Urbanization and genetic homogenization in the medieval Low Countries revealed through a ten-century paleogenomic study of the city of Sint-Truiden

Abstract

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.

Fig. 1

Sint-Truiden city center cemetery map. Two main burial groups at Trudoplein and Groenmarkt are highlighted by pink and green, respectively. Timeline of the main events mentioned in the text is shown to the right

Fig. 2

Sampling locations and genetic ancestry of the studied populations. A A map of the North Sea region with Early (EMA) and High (HMA) Middle Ages, Roman, and Late Iron Age (LIA) archeological sites used in data analyses, including genomes from Sint-Truiden (red), this study, and available reference data. PCA of selected modern (B) and ancient (C) genomes from Europe. PCA was run, after excluding closely related individuals, with FlashPCA2 without projection. B Modern population sources: 400 English, 191 French, 200 Irish, 190 Spanish, 443 Scandinavian (Danish, Norwegian, Swedish) and 400 Scottish/Welsh genomes from the UK Biobank; 112 Flemish and 195 Dutch genomes from the MinE consortium data [26, 27]. C 329 medieval/early modern imputed Sint-Truiden genomes and 8 Ypres individuals from this study, 20 Koksijde and 5 Wulpen individuals from Sasso et al. [6], 18 Iron Age French Gaul individuals from Fischer et al. 2022 [22], and 190 Early medieval genomes from Gretzinger et al. 2022 [5]

Fig. 3

qpAdm based Gaulish and Germanic ancestry estimates in Flemish and Dutch provinces. A Presented Gaulish (blue) and Germanic (orange) ancestry proportions represent the best fit qpAdm model (Additional file 1: Table S3) for each population tested. B Violin plot comparing Gaulish ancestry proportions between Groenmarkt and Trudoplein burials. C Violin plot comparing Gaulish ancestry proportions between early (pre-1286 AD) and late (post-1286 AD) phase burials in Groenmarkt. Light gray background in panels A–C refers to early phase burials, predating 1286, and dark gray background to later phase burials postdating 1286. D Map showing average Gaulish (blue) and Germanic (orange) ancestry proportions by the provinces of the Netherlands and Flanders of Belgium. West-Flanders and Limburg provinces of present-day Flanders for which we present a transect of time data are highlighted with a darker yellow background. EMA—Early Middle Ages, HMA—High Middle Ages, LMA—Late Middle Ages, PMA—post-Middle-Ages, MOD—modern controls from the MinE project data

Fig. 4

Genetic distances between the ancient and modern populations of the region. Genetic distances are presented as Fst × 1000000. Sint-Truiden time groups I = 675–999 AD (~ EMA), II = 1000–1286 (~ HMA), III/IV = 1287–1775, LIA = Late Iron Age, EMA = Early Middle Ages, HMA = High Middle Ages. BE-Limburg = Belgian Limburg, NL-Limburg = Dutch Limburg. Data sources: Sint-Truiden, this study; Koksijde, Sasso et al. [6]; West-Flanders, this study and Sasso et al. [6]; Early Medieval Netherlands, England and North Rhine-Westphalia, Germany – Gretzinger et al. 2022 [5]; Late Iron Age (LIA) France, Fischer et al. 2022 [22]; present-day Belgian and Dutch Limburg, the MiNE Consortium data [26, 27]; France, England and Spain, the UK Biobank data [32]

Fig. 5

Probability of individual connectedness (PiC) with modern and ancient populations. A Heatmap of probabilities (× 1000) of between individual sharing of > 7 cM segments within and among populations. Ancient population data (shown red) include data for Sint-Truiden and Ypres from this study, Early medieval (EMA) data from Gretzinger et al. 2022 [5], Sasso et al. [6], Late Iron Age (LIA) genomes from Fischer et al. 2022 [22], Viking Age (VA) data from Margaryan et al. 2020 [8], and Roman period data from Scheib et al. 2023 [23], Martiniano et al. 2016 [25] and Schiffels et al. 2016 [24]. Modern reference data include populations from the UK Biobank [32] and MinE Project data [26, 27]. ST-main – 318 genomes from the Sint-Truiden main group; ST-out—five outliers identified by PCA (Fig. 2). B. PiC scores estimated between present-day provinces of the Netherlands and Belgium, MinE project data [26, 27] and transect of time data from West Flanders ([6], this study) and Sint-Truiden (this study). Red stars on each map indicate the geographic location of the archeological sites with data

Fig. 6

Probabilities to observe genetic relatedness between Sint-Truiden burials. The probabilities of 1st–3rd degree relatedness are expressed as the ratio of observed relationships in the burial place and time with KIN and READ2 (Additional file 1: Table S8) and the total number of individual pairs with minimum aggregate coverage to detect them. The probability of 4–6th degree relatedness is expressed as the ratio of observed relationships with IBIS (Additional file 1: Table S9) and the total number of pairs of imputed individual genomes available from the burial place and time for the analyses

Fig. 7

Effective population size (Ne) over time. Effective population size (Ne) of the Sint-Truiden city center population between the eighth and the eighteenth century inferred by plotting the mean Ne estimated for each time group over its past 4 generations. The dark blue dotted line joins the different mean Ne estimates and the 95% confidence intervals obtained with bootstrap quantiles are represented by the light blue error bars

Fig. 8

Temporal distribution of the metagenomic findings. Individuals with pathogen findings and radiocarbon dates are presented for the subset of pathogens detected at least twice (Additional file 1: Table S16). HBV—hepatitis B virus, HHV—human betaherpesviruses. The mean value of the 95% range of the radiocarbon date of each individual is shown on the y axis, x axis values showing δ15N values