By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra–West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.

We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.

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Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom’s northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region.

We here describe fossil remains from three Lower and Middle Miocene localities of Anatolia, which we tentatively refer to chamaeleonids. The material comprises isolated tooth-bearing bones from the Early Miocene (MN 3) of Sabuncubeli (western Anatolia), the Early Miocene (MN 4) of Dededağ(western Anatolia), and the Middle Miocene (MN 5) of the world-renowned hominoid locality of Pasalar (northwestern Anatolia). If our identifications are correct, these specimens would represent the only fossil record of this group from Anatolia as well as the oldest occurrences of chameleons from Asia. Moreover, the recovery of these specimens across different Lower and Middle Miocene localities, suggest that these animals were a typical element of the Anatolian herpetofaunas of the early Neogene. Differences among the specimens from the three localities point to a higher taxonomic diversity of Miocene Anatolian chamaeleonids, however, based on such limited material, intraspecific or ontogenetic variation cannot be ruled out. The oldest among these occurrences, the Sabuncubeli material, coincides chronologically with the oldest chameleons, which had been previously described from Central Europe (MN 3). As such, this supports the recently suggested biogeographic scenario, according to which chamaeleonids dispersed from Afro-Arabia to Europe during the Burdigalian, via the "Gomphotherium Landbridge," through Anatolia and the Balkans. Finally, a few additional lizard and snake remains from the locality of Dededağare described, adding to the poorly known fossil herpetofaunas of Anatolia.