During this time, the influence on Crete by mainland centres intensified and Cretan resources were systematically exploited with the help of turning key palatial centres and cities like Knossos, Hagia Triada and Chania into outposts for the administration of large parts of the island 16. At the end of this conflict, the palatial period (Late Helladic IIIA-B) started with a few eminent polities centred in Mycenae, Tiryns, Pylos, Athens, Hagios Vasileios in Laconia, Thebes, Orchomenos and Dimini-to name only the most prominent ones 13, 14, 15. The competition between rising elites during the Shaft Grave period led to regional conflicts and culminated in the decline of many local dominions on the Greek mainland and possibly a first mainland military expedition to Crete during the fifteenth century 12. Only a few centuries later, during the late Middle Bronze Age (MBA Middle Helladic for the mainland), the first rich shaft graves of local elites appeared in southern mainland Greece, often displaying Minoan influences 11. With the emergence of the first palaces during the nineteenth century bc in the Middle Minoan period, the island’s societies transformed into a hitherto unknown sophistication in art, architecture and social practices. Crete does not seem to have suffered a comparable period of decline 9, 10. This disruption has been attributed to various factors, among them dramatic climatic changes 2, 4, 5 and the arrival of new groups 6, 7, 8. During the late third millennium bc, the Greek mainland witnessed a severe societal breakdown (at the end of Early Helladic II) with lasting impact until the later Middle Helladic period of the early second millennium 2, 3. Complex societies emerged, characterized by sophisticated architecture, metallurgy, sealing systems and the integration of the Aegean in the Bronze Age Eastern Mediterranean networks of exchange. The next major transformation in Aegean prehistory took place during the Early Bronze Age (EBA about 3100–2000 bc). Already during the seventh millennium bc, the first farming communities emerged in the Aegean, whereby the earliest evidence was unearthed on the island of Crete-that is, the oldest occupation level below the later palace of Knossos 1-but the origins of these populations remain ambiguous. The Aegean has long been recognized as a region of major importance for understanding transregional societal transformations between Europe and the Near East. Our results highlight the potential of archaeogenomic approaches in the Aegean for unravelling the interplay of genetic admixture, marital and other cultural practices. Biological and cultural connectedness within the Aegean is also supported by the finding of consanguineous endogamy practiced at high frequencies, unprecedented in the global ancient DNA record. Confirming previous findings for additional Central/Eastern European ancestry in the Greek mainland by the Middle Bronze Age, we additionally show that such genetic signatures appeared in Crete gradually from the seventeenth to twelfth centuries bc, a period when the influence of the mainland over the island intensified. In contrast, the end of the Neolithic period and the following Early Bronze Age were marked by ‘eastern’ gene flow, which was predominantly of Anatolian origin in Crete. We found that the early farmers from Crete shared the same ancestry as other contemporaneous Neolithic Aegeans. We have analysed newly generated genome-wide data from 102 ancient individuals from Crete, the Greek mainland and the Aegean Islands, spanning from the Neolithic to the Iron Age. The Neolithic and Bronze Ages were highly transformative periods for the genetic history of Europe but for the Aegean-a region fundamental to Europe’s prehistory-the biological dimensions of cultural transitions have been elucidated only to a limited extent so far. Nature Ecology & Evolution volume 7, pages 290–303 ( 2023) Cite this article Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean
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