205 ancient human samples from modern Georgia dating to 3500 BCE - 500 CE; 25 samples from Armenia dating to 400 - 200 BCE

Since prehistory, the Caucasus region has served as a hub for cultural, technological, and linguistic innovation. However, despite its dynamic history, the area between the Greater and Lesser Caucasus mountain ranges has received limited attention from archaeogenetic studies. Here, we present a genome-wide ancient DNA time transect comprising 205 individuals from 49 sites in Georgia and 25 individuals from Armenia, supplemented by 86 new radiocarbon dates. Spanning from the Early Bronze Age (c. 3500 BCE) to the so-called 'Migration Period' (c. 500 CE), these data reveal a persisting local gene pool that in the Middle and Late Bronze Age (c. 2600-1200 BCE) assimilated ancestry from two sources, Anatolia and the adjacent Eurasian Steppe. In subsequent periods, we document population growth and increasing genetic diversity. From the end of Late Antiquity (c. 3rd century CE) onward, we identify these interactions as individual ancestry outliers, often linked to urban centers – landmarks of the early Christianization in eastern Georgia. Several of the outliers with Central Eurasian Steppe ancestry manifest the cultural practice of artificial cranial deformations. However, 15 out of 20 individuals with such deformations were part of genetically local mating networks, indicating that this cultural practice was introduced by mobility from the Eurasian Steppes but adopted by local people. Our study underscores the value of high-resolution archaeogenetic time transects in capturing broad and fine-scale patterns of population history.