Biology subjects

Fehren-Schmitz, L.

Publications and source records attributed to Fehren-Schmitz, L..

8 recordsLinked to original sources

bioRxiv2026

On the Edge of Empire: Paleogenomic Insights into Roman Dacia

The Roman province of Dacia, located north of the Danube frontier, represented a key zone of cultural and demographic interaction during the Imperial period. However, the biological impact of Roman colonization in this region has not been characterized using genomic data. Here, we analyze genome-wide data from 34 individuals recovered from the Apulum-Dealul Furcilor necropolis, one of the largest funerary complexes in Roman Dacia. The genome-wide data reveal pronounced genetic heterogeneity within this population, reflecting its position at the intersection of Eastern Europe, the Mediterranean, and West Asia. Notably, we observe a sex-biased pattern of ancestry. Female individuals show stronger affinities to Eastern European, Steppe, and Caucasus-associated populations, suggesting the persistence of local or regionally connected genetic lineages. In contrast, male individuals display closer genetic relationships with Mediterranean and North African groups, including populations associated with Roman and Punic contexts, indicating male-mediated gene flow linked to long-distance mobility. These findings highlight the complex demographic processes shaping Roman frontier communities, where local and incoming populations were integrated through asymmetric social dynamics. Our results provide genomic evidence consistent with sex-biased admixture in Roman Dacia and underscore the role of frontier regions as hubs of genetic and cultural interaction within the Roman Empire.

genomics↗

bioRxiv2026

The Genomic Legacy of the Norman Conquest in Rural England

The Norman Conquest of 1066 CE reshaped the political and cultural landscape of England, yet its demographic consequences remain poorly understood, particularly outside elite and urban contexts where historical evidence is concentrated. Here, we investigate the population history of a rural English community spanning the Conquest using genome-wide ancient DNA from the Priory Orchard site, a cemetery in Godalming (Surrey) in use between the 9th and early 13th centuries CE. We generated genomic data from 78 individuals and established radiocarbon dates for 98 individuals from the site. Population genetic analyses place Priory Orchard individuals within the genetic continuum of early medieval populations from the North Sea region. Ancestry modelling indicates that this rural community carried substantial Scandinavian/Viking-related ancestry alongside a persistent Saxon-related component and a smaller French-related contribution. However, stratifying individuals by date, before and after 1066 CE, reveals no clear genome-wide discontinuity across the Conquest horizon, suggesting demographic continuity through this crucial political and social transition. This pattern is consistent with historical and archaeological evidence indicating that many of the most visible transformations following the Conquest occurred primarily among the elite. Our results provide the first genomic perspective on communities living through the Norman Conquest and indicate that rural southern England saw persistent migration links with other areas facing the North Sea rather than abrupt population replacement.

genetics↗

bioRxiv2026

Temporal shifts in polygenic traits track major epidemics in Western Eurasia

Infectious diseases are recognized as one of the strongest selective forces, exerting a profound influence on the genetic makeup of human populations over time. Recently, large-scale genome-wide association studies (GWAS) on immunological traits have underscored the notion that genetic predisposition to infectious diseases likely stems from the contribution of several thousand loci across the human genome. To model the polygenic inheritance of these traits, multiple variants can be combined into polygenic risk scores (PRS), which estimate an individuals genetic predisposition for a trait. By combining present-day GWAS statistics from large European biobanks with genomic data from more than 3,500 ancient individuals from Western Eurasia, we characterize temporal changes in four highly heritable infectious disease-related traits over a span of 10,000 years. In doing so, we account for variation in these traits across time, space, and genetic ancestries, and demonstrate that the observed patterns cannot be explained by genetic drift alone. Our findings suggest that major disease outbreaks in human history are associated with shifts in polygenic traits in human populations. Specifically, three events - the Justinian Plague, Antonine Plague, and early medieval measles outbreaks - coincide with significant shifts in the polygenic profiles of these traits. Using a Gene Ontology enrichment approach, we show that these shifts involve multiple systemic biological processes, with a consistent emphasis on metabolic pathways modulating immunological responses both directly and indirectly.

genomics↗

bioRxiv2026

Subsistence transition preceded population turnover in the eastern Colombian Andes

Northwest South America was a pivotal region for human dispersals and cultural exchange during the Holocene. The Altiplano Cundiboyacense, a high-altitude plateau in the Eastern Cordillera of the Northern Andes of Colombia, preserves one of the most continuous archaeological sequences in the Americas, spanning from late Pleistocene hunter-gatherer groups to final late Holocene Muisca chiefdoms. Increasing the regional ancient DNA sample size 11-fold, we report genome-wide data from 209 individuals who lived over a period of more than 7000 years. This includes hunter-gatherers from the early-middle (10,000-7000 BP) and middle (7000-4000 BP) Holocene, initial late Holocene people (4000-2500 BP) who have the first isotopic evidence of C-enriched diets (attributed to maize), and populations associated with increasing sedentism and food production in the Herrera (2200-1300 BP) and Muisca (1200-500 BP) Periods. Previous work identified a major population turnover distinguishing earlier groups from Herrera-Muisca Period populations, but the absence of individuals dating 6000-2000 BP in that study left unresolved whether this ancestry shift was gradual or abrupt and whether it accompanied the earliest isotopic evidence of dietary input from maize or coincided with the later emergence of Herrera culture. We show that individuals predating the Herrera Period form a lineage that persisted for over five millennia, with population structure driven by drift in small groups and no detectable external gene flow. Two individuals who lived [~]2800 years ago - one directly dated to 983-835 calBCE - exhibit genetic profiles entirely consistent with hunter-gatherer ancestry yet have isotopic values consistent with the incorporation of maize into their diets, indicating subsistence change without population replacement. The emergence of Herrera culture [~]2200 BP coincided with a sharp genetic break, reflecting the migration of people carrying ancestry diverged by up to ten millennia into the Sabana de Bogota and displacing previously established peoples. By co-analyzing ancient data with modern Native Americans, we show these later populations derived from a mixture [~]4000 years ago of groups related to Chibchan language speakers of lower Central America and ones related to present-day people at the Amazonian-Andean interface who may have lived along the Chibchan expansion route. In the Herrera and Muisca Periods, genetic substructure distinguishes people from the southern and northern Altiplano, consistent with the cultural differentiation of these regions in the archaeological record. IN BRIEFAncient DNA data from the eastern Colombian Andes reveal five millennia of population continuity during which C plants were incorporated into subsistence systems without population replacement, followed later by a major ancestry turnover involving a population with ancestry admixed between that found in Chibchan-related groups and at the Amazonian-Andean interface.

genetics↗

bioRxiv2025

Palaeogenomics reveals 1,500 years of population history of the peoples of the Chonos Archipelago, Chile.

The Chonos archipelago, located in northwestern Chilean Patagonia, was historically inhabited by an Indigenous sea-faring population known to the European colonists as the "Chono". Previous research has contextualized the human occupation of this region with radiocarbon dates and ancient mitochondrial genomes, offering a partial perspective on the history of its inhabitants. Here we present a paleogenomic analysis of 20 ancient human individuals from 6 archaeological sites, dated between 1,600-50 years before present (BP). We successfully captured over 100,000 SNPs from 15 of 20 individuals and recovered 12 full mitogenomes. All individuals presented unadmixed Indigenous South American ancestry and formed a separated genetic cluster relative to other ancient and modern South American genomes, indicating a unique Chonos ancestry. This Chonos ancestry falls within a broader cluster of late-Holocene Patagonian ancestry, most similar to the Kawesqar peoples who neighbour to the south. Within the Chonos, we distinguish a northern and southern ancestry cluster. The northern Chonos cluster exhibits some genetic connections to the present-time inhabitants of the neighbouring island of Chiloe, who are connected to Huilliche Indigenous history. Our findings reveal a point of contact between southern Chonos/Patagonian ancestry to the south and Mapuche ancestry to the north, and confirm that sea-faring subsistence was a knowledge transferred between Patagonian peoples.

genomics↗

bioRxiv2024

Optimised in-solution enrichment of over a million ancient human SNPs

In-solution hybridisation enrichment of genetic markers is a method of choice in paleogenomic studies, where the DNA of interest is generally heavily fragmented and contaminated with environmental DNA, and where the retrieval of genetic data comparable between individuals is challenging. Here, we benchmarked the commercial "Twist Ancient DNA" reagent from Twist Biosciences using sequencing libraries from ancestrally diverse ancient human samples with low to high endogenous DNA content (0.1-44%). For each library, we tested one and two rounds of enrichment, and assessed performance compared to deep shotgun sequencing. We find that the "Twist Ancient DNA" assay provides robust enrichment of [~]1.2M target SNPs without introducing allelic bias that may interfere with downstream population genetics analyses. Additionally, we show that pooling up to 4 sequencing libraries and performing two rounds of enrichment is both reliable and cost-effective for libraries with less than 27% endogenous DNA content. Above 38% endogenous content, a maximum of one round of enrichment is recommended for cost-effectiveness and to preserve library complexity. In conclusion, we provide researchers in the field of human paleogenomics with a comprehensive understanding of the strengths and limitations of different sequencing and enrichment strategies, and our results offer practical guidance for optimising experimental protocols.

genomics↗

bioRxiv2023

Allelic bias when performing in-solution enrichment of ancient human DNA

In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent--which enriches 1,237,207 genome-wide SNPs--since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g., Principal Components Analysis, [f]-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In [f]-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.

genomics↗

bioRxiv2018

The genomic landscape of western South America: Andes, Amazonia and Pacific Coast

Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here we explore the genetic structure of 177 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, with a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long distance genetic connections between speakers of the same language family suggest that languages had spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. With our results we emphasize the importance of including under-studied regions of the continent in high-resolution genetic studies, and we illustrate the potential of SNP chip arrays for informative regional scale analysis.

genetics↗