When tensions between the Christians and Muslims in Sicily in the first decades of the thirteenth century disrupted life on Frederick II's island, the emperor did what the Christian rulers of Iberia had done in the eleventh century: he removed the Muslims from his kingdom. Instead of expelling them, however, he deported them to Lucera, a town previously inhabited by Christians in Apulia, forty miles or so from the Adriatic Sea in the southern Italian peninsula. The first deportations began in the 1220s and continued for twenty years. By mid-century, Sicily's Muslim population no longer existed. Some had fled to North Africa while the majority had been settled in Lucera and small villages in the same region.
Rebellions of Muslims in villages around the island prompted Frederick to find ways to rid Sicily of them, but not to the point of depriving himself completely of their talents and uses. He shipped them off to Apulia, forced them to settle in Lucera, and put them to work in the service of the kingdom.
When Charles I of Anjou took possession of the colony in 1265, life became increasingly difficult for the inhabitants until, in 1300, Charles II decided to liquidate the colony entirely. He had all the Muslims in southern Italy sold into slavery, took the gold from their sale, and confiscated all of their property. Officials took inventory of all the grain and agricultural products stored there before carting them off to feed the Christian populations of southern Italy.
Sally McKee. "Review: Muslims in Medieval Italy: The Colony at Lucera, by Julie Taylor". The American Historical Review, October 2004.
Our estimates of NW African chromosome frequencies were highest in Iberia and Sicily, in accordance with the long-term Arab rule in these two areas. The chromosome frequencies in the two samples were not significantly different from each other (Fisher's exact test P=0.83) but were both significantly different from the peninsular Italy sample (P<0.01). An inspection of Table 1 reveals a non-random distribution of MNA [medieval North African] types in the Italian peninsula, with at least a twofold increase over the Italian average estimate in three geographically close samples across the southern Apennine mountains (East Campania, Northwest Apulia, Lucera). When pooled together, these three Italian samples displayed a local frequency of 4.7%, significantly different from the North and the rest of South Italy (P<0.01), but not from Iberia and Sicily (P=0.12 and P=0.33, respectively). Arab presence is historically recorded in these areas following Frederick II's relocation of Sicilian Arabs.
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Capelli et al. "Moors and Saracens in Europe: estimating the medieval North African male legacy in southern Europe". Eur J Hum Genet, 2009.