Periodic Reporting for period 1 - ALPGEN (Ancient genomics and the population history of the Circum-Alpine region)
Période du rapport: 2022-09-01 au 2025-02-28
The AlpGen project investigates the population history of prehistoric communities in the circum-Alpine region between roughly 5,000 and 600 BCE. This timeframe encompasses the rise and decline of the iconic Alpine lake settlements—remarkable pile-dwelling sites known for their exceptional preservation of organic material. Submerged under lake sediments, these sites have yielded wood, plant remains, textiles, and other rare artefacts that offer unparalleled insight into the lifeways of early agrarian societies in Central Europe. Despite this wealth of material culture, our understanding of the people themselves remains limited. Traditional burials are virtually absent, and human remains are rare, making it difficult to study the genetic makeup, health, and ancestry of these communities. AlpGen addresses this gap by applying cutting-edge ancient DNA methods to extract human and microbial DNA from chewed birch tar and other artefacts recovered from lake-dwelling sites. This approach represents a major innovation in ancient DNA research—enabling the study of past populations through artefacts rather than skeletal remains. Early results highlight the remarkable potential of these artefacts as sources of ancient biomolecules, revealing both individual and community-level genetic information. By analysing DNA preserved in chewed birch tar, AlpGen aims to trace genetic ancestry, demographic history, diet, and health, as well as to explore the evolution of the human oral microbiome in prehistoric Alpine populations. Ultimately, the project will provide crucial data on groups for whom conventional ancient DNA sources are lacking, significantly enriching our understanding of European population history. In doing so, AlpGen not only deepens our knowledge of the Alpine lake dwellers themselves but also sets the stage for broader applications of artefact-based ancient DNA research in archaeology worldwide.
The AlpGen project has made substantial progress during the last reporting period, with key developments in sample collection, wet-lab protocol optimization, and refinement of bioinformatic workflows. As part of this effort, we conducted two successful sampling trips, resulting in the collection of over 200 birch tar samples from 16 archaeological sites across the Alpine region—representing approximately two-thirds of our planned total. Each artefact has been carefully documented, photographed, and 3D-scanned, and the first scan catalogue is now available on our project website (www.alpgen.eu). Screening of over 100 samples has revealed excellent preservation of ancient DNA, providing a strong foundation for downstream analyses. To maximize DNA recovery, we have optimized laboratory protocols specifically for ancient DNA extraction from birch tar, including a newly developed non-invasive “leaching” method. This approach performs comparably to conventional invasive techniques, representing a major breakthrough that allows for high-quality DNA retrieval without damaging these rare archaeological objects. In parallel, we have advanced our bioinformatic pipelines for taxonomic classification of short metagenomic reads. These workflows minimize the risk of false-positive assignments and have already led to two manuscript submissions—one addressing the challenge of false positives in ancient metagenomic studies, and the other highlighting contamination issues in publicly available reference genomes. These insights reinforce AlpGen’s commitment to methodological rigor and underline the importance of careful validation in ancient genomics. Scientifically, the project has achieved a number of firsts. For the first time, we have successfully generated ancient human genomes directly from artefacts, producing over 40 partial genomes to date—marking a major advance in the field of ancient human genomics. In addition, sequencing of ancient oral microbiomes from these mastics has shown that they resemble modern human oral microbiomes more closely than those derived from dental calculus, opening new avenues for research into ancient microbial ecology and the evolution of the human oral microbiome. Together, these achievements represent a significant contribution to ancient DNA research and greatly enrich our understanding of the UNESCO-designated iconic Alpine lake settlements. As work continues, AlpGen is poised to provide transformative insights into the lives, health, ancestry, and environments of prehistoric lake-dwelling communities.
The AlpGen project has already delivered several high-impact results that push the boundaries of ancient DNA research and prehistoric archaeology. We have developed new protocols for extracting ancient DNA from archaeological mastics, including a non-invasive “leaching” method that preserves artefact integrity while enabling high-quality DNA recovery; these are currently being prepared for publication. Beyond chewed birch tar, we have shown that hafting and ceramic repair tar also preserve ancient DNA, broadening the range of usable materials—findings now under peer review. We have also optimised bioinformatic workflows to minimise false positives in ancient metagenomic analyses, with two manuscripts in preparation addressing methodological pitfalls and reference genome contamination. Notably, we have shown that ancient mastics preserve oral microbiomes more faithfully than dental calculus, and for the first time, recovered over 40 ancient human genomes directly from artefacts—results feeding into two major studies on European population history and oral microbiome evolution. These advances underscore the potential of artefact-based DNA research and point to the need for further sequencing, continued investment in lab and computational capacity, and broader collaboration and standardisation. By the end of the project, AlpGen will have produced open-access 3D scan catalogues, published protocols for both destructive and non-destructive DNA extraction, validated tools for low-biomass metagenomic analysis, and key insights into the ancestry, health, and microbial ecology of Alpine lake-dwelling populations—shared through at least four peer-reviewed articles, major conference presentations, and a planned travelling exhibition in the region.