone artifacts and a bone point recovered from Klasies River. To determine the chronological and cultural attribution of these artifacts, document bone-manufacturing techniques associated with the southern African MSA, and discuss the symbolic significance of the markings present on some of these objects we use (1) available contextual information; (2) morphometric comparison of Later Stone Age, Modern San, and purported Middle Stone Age projectile points; (3) analysis of the carbon/nitrogen content of bone tools and faunal remains from Peers and Blombos caves; and (4) microscopic analysis of traces of manufacture and use. Previously undescribed bone artifacts from Blombos Cave include a massive point manufactured on weathered bone, two complete awls and two awl tips manufactured on small-sized mammal and bird bone, a probable projectile point with a tang manufactured by knapping and scraping, a shaft fragment modified by percussion, used as retoucher and bearing a set of incised lines on the middle of the periosteal surface, and two fragments with possible engravings. The point from Peers Cave can be assigned to the Middle Stone Age and bears tiny markings reminiscent of those recorded on projectile points from Blombos and used as marks of ownership on San arrow points. The awl from Blombosch Sands and the bone point from Klasies River can be attributed to the Later Stone Age. Two notched objects from Klasies are attributed to the Middle Stone Age and interpreted as tools used on soft material; a third object bears possible deliberate symbolic engravings. Although low in number, the instances of bone artifacts attributable to the Middle Stone Age is increasing and demonstrates that the bone tools from Blombos Cave are not isolated instances. New discoveries of bone tools dating to this time period can be expected.

Extending the chronology of deposits at Blombos Cave, South Africa, back to 140 ka using optical dating of single and multiple grains of quartz.

Optically stimulated luminescence (OSL) measurements are reported for both single aliquots (of two different sizes) and single grains of quartz from deposits within Blombos Cave. Ages have been obtained for six sediments from the Middle Stone Age (MSA) occupation levels and for two sterile sands, one underlying the archaeological sediment and one overlying the Later Stone Age occupation levels. The ages for the archaeological sediments were obtained from single-grain measurements that enabled unrepresentative grains to be rejected. The MSA occupation levels have ages that, within error limits, are in stratigraphic order and fall between the OSL age for the oldest dune sand (143.2+/-5.5 ka) and a previously published OSL age for the sterile sand ( approximately 70 ka) that separates the Middle and Later Stone Age deposits. The earliest MSA archaeological phase, M3, from where fragments of ochre were found as well as human teeth, is dated to 98.9+/-4.5 ka, coinciding with the sea-level high of oxygen isotope substage 5c. The cave then appears to be unoccupied until oxygen isotope substage 5a on the basis of four OSL ages for archaeological phase M2, ranging from 84.6+/-5.8 to 76.8+/-3.1 ka; these levels contained large hearths and bone tools. An age of 72.7+/-3.1 ka was obtained for the final MSA archaeological phase, M1, from which deliberately engraved ochre and shell beads were recovered along with bifacial stone points. We conclude that the periods of occupation were determined by changes in sea level, with abundant sources of seafood available in times of high sea level and with the cave being closed by the accumulation of large dunes during periods of low sea level, such as during oxygen isotope stages 4 and 6.

The origin of modern human behavior.

Archaeology's main contribution to the debate over the origins of modern humans has been investigating where and when modern human behavior is first recognized in the archaeological record. Most of this debate has been over the empirical record for the appearance and distribution of a set of traits that have come to be accepted as indicators of behavioral modernity. This debate has resulted in a series of competing models that we explicate here, and the traits are typically used as the test implications for these models. However, adequate tests of hypotheses and models rest on robust test implications, and we argue here that the current set of test implications suffers from three main problems: (1) Many are empirically derived from and context-specific to the richer European record, rendering them problematic for use in the primarily tropical and subtropical African continent. (2) They are ambiguous because other processes can be invoked, often with greater parsimony, to explain their character. (3) Many lack theoretical justification. In addition, there are severe taphonomic problems in the application of these test implications across differing spans of time. To provide adequate tests of these models, archaeologists must first subject these test implications to rigorous discussion, which is initiated here.

Additional human remains from Blombos Cave, South Africa: (1999-2000 excavations).

The uppermost Middle Stone Age (MSA) layers at Blombos Cave contain high densities of Still Bay bifacial points. Information from other regional sites places the Still Bay prior to the Howiesons Poort industry, which has been dated at 65-70 ka. The Blombos Cave MSA strata have yielded nine human teeth or dental fragments. Four that were recovered during the 1997-1998 excavations have been published elsewhere. The remaining five were discovered during the 1999-2000 field seasons; these are described here. Three of the new specimens are deciduous teeth, and two are permanent premolar and molar crown fragments. The entire dental sample probably represents at least five and as many as seven individuals. The deciduous teeth from the upper MSA levels are likely to have been exfoliated in the cave. One deciduous tooth and the permanent tooth fragments from the lower MSA levels probably represent three individuals who died in or near the cave. The Blombos Cave premolars preserve horizontal circum-cervical striae suggestive of palliative tooth pick use. Approximately half of the permanent and deciduous crown diameters exceed those of recent Africans; for the remainder, the fossil values fall among modern African sample means. The Blombos Cave tooth crowns tend to be smaller than the majority of penecontemporaneous Neandertal teeth. The morphology of the Blombos Cave di is comparable to MSA homologues from the nearby, and presumably somewhat younger site of Die Kelders Cave 1.

Emergence of modern human behavior: Middle Stone Age engravings from South Africa.

In the Eurasian Upper Paleolithic after about 35,000 years ago, abstract or depictional images provide evidence for cognitive abilities considered integral to modern human behavior. Here we report on two abstract representations engraved on pieces of red ochre recovered from the Middle Stone Age layers at Blombos Cave in South Africa. A mean date of 77,000 years was obtained for the layers containing the engraved ochres by thermoluminescence dating of burnt lithics, and the stratigraphic integrity was confirmed by an optically stimulated luminescence age of 70,000 years on an overlying dune. These engravings support the emergence of modern human behavior in Africa at least 35,000 years before the start of the Upper Paleolithic.