Grey wolf genomic history reveals a dual ancestry of dogs.

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1-8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

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 genomic history of southeastern Europe.

Farming was first introduced to Europe in the mid-seventh millennium bc, and was associated with migrants from Anatolia who settled in the southeast before spreading throughout Europe. Here, to understand the dynamics of this process, we analysed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12000 and 500 bc. We document a west-east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe.

Ancient DNA of narrow-headed vole reveal common features of the Late Pleistocene population dynamics in cold-adapted small mammals.

The narrow-headed vole, collared lemming and common vole were the most abundant small mammal species across the Eurasian Late Pleistocene steppe-tundra environment. Previous ancient DNA studies of the collared lemming and common vole have revealed dynamic population histories shaped by climatic fluctuations. To investigate the extent to which species with similar adaptations share common evolutionary histories, we generated a dataset comprised the mitochondrial genomes of 139 ancient and 6 modern narrow-headed voles from several sites across Europe and northwestern Asia covering approximately the last 100 thousand years (kyr). We inferred Bayesian time-aware phylogenies using 11 radiocarbon-dated samples to calibrate the molecular clock. Divergence of the main mtDNA lineages across the three species occurred during marine isotope stages (MIS) 7 and MIS 5, suggesting a common response of species adapted to open habitat during interglacials. We identified several time-structured mtDNA lineages in European narrow-headed vole, suggesting lineage turnover. The timing of some of these turnovers was synchronous across the three species, allowing us to identify the main drivers of the Late Pleistocene dynamics of steppe- and cold-adapted species.

Early evidence for bear exploitation during MIS 9 from the site of Schöningen 12 (Germany).

A cutmarked bear metatarsal and phalanx from the German open-air sites of Schöningen 12 II-1 and 12 B, respectively, correlated with the interglacial optimum of MIS 9 (ca. 320 ka), provide early evidence for the exploitation of bear skins. Archaeological sites with evidence of bear exploitation from the Lower Paleolithic are rare, with only Boxgrove (United Kingdom) and Bilzingsleben (Germany) yielding cutmarked bear bones indicating skinning. We interpret these finds as evidence for bear hunting and primary access since bear skins are best extracted shortly after the animal's death. The very thin cutmarks found on the Schöningen specimens indicate delicate butchering and show similarities in butchery patterns to bears from other Paleolithic sites. The Eurasian Lower Paleolithic record does not show any evidence for the exploitation of bear meat; only Middle Paleolithic sites, such as Biache-Saint-Vaast (France; ca. 175 ka) and Taubach (Germany; ca. 120 ka), yield evidence for the exploitation of both skin and meat from bear carcasses. Bear skins have high insulating properties and might have played a role in the adaptations of Middle Pleistocene hominins to the cold and harsh winter conditions of Northwestern Europe.

Bayesian luminescence dating at Ghar-e Boof, Iran, provides a new chronology for Middle and Upper Paleolithic in the southern Zagros.

Ghar-e Boof is a Paleolithic cave site in Iran well known for its rich early Upper Paleolithic Rostamian assemblages. The site is located on the edge of the Dasht-e Rostam plain in the southern Zagros. Recent excavations by the members of the Tübingen-Iranian Stone Age Research Project at Ghar-e Boof also recovered well-stratified Middle Paleolithic assemblages. Here, we provide the first detailed luminescence chronology for the Middle and Upper Paleolithic of the site. More generally, our work is the first luminescence chronology for a Middle and Upper Paleolithic site in the Zagros Mountains region in Iran. The luminescence ages for the Upper Paleolithic of Ghar-e Boof agree with published 14C dates. We applied Bayesian models specifically designed for luminescence dating using the R package 'BayLum' to incorporate the well-established stratigraphic constraints, as well as the published 14C ages with our optically stimulated luminescence (OSL) ages to improve the precision of the chronological framework. The Bayesian chronology shows a significantly improved precision of the OSL ages in particular for the upper part of the sequence where 14C ages were available. The Bayesian OSL ages for the Rostamian horizons, archaeologicalhorizon (AH) III (a-b-c), and AH IV, fall in the range of 37-42 ka (68% credible interval [CI]). Moreover, we determined a series of dates between 45 and 81 ka (68% CI) for the Middle Paleolithic strata from AH IVd to AH VI. Our results point to a demographic shift in the populations responsible for the Middle Paleolithic and the Rostamian within three millennia. This major technological change accompanied by the rise of symbolic artifacts such as personal ornaments, may or may not reflect a replacement of Neanderthals by modern humans. While we are confident that the Rostamian was made by modern humans, available information does not allow us to be sure who made the local Middle Paleolithic.

Early anthropogenic use of hematite on Aurignacian ivory personal ornaments from Hohle Fels and Vogelherd caves, Germany.

The Aurignacian (ca. 43-35 ka) of southwestern Germany is well known for yielding some of the oldest artifacts related to symbolic behaviors, including examples of figurative art, musical instruments, and personal ornaments. Another aspect of these behaviors is the presence of numerous pieces of iron oxide (ocher); however, these are comparatively understudied, likely owing to the lack of painted artifacts from this region and time period. Several Aurignacian-aged carved ivory personal ornaments from the sites of Hohle Fels and Vogelherd contain traces of what appear to be red ocher residues. We analyzed these beads using a combination of macroanalytical and microanalytical methods, including scanning electron microscopy equipped with energy dispersive spectroscopy and Raman spectroscopy. We found that the residue is composed of the iron oxide mineral hematite (Fe2O3). Further analyses on associated archaeological sediments by X-ray diffraction revealed the absence of hematite and other iron oxide mineral phases, suggesting that the hematite residues were intentionally applied to the ivory personal ornaments by human agents. These findings have important implications as they represent evidence for the direct application of ocher on portable symbolic objects by early Homo sapiens in Europe. Furthermore, our results reveal shared behavioral practices from two key Aurignacian sites maintained over several millennia and illuminate aspects of pigment use and symbolic practices during a pivotal time in the cultural evolution of humans.

Ecosystem engineering in the Quaternary of the West Coast of South Africa.

Despite advances in our understanding of the geographic and temporal scope of the Paleolithic record, we know remarkably little about the evolutionary and ecological consequences of changes in human behavior. Recent inquiries suggest that human evolution reflects a long history of interconnections between the behavior of humans and their surrounding ecosystems (e.g., niche construction). Developing expectations to identify such phenomena is remarkably difficult because it requires understanding the multi-generational impacts of changes in behavior. These long-term dynamics require insights into the emergent phenomena that alter selective pressures over longer time periods which are not possible to observe, and are also not intuitive based on observations derived from ethnographic time scales. Generative models show promise for probing these potentially unexpected consequences of human-environment interaction. Changes in the uses of landscapes may have long term implications for the environments that hominins occupied. We explore other potential proxies of behavior and examine how modeling may provide expectations for a variety of phenomena.

The timing and spatiotemporal patterning of Neanderthal disappearance.

The timing of Neanderthal disappearance and the extent to which they overlapped with the earliest incoming anatomically modern humans (AMHs) in Eurasia are key questions in palaeoanthropology. Determining the spatiotemporal relationship between the two populations is crucial if we are to understand the processes, timing and reasons leading to the disappearance of Neanderthals and the likelihood of cultural and genetic exchange. Serious technical challenges, however, have hindered reliable dating of the period, as the radiocarbon method reaches its limit at ∼50,000 years ago. Here we apply improved accelerator mass spectrometry (14)C techniques to construct robust chronologies from 40 key Mousterian and Neanderthal archaeological sites, ranging from Russia to Spain. Bayesian age modelling was used to generate probability distribution functions to determine the latest appearance date. We show that the Mousterian ended by 41,030-39,260 calibrated years bp (at 95.4% probability) across Europe. We also demonstrate that succeeding 'transitional' archaeological industries, one of which has been linked with Neanderthals (Châtelperronian), end at a similar time. Our data indicate that the disappearance of Neanderthals occurred at different times in different regions. Comparing the data with results obtained from the earliest dated AMH sites in Europe, associated with the Uluzzian technocomplex, allows us to quantify the temporal overlap between the two human groups. The results reveal a significant overlap of 2,600-5,400 years (at 95.4% probability). This has important implications for models seeking to explain the cultural, technological and biological elements involved in the replacement of Neanderthals by AMHs. A mosaic of populations in Europe during the Middle to Upper Palaeolithic transition suggests that there was ample time for the transmission of cultural and symbolic behaviours, as well as possible genetic exchanges, between the two groups.

New electron spin resonance (ESR) ages from Geißenklösterle Cave: A chronological study of the Middle and early Upper Paleolithic layers.

Geißenklösterle Cave (Germany) is one of the most important Paleolithic sites in Europe, as it is characterized by human occupation during the Middle and early Upper Paleolithic. Aurignacian layers prior to 37-38 ka cal BP feature both musical and figurative art objects that are linked to the early arrival in Europe of Homo sapiens. Middle Paleolithic layers yielded lithic artifacts attributed to Homo neanderthalensis. Since human occupation at the site is attributed to both Neanderthals and modern humans, chronology is essential to clarify the issues of Neanderthal disappearance, modern human expansion in Europe, and the origin of the Aurignacian in Western Europe. Electron spin resonance (ESR) dating was performed on fossil tooth enamel collected from the Middle Paleolithic layers, which are beyond the radiocarbon dating range, and from the nearly sterile 'transitional' geological horizon (GH) 17 and the lower Aurignacian deposits, to cross-check ESR ages with previous radiocarbon, thermoluminescence and ESR age results. The Middle Paleolithic layers were dated between 94 ± 10 ka (GH 21) and 55 ± 6 ka (GH 18) by ESR on tooth enamel. Mean ages for GH 17, at 46 ± 3 ka, and for the lower Aurignacian layers, at 37 ± 3 ka, are in agreement with previous dating results, thus supporting the reliability of ESR chronology for the base of the sequence where dating comparisons are not possible. These results suggest that Neanderthals occupied the site from Marine Isotope Stage (MIS) 5 to the second half of MIS 3 and confirm the antiquity of early Aurignacian deposits. The presence of an almost sterile layer that separates Middle and Upper Paleolithic occupations could be related to the abandonment of the site by Neanderthals, possibly during Heinrich Stadial 5 (ca. 49-47 ka), thus before the arrival of H. sapiens in the area around 42 ka cal BP. These dates for the Middle Paleolithic of the Swabian Jura represent an important contribution to the prehistory of the region, where nearly all of the excavations were conducted decades ago and prior to the development of reliable radiometric dating beyond the range of radiocarbon.

Site fragmentation, hominin mobility and LCT variability reflected in the early Acheulean record of the Okote Member, at Koobi Fora, Kenya.

From its initial appearance at ∼1.7 Ma, the Acheulean was prevalent through a vast chronological span of hominin behavioural evolution that lasted nearly 1.5 million years. The origins and production patterns of large bifacial cutting tools ('LCTs') - the marker of the Acheulean techno-complex - and the systematic changes in this behaviour through time are gaining increasing interest in paleoanthropology. Here we provide a synthesis of early Acheulean LCT variation in a landscape context by analysing assemblages from four different quasi-contemporaneous (∼1.4 Ma) sites from the Koobi Fora Formation. We characterize this variation using both 3D geometric morphometric and descriptive approaches. The expansive lateral exposures of fluvial and lacustrine sediments, as well as the associated tephrostratigraphy of the Koobi Fora Formation provide the landscape context that enables these comparative analyses. Our study demonstrates that when multiple contemporaneous early Acheulean localities are analysed together, a broader picture of LCT variability is elucidated. Four sites at Koobi Fora appear to represent a single system of lithic economy, characterized by a discrete trajectory of changes in LCT size and shape. These sites have ranges of LCT forms which appear to represent different but overlapping stages on a single reduction trajectory. Certain sites exhibit the full reduction trajectory while others exhibit only fragments of this trajectory. Other inter-site lithic proxies further complement these patterns in LCT variability. We explore patterns of site function, mobility and hominin landscape use, all of which may be suggestive of a depth of planning in early Acheulean hominins wherein technological activities were undertaken in substantial anticipation of future needs.

Combined Non-invasive PIXE/PIGE Analyses of Mammoth Ivory from Aurignacian Archaeological Sites.

Among the earliest Homo sapiens societies in Eurasia, the Aurignacian phase of the Early Upper Paleolithic, approximately 40 000-30 000 years ago, mammoth ivory assumed great social and economic significance, and was used to create hundreds of personal ornaments as well as the earliest known works of three-dimensional figurative art in the world. This paper reports on the results of micro-PIXE/PIGE analyses of mammoth-ivory artifacts and debris from five major sites of Aurignacian ivory use. Patterns of variable fluorine content indicate regionally distinctive strategies of ivory procurement that correspond to apparent differences in human-mammoth interactions. Preserved trace elements (Br, Sr, Zn) indicate that differences at the regional level are applicable to sourcing Paleolithic ivory at the regional scale.

Chronometric investigations of the Middle to Upper Paleolithic transition in the Zagros Mountains using AMS radiocarbon dating and Bayesian age modelling.

The Middle to Upper Paleolithic transition is often linked with a bio-cultural shift involving the dispersal of modern humans outside of Africa, the concomitant replacement of Neanderthals across Eurasia, and the emergence of new technological traditions. The Zagros Mountains region assumes importance in discussions concerning this period as its geographic location is central to all pertinent hominin migration areas, pointing to both east and west. As such, establishing a reliable chronology in the Zagros Mountains is crucial to our understanding of these biological and cultural developments. Political circumstance, coupled with the poor preservation of organic material, has meant that a clear chronological definition of the Middle to Upper Paleolithic transition for the Zagros Mountains region has not yet been achieved. To improve this situation, we have obtained new archaeological samples for AMS radiocarbon dating from three sites: Kobeh Cave, Kaldar Cave, and Ghar-e Boof (Iran). In addition, we have statistically modelled previously published radiocarbon determinations for Yafteh Cave (Iran) and Shanidar Cave (Iraqi Kurdistan), to improve their chronological resolution and enable us to compare the results with the new dataset. Bayesian modelling results suggest that the onset of the Upper Paleolithic in the Zagros Mountains dates to 45,000-40,250 cal BP (68.2% probability). Further chronometric data are required to improve the precision of this age range.

The behavioral and cultural stratigraphic contexts of the lithic assemblages from Schöningen.

Within the various archaeological horizons in Schöningen, the presence of hominins is repeatedly demonstrated by the recovery of stone artifacts, broken bones, and bones with cut marks. The Spear Horizon, 13 II-4, with its ca. 1500 stone artifacts and ca. 12,000 faunal remains, represents by far the richest archaeological layers in Schöningen. Systematic waterscreening over a period of 15 years has fostered the recovery of numerous small flakes that otherwise would have remained undetected. Based on the stone artifacts published by H. Thieme and the lithic artifacts recovered from the ongoing excavations of the University of Tübingen and the Archaeological Heritage Office of Lower Saxony since 2008, we present here the main aspects of these lithic assemblages. The main features of the lithic assemblages recovered from the different find horizons and concentrations provide a consistent signature, suggesting a robust and repetitive technological strategy. The assemblages, which are made of local, high quality flint, lack handaxes and are clearly not related to the Acheulean. Intensely retouched scrapers, as well as denticulates, notched pieces, and points on thick flakes, angular debris, and non-anthropogenic thermal spalls are the most numerous retouched forms. The assemblages also contain a smaller number of thinner forms. Reduction sequences are short and Levallois technology is absent. Although some of the retouched forms are reminiscent of the Middle Paleolithic, the relatively non-standardized short reduction sequences technically oriented toward the production of thick and broad flakes are consistent with a classification in the late Lower Paleolithic.

Bone taphonomy of the Schöningen "Spear Horizon South" and its implications for site formation and hominin meat provisioning.

This paper presents the faunal remains from the new excavation area at the Lower Paleolithic site of Schöningen. The focus of the study is on the southern extension of the main find horizon (Spear Horizon South), which includes the layer that yielded the famous Schöningen spears (13 II-4). Taxonomic data corroborate previous studies, that hominins primarily hunted Equus mosbachensis, a large Pleistocene horse. Equid body part representation at the site suggests that the animals were hunted and butchered locally. There is no evidence for density-mediated attrition in the assemblage. Weathering damage is uncommon, though there is ample evidence that carnivores had access to the bone. Carnivore bite sizes were measured and compared to experimental data provided by previous authors. Based on relationships between bite size and carnivore behavior and body size, we conclude that the primary modifying agents were large carnivores (i.e., wolves or saber-toothed cats). Previous studies show that carnivores often had secondary access to the remains, after hominins. Cut marks are commonly arranged haphazardly on the bones. This may indicate that multiple hominins participated in the butchery of horse skeletons, or that they were butchered over the course of hours or days. Cut marks on axial elements are more "orderly," which probably reflects the physical logistics of orienting one's body in relation to a large carcass. These data differ from sites formed by Middle and Upper Paleolithic hominins, which might suggest that in later times, a system of organized meat provisioning was already in place. Taken together, the faunal evidence from the Spear Horizon South indicates that late Lower Paleolithic hominins using the site understood the behaviors of different prey species, hunted socially to take down large game, and successfully competed with large carnivores on the landscape for primary access to ungulate remains.

Overview and new results from large-scale excavations in Schöningen.

Archaeological finds including spears, other wooden artifacts, lithic artifacts, and bones with impact scars and cut marks document the repeated presence of hominins on the shoreline of an approximately 300,000 year old lake near Schöningen in Northern Germany. Continuing excavations have uncovered in the locality "Schöningen" at least 20 sites dating to the late Lower Paleolithic. Schöningen is therefore not only a singular archaeological site with remarkable finds; it is a vast locality that preserves a multifaceted archaeological landscape with numerous sites. Ongoing excavations have exposed several large surfaces with organic materials dating to MIS 9. In particular, recent excavations have uncovered new sections belonging to the original Spear Horizon from Schöningen 13 II-4 (the Horse Butchery Site). Current research in Schöningen places the exceptional artifacts within a spatial and environmental context, and provides a wealth of new information on the subsistence strategies and settlement dynamics of the inhabitants of these short-term lakeside occupations. Schöningen, with an overall excavated area of 9400 m(2), is one of the largest excavated archaeological localities from MIS 9. Here we present a summary of all the sites, as well as the most relevant excavated areas since 2008 (excavations Tübingen/NLD).

Residue and microwear analyses of the stone artifacts from Schöningen.

Stone artifacts from Schöningen 12 and 13 were examined microscopically to identify residues, wear, and manufacturing traces in order to clarify their possible anthropogenic origins and their function. We present evidence showing that the stone tools were used for working wood and hide and for cutting meat. The results from the use-wear and residue analyses proved complementary in several instances. Suggestive evidence of hafting was observed on a few pieces, which is particularly interesting given the identification of wooden hafts at the site. The positive results of this analysis demonstrate the efficacy and potential of these techniques for Lower Paleolithic sites such as Schöningen.

A new approach for deciphering between single and multiple accumulation events using intra-tooth isotopic variations: Application to the Middle Pleistocene bone bed of Schöningen 13 II-4.

It is often difficult to differentiate between archaeological bonebeds formed by one event such as a mass kill of a single herd, and those formed by multiple events that occurred over a longer period of time. The application of high temporal resolution studies such as intra-tooth isotopic profiles on archaeological mammal cohorts offers new possibilities for exploring this issue, allowing investigators to decipher between single and multiple accumulation events. We examined (18)O and (13)C isotopic variations from the enamel carbonate of 23 horse third molars from the Middle Pleistocene archaeological site of Schöningen. We employed a new approach to investigate processes of fossil accumulation that uses both bulk and intra-tooth isotopic variations and takes into account animal behavior, age at death and dental development to test the degree of isotopic affinity of animals from the same fossil assemblage. Oxygen and carbon isotope bulk values indicate that the horses from Schöningen 13 II-4 experienced relatively similar climatic and dietary regimes. Inter-individual differences of the bulk values of the horses sampled in the current study present nevertheless inter-individual variability similar to individuals from multi-layered localities. In addition, the intra-tooth isotopic variation of specimens of the same age at death seems to indicate that the studied cohort corresponds to a mix of individuals that recorded both similar and different isotopic histories. Finally, the conditions recorded in the isotopic signal shortly before death (i.e., for teeth not fully mineralized) varied between sampled individuals, suggesting possible differences in the seasonality of death. Considering those results, we discuss the possibility that the horses from Schöningen 13 II-4 correspond to an accumulation of different death events.

Characterizing the Lower Paleolithic bone industry from Schöningen 12 II: A multi-proxy study.

Although preservation of Paleolithic faunal assemblages from open-air settings is often poor, the Lower Paleolithic sites of Schöningen provide exceptionally well-preserved mammalian faunal material for investigating hominin/animal relationships. Pleistocene fossil assemblages, however, usually reflect a complex taphonomic history in which natural and anthropogenic processes are often superimposed. A number of examples of osseous finds that resemble tools were recently discovered in the MIS 9 deposits of Schöningen 12 II. Non-anthropogenic agents are known to produce surface modifications mimicking human artifacts and the identification of osseous remains used and/or deliberately modified by ancient hominins is often controversial in such old contexts. Multiple lines of evidence are thus useful for distinguishing between osseous artifacts and "eco-facts". In this paper, the recognition of the use of bone for different technological purposes by late Middle Pleistocene hominins is addressed through a multi-proxy study combining geoarcheology, bone taphonomy, zooarcheology, and use-wear analysis. This allowed the identification of the processes and agents responsible for the formation and modification of the different bone assemblages of Schöningen 12 II. Our analysis points to different types of bones having been likely used as tools. These results expand the diversity of the organic technological repertoire of the Middle Pleistocene hominins, making Schöningen 12 II a remarkable new source of information on osseous technology long before the Upper Paleolithic, the period traditionally viewed as the start of the systematic use of bone tools. Together with other observations of bone tools documented during the Lower and Middle Paleolithic, the results from Schöningen show that archeologists may have underestimated the diversity and importance of osseous technology among archaic hominins.