This paper presents an event stratigraphy based on data documenting lake-level changes as well as volcanic eruptions over the period 4500—3500 cal. BP from sediment sequences of Lakes Accesa in Tuscany (north-central Italy) and Maliq (Albania) in the central Mediterranean. The available data make it possible to recognise a tripartite climatic oscillation between c. 4300—3800 cal. BP. A phase characterised by drier conditions at c. 4100—3950 cal. BP appears to have been bracketed by two phases marked by wetter conditions and dated to c. 4300—4100 and 3950—3850 cal. BP, respectively. The deposition of the Avellino tephra occurred during the first humid phase, slightly before 4300 cal. BP, and that of an interplinian tephra AP2-AP4 (or Pr1) around 4050 cal. BP during the dry intermediate phase. This dry median episode may be related to the so-called ‘4.2 ka event’ observed in tropical areas as well as in northwestern Italy. A comparison of the Accesa lake-level record with palaeoclimatic terrestrial and marine records suggests that this complex climatic oscillation around 4300—3800 cal. BP affected the central and western Mediterranean area. The key position of the 4300—3800 cal. BP climatic oscillation at a crucial transition from mid to late Holocene in the Mediterranean and tropical areas, deserves major consideration in further investigations.

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.