Medieval Sicily, located at the intersection of Europe, North Africa and the Near East, experienced successive political and religious transitions under Byzantine, Aghlabid, Fatimid, Norman, and Swabian rule. While it is well established that these events led to multi-faith societies, the long-term genetic impact of regime change is unclear. To evaluate this potential impact, we applied ancient genomic analysis to 111 archaeological Sicilian individuals, leading to successful mitochondrial haplotype inferences for 67 individuals and genome-wide analyses for 32 individuals dated between the 5th and 15th centuries CE. In contrast to simple narratives of population replacement, the data indicate nuanced and unappreciated demographic shifts. Several individuals dating before the Islamic conquest of Sicily exhibit substantial North African ancestry, evidencing movement across the Mediterranean Sea before this conquest. Individuals buried in Islamic cemeteries during the 9th to 11th century were found to have diverse ancestries deriving from populations around the Mediterranean Basin, however, the same ancestry components are also found in earlier periods, limiting what can be inferred about intra-Mediterranean migrations in this dataset. Nonetheless, the Islamic period marks the appearance of individuals with distant ancestral origins, West Africa and Northern Europe. During the Norman period, Christian and Islamic burials show the same genetic diversity maintained for hundreds of years, however, by the late medieval period, the ancestry components shifted toward modern European populations. Altogether, the study demonstrates the value of examining recent periods with ancient DNA methodologies to better understand how culture, identity and mobility impacted demography in the past. ✉ * E-mail: aurore.monnereau@palaeome.org (AM); nathan.wales@york.ac.uk (NW) 24 6 2026 21 6 e0350298 e0350298 25 6 2026 © 2026 Monnereau et al This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract Medieval Sicily, located at the intersection of Europe, North Africa and the Near East, experienced successive political and religious transitions under Byzantine, Aghlabid, Fatimid, Norman, and Swabian rule. Introduction Between the 5th and 15th centuries CE, the Mediterranean world and its surrounding regions experienced profound transformations, including the fragmentation of the Western Roman Empire, the expansion of Islamic politics, the military and religious mobilisations of the Crusades, and recurrent demographic crises such as the Black Death. Within this wider context, medieval Sicily occupied a position of exceptional strategic and economic importance. Its fertile plains and central location within the Mediterranean basin made it a critical hub in the networks of trade, conflict, and cultural transmission that connected Latin Christendom, the Islamic world, and the Byzantine East. As a result, the island became the target of successive powers, including the Byzantine Empire, Arab emirates, Norman rulers, the Hohenstaufen, and the Crown of Aragon. Each of them was seeking to control its ports and influence over the central Mediterranean. Following the fall of the Roman Empire and then decades of control by Vandals and Goths [ 1 ], Sicily was governed by Byzantines from 535–827 CE [ 2 ], by Sunni and Shıʿa Muslims in the 9th and 10th centuries [ 3 ], and finally by Christian dynasties [ 4 , 5 ]. While historical sources chronicle Sicily’s battles and coronations, less information is available to track the impact of medieval regime change on local populations. Rather, age ranges of some individuals span several centuries, such as individual GABN5 buried at the site of La Gancia in west Palermo, whose calibrated date of 685–970 CE overlaps with rule by the Byzantines, the Aghlabid dynasty (Sunni Muslim), and the Fatimid Caliphate (Shıʿa Muslim). To accommodate the limits of the wide age estimates, we present the genetic data using the mean age of the calibrated radiocarbon date corrected for the MRE ( Fig 2 ) using this simplified chronological framework of five major periods of medieval Sicily: Fig 2 Chronological distribution of individuals tested, listed by site and presented with associated periods and key historical dates: 535 CE Byzantine conquest of Sicily, 827 CE Aghlabid invasion of Sicily, 909 CE Start of Fātimids caliphate, 1061 CE Norman invasion of Sicily, 1198 Swabian governance, and 1266 CE Angevin kings control Sicily. Sites are ordered in a largely west-to-east continuum, as shown in Fig 1 . Identification of structured populations within non-African individuals in medieval Sicily We conducted an outgroup- F 3 statistical analysis to formally test genetic relationships between medieval Sicilian individuals in the PCA for Western Europe, Middle East and North Africa and assess potential links between either the burial rites or time periods. Medieval individuals are ordered according to the mean calibration radiocarbon age and other individuals are sorted within the respective time period by the amount of Anatolian Neolithic ancestry. The burial rite for the medieval individuals is provided after the identifier: C = Christian, I = Islamic, N = Non-Islamic (Christian or Jewish) and U = Undetermined. This observation is consistent with Moot et al.’s [ 40 ] interpretation of a shift toward eastern Mediterranean ancestries in the Roman Empire through gene flow. The cumulative impact of eastern ancestries introduced during the Neolithic, Bronze Age, Iron Age to the Roman Period creates a complex genetic background that can make it more difficult to disentangle the later contributions from the Near and Middle East in Sicily during the Middle Ages.

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