Imputed genomes and haplotype-based analyses of the Picts of early medieval Scotland reveal fine-scale relatedness between Iron Age, early medieval and the modern people of the UK.

There are longstanding questions about the origins and ancestry of the Picts of early medieval Scotland (ca. 300-900 CE), prompted in part by exotic medieval origin myths, their enigmatic symbols and inscriptions, and the meagre textual evidence. The Picts, first mentioned in the late 3rd century CE resisted the Romans and went on to form a powerful kingdom that ruled over a large territory in northern Britain. In the 9th and 10th centuries Gaelic language, culture and identity became dominant, transforming the Pictish realm into Alba, the precursor to the medieval kingdom of Scotland. To date, no comprehensive analysis of Pictish genomes has been published, and questions about their biological relationships to other cultural groups living in Britain remain unanswered. Here we present two high-quality Pictish genomes (2.4 and 16.5X coverage) from central and northern Scotland dated from the 5th-7th century which we impute and co-analyse with >8,300 previously published ancient and modern genomes. Using allele frequency and haplotype-based approaches, we can firmly place the genomes within the Iron Age gene pool in Britain and demonstrate regional biological affinity. We also demonstrate the presence of population structure within Pictish groups, with Orcadian Picts being genetically distinct from their mainland contemporaries. When investigating Identity-By-Descent (IBD) with present-day genomes, we observe broad affinities between the mainland Pictish genomes and the present-day people living in western Scotland, Wales, Northern Ireland and Northumbria, but less with the rest of England, the Orkney islands and eastern Scotland-where the political centres of Pictland were located. The pre-Viking Age Orcadian Picts evidence a high degree of IBD sharing across modern Scotland, Wales, Northern Ireland, and the Orkney islands, demonstrating substantial genetic continuity in Orkney for the last ~2,000 years. Analysis of mitochondrial DNA diversity at the Pictish cemetery of Lundin Links (n = 7) reveals absence of direct common female ancestors, with implications for broader social organisation. Overall, our study provides novel insights into the genetic affinities and population structure of the Picts and direct relationships between ancient and present-day groups of the UK.

Multi-isotope zooarchaeological investigations at Abri du Maras: The paleoecological and paleoenvironmental context of Neanderthal subsistence strategies in the Rhône Valley during MIS 3.

The exploitation of mid- and large-sized herbivores (ungulates) was central to hominin subsistence across Late Pleistocene Europe. Reconstructing the paleoecology of prey-taxa is key to better understanding procurement strategies, decisions and behaviors, and the isotope analysis of faunal bones and teeth found at archaeological sites represent a powerful means of accessing information about past faunal behaviors. These isotope zooarchaeological approaches also have a near-unique ability to reveal environmental conditions contemporary to the human activities that produced these remains. Here, we present the results of a multi-isotope, multitissue study of ungulate remains from the Middle Paleolithic site of Abri du Maras, southern France, providing new insights into the living landscapes of the Rhône Valley during MIS 3 (level 4.2 = 55 ± 2 to 42 ± 3 ka; level 4.1 = 46 ± 3 to 40 ± 3 ka). Isotope data (carbon, nitrogen) reveal the dietary niches of different ungulate taxa, including the now-extinct giant deer (Megaloceros). Oxygen isotope data are consistent with a mild seasonal climate during level 4.2, where horse (Equus), bison (Bison), and red deer (Cervus elaphus) were exploited year-round. Strontium and sulfur isotope analyses provide new evidence for behavioral plasticity in Late Pleistocene European reindeer (Rangifer) between level 4.2 and level 4.1, indicating a change from the migratory to the sedentary ecotype. In level 4.1, the strong seasonal nature of reindeer exploitation, combined with their nonmigratory behavior, is consistent with a seasonally restricted use of the site by Neanderthals at that time or the preferential hunting of reindeer when in peak physical condition during the autumn.

Megalithic tombs in western and northern Neolithic Europe were linked to a kindred society.

Paleogenomic and archaeological studies show that Neolithic lifeways spread from the Fertile Crescent into Europe around 9000 BCE, reaching northwestern Europe by 4000 BCE. Starting around 4500 BCE, a new phenomenon of constructing megalithic monuments, particularly for funerary practices, emerged along the Atlantic façade. While it has been suggested that the emergence of megaliths was associated with the territories of farming communities, the origin and social structure of the groups that erected them has remained largely unknown. We generated genome sequence data from human remains, corresponding to 24 individuals from five megalithic burial sites, encompassing the widespread tradition of megalithic construction in northern and western Europe, and analyzed our results in relation to the existing European paleogenomic data. The various individuals buried in megaliths show genetic affinities with local farming groups within their different chronological contexts. Individuals buried in megaliths display (past) admixture with local hunter-gatherers, similar to that seen in other Neolithic individuals in Europe. In relation to the tomb populations, we find significantly more males than females buried in the megaliths of the British Isles. The genetic data show close kin relationships among the individuals buried within the megaliths, and for the Irish megaliths, we found a kin relation between individuals buried in different megaliths. We also see paternal continuity through time, including the same Y-chromosome haplotypes reoccurring. These observations suggest that the investigated funerary monuments were associated with patrilineal kindred groups. Our genomic investigation provides insight into the people associated with this long-standing megalith funerary tradition, including their social dynamics.

Palaeoproteomic analyses of dog palaeofaeces reveal a preserved dietary and host digestive proteome.

The domestic dog has inhabited the anthropogenic niche for at least 15 000 years, but despite their impact on human strategies, the lives of dogs and their interactions with humans have only recently become a subject of interest to archaeologists. In the Arctic, dogs rely exclusively on humans for food during the winter, and while stable isotope analyses have revealed dietary similarities at some sites, deciphering the details of provisioning strategies have been challenging. In this study, we apply zooarchaeology by mass spectrometry (ZooMS) and liquid chromatography tandem mass spectrometry to dog palaeofaeces to investigate protein preservation in this highly degradable material and obtain information about the diet of domestic dogs at the Nunalleq site, Alaska. We identify a suite of digestive and metabolic proteins from the host species, demonstrating the utility of this material as a novel and viable substrate for the recovery of gastrointestinal proteomes. The recovered proteins revealed that the Nunalleq dogs consumed a range of Pacific salmon species (coho, chum, chinook and sockeye) and that the consumed tissues derived from muscle and bone tissues as well as roe and guts. Overall, the study demonstrated the viability of permafrost-preserved palaeofaeces as a unique source of host and dietary proteomes.

Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.

Domestic dogs have been central to life in the North American Arctic for millennia. The ancestors of the Inuit were the first to introduce the widespread usage of dog sledge transportation technology to the Americas, but whether the Inuit adopted local Palaeo-Inuit dogs or introduced a new dog population to the region remains unknown. To test these hypotheses, we generated mitochondrial DNA and geometric morphometric data of skull and dental elements from a total of 922 North American Arctic dogs and wolves spanning over 4500 years. Our analyses revealed that dogs from Inuit sites dating from 2000 BP possess morphological and genetic signatures that distinguish them from earlier Palaeo-Inuit dogs, and identified a novel mitochondrial clade in eastern Siberia and Alaska. The genetic legacy of these Inuit dogs survives today in modern Arctic sledge dogs despite phenotypic differences between archaeological and modern Arctic dogs. Together, our data reveal that Inuit dogs derive from a secondary pre-contact migration of dogs distinct from Palaeo-Inuit dogs, and probably aided the Inuit expansion across the North American Arctic beginning around 1000 BP.

Oxygen isotope analysis of human bone phosphate evidences weaning age in archaeological populations.

Here we report bone phosphate oxygen (δ(18)Op) values from perinates/neonates and infants (<3.5 years; n = 32); children (4-12 years; n = 12); unsexed juveniles (16-18 years; n = 2); and adult bones (n = 17) from Wharram Percy, North Yorkshire, England, in order to explore the potential of this method to investigate patterns of past breastfeeding and weaning. In prior studies, δ(15)N and δ(13)C analyses of bone collagen have been utilized to explore weaning age in this large and well-studied assemblage, rendering this material highly appropriate for the testing and development of this alternative method targeting the inorganic phase of bone. Data produced reveal (18)O-enrichment in the youngest perinatal/neonatal and infant samples, and an association between age and bone δ(18)Op (and previously-published δ(15)N values), with high values in both these isotope systems likely due to breastfeeding. After the age of 2-3 years, δ(18)Op values are lower, and all children between the ages of 4 and 12, along with the vast majority of sub-adults and adults sampled (aged 16 to >50 years), have δ(18)Op values consistent with the consumption of local modern drinking water. The implications of this study for the reconstruction of weaning practices in archaeological populations are discussed, including variations observed with bone δ(15)Ncoll and δ(18)Op co-analysis and the influence of culturally-modified drinking water and seasonality. The use of this method to explore human mobility and palaeoclimatic conditions are also discussed with reference to the data presented.

Carbon, nitrogen, and sulfur elemental and isotopic variations in mouse hair and bone collagen during short-term graded calorie restriction.

This study characterized the effect of calorie restriction (CR) on elemental content and stable isotope ratio measurements of bone "collagen" and hair keratin. Adult mice on graded CR (10-40%; 84 days) showed decreased hair δ 15N, δ 13C, and δ 34S values (significantly for δ 15N) with increasing CR, alongside a significant increase in bone "collagen" δ 15N values and a decrease in "collagen" δ 13C values. We propose this was likely due to the intensified mobilization of endogenous proteins, as well as lipids in newly synthesized "collagen". Elemental analysis of bone "collagen" revealed decreased carbon, nitrogen, and sulfur % content with increasing CR which is attributed to a change in the in vivo bone "collagen" structure with extent of CR. This complexity challenges the use of elemental indicators in the assessment of collagen quality in archaeological studies where nutritional stress may be a factor.

Multi-isotope reconstruction of Late Pleistocene large-herbivore biogeography and mobility patterns in Central Europe.

Interpretations of Late Pleistocene hominin adaptative capacities by archaeologists have focused heavily on their exploitation of certain prey and documented contemporary behaviours for these species. However, we cannot assume that animal prey-taxa ecology and ethology were the same in the past as in the present, or were constant over archaeological timescales. Sequential isotope analysis of herbivore teeth has emerged as a particularly powerful method of directly reconstructing diet, ecology and mobility patterns on sub-annual scales. Here, we apply 87Sr/86Sr isotope analysis, in combination with δ18O and δ13C isotope analysis, to sequentially sampled tooth enamel of prevalent herbivore species that populated Europe during the Last Glacial Period, including Rangifer tarandus, Equus sp. and Mammuthus primigenius. Our samples come from two open-air archaeological sites in Central Germany, Königsaue and Breitenbach, associated with Middle Palaeolithic and early Upper Palaeolithic cultures, respectively. We identify potential inter- and intra-species differences in range size and movement through time, contextualised through insights into diet and the wider environment. However, homogeneous bioavailable 87Sr/86Sr across large parts of the study region prevented the identification of specific migration routes. Finally, we discuss the possible influence of large-herbivore behaviour on hominin hunting decisions at the two sites.

The ecology, subsistence and diet of ~45,000-year-old Homo sapiens at Ilsenhöhle in Ranis, Germany.

Recent excavations at Ranis (Germany) identified an early dispersal of Homo sapiens into the higher latitudes of Europe by 45,000 years ago. Here we integrate results from zooarchaeology, palaeoproteomics, sediment DNA and stable isotopes to characterize the ecology, subsistence and diet of these early H. sapiens. We assessed all bone remains (n = 1,754) from the 2016-2022 excavations through morphology (n = 1,218) or palaeoproteomics (zooarchaeology by mass spectrometry (n = 536) and species by proteome investigation (n = 212)). Dominant taxa include reindeer, cave bear, woolly rhinoceros and horse, indicating cold climatic conditions. Numerous carnivore modifications, alongside sparse cut-marked and burnt bones, illustrate a predominant use of the site by hibernating cave bears and denning hyaenas, coupled with a fluctuating human presence. Faunal diversity and high carnivore input were further supported by ancient mammalian DNA recovered from 26 sediment samples. Bulk collagen carbon and nitrogen stable isotope data from 52 animal and 10 human remains confirm a cold steppe/tundra setting and indicate a homogenous human diet based on large terrestrial mammals. This lower-density archaeological signature matches other Lincombian-Ranisian-Jerzmanowician sites and is best explained by expedient visits of short duration by small, mobile groups of pioneer H. sapiens.

Stable isotopes show Homo sapiens dispersed into cold steppes ~45,000 years ago at Ilsenhöhle in Ranis, Germany.

The spread of Homo sapiens into new habitats across Eurasia ~45,000 years ago and the concurrent disappearance of Neanderthals represents a critical evolutionary turnover in our species' history. 'Transitional' technocomplexes, such as the Lincombian-Ranisian-Jerzmanowician (LRJ), characterize the European record during this period but their makers and evolutionary significance have long remained unclear. New evidence from Ilsenhöhle in Ranis, Germany, now provides a secure connection of the LRJ to H. sapiens remains dated to ~45,000 years ago, making it one of the earliest forays of our species to central Europe. Using many stable isotope records of climate produced from 16 serially sampled equid teeth spanning ~12,500 years of LRJ and Upper Palaeolithic human occupation at Ranis, we review the ability of early humans to adapt to different climate and habitat conditions. Results show that cold climates prevailed across LRJ occupations, with a temperature decrease culminating in a pronounced cold excursion at ~45,000-43,000 cal BP. Directly dated H. sapiens remains confirm that humans used the site even during this very cold phase. Together with recent evidence from the Initial Upper Palaeolithic, this demonstrates that humans operated in severe cold conditions during many distinct early dispersals into Europe and suggests pronounced adaptability.

Maritime adaptations and dietary variation in prehistoric Western Alaska: stable isotope analysis of permafrost-preserved human hair.

The reconstruction of diet and subsistence strategies is integral in understanding early human colonizations and cultural adaptations, especially in the Arctic-one of the last areas of North America to be permanently inhabited. However, evidence for early subsistence practices in Western Alaska varies, particularly with regards to the emergence, importance, and intensity of sea mammal hunting. Here, we present stable carbon and nitrogen isotope data from permafrost-preserved human hair from two new prehistoric sites in Western Alaska, providing a direct measure of diet. The isotope evidence indicates a heavy reliance on sea mammal protein among the earlier Norton-period group (1,750 ± 40 cal BP), confirming that the complex hunting technologies required to intensively exploit these animals were most likely already in place in this region by at least the beginning of 1st millennium AD. In contrast, analysis of the more recent Thule-period hair samples (650 ± 40 cal BP; 570 ± 30 cal BP) reveals a more mixed diet, including terrestrial animal protein. Sequential isotope analysis of two longer human hair locks indicates seasonal differences in diet in a single Norton-period individual but demonstrates little dietary variation in a Thule-period individual. These analyses provide direct evidence for dietary differences among Alaska's early Eskimo groups and confirm the antiquity of specialized sea mammal hunting and procurement technologies. The results of this study have implications for our understanding of human adaptation to maritime and high-latitude environments, and the geographical and temporal complexity in early Arctic subsistence.

Out of the frying pan? Streamlining the ethics review process of multisite qualitative research projects.

This paper describes the ethics approval processes for two multicentre, nationwide, qualitative health service research projects. The paper explains that the advent of the National Ethics Application Form has brought many improvements, but that attendant processes put in place at local health network and Human Research Ethics Committee levels may have become significantly more complicated, particularly for innovative qualitative research projects. The paper raises several questions based on its analysis of ethics application processes currently in place. WHAT IS KNOWN ABOUT THE TOPIC? The complexity of multicentre research ethics applications for research in health services has been addressed by the introduction of the National Ethics Application Form. Uptake of the form across the country's human research ethics committees has been uneven. WHAT DOES THIS PAPER ADD? This paper adds detailed insight into the ethics application process as it is currently enacted across the country. The paper details this process with reference to difficulties faced by multisite and qualitative studies in negotiating access to research sites, ethics committees' relative unfamiliarity with qualitative research , and apparent tensions between harmonisation and local sites' autonomy in approving research. WHAT ARE THE IMPLICATIONS FOR PRACTITIONERS? Practitioners aiming to engage in research need to be aware that ethics approval takes place in an uneven procedural landscape, made up of variable levels of ethics approval harmonization and intricate governance or site-specific assessment processes.

Comparison between strip sampling and laser ablation methods to infer seasonal movements from intra-tooth strontium isotopes profiles in migratory caribou.

Strontium isotopes analysis is a powerful tool in the study of past animal movements, notably the sequential analysis of tooth enamel to reconstruct individual movements in a time-series. Compared to traditional solution analysis, high resolution sampling using laser-ablation multi-collector inductively coupled plasma mass spectrometry (LA-MC-ICP-MS) has the potential to reflect fine scale mobility. However, the averaging of the 87Sr/86Sr intake during the enamel mineralization process may limit fine scale inferences. We compared solution and LA-MC-ICP-MS 87Sr/86Sr intra-tooth profiles from the second and third molars of 5 caribou from the Western Arctic herd, Alaska. Profiles from both methods showed similar trends, reflecting the seasonal migratory movements, but LA-MC-ICP-MS profiles showed a less damped 87Sr/86Sr signal than solution profiles. Geographic assignments of the profile endmembers to the known summer and winter ranges were consistent between methods and with the expected timing of enamel formation but showed discrepancy at a finer scale. Variations on LA-MC-ICP-MS profiles, consistent with expected seasonal movements, suggested more than an admixture of the endmember values. However, more work in understanding enamel formation in Rangifer, and other ungulates, and how 87Sr/86Sr daily intake translates into enamel are needed to assess the real resolution that can be achieved with LA-MC-ICP-MS.

Multi-isotope analysis of bone collagen of Late Pleistocene ungulates reveals niche partitioning and behavioural plasticity of reindeer during MIS 3.

Here we present stable carbon, nitrogen and sulfur isotope ratios of collagen extracted from Rangifer, Equus and Bison bone (n = 128) from different stratigraphic levels at the chronologically well-constrained Middle and Upper Palaeolithic site of Les Cottés, France. Samples were taken from five phases of site use (US08, US06, US04 [upper and lower], and US02; ~ 45.8-35.3 ka cal BP) to explore the dietary and spatial palaeoecology of these ungulate species during MIS 3, and the contemporary climate. Temporal trends in δ15N values of all species broadly align with other climatic indicators at the site and the lowest values in US04 correspond to the Heinrich 4 cooling event, reflecting changes in the composition of soil/plant nitrogen at this time. Rangifer collagen is 13C-enriched compared to the other species throughout, consistent with lichen consumption. However, this isotopic niche partitioning between Rangifer and Equus/Bison is most extensive during US04, indicating plasticity in reindeer feeding behaviour, and potentially overall increased lichen biomass during this cooler/more arid phase. Rangifer δ34S values are consistently lower than Equus and Bison, which could be indicative of their more extensive spatial ranges incorporating greater inland areas. Equus and Bison demonstrate a significant decrease in δ34S values through time, which may be linked to contemporary climatic decline.

Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain.

The prevalence of chronic, non-communicable diseases has risen sharply in recent decades, especially in industrialized countries. While several studies implicate the microbiome in this trend, few have examined the evolutionary history of industrialized microbiomes. Here we sampled 235 ancient dental calculus samples from individuals living in Great Britain (∼2200 BCE to 1853 CE), including 127 well-contextualized London adults. We reconstructed their microbial history spanning the transition to industrialization. After controlling for oral geography and technical biases, we identified multiple oral microbial communities that coexisted in Britain for millennia, including a community associated with Methanobrevibacter, an anaerobic Archaea not commonly prevalent in the oral microbiome of modern industrialized societies. Calculus analysis suggests that oral hygiene contributed to oral microbiome composition, while microbial functions reflected past differences in diet, specifically in dairy and carbohydrate consumption. In London samples, Methanobrevibacter-associated microbial communities are linked with skeletal markers of systemic diseases (for example, periostitis and joint pathologies), and their disappearance is consistent with temporal shifts, including the arrival of the Second Plague Pandemic. This suggests pre-industrialized microbiomes were more diverse than previously recognized, enhancing our understanding of chronic, non-communicable disease origins in industrialized populations.

Strontium isotope evidence for migration in late Pleistocene Rangifer: implications for Neanderthal hunting strategies at the Middle Palaeolithic site of Jonzac, France.

In order to understand the behaviours and subsistence choices of Palaeolithic hunter-gatherers, it is essential to understand the behavioural ecology of their prey. Here, we present strontium isotope data from sequentially-sampled enamel from three reindeer (Rangifer tarandus ssp.) and a single bison (Bison cf. priscus) from the late Middle Palaeolithic site of Jonzac (Chez-Pinaud), France. The results are used to investigate the ranging and migratory behaviours of these important prey species. We found that the bison had isotope values most consistent with a local range, while the three reindeer had values indicating a seasonal migration pattern. Due to the similarity of the patterning of two of the three reindeer and in conjunction with zooarchaeological results, we suggest that they may have been from the same herd, were likely killed around the same point during their seasonal round and may therefore be the product of a single hunting event or a small number of successive hunting events. The isotope analyses complement the zooarchaeological data and have allowed greater insight into the palaeoecology of these species, the palaeoenvironment, and Neanderthal site use and hunting strategies.

Subarctic climate for the earliest Homo sapiens in Europe.

The expansion of Homo sapiens across Eurasia marked a major milestone in human evolution that would eventually lead to our species being found across every continent. Current models propose that these expansions occurred only during episodes of warm climate, based on age correlations between archaeological and climatic records. Here, we obtain direct evidence for the temperatures faced by some of these humans through the oxygen isotope analysis of faunal remains from Bacho Kiro Cave, Bulgaria, the earliest clear record of H. sapiens in Europe. The results indicate that humans ∼45,000 years ago experienced subarctic climates with far colder climatic conditions than previously suggested. This demonstrates that the early presence of H. sapiens in Europe was not contingent on warm climates. Our results necessitate the revision of key models of human expansion and highlight the need for a less deterministic role of climate in the study of our evolutionary history.

Reconstructing Late Pleistocene paleoclimate at the scale of human behavior: an example from the Neandertal occupation of La Ferrassie (France).

Exploring the role of changing climates in human evolution is currently impeded by a scarcity of climatic information at the same temporal scale as the human behaviors documented in archaeological sites. This is mainly caused by high uncertainties in the chronometric dates used to correlate long-term climatic records with archaeological deposits. One solution is to generate climatic data directly from archaeological materials representing human behavior. Here we use oxygen isotope measurements of Bos/Bison tooth enamel to reconstruct summer and winter temperatures in the Late Pleistocene when Neandertals were using the site of La Ferrassie. Our results indicate that, despite the generally cold conditions of the broader period and despite direct evidence for cold features in certain sediments at the site, Neandertals used the site predominantly when climatic conditions were mild, similar to conditions in modern day France. We suggest that due to millennial scale climate variability, the periods of human activity and their climatic characteristics may not be representative of average conditions inferred from chronological correlations with long-term climatic records. These results highlight the importance of using direct routes, such as the high-resolution archives in tooth enamel from anthropogenically accumulated faunal assemblages, to establish climatic conditions at a human scale.

CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content.

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.

The genetic prehistory of the New World Arctic.

The New World Arctic, the last region of the Americas to be populated by humans, has a relatively well-researched archaeology, but an understanding of its genetic history is lacking. We present genome-wide sequence data from ancient and present-day humans from Greenland, Arctic Canada, Alaska, Aleutian Islands, and Siberia. We show that Paleo-Eskimos (~3000 BCE to 1300 CE) represent a migration pulse into the Americas independent of both Native American and Inuit expansions. Furthermore, the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population, representing the ancestors of present-day Inuit, with evidence of past gene flow between these lineages. Despite periodic abandonment of major Arctic regions, a single Paleo-Eskimo metapopulation likely survived in near-isolation for more than 4000 years, only to vanish around 700 years ago.