BACKGROUND: Processes shaping the formation of the present-day population structure in highly urbanized Northern Europe are still poorly understood. Gaps remain in our understanding of when and how currently observable regional differences emerged and what impact city growth, migration, and disease pandemics during and after the Middle Ages had on these processes. RESULTS: We perform low-coverage sequencing of the genomes of 338 individuals spanning the eighth to the eighteenth centuries in the city of Sint-Truiden in Flanders, in the northern part of Belgium. The early/high medieval Sint-Truiden population was more heterogeneous, having received migrants from Scotland or Ireland, and displayed less genetic relatedness than observed today between individuals in present-day Flanders. We find differences in gene variants associated with high vitamin D blood levels between individuals with Gaulish or Germanic ancestry. Although we find evidence of a Yersinia pestis infection in 5 of the 58 late medieval burials, we were unable to detect a major population-scale impact of the second plague pandemic on genetic diversity or on the elevated differentiation of immunity genes. CONCLUSIONS: This study reveals that the genetic homogenization process in a medieval city population in the Low Countries was protracted for centuries. Over time, the Sint-Truiden population became more similar to the current population of the surrounding Limburg province, likely as a result of reduced long-distance migration after the high medieval period, and the continuous process of local admixture of Germanic and Gaulish ancestries which formed the genetic cline observable today in the Low Countries.

• Keywords
• Flanders, Low countries, Medieval, Migration, Palaeo-genomics, Plague, Urbanization,
• MeSH
• History, Medieval MeSH
• Genetic Variation MeSH
• Genome, Human MeSH
• Genomics MeSH
• Humans MeSH
• Plague epidemiology   history   genetics   MeSH
• Genetics, Population MeSH
• Urbanization * history   MeSH
• Check Tag
• History, Medieval MeSH
• Humans MeSH
• Publication type
• Journal Article MeSH
• Historical Article MeSH
• Geographicals
• Belgium MeSH

qpAdm is a statistical tool that is often used for testing large sets of alternative admixture models for a target population. Despite its popularity, qpAdm remains untested on 2D stepping stone landscapes and in situations with low prestudy odds (low ratio of true to false models). We tested high-throughput qpAdm protocols with typical properties such as number of source combinations per target, model complexity, model feasibility criteria, etc. Those protocols were applied to admixture graph-shaped and stepping stone simulated histories sampled randomly or systematically. We demonstrate that false discovery rates of high-throughput qpAdm protocols exceed 50% for many parameter combinations since: (1) prestudy odds are low and fall rapidly with increasing model complexity; (2) complex migration networks violate the assumptions of the method; hence, there is poor correlation between qpAdm P-values and model optimality, contributing to low but nonzero false-positive rate and low power; and (3) although admixture fraction estimates between 0 and 1 are largely restricted to symmetric configurations of sources around a target, a small fraction of asymmetric highly nonoptimal models have estimates in the same interval, contributing to the false-positive rate. We also reinterpret large sets of qpAdm models from 2 studies in terms of source-target distance and symmetry and suggest improvements to qpAdm protocols: (1) temporal stratification of targets and proxy sources in the case of admixture graph-shaped histories, (2) focused exploration of few models for increasing prestudy odds; and (3) dense landscape sampling for increasing power and stringent conditions on estimated admixture fractions for decreasing the false-positive rate.

• Keywords
• qpAdm, admixture graphs, archaeogenetics, genetic admixture, simulation, stepping stone models,
• MeSH
• Humans MeSH
• Models, Genetic * MeSH
• Genetics, Population * methods   MeSH
• Software * MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH

The Huns appeared in Europe in the 370s, establishing an Empire that reshaped West Eurasian history. Yet until today their origins remain a matter of extensive debate. Traditional theories link them to the Xiongnu, the founders of the first nomadic empire of the Mongolian steppe. The Xiongnu empire dissolved, however, ~300 y before the Huns appeared in Europe, and there is little archaeological and historical evidence of Huns in the steppe during this time gap. Furthermore, despite the rich 5th to 6th centuries current era (CE) archaeological record of the Carpathian Basin, the cultural elements of connections with the steppe are limited to few findings and even fewer solitary eastern-type burials. In this study, we coanalyze archaeological evidence with 35 newly sequenced and published genomic data for a total of 370 individuals-from 5th to 6th century CE contexts in the Carpathian Basin including 10 Hun-period eastern-type burials, 2nd to 5th century sites across Central Asia and 2nd c. before current era (BCE) to 1st c. CE Xiongnu period sites across the Mongolian steppe. We find no evidence for the presence of a large eastern/steppe descent community among the Hun- and post-Hun-period Carpathian Basin population. We also observe a high genetic diversity among the eastern-type burials that recapitulates the variability observed across the Eurasian Steppe. This suggests a mixed origin of the incoming steppe conquerors. Nevertheless, long-shared genomic tracts provide compelling evidence of genetic lineages directly connecting some individuals of the highest Xiongnu-period elite with 5th to 6th century CE Carpathian Basin individuals, showing that some European Huns descended from them.

• Keywords
• Huns, Middle Ages, Xiongnu, ancient DNA, trans-Eurasian mobility,
• MeSH
• Archaeology MeSH
• History, Ancient MeSH
• Genome, Human * MeSH
• Humans MeSH
• Human Migration * history   MeSH
• DNA, Ancient * analysis   MeSH
• Check Tag
• History, Ancient MeSH
• Humans MeSH
• Publication type
• Journal Article MeSH
• Historical Article MeSH
• Geographicals
• Europe MeSH
• Names of Substances
• DNA, Ancient * MeSH

qpAdm is a statistical tool that is often used for testing large sets of alternative admixture models for a target population. Despite its popularity, qpAdm remains untested on two-dimensional stepping-stone landscapes and in situations with low pre-study odds (low ratio of true to false models). We tested high-throughput qpAdm protocols with typical properties such as number of source combinations per target, model complexity, model feasibility criteria, etc. Those protocols were applied to admixture-graph-shaped and stepping-stone simulated histories sampled randomly or systematically. We demonstrate that false discovery rates of high-throughput qpAdm protocols exceed 50% for many parameter combinations since: 1) pre-study odds are low and fall rapidly with increasing model complexity; 2) complex migration networks violate the assumptions of the method, hence there is poor correlation between qpAdm p-values and model optimality, contributing to low but non-zero false positive rate and low power; 3) although admixture fraction estimates between 0 and 1 are largely restricted to symmetric configurations of sources around a target, a small fraction of asymmetric highly non-optimal models have estimates in the same interval, contributing to the false positive rate. We also re-interpret large sets of qpAdm models from two studies in terms of source-target distance and symmetry and suggest improvements to qpAdm protocols: 1) temporal stratification of targets and proxy sources in the case of admixture-graph-shaped histories; 2) focused exploration of few models for increasing pre-study odds; 3) dense landscape sampling for increasing power and stringent conditions on estimated admixture fractions for decreasing the false positive rate.

• Keywords
• admixture graphs, archaeogenetics, genetic admixture, qpAdm, simulation, stepping-stone models,
• Publication type
• Journal Article MeSH
• Preprint MeSH

After a long-distance migration, Avars with Eastern Asian ancestry arrived in Eastern Central Europe in 567 to 568 CE and encountered groups with very different European ancestry1,2. We used ancient genome-wide data of 722 individuals and fine-grained interdisciplinary analysis of large seventh- to eighth-century CE neighbouring cemeteries south of Vienna (Austria) to address the centuries-long impact of this encounter1,2. We found that even 200 years after immigration, the ancestry at one site (Leobersdorf) remained dominantly East Asian-like, whereas the other site (Mödling) shows local, European-like ancestry. These two nearby sites show little biological relatedness, despite sharing a distinctive late-Avar culture3,4. We reconstructed six-generation pedigrees at both sites including up to 450 closely related individuals, allowing per-generation demographic profiling of the communities. Despite different ancestry, these pedigrees together with large networks of distant relatedness show absence of consanguinity, patrilineal pattern with female exogamy, multiple reproductive partnerships (for example, levirate) and direct correlation of biological connectivity with archaeological markers of social status. The generation-long genetic barrier was maintained by systematically choosing partners with similar ancestry from other sites in the Avar realm. Leobersdorf had more biological connections with the Avar heartlands than with Mödling, which is instead linked to another site from the Vienna Basin with European-like ancestry. Mobility between sites was mostly due to female exogamy pointing to different marriage networks as the main driver of the maintenance of the genetic barrier.

• MeSH
• Asian People genetics   MeSH
• White MeSH
• White People genetics   MeSH
• History, Ancient MeSH
• Genome, Human genetics   MeSH
• Culture * MeSH
• Humans MeSH
• Human Migration * history   MeSH
• Consanguinity MeSH
• Reproductive Isolation * MeSH
• Pedigree MeSH
• Reproduction * genetics   MeSH
• DNA, Ancient * analysis   MeSH
• Check Tag
• History, Ancient MeSH
• Humans MeSH
• Male MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Historical Article MeSH
• Geographicals
• Austria MeSH
• Names of Substances
• DNA, Ancient * MeSH

During the Hungarian Conquest in the 10th century CE, the early medieval Magyars, a group of mounted warriors from Eastern Europe, settled in the Carpathian Basin. They likely introduced the Hungarian language to this new settlement area, during an event documented by both written sources and archaeological evidence. Previous archaeogenetic research identified the newcomers as migrants from the Eurasian steppe. However, genome-wide ancient DNA from putative source populations has not been available to test alternative theories of their precise source. We generated genome-wide ancient DNA data for 131 individuals from candidate archaeological contexts in the Circum-Uralic region in present-day Russia. Our results tightly link the Magyars to people of the Early Medieval Karayakupovo archaeological horizon on both the European and Asian sides of the southern Urals. Our analyes show that ancestors of the people of the Karayakupovo archaeological horizon were established in the Southern Urals by the Iron Age and that their descendants persisted locally in the Volga-Kama region until at least the 14th century.

• Publication type
• Journal Article MeSH
• Preprint MeSH

From AD 567-568, at the onset of the Avar period, populations from the Eurasian Steppe settled in the Carpathian Basin for approximately 250 years1. Extensive sampling for archaeogenomics (424 individuals) and isotopes, combined with archaeological, anthropological and historical contextualization of four Avar-period cemeteries, allowed for a detailed description of the genomic structure of these communities and their kinship and social practices. We present a set of large pedigrees, reconstructed using ancient DNA, spanning nine generations and comprising around 300 individuals. We uncover a strict patrilineal kinship system, in which patrilocality and female exogamy were the norm and multiple reproductive partnering and levirate unions were common. The absence of consanguinity indicates that this society maintained a detailed memory of ancestry over generations. These kinship practices correspond with previous evidence from historical sources and anthropological research on Eurasian Steppe societies2. Network analyses of identity-by-descent DNA connections suggest that social cohesion between communities was maintained via female exogamy. Finally, despite the absence of major ancestry shifts, the level of resolution of our analyses allowed us to detect genetic discontinuity caused by the replacement of a community at one of the sites. This was paralleled with changes in the archaeological record and was probably a result of local political realignment.

• MeSH
• Archaeology * methods   MeSH
• Family Characteristics * ethnology   history   MeSH
• History, Medieval MeSH
• Adult MeSH
• Genomics MeSH
• Cemeteries history   MeSH
• Humans MeSH
• Adolescent MeSH
• Young Adult MeSH
• Grassland * MeSH
• Consanguinity MeSH
• Politics MeSH
• Pedigree * MeSH
• DNA, Ancient * analysis   MeSH
• Check Tag
• History, Medieval MeSH
• Adult MeSH
• Humans MeSH
• Adolescent MeSH
• Young Adult MeSH
• Male MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Historical Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Asia ethnology   MeSH
• Europe ethnology   MeSH
• Names of Substances
• DNA, Ancient * MeSH

Investigation into the nexus of human-environmental behavior has seen increasing collaboration of archaeologists, historians, and paleo-scientists. However, many studies still lack interdisciplinarity and overlook incompatibilities in spatiotemporal scaling of environmental and societal data and their uncertainties. Here, we argue for a strengthened commitment to collaborative work and introduce the "dahliagram" as a tool to analyze and visualize quantitative and qualitative knowledge from diverse disciplinary sources and epistemological backgrounds. On the basis of regional cases of past human mobility in eastern Africa, Inner Eurasia, and the North Atlantic, we develop three dahliagrams that illustrate pull and push factors underlying key phases of population movement across different geographical scales and over contrasting periods of time since the end of the last Ice Age. Agnostic to analytical units, dahliagrams offer an effective tool for interdisciplinary investigation, visualization, and communication of complex human-environmental interactions at a diversity of spatiotemporal scales.

• MeSH
• Communication * MeSH
• Humans MeSH
• Research Design MeSH
• Knowledge * MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH