A Transient Pulse of Genetic Admixture from the Crusaders in the Near East Identified from Ancient Genome Sequences

Abstract

During the medieval period, hundreds of thousands of Europeans migrated to the Near East to take part in the Crusades, and many of them settled in the newly established Christian states along the Eastern Mediterranean coast. Here, we present a genetic snapshot of these events and their aftermath by sequencing the whole genomes of 13 individuals who lived in what is today known as Lebanon between the 3^rd and 13^th centuries CE. These include nine individuals from the "Crusaders' pit" in Sidon, a mass burial in South Lebanon identified from the archaeology as the grave of Crusaders killed during a battle in the 13^th century CE. We show that all of the Crusaders' pit individuals were males; some were Western Europeans from diverse origins, some were locals (genetically indistinguishable from present-day Lebanese), and two individuals were a mixture of European and Near Eastern ancestries, providing direct evidence that the Crusaders admixed with the local population. However, these mixtures appear to have had limited genetic consequences since signals of admixture with Europeans are not significant in any Lebanese group today-in particular, Lebanese Christians are today genetically similar to local people who lived during the Roman period which preceded the Crusades by more than four centuries.

Keywords: Lebanon; Roman period; Sidon; aDNA; medieval period; population history; whole-genome sequences.

Figure 1

Principal Components Analysis of West Eurasians Eigenvectors were inferred using present-day populations (gray points) and the ancient samples (colored shapes) were projected onto the plot. The new ancient samples from the Roman period (Lebanon_RP) are represented by solid pink circles and the new ancient samples from the Crusaders period (Crusaders’ pit) are shown in pink squares with black circles. In addition, two samples discussed individually in the text are annotated with their IDs (SI-41 and SI-53) on the plot.

Figure 2

Contrast between Europeans and Near Easterners from Their Genetic Affinity to WHG The statistic f4(Lebanon_RP, A; WHG, Chimpanzee) is significantly negative when A is a European population. The ancient individuals from the Crusaders’ pit are represented by pink squares with black circles. We plot the f4 statistic value and ±3 standard errors.

Figure 3

Admixed Individuals in the Crusaders’ Pit (A) ADMIXTURE plot of the HO set using ∼80,000 transversions and showing results from K = 17 in a supervised run with references: Anatolia_N, Iran_N, EHG, WHG, Levant_N, Atayal, Chipewyan, Eskimo, Hadza, Mala, Mbuti, Nganasan, Onge, Papuan, Quechua, Taa_West, and Yoruba. We show results from the ancient individuals from the Crusaders’ pit in addition to the median of the ancestry proportions found in modern populations. (B) The position on the PCA of two individuals found in the Crusaders’ pit can be explained by admixture. Simulated (first generation) hybrid samples (gray crosses, with some highlighted in color as indicated on the figure) consisting of genomes with positions represented by an allele from a Near Easterner (orange circles) and an allele from a modern European (blue circles) show intermediate positions on the PCA and overlap with the ancient individuals SI-41 and SI-53. (C) Individuals SI-41 and SI-53 can be successfully modeled as mixture of Europeans and Near Easterners using qpAdm. We show the p values for rank = 1 and annotate the models with the top values.