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.

The population genomic legacy of the second plague pandemic

Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.¹ It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).² Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17^th-19^th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large F_ST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.

Sustainable phosphorus management in soil using bone apatite

Soil fertility and phosphorus management by bone apatite amendment are receiving increasing attention, yet further research is needed to integrate the physicochemical and mineralogical transformation of bone apatite and their impact on the supply and storage of phosphorus in soil. This study has examined bone transformation in the field over a span of 10-years using a set of synchrotron-based microscopic and spectroscopic techniques. Transmission X-ray microscopy (TXM) observations reveal the in-situ deterioration of bone osteocyte-canaliculi system and sub-micron microbial tunneling within a year. Extensive organic decomposition, secondary mineral formation and re-mineralization of apatite are evident from the 3rd year. The relative ratio of (v₁ + v₃) PO₄^3- to v₃ CO₃^2- and to amide I increase, and the v_3c PO₄^3- peak exhibits a blue-shift in less than 3 years. The carbonate substitution of bone hydroxyapatite (HAp) to AB-type CHAp, and phosphate crystallographic rearrangement become apparent after 10 years' aging. The overall CO₃^2- peak absorbance increases over time, contributing to a higher acid susceptibility in the aged bone. The X-ray Photoelectron Spectroscopy (XPS) binding energies for Ca (2p), P (2p) and O (1s) exhibit a red-shift after 1 year because of organo-mineral interplay and a blue-shift starting from the 3rd year as a result of the de-coupling of mineral and organic components. Nutrient supply to soil occurs within months via organo-mineral decoupling and demineralization. More phosphorus has been released from the bones and enriched in the associated and adjacent soils over time. Lab incubation studies reveal prominent secondary mineral formation via re-precipitation at a pH similar to that in soil, which are highly amorphous and carbonate substituted and prone to further dissolution in an acidic environment. Our high-resolution observations reveal a stage-dependent microbial decomposition, phosphorus dissolution and immobilization via secondary mineral formation over time. The active cycling of phosphorus within the bone and its interplay with adjacent soil account for a sustainable supply and storage of phosphorus nutrients.

Systematic changes of bone hydroxyapatite along a charring temperature gradient: An integrative study with dissolution behavior

The applicability of bone char as a long-term phosphorus nutrient source was assessed by integrating their mineral transformation and physicochemical properties with their dissolution behavior. We have explored synchrotron-based spectroscopic and imaging techniques (FTIR, XRD, and TXM) to investigate the physicochemical changes of bone and bone char along a charring temperature gradient (300-1200 °C) and used a lab incubation experiment to study their dissolution behaviors in solutions of different pH (4, 6, and 6.9). The thermal decomposition of inorganic carbonate (CO₃^2-) and the loss of organic components rendered a crystallographic rearrangement (blueshift of the PO₄^3- peak) and mineral transformation with increasing temperatures. The mineral transformation from B-type to AB- and A-type carbonate substitution occurred mainly at <700 °C, while the transformation from carbonated hydroxyapatite (CHAp) to more mineralogically and chemically stable HAp occurred at >800 °C. The loss of inorganic carbonate and the increase of structural OH^- with increasing temperatures explained the change of pH buffering capacity and increase of pH and their dissolution behaviors. The higher peak area ratios of phosphate to carbonate and phosphate to amide I band with increasing temperatures corroborated the higher stability and resistivity to acidic dissolution by bone chars made at higher temperatures. Our findings suggest that bone char made at low to intermediate temperatures can be a substantial source of phosphorus for soil fertility via waste management and recycling. The bone char made at 500 °C exhibited a high pH buffering capacity in acidic and near-neutral solutions. The 700 °C bone char was proposed as a suitable liming agent for raising the soil pH and abating soil acidity. Our study has underpinned the systematic changes of bone char and interlinked the charring effect with their dissolution behavior, providing a scientific base for understanding the applicability of different bone chars as suitable P-fertilizers.

Bone biodeterioration-The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community

Bacteria play an important role in the degradation of bone material. However, much remains to be learnt about the structure of their communities in degrading bone, and how the depositional environment influences their diversity throughout the exposure period. We genetically profiled the bacterial community in an experimental series of pig bone fragments (femur and humeri) deposited at different well-defined environments in Denmark. The bacterial community in the bone fragments and surrounding depositional environment were studied over one year, and correlated with the bioerosion damage patterns observed microscopically in the bones. We observed that the bacterial communities within the bones were heavily influenced by the local microbial community, and that the general bone microbial diversity increases with time after exposure. We found the presence of several known collagenase producing bacterial groups, and also observed increases in the relative abundance of several of these in bones with tunneling. We anticipate that future analyses using shotgun metagenomics on this and similar datasets will be able to provide insights into mechanisms of microbiome driven bone degradation.

Population genomics of the Viking world

The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history^1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.

Population genomics of the Viking world

The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history^1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.

Osteoporosis in a population from medieval Norway

Modern populations from Norway and England differ in their experience of osteoporosis, the former showing lower bone mineral density (BMD) and a higher fragility fracture rate. The aim of the present work was to investigate whether this was also the case during the Middle Ages. Age-dependent loss of BMD in the proximal femur was assessed using dual X-ray absorptiometry (DXA) in male and female adult skeletons from a cemetery in the medieval town of Trondheim, Norway. Fracture prevalence was also investigated. Results were compared with those previously reported for a skeletal series from Wharram Percy, a deserted medieval village in England. Results indicate that peak BMD and patterns of age-related loss of BMD in the Norwegian and the English group were similar. Among females, the prevalence of osteoporotic fractures was greater in the Norwegian than in the English population. The BMD results suggest that differences in BMD between English and Norwegians are of recent origin, although given the fairly modest sample sizes, further work is needed to confirm this. Reasons for the greater prevalence of osteoporotic fractures in women in the Norwegian skeletal series are unclear, but the colder climate and greater frequency of hard surfaces may have meant that falls were more frequent, and when they occurred, were more likely to result in fractures than in the rural English group.

Paleopathological and biomolecular study of tuberculosis in a medieval skeletal collection from England

Nine human skeletons of medieval date from a rural English burial site show signs of skeletal tuberculosis. They were subject to polymerase chain reaction (PCR) assays aimed at detecting traces of DNA from infecting mycobacteria, with the purpose both of confirming the paleopathological diagnosis of tuberculosis and determining in individual cases whether disease was due to M. tuberculosis or M. bovis. In all nine cases, evidence for M. tuberculosis complex DNA was found, and in all instances it appeared that disease was due to M. tuberculosis rather than M. bovis. The significance of the findings for understanding tuberculous infection in rural agrarian communities in medieval England is discussed.