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.
