Biology subjects

Philippsen, B.

Publications and source records attributed to Philippsen, B..

4 recordsLinked to original sources

bioRxiv2026

The Genomic Landscape of Post-Black Death Epidemics in Northern Europe and the Caucasus

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.

genetics↗

bioRxiv2026

Genomic impact of the second plague pandemic on three human populations

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.

genomics↗

bioRxiv2026

Walrus Population-specific Marine Reservoir Offsets (ΔR) for Calibration of Radiocarbon Dates: Implications for Arctic Chronologies and Medieval Trade

Walruses have long played a vital role in Arctic subsistence and commercial economies, yet accurate radiocarbon dating of walrus-derived archaeological materials is complicated by regional variation in marine reservoir effects. This study presents new {Delta}R values derived from 31 new and 15 legacy radiocarbon dates on known-age walrus specimens spanning multiple populations of Odobenus rosmarus rosmarus and O. r. divergens. The results reveal substantial inter-population variability, with {Delta}R values ranging from -140 (Franz Josef Land) to +295 (Pacific), underscoring the importance of population-specific calibration. A pooled {Delta}R of +17{+/-}12 was calculated for western Greenland and the Canadian Arctic--regions central to the medieval Norse ivory trade--and applied to 12 walrus rostra and ivory artefacts excavated in Trondheim, Norway. The resulting calibrated dates are from the 11th to early 14th centuries CE, confirming that seemingly anomalous post-15th-century finds are residual rather than evidence of continued trade. An alternative {Delta}R estimate of -110{+/-}35, derived solely from archaeological context dates, suggests potential time lags between harvest and deposition. These findings demonstrate the value of known-age walrus {Delta}R data for refining chronologies of Arctic exploitation and long-distance trade, while highlighting the need for provenance studies in archaeological dating and both the pertinence and limitations of mollusk-based reservoir corrections.

paleontology↗

bioRxiv2025

Sedimentary ancient DNA metagenomic analysis provides new insights into farming in central Norway from the Bronze Age to late Medieval period

Sedimentary ancient DNA (sedaDNA) has been proposed as a key methodology for reconstructing paleoclimates and biodiversity over time. To a lesser extent, it has been explored as a complementary tool for reconstructing human-driven local environmental changes over time, such as those explored in open air archaeological sites. Our study employs a sedaDNA metagenomic approach to investigate land use and environmental change at the archaeological site of Torg[a]rdsletta in central Norway, spanning from the Bronze Age through the Medieval period. Stratigraphic sediment samples reveal temporal shifts in plant, animal and microbial communities, reflecting evolving human practices and climatic conditions. Progression through the layers indicate signs or land clearance, cultivation and animal husbandry in the region. Notably, a significant reduction in microbial and plant diversity during periods of climatic upheaval--such as the AD 536-540 volcanic event--correlates with landscape and societal adjustments. The findings demonstrate that sedaDNA complements traditional proxies, providing high-resolution insights into past land use, environmental interactions, and societal organization. The successful extraction of ancient genetic material underscores sedaDNAs potential to reconstruct dynamic prehistoric landscapes and anthropogenic impacts, offering further potential for understanding long-term human-environment relationships in Scandinavia.

genomics↗