A double-blind comparison of morphological and collagen fingerprinting (ZooMS) methods of skeletal identifications from Paleolithic contexts

Modeling the subsistence strategies of prehistoric groups depends on the accuracy of the faunal identifications that provide the basis for these models. However, our knowledge remains limited about the reproducibility of published taxonomic identifications and how they accurately reflect the range of species deposited in the archaeological record. This study compares taxonomic identifications at three Paleolithic sites (Saint-Césaire and Le Piage in France, Crvena Stijena in Montenegro) characterized by high levels of fragmentation. Identifications at these sites were derived using two methods: morphological identification and collagen fingerprinting, the latter a peptide-based approach known as ZooMS. Using a double-blind experimental design, we show that the two methods give taxonomic profiles that are statistically indistinguishable at all three sites. However, rare species and parts difficult to identify such as ribs seem more frequently associated with errors of identification. Comparisons with the indeterminate fraction indicate that large game is over-represented in the ZooMS sample at two of the three sites. These differences possibly signal differential fragmentation of elements from large species. Collagen fingerprinting can produce critical insights on the range distribution of animal prey in the past while also contributing to improved models of taphonomic processes and subsistence behavior.

Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants.

New insights on interpersonal violence in the Late Pleistocene based on the Nile valley cemetery of Jebel Sahaba

The remains of 61 individuals buried in the cemetery of Jebel Sahaba (site 117) offer unique and substantial evidence to the emergence of violence in the Nile Valley at the end of the Late Pleistocene. Excavated and assessed in the 1960s, some of the original findings and interpretations are disputed. A full reanalysis of the timing, nature and extent of the violence was conducted through the microscopic characterization of the nature of each osseous lesion, and the reassessment of the archaeological data. Over 100 previously undocumented healed and unhealed lesions were identified on both new and/or previously identified victims, including several embedded lithic artefacts. Most trauma appears to be the result of projectile weapons and new analyses confirm for the first time the repetitive nature of the interpersonal acts of violence. Indeed, a quarter of the skeletons with lesions exhibit both healed and unhealed trauma. We dismiss the hypothesis that Jebel Sahaba reflects a single warfare event, with the new data supporting sporadic and recurrent episodes of inter-personal violence, probably triggered by major climatic and environmental changes. At least 13.4 ka old, Jebel Sahaba is one of the earliest sites displaying interpersonal violence in the world.

Characterisation of charred organic matter in micromorphological thin sections by means of Raman spectroscopy

Burned or charred organic matter in anthropogenic combustion features may provide important clues about past human activities related to fire. To interpret archaeological hearths, a correct identification of the organic source material is key. In the present work, Raman spectroscopy is applied to characterise the structural properties of char produced in laboratory heating- and open-fire experiments. This reference data set is compared to analyses of three different archaeological sites with Middle Palaeolithic combustion contexts. The results show that it is possible to determine whether a charred fragment is the product of burning animal-derived matter (e.g. meat) or plant-derived matter (e.g. wood) by plotting a few Raman spectral parameters (i.e. position of G and D bands, and intensity ratios H _D/H _G and H _V/H _G) against one another. The most effective parameters for discriminating animal- from plant-derived matter are the position of the G band and the H _V/H _G intensity ratio. This method can be applied on raw sample material and on uncovered micromorphological thin sections. The latter greatly compliments micromorphology by providing information about char fragments without any clear morphological characteristics. This study is the first of its kind and may provide archaeologists with a robust new method to distinguish animal- from plant-derived char in thin sections.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12520-020-01263-3.

The evolutionary history of Neanderthal and Denisovan Y chromosomes

Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.

Biocultural diversity in Late Pleistocene/Early Holocene Africa: Olduvai Hominid 1 (Tanzania) biological affinity and intentional body modification

OBJECTIVES

The dentition of Olduvai Hominid 1 (OH1) exhibits an anomalous pattern of dental wear that was originally attributed to either intentional cultural modification (filing) or plant processing behaviors. A differential diagnosis of the wear and assessment of the biological affinity of OH1 is presented.

MATERIALS AND METHODS

Macroscopic and microscopic observations of all labial and buccal tooth surfaces were undertaken to assess wear patterns. A multivariate analysis of mandibular morphology of OH1 compared to other Late Pleistocene, Holocene, and recent modern humans was used to ascertain biological affinity.

RESULTS

The morphological variation of the OH1 mandible is closely aligned with variation in penecontemporaneous fossils from Africa and outside that of recent humans. The concave wear facets exposing dentin on the labial surfaces of all three preserved mandibular incisors is confirmed. Substantial loss of labial/buccal surfaces was documented on the surfaces of all in situ maxillary and mandibular canines, premolars, and molars ranging from distinct facets with well-defined edges, to blunting or "polishing" around areas of maximum buccal curvature. The wear on both the anterior and postcanine teeth closely resemble that caused by adornments ("labrets") worn in lower-lip and buccal facial piercings known from bioarchaeological and ethnographic contexts. The wear pattern suggests that the OH1 wore three facial piercings-two buccal/lateral and a medial one in the lower lip.

DISCUSSION

Our findings suggest that the expression of social identities through intentional body modification is more diverse than previously documented elsewhere in Africa during the Late Pleistocene (i.e., ablation) and Early Holocene (i.e., ablation, chipping, and filing).

Ancient West African foragers in the context of African population history

Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children-two of whom were buried approximately 8,000 years ago and two 3,000 years ago-from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group1-11. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region12,13. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today-as well as speakers of Bantu languages from across the continent-are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.

Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals

A fully sequenced high-quality genome has revealed in 2010 the existence of a human population in Asia, the Denisovans, related to and contemporaneous with Neanderthals. Only five skeletal remains are known from Denisovans, mostly molars; the proximal fragment of a fifth finger phalanx used to generate the genome, however, was too incomplete to yield useful morphological information. Here, we demonstrate through ancient DNA analysis that a distal fragment of a fifth finger phalanx from the Denisova Cave is the larger, missing part of this phalanx. Our morphometric analysis shows that its dimensions and shape are within the variability of Homo sapiens and distinct from the Neanderthal fifth finger phalanges. Thus, unlike Denisovan molars, which display archaic characteristics not found in modern humans, the only morphologically informative Denisovan postcranial bone identified to date is suggested here to be plesiomorphic and shared between Denisovans and modern humans.

Reconstructing the genetic history of late Neanderthals

Although it is known that Neandertals contributed DNA to modern humans1,2, not much is known about the genetic diversity of Neandertals or the relationship between late Neandertal populations at the time when their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neandertal individuals has been limited by poor preservation of endogenous DNA3 and large amounts of microbial and present-day human DNA that contaminate Neandertal skeletal remains3–5. Here we use hypochlorite treatment6 of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five 39,000- to 47,000-year-old Neandertals (i.e. late Neandertals), thereby doubling the number of Neandertals for which genome sequences are available. Genetic similarity among late Neandertals is well predicted by their geographical location, and comparison to the genome of an older Neandertal from the Caucasus2,7 indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neandertal history. We find that the bulk of Neandertal gene flow into early modern humans originated from one or more source populations that diverged from the Neandertals studied here at least 70,000 years ago, but after they split from a previously sequenced Neandertal from Siberia2 ~150,000 years ago. Although four of these Neandertals post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.

Neandertal cannibalism and Neandertal bones used as tools in Northern Europe

Almost 150 years after the first identification of Neandertal skeletal material, the cognitive and symbolic abilities of these populations remain a subject of intense debate. We present 99 new Neandertal remains from the Troisième caverne of Goyet (Belgium) dated to 40,500–45,500 calBP. The remains were identified through a multidisciplinary study that combines morphometrics, taphonomy, stable isotopes, radiocarbon dating and genetic analyses. The Goyet Neandertal bones show distinctive anthropogenic modifications, which provides clear evidence for butchery activities as well as four bones having been used for retouching stone tools. In addition to being the first site to have yielded multiple Neandertal bones used as retouchers, Goyet not only provides the first unambiguous evidence of Neandertal cannibalism in Northern Europe, but also highlights considerable diversity in mortuary behaviour among the region’s late Neandertal population in the period immediately preceding their disappearance.

Late Stone Age human remains from Ishango (Democratic Republic of Congo): New insights on Late Pleistocene modern human diversity in Africa

Although questions of modern human origins and dispersal are subject to intense research within and outside Africa, the processes of modern human diversification during the Late Pleistocene are most often discussed within the context of recent human genetic data. This situation is due largely to the dearth of human fossil remains dating to the final Pleistocene in Africa and their almost total absence from West and Central Africa, thus limiting our perception of modern human diversification within Africa before the Holocene. Here, we present a morphometric comparative analysis of the earliest Late Pleistocene modern human remains from the Central African site of Ishango in the Democratic Republic of Congo. The early Late Stone Age layer (eLSA) of this site, dated to the Last Glacial Maximum (25-20 Ky), contains more than one hundred fragmentary human remains. The exceptional associated archaeological context suggests these remains derived from a community of hunter-fisher-gatherers exhibiting complex social and cognitive behaviors including substantial reliance on aquatic resources, development of fishing technology, possible mathematical notations and repetitive use of space, likely on a seasonal basis. Comparisons with large samples of Late Pleistocene and early Holocene modern human fossils from Africa and Eurasia show that the Ishango human remains exhibit distinctive characteristics and a higher phenotypic diversity in contrast to recent African populations. In many aspects, as is true for the inner ear conformation, these eLSA human remains have more affinities with Middle to early Late Pleistocene fossils worldwide than with extant local African populations. In addition, cross-sectional geometric properties of the long bones are consistent with archaeological evidence suggesting reduced terrestrial mobility resulting from greater investment in and use of aquatic resources. Our results on the Ishango human remains provide insights into past African modern human diversity and adaptation that are consistent with genetic theories about the deep sub-structure of Late Pleistocene African populations and their complex evolutionary history of isolation and diversification.

The genetic history of Ice Age Europe

Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000-7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3-6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ~35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.

Pleistocene Mitochondrial Genomes Suggest a Single Major Dispersal of Non-Africans and a Late Glacial Population Turnover in Europe

How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [1, 2]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [3-5]; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa [6-9]. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa [3-5, 8, 9]. The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.

La Ferrassie 8 Neandertal child reloaded: New remains and re-assessment of the original collection

The first evidence of the partial infant Neandertal skeleton La Ferrassie 8 (LF8) was discovered in 1970, although most of the remains were found in 1973 as part of the 1968-1973 work at the site by H. Delporte. This individual and the other Neandertal children from La Ferrassie were published in the early 1980s by J.-L. Heim, and since then LF8 has been regarded as coming from a poorly documented excavation. The recent rediscovery of the box that contained the hominin bones given by Delporte to Heim in the Muséum national d'Histoire naturelle (MNHN) collection provided new fossils and helped to locate LF8 in the site: level M2 in square 1. Two visits to the Musée d'Archéologie nationale et Domaine national de Saint-Germain-en-Laye (MAN) yielded additional fossil remains from both the 1970 and 1973 excavations and resulted in the discovery of all of the notes from the excavation of H. Delporte between 1968 and 1973. Here the new fossil remains (47 after performing all possible refits), representing significant portions of the cranium, mandible, and vertebral column together with fragmentary hand and costal remains, are described. Unsurprisingly, the morphology of the bony labyrinth and of a complete stapes from the nearly complete left temporal show clear Neandertal affinities. Additionally, a complete reassessment of the original LF8 collection has resulted in the identification of several errors in the anatomical determination. Despite the significant increase in the anatomical representation of LF8, the skeletal remains are still limited to the head, thorax, pelvis, and four hand phalanges, with some very fragile elements relatively well preserved. Different hypotheses are proposed to explain this anatomical representation, which can be tested during future fieldwork.

Middle pleistocene human remains from Tourville-la-Rivière (Normandy, France) and their archaeological context

Despite numerous sites of great antiquity having been excavated since the end of the 19th century, Middle Pleistocene human fossils are still extremely rare in northwestern Europe. Apart from the two partial crania from Biache-Saint-Vaast in northern France, all known human fossils from this period have been found from ten sites in either Germany or England. Here we report the discovery of three long bones from the same left upper limb discovered at the open-air site of Tourville-la-Rivière in the Seine Valley of northern France. New U-series and combined US-ESR dating on animal teeth produced an age range for the site of 183 to 236 ka. In combination with paleoecological indicators, they indicate an age toward the end of MIS 7. The human remains from Tourville-la-Rivière are attributable to the Neandertal lineage based on morphological and metric analyses. An abnormal crest on the left humerus represents a deltoid muscle enthesis. Micro- and or macro-traumas connected to repetitive movements similar to those documented for professional throwing athletes could be origin of abnormality.

Temporal labyrinths of eastern Eurasian Pleistocene humans

One of the morphological features that has been identified as uniquely derived for the western Eurasian Neandertals concerns the relative sizes and positions of their semicircular canals. In particular, they exhibit a relatively small anterior canal, a relatively larger lateral one, and a more inferior position of the posterior one relative to the lateral one. These discussions have not included full paleontological data on eastern Eurasian Pleistocene human temporal labyrinths, which have the potential to provide a broader context for assessing Pleistocene Homo trait polarities. We present the temporal labyrinths of four eastern Eurasian Pleistocene Homo, one each of Early (Lantian 1), Middle (Hexian 1), and Late (Xujiayao 15) Pleistocene archaic humans and one early modern human (Liujiang 1). The labyrinths of the two earlier specimens and the most recent one conform to the proportions seen among western early and recent modern humans, reinforcing the modern human pattern as generally ancestral for the genus Homo. The labyrinth of Xujiayao 15 is in the middle of the Neandertal variation and separate from the other samples. This eastern Eurasian labyrinthine dichotomy occurs in the context of none of the distinctive Neandertal external temporal or other cranial features. As such, it raises questions regarding possible cranial and postcranial morphological correlates of Homo labyrinthine variation, the use of individual "Neandertal" features for documenting population affinities, and the nature of late archaic human variation across Eurasia.

First early hominin from central Africa (Ishango, Democratic Republic of Congo)

Despite uncontested evidence for fossils belonging to the early hominin genus Australopithecus in East Africa from at least 4.2 million years ago (Ma), and from Chad by 3.5 Ma, thus far there has been no convincing evidence of Australopithecus, Paranthropus or early Homo from the western (Albertine) branch of the Rift Valley. Here we report the discovery of an isolated upper molar (#Ish25) from the Western Rift Valley site of Ishango in Central Africa in a derived context, overlying beds dated to between ca. 2.6 to 2.0 Ma. We used µCT imaging to compare its external and internal macro-morphology to upper molars of australopiths, and fossil and recent Homo. We show that the size and shape of the enamel-dentine junction (EDJ) surface discriminate between Plio-Pleistocene and post-Lower Pleistocene hominins, and that the Ishango molar clusters with australopiths and early Homo from East and southern Africa. A reassessment of the archaeological context of the specimen is consistent with the morphological evidence and suggest that early hominins were occupying this region by at least 2 Ma.

Modern human cranial diversity in the Late Pleistocene of Africa and Eurasia: evidence from Nazlet Khater, Peştera cu Oase, and Hofmeyr

The origin and evolutionary history of modern humans is of considerable interest to paleoanthropologists and geneticists alike. Paleontological evidence suggests that recent humans originated and expanded from an African lineage that may have undergone demographic crises in the Late Pleistocene according to archaeological and genetic data. This would suggest that extant human populations derive from, and perhaps sample a restricted part of the genetic and morphological variation that was present in the Late Pleistocene. Crania that date to Marine Isotope Stage 3 should yield information pertaining to the level of Late Pleistocene human phenotypic diversity and its evolution in modern humans. The Nazlet Khater (NK) and Hofmeyr (HOF) crania from Egypt and South Africa, together with penecontemporaneous specimens from the Peştera cu Oase in Romania, permit preliminary assessment of variation among modern humans from geographically disparate regions at this time. Morphometric and morphological comparisons with other Late Pleistocene modern human specimens, and with 23 recent human population samples, reveal that elevated levels of variation are present throughout the Late Pleistocene. Comparison of Holocene and Late Pleistocene craniometric variation through resampling analyses supports hypotheses derived from genetic data suggesting that present phenotypic variation may represent only a restricted part of Late Pleistocene human diversity. The Nazlet Khater, Hofmeyr, and Oase specimens provide a unique glimpse of that diversity.