The genetic history of Scandinavia from the Roman Iron Age to the present.

We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.

Abnormal (Hydroxy)proline Deuterium Content Redefines Hydrogen Chemical Mass.

Analyzing the δ2H values in individual amino acids of proteins extracted from vertebrates, we unexpectedly found in some samples, notably bone collagen from seals, more than twice as much deuterium in proline and hydroxyproline residues than in seawater. This corresponds to at least 4 times higher δ2H than in any previously reported biogenic sample. We ruled out diet as a plausible mechanism for such anomalous enrichment. This finding puts into question the old adage that "you are what you eat".

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation.

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57× coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500-6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans.

Moose genomes reveal past glacial demography and the origin of modern lineages.

BACKGROUND: Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America. RESULTS: We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines. CONCLUSIONS: Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.

Identification of microbial pathogens in Neolithic Scandinavian humans.

With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.

Mitochondrial DNA and Y-chromosomal diversity in ancient populations of domestic sheep (Ovis aries) in Finland: comparison with contemporary sheep breeds.

BACKGROUND: Several molecular and population genetic studies have focused on the native sheep breeds of Finland. In this work, we investigated their ancestral sheep populations from Iron Age, Medieval and Post-Medieval periods by sequencing a partial mitochondrial DNA D-loop and the 5'-promoter region of the SRY gene. We compared the maternal (mitochondrial DNA haplotypes) and paternal (SNP oY1) genetic diversity of ancient sheep in Finland with modern domestic sheep populations in Europe and Asia to study temporal changes in genetic variation and affinities between ancient and modern populations. RESULTS: A 523-bp mitochondrial DNA sequence was successfully amplified for 26 of 36 sheep ancient samples i.e. five, seven and 14 samples representative of Iron Age, Medieval and Post-Medieval sheep, respectively. Genetic diversity was analyzed within the cohorts. This ancient dataset was compared with present-day data consisting of 94 animals from 10 contemporary European breeds and with GenBank DNA sequence data to carry out a haplotype sharing analysis. Among the 18 ancient mitochondrial DNA haplotypes identified, 14 were present in the modern breeds. Ancient haplotypes were assigned to the highly divergent ovine haplogroups A and B, haplogroup B being the major lineage within the cohorts. Only two haplotypes were detected in the Iron Age samples, while the genetic diversity of the Medieval and Post-Medieval cohorts was higher. For three of the ancient DNA samples, Y-chromosome SRY gene sequences were amplified indicating that they originated from rams. The SRY gene of these three ancient ram samples contained SNP G-oY1, which is frequent in modern north-European sheep breeds. CONCLUSIONS: Our study did not reveal any sign of major population replacement of native sheep in Finland since the Iron Age. Variations in the availability of archaeological remains may explain differences in genetic diversity estimates and patterns within the cohorts rather than demographic events that occurred in the past. Our ancient DNA results fit well with the genetic context of domestic sheep as determined by analyses of modern north-European sheep breeds.

Microsatellite genotyping reveals end-Pleistocene decline in mammoth autosomal genetic variation.

The last glaciation was a dynamic period with strong impact on the demography of many species and populations. In recent years, mitochondrial DNA sequences retrieved from radiocarbon-dated remains have provided novel insights into the history of Late Pleistocene populations. However, genotyping of loci from the nuclear genome may provide enhanced resolution of population-level changes. Here, we use four autosomal microsatellite DNA markers to investigate the demographic history of woolly mammoths (Mammuthus primigenius) in north-eastern Siberia from before 60 000 years ago up until the species' final disappearance c.4000 years ago. We identified two genetic groups, implying a marked temporal genetic differentiation between samples with radiocarbon ages older than 12 thousand radiocarbon years before present (ka) and those younger than 9ka. Simulation-based analysis indicates that this dramatic change in genetic composition, which included a decrease in individual heterozygosity of approximately 30%, was due to a multifold reduction in effective population size. A corresponding reduction in genetic variation was also detected in the mitochondrial DNA, where about 65% of the diversity was lost. We observed no further loss in genetic variation during the Holocene, which suggests a rapid final extinction event.

Conformity in diversity? Isotopic investigations of infant feeding practices in two iron age populations from Southern Öland, Sweden.

This article presents the results of a study of infant diet at two Iron Age sites on the island of Öland, Sweden. The cemetery at Bjärby contained a large number of subadults who had survived the earliest years of life, whereas most individuals at Triberga had died by 6 months of age. To investigate whether differences in infant feeding could explain the different mortality rates, the carbon, nitrogen, and sulfur stable isotope ratios of bone and tooth dentin collagen from the two sites were analyzed. Twenty-two samples from Triberga and 102 from Bjärby yielded data that could be included in the carbon and nitrogen analysis. Twelve samples from Triberga and 42 from Bjärby were included in the sulfur analysis. The results for carbon (δ(13) C: Triberga X = -18.8, s.d. = 1.1; Bjärby X = -19.8, s.d. = 0.4), nitrogen (δ(15) N: Triberga X = 12.9, s.d. = 1.5; Bjärby X = 13.4, s.d. = 1.4), and sulfur (δ(34) S: Triberga X = 8.1, s.d. = 1.1; Bjärby X = 5.8, s.d. = 1.3) suggest that diet was broadly similar at both sites and based on terrestrial resources. At Bjärby, females and high-status individuals consumed higher-trophic level protein than other males from early childhood onward. There was some indication that the contribution of marine resources to the diet may also have differed between the sexes at Triberga. No consistent differences in breast milk intake were observed between the two sites, but there was substantial variation at each. This variation may reflect an influence of gender and social status on infant feeding decisions.

Species-specific reservoir effect estimates: A case study of archaeological marine samples from the Bering Strait.

Due to the marine reservoir effect, radiocarbon dates of marine samples require a correction. Marine reservoir effects, however, may vary among different marine species within a given body of water. Factors such as diet, feeding depth and migratory behaviour all affect the 14C date of a marine organism. Moreover, there is often significant variation within single marine species. Whilst the careful consideration of the ΔR values of a single marine species in a given location is important, so too is the full range of ΔR values within an ecosystem. This paper illustrates this point, using a sample pairing method to estimate the reservoir effects in 17 marine samples, of eight different species, from the archaeological site of Ekven (Eastern Chukotka, Siberia). An OxCal model is used to assess the strength of these estimates. The marine reservoir effects of samples passing the model range from ΔR (Marine20) = 136 ± 41-ΔR = 460 ± 40. Marine reservoir effect estimates of these samples and other published samples are used to explore variability in the wider Bering Strait region. The archaeological implications of this variability are also discussed. The calibrating of 14C dates from human bone collagen, for example, could be improved by applying a dietary relevant marine reservoir effect correction. For humans from the site of Ekven, a ΔR (Marine20) correction of 289 ± 124 years or reservoir age correction of 842 ± 123 years is suggested.

Approaches to osteoporosis in paleopathology: How did methodology shape bone loss research?

OBJECTIVE: This paper will review how different methods employed to study bone loss in the past were used to explore different questions and aspects of bone loss, how methodology has changed over time, and how these different approaches have informed our understanding of bone loss in the past. MATERIALS AND METHODS: A review and discussion is conducted on research protocols and results of 84 paleopathology publications on bone loss in archaeological skeletal collections published between 1969 and 2021. CONCLUSIONS: The variety in research protocols confounds accurate meta-analysis of previously published research; however, more recent publications incorporate a combination of bone mass and bone quality based methods. Biased sample selection has resulted in a predominance of European and Medieval publications, limiting more general observations on bone loss in the past. Collection of dietary or paleopathological covariables is underemployed in the effort to interpret bone loss patterns. SIGNIFICANCE: Paleopathology publications have demonstrated differences in bone loss between distinct archaeological populations, between sex and age groups, and have suggested factors underlying observed differences. However, a lack of a gold standard has encouraged the use of a wide range of methods. Understanding how this array of methods effects results is crucial in contextualizing our knowledge of bone loss in the past. LIMITATIONS: The development of a research protocol is also influenced by available expertise, available equipment, restrictions imposed by the curator, and site-specific taphonomic aspects. These factors will likely continue to cause (minor) biases even if a best practice can be established. SUGGESTIONS FOR FUTURE RESEARCH: Greater effort to develop uniform terminology and operational definitions of osteoporosis in skeletal remains, as well as the expansion of time scale and geographical areas studied. The Next-Generation Sequencing revolution has also opened up the possibility of ancient DNA analyses to study genetic predisposition to bone loss in the past.

Predicting sample success for large-scale ancient DNA studies on marine mammals.

In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic and surrounding regions. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly within species according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.

High frequency of lactose intolerance in a prehistoric hunter-gatherer population in northern Europe.

BACKGROUND: Genes and culture are believed to interact, but it has been difficult to find direct evidence for the process. One candidate example that has been put forward is lactase persistence in adulthood, i.e. the ability to continue digesting the milk sugar lactose after childhood, facilitating the consumption of raw milk. This genetic trait is believed to have evolved within a short time period and to be related with the emergence of sedentary agriculture. RESULTS: Here we investigate the frequency of an allele (-13910*T) associated with lactase persistence in a Neolithic Scandinavian population. From the 14 individuals originally examined, 10 yielded reliable results. We find that the T allele frequency was very low (5%) in this Middle Neolithic hunter-gatherer population, and that the frequency is dramatically different from the extant Swedish population (74%). CONCLUSIONS: We conclude that this difference in frequency could not have arisen by genetic drift and is either due to selection or, more likely, replacement of hunter-gatherer populations by sedentary agriculturalists.

Temporal genetic change in the last remaining population of woolly mammoth.

During the Late Pleistocene, the woolly mammoth (Mammuthus primigenius) experienced a series of local extinctions generally attributed to human predation or environmental change. Some small and isolated populations did however survive far into the Holocene. Here, we investigated the genetic consequences of the isolation of the last remaining mammoth population on Wrangel Island. We analysed 741 bp of the mitochondrial DNA and found a loss of genetic variation in relation to the isolation event, probably caused by a demographic bottleneck or a founder event. However, in spite of ca 5000 years of isolation, we did not detect any further loss of genetic variation. Together with the relatively high number of mitochondrial haplotypes on Wrangel Island near the final disappearance, this suggests a sudden extinction of a rather stable population.

Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses.

Multiple geographical regions have been proposed for the domestication of Equus caballus. It has been suggested, based on zooarchaeological and genetic analyses that wild horses from the Iberian Peninsula were involved in the process, and the overrepresentation of mitochondrial D1 cluster in modern Iberian horses supports this suggestion. To test this hypothesis, we analysed mitochondrial DNA from 22 ancient Iberian horse remains belonging to the Neolithic, the Bronze Age and the Middle Ages, against previously published sequences. Only the medieval Iberian sequence appeared in the D1 group. Neolithic and Bronze Age sequences grouped in other clusters, one of which (Lusitano group C) is exclusively represented by modern horses of Iberian origin. Moreover, Bronze Age Iberian sequences displayed the lowest nucleotide diversity values when compared with modern horses, ancient wild horses and other ancient domesticates using nonparametric bootstrapping analyses. We conclude that the excessive clustering of Bronze Age horses in the Lusitano group C, the observed nucleotide diversity and the local continuity from wild Neolithic Iberian to modern Iberian horses, could be explained by the use of local wild mares during an early Iberian domestication or restocking event, whereas the D1 group probably was introduced into Iberia in later historical times.

Diet patterns in medieval to early modern (14th-early 20th c.) coastal communities in Lithuania.

Coastal residents are quite often expected to consume a significant amount of aquatic resources, though historical evidence often reveals a rather complex diet. To better understand the actual consumption and the distribution of various foods, stable isotope (δ13C and δ15N) analyses were employed to skeletal remains from three coastal communities, Palanga, Kretinga and Smelte, ranging in date from the medieval period to the early modern ages (14th-early 20th c.) near the Curonian Lagoon and the Baltic Sea in Lithuania. Animal bones from the region, covering the same time periods, were also analysed. Stable isotope results were compared with historical records. According to historical sources different types of diet were prevalent during that period of time: Medieval Prussian-Lithuanian peasant, Lithuanian fisherman, German urban, and religious-based. Elevated δ15N values for Smelte samples suggest a diet consisting of considerable amounts of freshwater fish protein, which is in contrast to historical sources. There were no significant differences in stable isotope values between males and females, while subadult δ15N values were significantly higher than adult ones, indicating that those children were breastfed for an extended period. Meanwhile, Palanga and Kretinga samples had isotope values suggesting a high reliance on terrestrial resources and a peasant type of diet.

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) 87Sr/86Sr isotope data from scythian Iron age barrows in Altai, Russia.

This paper reports LA-ICP-MS 87Sr/86Sr isotopic data collected from archaeological human remains uncovered in Manzherok region, Altai Republic, Russian Federation ("Mobility of nomads in central Asia: chronology and 87Sr/86Sr isotope evidence from the Pazyryk barrows of northern Altai, Russia" [1]. The skeletal remains derive from Scythian barrows dated to 6th - 3rd century BC located at Chultukov Log 1 cemetery. The Chultukov Log cemetery, located approximately 470km south of Novosibirsk, is considered the biggest nomadic burial ground in the Upper Altai and the Sayan Mountains. To enrich the information on prehistoric mobility of ancient nomadic populations in Central Asia, strontium isotopic data were collected using a Nu plasma (II) MC-ICP-MS equipped with ESI NWR193-based laser ablation system from premolar teeth of 8 adult individuals (4 males and 4 females), associated mainly with the Pazyryk culture. Additionally, we report bioavailable strontium data from single Equus caballus specimen (found at Chultukov Log 9 settlement) from Manzherok territory. In this study we have successfully applied and tested new in-depth decontamination protocol for total (<95%) removal of contaminants, necrotic tissue and dental calculus in archaeological materials based on a clinical irrigation procedure with NaOCl and EDTA. Strontium LA-ICP-MS 87Sr/86Sr isotopic data presented in this paper were obtained from prehistoric human teeth previously decontaminated according to this method. These data will provide valuable resources for isotopic analyses of prehistoric transportation systems in Central Asia, including residential mobility of ancient nomads inhabiting steppe zone, Mongolia and NW China.

Genetic turnovers and northern survival during the last glacial maximum in European brown bears.

The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid-Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter-specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought.

Temporal fluctuation in North East Baltic Sea region cattle population revealed by mitochondrial and Y-chromosomal DNA analyses.

BACKGROUND: Ancient DNA analysis offers a way to detect changes in populations over time. To date, most studies of ancient cattle have focused on their domestication in prehistory, while only a limited number of studies have analysed later periods. Conversely, the genetic structure of modern cattle populations is well known given the undertaking of several molecular and population genetic studies. RESULTS: Bones and teeth from ancient cattle populations from the North-East Baltic Sea region dated to the Prehistoric (Late Bronze and Iron Age, 5 samples), Medieval (14), and Post-Medieval (26) periods were investigated by sequencing 667 base pairs (bp) from the mitochondrial DNA (mtDNA) and 155 bp of intron 19 in the Y-chromosomal UTY gene. Comparison of maternal (mtDNA haplotypes) genetic diversity in ancient cattle (45 samples) with modern cattle populations in Europe and Asia (2094 samples) revealed 30 ancient mtDNA haplotypes, 24 of which were shared with modern breeds, while 6 were unique to the ancient samples. Of seven Y-chromosomal sequences determined from ancient samples, six were Y2 and one Y1 haplotype. Combined data including Swedish samples from the same periods (64 samples) was compared with the occurrence of Y-chromosomal haplotypes in modern cattle (1614 samples). CONCLUSIONS: The diversity of haplogroups was highest in the Prehistoric samples, where many haplotypes were unique. The Medieval and Post-Medieval samples also show a high diversity with new haplotypes. Some of these haplotypes have become frequent in modern breeds in the Nordic Countries and North-Western Russia while other haplotypes have remained in only a few local breeds or seem to have been lost. A temporal shift in Y-chromosomal haplotypes from Y2 to Y1 was detected that corresponds with the appearance of new mtDNA haplotypes in the Medieval and Post-Medieval period. This suggests a replacement of the Prehistoric mtDNA and Y chromosomal haplotypes by new types of cattle.

Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process.

The European Neolithization process started around 12 000 years ago in the Near East. The introduction of agriculture spread north and west throughout Europe and a key question has been if this was brought about by migrating individuals, by an exchange of ideas or a by a mixture of these. The earliest farming evidence in Scandinavia is found within the Funnel Beaker Culture complex (Trichterbecherkultur, TRB) which represents the northernmost extension of Neolithic farmers in Europe. The TRB coexisted for almost a millennium with hunter-gatherers of the Pitted Ware Cultural complex (PWC). If migration was a substantial part of the Neolithization, even the northerly TRB community would display a closer genetic affinity to other farmer populations than to hunter-gatherer populations. We deep-sequenced the mitochondrial hypervariable region 1 from seven farmers (six TRB and one Battle Axe complex, BAC) and 13 hunter-gatherers (PWC) and authenticated the sequences using postmortem DNA damage patterns. A comparison with 124 previously published sequences from prehistoric Europe shows that the TRB individuals share a close affinity to Central European farmer populations, and that they are distinct from hunter-gatherer groups, including the geographically close and partially contemporary PWC that show a close affinity to the European Mesolithic hunter-gatherers.

Dietary variation in arctic foxes (Alopex lagopus)-an analysis of stable carbon isotopes.

We used stable carbon isotopes to analyse individual variation in arctic fox diet. We extracted collagen from bones (the lower jaw), and measured stable carbon isotopes. The foxes came from three different localities: Iceland, where both microtines and reindeer are rare; west Greenland, where microtines are absent; and Sweden, where scat analyses showed the primary food to be microtine rodents and reindeer. The Icelandic samples included foxes from both coastal and inland habitats, the Swedish sample came from an inland area, and the Greenland sample from coastal sites. The spatial variation in the isotopic pattern followed a basic division between marine and terrestrial sources of protein. Arctic foxes from inland sites had δ13C values of -21.4 (Iceland) and -20.4‰ (Sweden), showing typical terrestrial values. Coastal foxes from Greenland had typical marine values of -14.9‰, whereas coastal foxes from Iceland had intermediate values of -17.7‰. However, there was individual variation within each sample, probably caused by habitat heterogeneity and territoriality among foxes. The variation on a larger scale was related to the availability of different food items. These results were in accordance with other dietary analyses based on scat analyses. This is the first time that stable isotopes have been used to reveal individual dietary patterns. Our study also indicated that isotopic values can be used on a global scale.