The genetic history of the Southern Caucasus from the Bronze Age to the Early Middle Ages: 5,000 years of genetic continuity despite high mobility

The Caucasus was a hub for cultural and technological innovation in prehistory, yet the population history between the Greater and Lesser Caucasus remains insufficiently understood. We present genome-wide data of 205 individuals from modern Georgia and 25 from Armenia, spanning the period from the Bronze Age (BA) to the "Migration Period" (c. 3500 BCE-700 CE). Our results reveal a persisting local gene pool that, during the Middle-Late BA, absorbed additional ancestry from Anatolia and the neighboring Eurasian Steppe. In subsequent periods, we document population growth and increasing genetic diversity, supported by a high rate of individual ancestry outliers, particularly in urban centers of eastern Georgia. Among 20 Medieval individuals with artificially deformed skulls, 15 were part of local mating networks and five derived ancestry from the Eurasian Steppe, suggesting that cranial modification arrived with nomadic groups but became a locally adopted cultural practice.