Genomic and strontium isotope variation reveal immigration patterns in a viking age town

Abstract: The impact of human mobility on the northern Euro- pean urban populations during the Viking and Early Middle Ages and its repercussions in Scandinavia it- self are still largely unexplored. Our study of the de- mographics in the final phase of the Viking era is the first comprehensive multidisciplinary investiga- tion that includes genetics, isotopes, archaeology, and osteology on a larger scale. This early Christian dataset is particularly important as the earlier com- mon pagan burial tradition during the Iron Age was cremation, hindering large-scale DNA analyses. We present genome-wide sequence data from 23 indi- viduals from the 10th to 12th century Swedish town of Sigtuna. The data revealed high genetic diversity among the early urban residents. The observed vari- ation exceeds the genetic diversity in distinct mod- ern-day and Iron Age groups of central and northern Europe. Strontium isotope data suggest mixed local and non-local origin of the townspeople..

The history of the Polynesians inferred from high resolution HLA data.

Numerous scientific investigations have been undertaken to answer the question of Polynesian origins. Most archaeological and linguistic evidence and previous studies in population genetics suggested that Remote Oceania was settled from the west. The human colonization of the Pacific began with the settlement of Australia and Papua New Guinea (PNG) at least 40,000 years ago, and was followed by the settlement of Remote Oceania, starting about 3,500 years ago. Most scholars agree that present-day Polynesians originated in Southeast Asia, and first entered the region as Neolithic agriculturalists. But the questions of the character of colonization and the extent of the Melanesian contribution to the Polynesian gene pool, as well possible South American contacts, still prevail. Certain plants, such as the sweet potato and bottle gourd, indicate some contacts with South America. Moreover, the Norwegian explorer Thor Heyerdahl showed that a voyage from South America was physically possible, even though no direct evidence of Amerindian ancestry has been found. Interestingly, recent research on the HLA system showed a significant South American genetic component in Easter Island. In order to address the issue of possible ancient contacts between Polynesia and South America, and to investigate the genetic affinities of the Eastern Polynesians, 52 human genomic DNA samples from three locations in Eastern Polynesia (Southern Marquesas, Mangareva and Western Samoa) were tested for HLA polymorphisms. The results indicate that the Eastern Polynesians are principally derived from Southeast Asia. Some recent European admixture was detected, most likely due to post-European contacts. Several polymorphisms point to a possible North Asian connection (DRB1*0405 and DRB1*1201) and other, rare elements (e.g. A*0212, B*3905 and DRB1*1402) are clear evidence of South American admixture. No significant Melanesian ancestry was found. Phylogenetic analysis showed that the Polynesians studied did not differ significantly from Southeast Asian populations of mixed origins (such as Malay, Filipino, East Timorese and Moluccans) but have very little in common with the present-day inhabitants of Papua New Guinea. The results, however, could be the effect of sampling variance or genetic drift in Polynesia. In general, the HLA polymorphisms observed in this study give further support to the ‘Express train’ model of the colonization of the Pacific

aMeta : an accurate and memory-efficient ancient metagenomic profiling workflow

Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory

Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

Background After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data. Results Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses. Conclusions We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field

Human population dynamics and Yersinia pestis in ancient northeast Asia

We present genome-wide data from 40 individuals dating to c.16,900 to 550 years ago in northeast Asia. We describe hitherto unknown gene flow and admixture events in the region, revealing a complex population history. While populations east of Lake Baikal remained relatively stable from the Mesolithic to the Bronze Age, those from Yakutia and west of Lake Baikal witnessed major population transformations, from the Late Upper Paleolithic to the Neolithic, and during the Bronze Age, respectively. We further locate the Asian ancestors of Paleo-Inuits, using direct genetic evidence. Last, we report the most northeastern ancient occurrence of the plague-related bacterium, Yersinia pestis. Our findings indicate the highly connected and dynamic nature of northeast Asia populations throughout the Holocene.De två första författarna delar förstaförfattarskapet.</p

Investigating Holocene human population history in North Asia using ancient mitogenomes

Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c. 13,790 BP and c. 1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene

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.Günther T., Malmström H., Svensson E.M., Omrak A., Sánchez-Quinto F, Kılınç G.M., Krzewinska M., Eriksson G., Fraser M., Edlund H., Munters A.R., Coutinho A., Simões L.G., Vicente M., Sjölander A., Sellevold B.J., Jørgensen R., Claes P., Shriver M.D., Valdiosera C., Netea M.G., Apel J., Lidén K., Skar B., Storå J., Götherström A., Jakobsson M., ''Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation'', PLoS Biology, vol. 16, no. 1, pp. e2003703, 22 pp., January 9, 2018.status: publishe

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

Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age

The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups. By analysing 91 Bronze Age genomes from East-Central Europe, the authors discovered that Middle Bronze Age populations were formed by an admixture event involving hunter-gatherers and that the social structure of resulting population was primarily patrilocal