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.

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.

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.

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.

Population dynamics in pre-Inca human groups from the Osmore Valley, the Azapa Valley and the coast of the South Central Andes.

The present study applies a dental morphological perspective to the understanding of the complex pre-contact population history of the South Central Andes, through the detection of the underlying dynamics, and the assessment of the biological ties among groups. It presents an analysis of 1591 individuals from 66 sites that date from the Archaic to the Late Intermediate phases from Bolivia, Chile and Peru. The results suggest this area is characterized by significant movement of people and cultures and, at the same time, by long standing population continuity, and highlight the need for wider perspectives capable of taking into account both the different micro-regional realities and the region in its entirety.

Ancient Rome: A genetic crossroads of Europe and the Mediterranean.

Ancient Rome was the capital of an empire of ~70 million inhabitants, but little is known about the genetics of ancient Romans. Here we present 127 genomes from 29 archaeological sites in and around Rome, spanning the past 12,000 years. We observe two major prehistoric ancestry transitions: one with the introduction of farming and another prior to the Iron Age. By the founding of Rome, the genetic composition of the region approximated that of modern Mediterranean populations. During the Imperial period, Rome's population received net immigration from the Near East, followed by an increase in genetic contributions from Europe. These ancestry shifts mirrored the geopolitical affiliations of Rome and were accompanied by marked interindividual diversity, reflecting gene flow from across the Mediterranean, Europe, and North Africa.

The Middle Pleistocene (MIS 12) human dental remains from Fontana Ranuccio (Latium) and Visogliano (Friuli-Venezia Giulia), Italy. A comparative high resolution endostructural assessment.

The penecontemporaneous Middle Pleistocene sites of Fontana Ranuccio (Latium) and Visogliano (Friuli-Venezia Giulia), set c. 450 km apart in central and northeastern Italy, respectively, have yielded some among the oldest human fossil remains testifying to a peopling phase of the Italian Peninsula broadly during the glacial MIS 12, a stage associated with one among the harshest climatic conditions in the Northern hemisphere during the entire Quaternary period. Together with the large samples from Atapuerca Sima de los Huesos, Spain, and Caune de l'Arago at Tautavel, France, the remains from Fontana Ranuccio and Visogliano are among the few mid-Middle Pleistocene dental assemblages from Western Europe available for investigating the presence of an early Neanderthal signature in their inner structure. We applied two- three-dimensional techniques of virtual imaging and geometric morphometrics to the high-resolution X-ray microtomography record of the dental remains from these two Italian sites and compared the results to the evidence from a selected number of Pleistocene and extant human specimens/samples from Europe and North Africa. Depending on their preservation quality and on the degree of occlusal wear, we comparatively assessed: (i) the crown enamel and radicular dentine thickness topographic variation of a uniquely represented lower incisor; (ii) the lateral crown tissue proportions of premolars and molars; (iii) the enamel-dentine junction, and (iv) the pulp cavity morphology of all available specimens. Our analyses reveal in both samples a Neanderthal-like inner structural signal, for some aspects also resembling the condition shown by the contemporary assemblage from Atapuerca SH, and clearly distinct from the recent human figures. This study provides additional evidence indicating that an overall Neanderthal morphological dental template was preconfigured in Western Europe at least 430 to 450 ka ago.

Social reorganization and biological change: An examination of stature variation among Iron Age Samnites from Abruzzo, central Italy.

Stature is a sensitive indicator of overall environmental quality experienced during growth and development, and can provide insights on a population's 'well-being'. This study investigated changes in estimated adult stature in a large (N=568) sample of Samnite Iron Age (800-27 BCE) people from central Italy, during a period of increasing sociopolitical complexity. Stature was analyzed diachronically, between sexes, and across social strata inferred using the 'Status Index' based on funerary treatment. It was expected: 1) a decrease in stature from the Orientalizing-Archaic period (O-A) to the fifth century BC (V SEC) and the following Hellenistic period (ELL), due to population increase and urbanization; 2) social status to positively influence the attainment of the full stature potential; 3) sexual dimorphism to be higher in more stratified groups. Results revealed no significant diachronic changes in stature (females: O-A: 154.2cm,V SEC: 154.2cm, and ELL: 153.6cm; males: O-A: 165.0cm,V SEC: 165.2cm, and ELL: 165.0cm) or sexual dimorphism. High-status males were taller than low-status (p=0.021), possibly due to a better diet, but only in the Orientalizing-Archaic period. Nonsignificant changes in females suggest either differential access to resources in women, or a better buffering from environmental optima or crises. The results of this study highlight the complex interrelation between social factors and human growth, and stress the importance of understanding the specific mechanisms leading to variation in adult stature.

Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes.

Rare mitochondrial lineages with relict distributions can sometimes be disproportionately informative about deep events in human prehistory. We have studied one such lineage, haplogroup R0a, which uniquely is most frequent in Arabia and the Horn of Africa, but is distributed much more widely, from Europe to India. We conclude that: (1) the lineage ancestral to R0a is more ancient than previously thought, with a relict distribution across the Mediterranean/Southwest Asia; (2) R0a has a much deeper presence in Arabia than previously thought, highlighting the role of at least one Pleistocene glacial refugium, perhaps on the Red Sea plains; (3) the main episode of dispersal into Eastern Africa, at least concerning maternal lineages, was at the end of the Late Glacial, due to major expansions from one or more refugia in Arabia; (4) there was likely a minor Late Glacial/early postglacial dispersal from Arabia through the Levant and into Europe, possibly alongside other lineages from a Levantine refugium; and (5) the presence of R0a in Southwest Arabia in the Holocene at the nexus of a trading network that developed after ~3 ka between Africa and the Indian Ocean led to some gene flow even further afield, into Iran, Pakistan and India.

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.

A health assessment for imperial Roman burials recovered from the necropolis of San Donato and Bivio CH, Urbino, Italy.

Imperial Roman burials recovered from the sites of San Donato and Bivio CH, located in the city of Urbino, Italy were examined for skeletal lesions. Observed pathologies include arthritis, trauma, periostitis, cranial pitting and enamel hypoplasia. All of the adults exhibited at least one enamel hypoplasia. In general, the adult males exhibit greater rates of skeletal pathologies than the females. Clearly, chronic health problems appear to be common among all adults; nearly 89% of them exhibit at least one form of skeletal lesion. This is in stark contrast to what is seen for the sub-adults. Only one sub-adult showed skeletal lesions. Acute health problems may have been the primary contributing factors for the death of the children recovered from the site. Despite previous research and attention to malaria as a critical health problem of Roman sub-adults, it does not seem to be an issue for this burial sample. We compare the frequency of cranial pitting and periostitis for the Urbino burials to several other Imperial Roman skeletal samples as a means to assess the potential for malaria and other casual factors for the observed lesions. In conclusion, we see the extreme rate of skeletal lesions for this community as indication of an extremely poor quality of life for these Romans.

Italian populations during the Copper Age: assessment of biological affinities through morphological dental traits.

The Copper Age (3rd millennium BC) was characterized by considerable socioeconomic transformations and coincided with the discovery of metallurgy. In this study we reconstruct the peopling of Italy during this period on the basis of dental morphology traits. Dental remains from 41 sites throughout Italy were analyzed; only three of the sites (Laterza and two from Sicily) span from the late Copper Age to the early Bronze Age. To work with adequate samples, we pooled the collections into nine geographically and culturally homogeneous groups. Dental morphological traits were scored on 8,891 teeth from 1,302 individuals using the ASUDAS scale. The correlation between the mean measure of divergence and geographic distances (calculated as air distances) was computed. Multidimensional scaling with the minimum spanning tree and maximum-likelihood methods was applied to assess the relationships between groups. The results revealed a substantial genetic homogeneity among the populations throughout the Italian peninsula during the Copper Age with the exception of Sardinia, which tends to diverge from the continental samples. Phenetic and geographic distances correlate highly significantly only when the southern samples from Sicily and Laterza are removed from the analysis, which indicates that these groups may have experienced genetic admixture with external populations.

Newly recognized Pleistocene human teeth from Tabun Cave, Israel.

Seven human teeth from Tabun Cave, Israel, curated at the Natural History Museum London since 1955, are of uncertain provenance and identity. They are all from the upper dentition, without duplications, and are characterized by a similar preservation. The Catalogue of Fossil Hominids (1975) suggested that they might have derived from Tabun Layer A (Bronze Age to Recent). However, one of us (AC) noted some distinctive features of these teeth that warranted further study. They are here assigned to a single individual, Tabun BC7. Their morphology and metrics were then compared with the frequency of Late Pleistocene and Early Holocene groups from Europe, North Africa and Middle East. A fragment of the right M3 crown of Tabun BC7 was removed for ESR and U-analysis, and it was determined that only samples from Layer B have similar dose values. Using the sediment dose values of layer B, preliminary age estimates of 82 +/- 14 ka (early U-uptake) and 92+/-18 ka (linear uptake) were obtained. U-series disequilibrium determined from other samples attributed to Layer B resulted in a U-uptake history close to linear uptake, giving a very comparable age estimate of 90(+30)(-16) ka. The dose value previously obtained on an enamel fragment from the Tabun C1 dentition is nearly double the value measured for BC7, and tentative age estimates for C1 were in the range of 143+/-37 ka. However, due to uncertainties in the exact provenance of the human fossils, we cannot confirm that C1 is older than the new tooth sampled here, and both C1 and BC7 can be attributed to Layer B on chronological grounds. On the basis of chronology, dental morphology and metrics, the specimen named Tabun BC7 was identified as a probable Neanderthal.