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.

The stratigraphy and formation of Middle Stone Age deposits in Cave 1B, Klasies River Main site, South Africa, with implications for the context, age, and cultural association of the KRM 41815/SAM-AP 6222 human mandible.

Cave 1B, in the Klasies River Main site complex (KRM), is best known for the recovery of the KRM 41815/SAM-AP 6222 human mandible. After initial skepticism over the modernity of this specimen, it is accepted that the mix of archaic and modern traits it displays is characteristic of early Homo sapiens individuals. Different authors have associated this specimen with the Middle Stone Age (MSA) I and II/Mossel Bay cultural phases, but the published data do not allow an unambiguous attribution. KRM 41815's frequent use in studies of the evolution of the human mandible, and its well-developed chin, makes clarifying its age and context important objectives. The field and micromorphology observations presented here provide greater insight into the stratigraphy and formation of the sequence exposed in the PP38 excavation. There are three major divisions: the basal Light Brown Sand (LBS) Member (not excavated), the Rubble Sand (RS) Member (MSA I), and the Shell and Sand Dark Carbonized (SASDC) Submember (MSA II). Cultural stratigraphy based on lithic artifacts remains the only way to make secure (but broad) temporal correlations with the rest of the site complex. This investigation shows that a range of anthropogenic, geogenic, and biogenic processes contributed to the deposition and post-depositional alteration of the identified microfacies. Short depositional hiatuses are reasonably common, and a significant hiatus was identified between the RS and SASDC. The impact of post-depositional processes on the RS is significant, with anthropogenic deposits poorly preserved. In comparison, the SASDC is dominated by hearths contained within deposits rich in reworked anthropogenic materials known as carbonized partings. Small shell disposal features are also present. The distribution of these anthropogenic features suggests continuity in the management of space throughout the MSA II occupations, from before 110 ka. New stratigraphic correlations indicate that KRM 41815 is unambiguously associated with the MSA I. Therefore, it predates 110 ka, with a lower age limit potentially in Marine Isotope Stage 6.

Cooked starchy food in hearths ca. 120 kya and 65 kya (MIS 5e and MIS 4) from Klasies River Cave, South Africa.

Plant carbohydrates currently constitute 55-80% of the modern human diet (FAO and WHO, 1997) and some of today's key global health issues are associated with excessive carbohydrate consumption. However, starch carbohydrate is still a poorly understood element of modern human diet and our past starch diet may provide insights for future research. Despite an archaeological narrative that links our early hominin ancestors to a diet that is rich in roots and tubers, there is little deep time archaeological evidence of human plant starch consumption. Geneticists hypothesise that the duplication of starch digestion genes in early Homo sapiens (∼300 kya), is an adaptive response to an increased starch diet. Here we offer the earliest evidence of identified fragments of charred starch plant tissue (parenchyma) from cave and rock shelter hearths dated to Marine Isotope Stage (MIS) 5e and MIS 4, from the Middle Stone Age (MSA) site of Klasies River main site, South Africa (34.06°S, 24.24°E).

Human (Clovis)-gomphothere (Cuvieronius sp.) association ∼ 13,390 calibrated yBP in Sonora, Mexico.

The earliest known foragers to populate most of North America south of the glaciers [∼ 11,500 to ≥ ∼ 10,800 (14)C yBP; ∼ 13,300 to ∼ 12,800 calibrated (Cal) years] made distinctive "Clovis" artifacts. They are stereotypically characterized as hunters of Pleistocene megamammals (mostly mammoth) who entered the continent via Beringia and an ice-free corridor in Canada. The origins of Clovis technology are unclear, however, with no obvious evidence of a predecessor to the north. Here we present evidence for Clovis hunting and habitation ∼ 11,550 yBP (∼ 13,390 Cal years) at "El Fin del Mundo," an archaeological site in Sonora, northwestern Mexico. The site also includes the first evidence to our knowledge for gomphothere (Cuvieronius sp.) as Clovis prey, otherwise unknown in the North American archaeological record and terminal Pleistocene paleontological record. These data (i) broaden the age and geographic range for Clovis, establishing El Fin del Mundo as one of the oldest and southernmost in situ Clovis sites, supporting the hypothesis that Clovis had its origins well south of the gateways into the continent, and (ii) expand the make-up of the North American megafauna community just before extinction.

A forager-herder trade-off, from broad-spectrum hunting to sheep management at Asikli Höyük, Turkey.

Asikli Höyük is the earliest known preceramic Neolithic mound site in Central Anatolia. The oldest Levels, 4 and 5, spanning 8,200 to approximately 9,000 cal B.C., associate with round-house architecture and arguably represent the birth of the Pre-Pottery Neolithic in the region. Results from upper Level 4, reported here, indicate a broad meat diet that consisted of diverse wild ungulate and small animal species. The meat diet shifted gradually over just a few centuries to an exceptional emphasis on caprines (mainly sheep). Age-sex distributions of the caprines in upper Level 4 indicate selective manipulation by humans by or before 8,200 cal B.C. Primary dung accumulations between the structures demonstrate that ruminants were held captive inside the settlement at this time. Taken together, the zooarchaeological and geoarchaeological evidence demonstrate an emergent process of caprine management that was highly experimental in nature and oriented to quick returns. Stabling was one of the early mechanisms of caprine population isolation, a precondition to domestication.

Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep (Ovis aries).

Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Asikli Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Asikli Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Asikli Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations.

High-resolution sediment analysis reveals Middle Bronze Age byre-houses at the site of Oppeano (Verona province, NE Italy).

High-resolution sediment analysis allowed us to identify two Middle Bronze Age (MBA 1, 1650-1550 cal a BCE) byre-houses at the waterlogged site of Oppeano "4D", south of Verona (Veneto region, NE Italy). The site lies in a low-lying valley incised by the Adige River in its LGM alluvial fan. In this fluvio-palustrine environment burial and taphonomic conditions were such that the archaeological record was extremely well preserved. The wooden elements making up basal parts of nine 'huts' were in fact exposed at Oppeano, and so were their internal accretion deposits. These featured finely laminated dung units deriving from the stalling of small herbivores, possibly ovicaprids, intercalated with repeated accumulations of wood ash. This was produced in large and multi-stratified hearths that were exposed within each hut. Organic petrology provided evidence of the production of wood tar inside one of the studied structures. At Oppeano 4D it was thus demonstrated that these structures were not just byres or stables, but spaces that housed humans together with animals at least during some periods of the year, hence byre-houses. The identification of byre-houses in a Middle Bronze Age settlement is key for the reconstruction of socio-economic aspects of Bronze Age economy and production systems.

Early Middle Stone Age personal ornaments from Bizmoune Cave, Essaouira, Morocco.

Ornaments such as beads are among the earliest signs of symbolic behavior among human ancestors. Their appearance signals important developments in both cognition and social relations. This paper describes and presents contextual information for 33 shell beads from Bizmoune Cave (southwest Morocco). Many of the beads come as deposits dating to ≥142 thousand years, making them the oldest shell beads yet recovered. They extend the dates for the first appearance of this behavior into the late Middle Pleistocene. The ages and ubiquity of beads in Middle Stone Age (MSA) sites in North Africa provide further evidence of the potential importance of these artifacts as signals of identity. The early and continued use of Tritia gibbosula and other material culture traits also suggest a remarkable degree of cultural continuity among early MSA Homo sapiens groups across North Africa.

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.