Hannes Schroeder

Historical narratives of early colonization in Quebec frequently portray French–Indigenous relations as cooperative and characterized by admixture; which are often mobilized in modern debates on false-indigeneity. These narratives have been studied through genealogical, genetic, and bioarchaeological analyses, yet individuals of African descent remain mostly absent from them, while Indigenous peoples are framed largely in relation to colonists. Notre-Dame Cemetery (1683–1796) in Tiohtià:ke-Montréal offers a unique window onto one of the earliest urban colonial populations in Nouvelle France, but previous bioarchaeological studies have produced conflicting interpretations regarding the presence of non-European or admixed individuals. Here, we generated ancient DNA from 45 individuals and applied genotype imputation, runs-of-homozygosity, and identity-by-descent analyses to reevaluate genetic relatedness and cemetery organization. Our results show exclusively French European ancestry. We observe low levels of close-kin unions and identify several genetic lineages distributed across the cemetery’s successive burial phases rather than family clustering or religious ordering. The spatial organization of the graves is consistent with rapid demographic growth, with successive burials overlapping one another, before being disrupted by urban development. Rooted in Indigenous decolonial frameworks, these findings challenge the ‘admixed founding population’ narrative, aligning with historical evidence of Indigenous and African-descended marginalization while highlighting the social inequalities shaping this colonial urban cemetery. Québec’s bioarchaeological practices must move beyond blood ties as the sole measure of kinship and commit to legal frameworks that better reflect reciprocal obligations of care, in order to overcome the colonial structures that still define heritage.

Ancient DNA (aDNA) analysis has transformed how we study human migration, species dispersals and environmental change, but poor preservation remains a major challenge. This is especially true in tropical settings, where hot and humid conditions accelerate DNA decay. Because aDNA work is destructive, knowing how long DNA survives and under what conditions is crucial for selecting samples likely to yield meaningful data while minimizing damage. Here, we analyse low-coverage shotgun data from over 300 human samples from 33 archaeological sites (3300–400 cal. BP) in the Caribbean to evaluate the effects of sample age, sample type and burial context on DNA preservation. Preservation varied markedly both between and within sites, with sample type and burial context exerting strong effects. Macroscopic inspection, though imperfect, proved a useful first line predictor of molecular preservation. Decay-rate modelling indicates that DNA decays roughly 4× faster in the Caribbean than in temperate regions and about 14× faster than in subpolar settings. Under these conditions we predict that recovery from remains significantly older than approximately 5000 years will be challenging. Encouragingly, this window encompasses most of the region's human history, indicating that much of it remains accessible to aDNA analysis, provided suitable samples can be found and appropriate excavation and post-excavation protocols are followed.

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 use of Saccharomyces cerevisiae to ferment alcoholic beverages is an ancient tradition, with genetic evidence indicating origins in Neolithic Asia, although the domestication process of the species is not fully understood. Kveik is a group of traditional yeasts used in farmhouse brewing in western Norway preserved through generations of rural brewing practice. While recent studies have highlighted the distinctiveness of kveik, its precise phylogenetic position, genetic diversity, and domestication history remain unclear. We performed whole-genome sequencing on 64 isolates from 25 traditional brewing cultures from Western Norway selected using cultural heritage criteria and generated telomere-to-telomere assemblies for selected strains. Phylogenomic and population genetic analyses reveal that kveik strains form a paraphyletic and early-diverging group with respect to other domesticated S. cerevisiae strains. Most strains exhibit low diversity among isolates from the same brewing culture, strong geographic clustering, and little evidence of gene flow or admixture. Mitochondrial genomes and Ty1 retrotransposon profiles corroborate this distinct lineage history. We further show that previously reported signals of gene flow between kveik and Asian fermentation strains are likely artifacts caused by population structure and selection. Divergence time estimates suggest that the common ancestor of beer, kveik, and other liquid-phase fermenting strains originated from ancestral populations 4,000 to 8,000 years ago. Our genomic resource sheds light on yeast evolution and domestication. Kveik likely comprises some of the oldest domesticated lineages in continuous use until today, connecting intangible cultural heritage to an early genetic origin.

In the mid-19th century, St Helena became a key receiving point for Africans “liberated” from illegal slave ships by the British Royal Navy. Of the ~27,000 landed, ~8000 died soon after arrival and were buried locally. In connection with a broader community-led commemorative effort, we analyzed tooth enamel strontium isotope ( ⁸⁷ Sr/ ⁸⁶ Sr) data for 152 individuals, including high-resolution intratooth profiles, to identify likely origins and infer forced movements before embarkation. Isoscape-based probabilistic assignment, integrated with historical evidence and published ancient DNA data, constrains homelands ranging from coastal Central Africa to far inland areas, revealing long-distance movements, sometimes beginning in childhood. By refining provenance, these data informed local decisions about care and potential repatriation, highlighting the complexities of return and ultimately supporting reburial on St Helena.

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.

The use of Saccharomyces cerevisiae to ferment alcoholic beverages is an ancient tradition, with genetic evidence indicating origins in Neolithic Asia, although the domestication process of the species is not fully understood. Kveik is a group of traditional yeasts used in farmhouse brewing in western Norway preserved through generations of rural brewing practice. While recent studies have highlighted the distinctiveness of kveik, its precise phylogenetic position, genetic diversity, and domestication history remain unclear. We performed whole-genome sequencing on 64 isolates from 25 traditional brewing cultures from Western Norway selected using cultural heritage criteria, and generated telomere-to-telomere (T2T) assemblies for selected strains. Phylogenomic and population genetic analyses reveal that kveik strains form a paraphyletic and early diverging group with respect to other domesticated S. cerevisiae strains. Most strains exhibit low diversity among isolates from the same brewing culture, strong geographic clustering, and little evidence of gene-flow or admixture. Mitochondrial genomes and Ty1 retrotransposon profiles corroborate this distinct lineage history. We further show that previously reported signals of gene flow between kveik and Asian fermentation strains are likely artifacts caused by population structure and selection. Divergence time estimates suggest that the common ancestor of beer, kveik, and other liquid-phase fermenting strains originated from ancestral populations 4,000 to 8,000 years ago. Our genomic resource sheds light on yeast evolution and domestication. Kveik likely comprises some of the oldest domesticated lineages in continuous use until today, connecting intangible cultural heritage to an early genetic origin. Significance statement: Yeast has been used to brew beer and ferment food for thousands of years, but we still do not fully understand how and where the different domesticated strains we are using today arose. We sequenced the largest collection of Norwegian farmhouse yeasts (kveik) to date, from cultures used by rural traditional brewers for generations. Our genetic analyses show that kveik forms a distinct and early branch among European brewing yeasts. This shows that historical traditions have created unique local types of yeast and helps us better understand and preserve the diversity of domesticated yeasts.

The transition to agriculture was a transformative process in human history with wide-ranging demographic and social consequences¹. Across South America, agriculture was adopted at different times and through diverse pathways, resulting in a mosaic of regionally distinct farming histories^2,3. The Uspallata Valley, at the southern frontier of Andean farming, offers a unique opportunity to examine a case of late adoption of agriculture. Here we show that agriculture in the Uspallata Valley was adopted by local hunter-gatherers, as evidenced by genetic continuity between pre-farming and farming populations inferred from 46 newly sequenced ancient human genomes. These groups carried a distinct genetic component in Indigenous American diversity, indicating a unique population history in the region. Palaeodietary isotopes (δ¹³C/δ¹⁵N) reveal fluctuating maize intake consistent with flexible farming. Strontium isotopes (⁸⁷Sr/⁸⁶Sr) indicate the arrival of migrants from nearby regions between around 810-700 cal years BP, shortly before the Inka expansion. Genomic and isotopic analyses show that these migrants belonged to the same regional metapopulation as local groups, relied heavily on maize, probably moved in matrilineally organized family groups, exhibited stress markers (including malnutrition and diseases, such as tuberculosis, as confirmed by pathogen genomics) and experienced a long-term demographic decline. Our results suggest that these groups used social organization and migration as resilience strategies in the face of a multidimensional crisis.

Narratives about the motivations and conditions for mass violence as a persistent feature of conflict throughout human history have evolved in complexity and materiality. Victims of these events are key for understanding the evolution and transformative power of violent behaviour as it developed from simple intergroup conflict to more strategic mass violence. Here we present the results of a bioarchaeological study of 77 and biomolecular analysis of 25 individuals from a ninth-century BCE mass grave from Gomolava in the Carpathian Basin, Southeast Europe. The site is located at the interface of complex sociospatial relations, divergent cultural traditions and values, and competing ideologies of landscape use. We show that excessive lethal violence enacted mostly on women and children suggests a selective demographic bias. The people buried together shared few, even distant, genetic relationships, and so their killing presents striking evidence for an episode of cross-regional conflict and an underlying aggressive shift in power, violence and gender relations in the region. Gomolava provides evidence consistent with deliberate annihilation of select sections of a regional population as a motivation for mass violence behaviour in later prehistoric Europe. It also shines new light on the socioeconomic agency and importance of women and young individuals in later European prehistory.

As the practice and business of personal DNA ancestry testing continue to expand globally, understanding people’s interest in their genetic history, and how the results influence attitudes about the past, is being called for. Such insight is especially relevant to archaeologists and heritage researchers. Yet the motivations for taking direct-to-consumer DNA tests and their effects remain poorly understood in a European context. This paper presents the results of a nationwide survey carried out by The Centre for Critical Heritage Studies, University of Gothenburg, in collaboration with the Swedish Society for Genetic Genealogy. The aim was to identify social and cultural attitudes among people who decided to take a personal DNA test in Sweden. Nearly 900 individuals answered the survey. Based on the results, we identify a distinction between family genealogies and personal genetic history versus national history and collective identity. While the majority of respondents are interested in history and archaeology, their interest in family genealogies is specifically linked to individual stories and possible links to existing/unknown family members. This suggests that DNA-testing provides a new and different take on family histories compared to historically-documented genealogies. It also suggests that the link to polarizing debates on ethnonational belonging, highlighted in relation to public responses to ancient DNA studies in archaeology, remains muted as regards personal DNA tests.