The final disappearance of the aurochs ( Bos primigenius ) from Poland in the 17th century marked the culmination of a decline that had begun as early as the Atlantic period. Although human activities primarily drove its extinction, the reasons for its earlier disappearance in Scandinavia remain uncertain. This study investigates the immigration and extinction dynamics of the Scandinavian aurochs during the Holocene. Utilising phylogenetic and palaeogenetic data, we trace its postglacial colonisation from a Western European refugium, delimiting the period of connectivity with the main European population before the land bridge was severed by rising sea levels. Genetic analyses further point to inbreeding and genetic drift, exacerbated by population bottlenecks and geographical isolation, diminishing resilience over time. Population modelling indicates a classic boom-bust pattern correlated with intensified human settlement and hunting. Despite environmental conditions initially permitting persistence amidst increasing forest cover, subsequent habitat loss and human pressures accelerated demographic decline. Our integrated approach indicates that the extinction resulted from a synergistic effect of habitat fragmentation and degradation, genetic depletion, and prolonged anthropogenic pressures. These findings highlight the complex, multifactorial processes underlying species extinction and emphasise the importance of cross-disciplinary methods in palaeoecological research.
Abstract One of the most devastating events in human history, the Black Death (c.1347-1353), marked the beginning of the Second Plague Pandemic. After initially receding, plague returned in intermittent outbreaks throughout Europe, beginning with the pestis secunda . Despite its significance, the post-Black Death epidemiology of Yersinia pestis remains poorly understood. Here, we report 23 new Y. pestis genomes recovered from Second Plague Pandemic contexts across Scandinavia, the Netherlands, Iceland, and Armenia, spanning approximately 270 years. Applying a reproducible mutation-filtering pipeline to assess genetic diversity, we report both Black Death and post-Black Death lineages and document multiple waves of plague at individual cemetery sites. We identify four pestis secunda genomes, including three from Armenia, supporting the eastward dissemination of this lineage prior to its disappearance from Europe. We also resolve a previously under-characterised Branch 1A sub-lineage of Y. pestis and provide the first genomic evidence of plague in Iceland, resolving longstanding uncertainty over its presence on the island. Finally, by calling variants against a reconstructed ancestral reference, we identify clade-defining mutations, including nonsynonymous changes in metabolic and biofilm-related genes with predicted structural effects that may have contributed to shaping the epidemiological dynamics of the Second Plague Pandemic.
The second plague pandemic (early 14th-early 19th centuries), which was caused by Yersinia pestis, had a profound demographic, socio-economic and cultural impact across Eurasia and North Africa. Many regions in Europe and the Middle East are estimated to have lost 40-60% of their human populations, with some areas suffering even higher mortality. Whether exposure to Y. pestis drove strong positive selection on protective genetic variants in the human genome, and how it shaped migration patterns, remains debated, despite several recent studies based on ancient DNA. Here, we analyse a markedly larger, higher coverage, and geographically diverse dataset based on shotgun sequencing of genomes from 529 ancient individuals to a mean depth 8.8x dating to either before or after the arrival of the pandemic at three sites in northern Europe: Trondheim (Norway), Lund (Sweden) and Vilnius (Lithuania). Genome-wide scans for signatures of selection provide no evidence for strong positive selection acting on specific genetic variants driven by Y. pestis exposure: we neither replicate selection signatures reported by previous studies nor identify new genome-wide significant candidates. However, for all three sites, we observe evidence for a reduction in long-range immigration, indicated by a drop in the diversity of ancestry that followed the arrival of Y. pestis and broadly coincided with the end of the Viking Age, Christianisation and the onset of the Little Ice Age. Our results shed important light on the demographic impact of major sociohistorical changes that occurred during the late Medieval period in Scandinavia and the Baltic region and link Christianisation to increased diversity in ancestry before the pandemic.
This study employs an interdisciplinary approach to investigate diet at the Swedish town of Nya Lodose (1473-1624 CE). The primary aim is to determine the proportions of aquatic and terrestrial foods consumed in the diet and to examine whether these proportions shifted after the Reformation in 1527. A secondary aim is to analyze variations in diet related to biological sex or social status. delta C-13 and delta N-15 stable isotope ratio analysis of bulk rib collagen from humans (n = 71) and fauna (n = 202) was conducted, and the results show the sampled individuals have similar isotopic compositions, with mean delta C-13 values of -19.9 +/- 0.7 parts per thousand and delta N-15 values of 12.6 +/- 1.0 parts per thousand. These isotopic values suggest a diet rich in animal protein, mainly beef, with some consumption of aquatic resources. The Bayesian mixing model FRUITS was used to estimate the relative consumption of livestock, marine fish, and freshwater/pelagic fish. Modelling indicates an average aquatic protein intake of similar to 15-16% for females and similar to 20-24% for males. Comparing isotopic data from before and after the Reformation reveals no major changes in diet, although the post-Reformation period saw a small increase in fish intake in males and a diversification in diet in both sexes. The isotopic data suggest a slight but statistically significant difference in diet between males and females. Females had a less varied diet than males, with males having greater access to fish. After the Reformation, dietary differences between the sexes became marginally more pronounced.
