Population genomics of post-glacial western Eurasia.

Western Eurasia witnessed several large-scale human migrations during the Holocene1-5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.

Density separation of petrous bone powders for optimized ancient DNA yields.

Density separation is a process routinely used to segregate minerals, organic matter, and even microplastics, from soils and sediments. Here we apply density separation to archaeological bone powders before DNA extraction to increase endogenous DNA recovery relative to a standard control extraction of the same powders. Using nontoxic heavy liquid solutions, we separated powders from the petrous bones of 10 individuals of similar archaeological preservation into eight density intervals (2.15 to 2.45 g/cm3, in 0.05 increments). We found that the 2.30 to 2.35 g/cm3 and 2.35 to 2.40 g/cm3 intervals yielded up to 5.28-fold more endogenous unique DNA than the corresponding standard extraction (and up to 8.53-fold before duplicate read removal), while maintaining signals of ancient DNA authenticity and not reducing library complexity. Although small 0.05 g/cm3 intervals may maximally optimize yields, a single separation to remove materials with a density above 2.40 g/cm3 yielded up to 2.57-fold more endogenous DNA on average, which enables the simultaneous separation of samples that vary in preservation or in the type of material analyzed. While requiring no new ancient DNA laboratory equipment and fewer than 30 min of extra laboratory work, the implementation of density separation before DNA extraction can substantially boost endogenous DNA yields without decreasing library complexity. Although subsequent studies are required, we present theoretical and practical foundations that may prove useful when applied to other ancient DNA substrates such as teeth, other bones, and sediments.

A minimally destructive protocol for DNA extraction from ancient teeth.

Ancient DNA sampling methods-although optimized for efficient DNA extraction-are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.

Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus.

Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.

Human auditory ossicles as an alternative optimal source of ancient DNA.

DNA recovery from ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that ancient DNA analysis will produce useable results.

Early life of Neanderthals.

The early onset of weaning in modern humans has been linked to the high nutritional demand of brain development that is intimately connected with infant physiology and growth rate. In Neanderthals, ontogenetic patterns in early life are still debated, with some studies suggesting an accelerated development and others indicating only subtle differences vs. modern humans. Here we report the onset of weaning and rates of enamel growth using an unprecedented sample set of three late (∼70 to 50 ka) Neanderthals and one Upper Paleolithic modern human from northeastern Italy via spatially resolved chemical/isotopic analyses and histomorphometry of deciduous teeth. Our results reveal that the modern human nursing strategy, with onset of weaning at 5 to 6 mo, was present among these Neanderthals. This evidence, combined with dental development akin to modern humans, highlights their similar metabolic constraints during early life and excludes late weaning as a factor contributing to Neanderthals' demise.

Virtual histology of archaeological human deciduous prenatal enamel through synchrotron X-ray computed microtomography images.

Virtual histology is increasingly utilized to reconstruct the cell mechanisms underlying dental morphology for fragile fossils when physical thin sections are not permitted. Yet, the comparability of data derived from virtual and physical thin sections is rarely tested. Here, the results from archaeological human deciduous incisor physical sections are compared with virtual ones obtained by phase-contrast synchrotron radiation computed microtomography (SRµCT) of intact specimens using a multi-scale approach. Moreover, virtual prenatal daily enamel secretion rates are compared with those calculated from physical thin sections of the same tooth class from the same archaeological skeletal series. Results showed overall good visibility of the enamel microstructures in the virtual sections which are comparable to that of physical ones. The highest spatial resolution SRµCT setting (effective pixel size = 0.9 µm) produced daily secretion rates that matched those calculated from physical sections. Rates obtained using the lowest spatial resolution setup (effective pixel size = 2.0 µm) were higher than those obtained from physical sections. The results demonstrate that virtual histology can be applied to the investigated samples to obtain reliable and quantitative measurements of prenatal daily enamel secretion rates.

Growth of Neanderthal infants from Krapina (120-130 ka), Croatia.

Modern humans have a slow and extended period of childhood growth, but to what extent this ontogenetic pathway was present in Neanderthals is debated. Dental development, linked to the duration of somatic growth across modern primates, is the main source for information about growth and development in a variety of fossil primates, including humans. Studies of Neanderthal permanent teeth report a pace of development either similar to recent humans or relatively accelerated. Neanderthal milk teeth, which form and emerge before permanent teeth, provide an opportunity to determine which pattern was present at birth. Here we present a comparative study of the prenatal and early postnatal growth of five milk teeth from three Neanderthals (120 000-130 000 years ago) using virtual histology. Results reveal regions of their milk teeth formed quickly before birth and over a relatively short period of time after birth. Tooth emergence commenced towards the earliest end of the eruption schedules displayed by extant human children. Advanced dental development is consistent with expectations for Neanderthal infant feeding.

Lead in Archeological Human Bones Reflecting Historical Changes in Lead Production.

Forty years ago, in a seminal paper published in Science, Settle and Patterson used archeological and historical data to estimate the rates of worldwide lead production since the discovery of cupellation, approximately 5000 years ago. Here, we record actual lead exposure of a human population by direct measurements of the concentrations of lead in petrous bones of individuals representing approximately 12 000 years of inhabitation in Italy. This documentation of lead pollution throughout human history indicates that, remarkably, much of the estimated dynamics in lead production is replicated in human exposure. Thus, lead pollution in humans has closely followed anthropogenic lead production. This observation raises concerns that the forecasted increase in the production of lead and other metals might affect human health in the near future.

Economic access influences degenerative spine disease outcomes at rural Late Medieval Villamagna (Lazio, IT).

OBJECTIVES: Degenerative joint disease in the spine is heavily influenced by genetic, environmental, and epigenetic factors, as well as exacerbated by physical activity and injury. The objective of this study was to investigate the multivariate relationship between known predictors of degenerative joint disease in the spine, such as age and sex, with mortuary indicators of economic access such as grave inclusions, burial location, and burial type. MATERIALS AND METHODS: The presence and severity of vertebral osteophytosis (VO) and vertebral osteoarthritis (VOA) was recorded for the vertebral columns of N = 106 adult individuals from the Late Medieval period at the rural monastery of San Pietro at Villamagna in Lazio, Italy (1300-1450 AD). Multiple skeletal indicators of degenerative joint disease, morphological sex, and age were compared with differences in mortuary treatment across four regions of the spine. RESULTS: There are marked differences in severe joint disease outcome between groups with more and less economic access. Relative risk ratios suggest that males and females with less economic access have elevated risk for VO and VOA in specific spine regions, although this effect is reduced among females. DISCUSSION: Current research on the consequences of economic and social inequality point to the important role of economic inequality in shaping disease outcomes. Our results suggest that biocultural effects of reduced economic access at the intraclass level may increase vulnerability to the downstream effects of risk exposure (e.g., biomechanical injure, physical activity, biochemical imbalance), and ultimately increase the risk and prevalence for severe degenerative disease outcomes in medieval Italy.

Making sense of medieval mouths: Investigating sex differences of dental pathological lesions in a late medieval Italian community.

OBJECTIVES: Bioarchaeological investigations of sex-based differences in the prevalence of dental pathological lesions, particularly caries, have drawn considerable attention, and out of this work, two dominant models have emerged. Traditionally, the first model interprets sex-related patterns in caries as a product of gendered differences in diet. A more recent model interprets a generally higher propensity for caries prevalence in females in light of reproductive ecology. To test the hypothesis that females have higher risk of caries in accordance with reproductive ecology, we examined and analyzed caries prevalence and other potentially synergistic oral pathological lesions in a late medieval (A.D. 1300-1500) Italian archaeological sample. MATERIALS AND METHODS: We examined sex- and age-related prevalence in caries and other oral pathological lesions in a late medieval Italian skeletal assemblage excavated from Villamagna consisting of 38 females and 37 males (n = 1,534 teeth). We examined age- and sex-related patterns in six dental traits: antemortem tooth loss, caries, calculus, periapical inflammation, tooth wear, and periodontitis. RESULTS: Significant age-related increases in antemortem tooth loss, caries, calculus, and tooth wear were observed in both males and females. However, there was a lack of expected sex differences in oral pathological lesions, with instead older males exhibiting significantly more antemortem tooth loss and corrected caries than females. DISCUSSION: Results are discussed in relation to the ethnohistoric context of medieval rural dietary practices as well as biomedical salivary literature, which suggest that dietary changes throughout the life course may have facilitated trade-offs that buffered females from higher rates of dental pathological lesions.

The endocast of the one-million-year-old human cranium from Buia (UA 31), Danakil Eritrea.

OBJECTIVES: The Homo erectus-like cranium from Buia (UA 31) was found in the Eritrean Danakil depression and dated to 1 million years. Its outer morphology displays archaic traits, as well as distinctive and derived characters. The present study provides the description and metric comparison of its endocranial anatomy. MATERIALS AND METHODS: UA 31 was originally filled by a diffuse concretion. Following its removal and cleaning, the endocast (995 cc) was reconstructed after physical molding and digital scan. Its morphology is here compared with specimens belonging to different human taxa, taking into account endocranial metrics, cortical traits, and craniovascular features. RESULTS: The endocast is long and narrow when compared to the H. erectus/ergaster hypodigm, although its proportions are compatible with the morphology displayed by all archaic and medium-brained human species. The occipital areas display a pronounced bulging, the cerebellum is located in a posterior position, and the middle meningeal vessels are more developed in the posterior regions. These features are common among specimens attributed to H. erectus s.l., particularly the Middle Pleistocene endocasts from Zhoukoudian. The parietal lobes are markedly bossed. This lateral bulging is associated with the lower parietal circumvolutions, as in other archaic specimens. This pronounced parietal curvature is apparently due to a narrow cranial base, more than to wider parietal areas. CONCLUSIONS: The endocast of UA 31 shows a general plesiomorphic phenotype, with some individual features (e.g., dolichocephaly and rounded lower parietal areas) which confirm a remarkable degree of morphological variability within the H. erectus/ergaster hypodigm. Am J Phys Anthropol 160:458-468, 2016. © 2016 Wiley Periodicals, Inc.

A bioarchaeological approach to the reconstruction of changes in military organization among Iron Age Samnites (Vestini) From Abruzzo, Central Italy.

The Samnites were an Iron Age population that shifted from warlike mountain dwellers to the largest sociopolitical unit of central Italy, able to dispute with Rome the domination over the peninsula. Archaeological and historical evidence suggests that this major shift in the scale of conflict may have involved a reorganization of the military system, which changed from an elite militia to a conscript or standing army from the Orientalizing-Archaic (800-500 BC) to Hellenistic times (400-27 BC). We propose a bioarchaeological framework jointly analyzing skeletal properties and funerary treatment in male Samnites to investigate on this shift in military organization. We anticipated that, when Samnites had an elite militia, the warring force was constituted by the wealthier segments of the society. Conversely, we expected the warring force of the standing/conscript army to be mainly drawn from the lower social strata. We considered high asymmetry in J, a measure of humeral torsional rigidity (calculated via cross-sectional geometry, CSG) as a proxy for pre- and peri-adolescent-onset weapon training. The social standing of the individual was approximated via funerary treatment analysis (Status Index). Results show that in the Orientalizing-Archaic period, humeral asymmetry and Status Index are positively correlated, and the high-status subsample shows significantly higher asymmetry than the low-status subsample. Among Hellenistic Samnites, no correlation between Status Index and humeral asymmetry is present, and the low-status subsample is the most lateralized. Results support the use of CSG in a strong theoretical framework to investigate past changes in military organization and their correlates in terms of sociopolitical development, alterations of power relationships, and warfare.

The late Early Pleistocene human dental remains from Uadi Aalad and Mulhuli-Amo (Buia), Eritrean Danakil: macromorphology and microstructure.

Fieldwork performed during the last 15 years in various Early Pleistocene East African sites has significantly enlarged the fossil record of Homo erectus sensu lato (s.l.). Additional evidence comes from the Danakil Depression of Eritrea, where over 200 late Early to early Middle Pleistocene sites have been identified within a ∼1000 m-thick sedimentary succession outcropping in the Dandiero Rift Basin, near Buia. Along with an adult cranium (UA 31), which displays a blend of H. erectus-like and derived morpho-architectural features and three pelvic remains, two isolated permanent incisors (UA 222 and UA 369) have also been recovered from the 1 Ma (millions of years ago) Homo-bearing outcrop of Uadi Aalad. Since 2010, our surveys have expanded to the nearby (4.7 km) site of Mulhuli-Amo (MA). This is a fossiliferous area that has been preliminarily surveyed because of its exceptional concentration of Acheulean stone tools. So far, the site has yielded 10 human remains, including the unworn crown of a lower permanent molar (MA 93). Using diverse analytical tools (including high resolution µCT and µMRI), we analysed the external and internal macromorphology and microstructure of the three specimens, and whenever possible compared the results with similar evidence from early Homo, H. erectus s.l., H. antecessor, H. heidelbergensis (from North Africa), Neanderthals and modern humans. We also assessed the UA 369 lower incisor from Uadi Aalad for root completion timing and showed that it compares well with data for root apex closure in modern human populations.

A genetic history of continuity and mobility in the Iron Age central Mediterranean.

The Iron Age was a dynamic period in central Mediterranean history, with the expansion of Greek and Phoenician colonies and the growth of Carthage into the dominant maritime power of the Mediterranean. These events were facilitated by the ease of long-distance travel following major advances in seafaring. We know from the archaeological record that trade goods and materials were moving across great distances in unprecedented quantities, but it is unclear how these patterns correlate with human mobility. Here, to investigate population mobility and interactions directly, we sequenced the genomes of 30 ancient individuals from coastal cities around the central Mediterranean, in Tunisia, Sardinia and central Italy. We observe a meaningful contribution of autochthonous populations, as well as highly heterogeneous ancestry including many individuals with non-local ancestries from other parts of the Mediterranean region. These results highlight both the role of local populations and the extreme interconnectedness of populations in the Iron Age Mediterranean. By studying these trans-Mediterranean neighbours together, we explore the complex interplay between local continuity and mobility that shaped the Iron Age societies of the central Mediterranean.

Microgeographic differentiation in historical Yemen inferred by morphometric distances.

This study analyzed the variations in space of 8 body dimensions and 11 measures of the head of 1,244 adult Yemenite males, collected in 1933/34 by Coon in Yemen and in Hadhramawt. The aim was to evaluate the presence of geographic microdifferentiation of the populations settled in the different regions of Yemen at the time. Coon sub-divided the sample into six geographical areas according to birthplace and ethnicity of the individuals: Tihamah, the Western Mountains, the Central Plateau, the South Coast, the Eastern Mountains, and Hadhramawt. The results of ANCOVA (age as covariate) show that the observed differences of all variables among the six groups were highly statistically significant. Tukey's post-hoc test reveals higher statistically significant differences among four main groups: (1) Tihamah; (2) the Western Mountains and Central Plateau; (3) the Eastern Mountains; and (4) the Southern Coast and Hadhramawt. Multiple discriminant analysis carried out using only the data of the 11 measures of the head, the more "genetically" determined variables, confirmed these differences. Indeed, the first canonical variate well separates the groups with the Tihamah, Southern Coast and Hadhramawt on the one side and the Eastern Mountains, Western Mountains and Central Plateau on the other. The second canonical variate separates the Tihamah, Western Mountains and Central Plateau from the Eastern Mountains, Southern Coast and Hadhramawt. In conclusion, the Yemenite population seems to be composed of three morphologically distinct groups and an Eastern Mountains group which is positioned between the group formed by the Southern Coast and Hadhramawt and the Western Mountains and Central Plateau group. The Tihamah is the most distant from all the other groups. These differences are probably due to the presence/absence of geographical and cultural barriers that have favored/blocked the gene flow over the years. Indeed, the entire coastal bell, through the centuries, has constituted one of the principal commercial routes between the East, Africa, and the eastern Mediterranean, while the high inland mountains have isolated the remaining communities. This data is also confirmed by genetic studies. Finally, the average height (162.6 cm) of the global Yemenite population, compared to data from the other six middle-eastern Arab countries and Egypt, was found to be 3-6 cm less. This characteristic will be further studied, analyzing variations in average height according to the different age classes in order to evaluate any possible secular changes.

Salorno-Dos de la Forca (Adige Valley, Northern Italy): A unique cremation site of the Late Bronze Age.

The archaeological site of Salorno-Dos de la Forca (Bozen, Alto Adige) provides one of the rarest and most significant documentations of cremated human remains preserved from an ancient cremation platform (ustrinum). The pyre area, located along the upper Adige valley, is dated to the Late Bronze Age (ca. 1150-950 BCE) and has yielded an unprecedented quantity of cremated human remains (about 63.5 kg), along with burnt animal bone fragments, shards of pottery, and other grave goods made in bronze and animal bone/antler. This study focuses on the bioanthropological analysis of the human remains and discusses the formation of the unusual burnt deposits at Salorno through comparisons with modern practices and protohistoric and contemporaneous archaeological deposits. The patterning of bone fragmentation and commingling was investigated using spatial data recorded during excavation which, along with the bioanthropological and archaeological data, are used to model and test two hypotheses: Salorno-Dos de la Forca would be the result of A) repeated primary cremations left in situ; or B) of residual material remaining after select elements were removed for internment in urns or burials to unknown depositional sites. By modelling bone weight and demographic data borrowed from regional affine contexts, the authors suggest that this cremation site may have been used over several generations by a small community-perhaps a local elite. With a quantity of human remains that exceeds that of any other coeval contexts interpreted as ustrina, Salorno may be the product of a complex series of rituals in which the human cremains did not receive individual burial, but were left in situ, in a collective/communal place of primary combustion, defining an area of repeated funeral ceremonies involving offerings and libations across a few generations. This would represent a new typological and functional category that adds to the variability of mortuary customs at the end of the Bronze Age in the Alpine are, at a time in which "globalising" social trends may have stimulated the definition of more private identities.

A new methodology to estimate flat foot in skeletal remains - the example of Mediterranean collections.

Flat feet (pes planus) are considered a postural defect caused by the collapse of the longitudinal arch, producing complete or near-complete contact of the sole of the foot with the ground. Pes planus has been well-studied in clinical literature and paleoanthropology but has not been approached extensively in bioarchaeology. The main difficulty is related to the diagnosis of this pathology based exclusively on bone remains. In this work, we propose a metric and morphological method to discriminate flat foot in dry bones. Thus, we studied 390 pairs of adult feet in a fair state of preservation from archaeological contexts from Spain, Italy, and Oman. Morphological variability, angles, and dimensions of both the normal bones and the bones displaying flat foot characteristics were analyzed. We found a correlation between the presence of flat foot and some morphological and metric features, mainly in the subtalar and Chopart joints. These results are expressed through a combination of morphological and metric variables, which are useful to discriminate between these two groups. No markedly significant differences of flat foot frequencies between the Spanish and Italian series were found across centuries. However, we noticed a notable increase of the prevalence of flat foot in the contemporary collection, possibly due to the consequences of a rise in life expectancy and modern styles of footwear.

Multipronged dental analyses reveal dietary differences in last foragers and first farmers at Grotta Continenza, central Italy (15,500-7000 BP).

This paper provides results from a suite of analyses made on human dental material from the Late Palaeolithic to Neolithic strata of the cave site of Grotta Continenza situated in the Fucino Basin of the Abruzzo region of central Italy. The available human remains from this site provide a unique possibility to study ways in which forager versus farmer lifeways affected human odonto-skeletal remains. The main aim of our study is to understand palaeodietary patterns and their changes over time as reflected in teeth. These analyses involve a review of metrics and oral pathologies, micro-fossils preserved in the mineralized dental plaque, macrowear, and buccal microwear. Our results suggest that these complementary approaches support the assumption about a critical change in dental conditions and status with the introduction of Neolithic foodstuff and habits. However, we warn that different methodologies applied here provide data at different scales of resolution for detecting such changes and a multipronged approach to the study of dental collections is needed for a more comprehensive and nuanced understanding of diachronic changes.