The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.
1) the main pulse of Indo-Europeans, the proto-Greeks, arrived ~2300 BCE to “mainland Greece” (i.e., the north). This notwithstanding other earlier contacts noted in the text between the Pontic steppe and the Balkans
2) The Minoans and other peoples of the Aegean did not have this ancestry. This is not surprising. But, this works seems to confirm a likely pulse of ancestry into the Aegean ~4000 BCE with roots in eastern Anatolia and/or the Caucasus. This is a minority component, but seems correlated with the arrival of Y chromosomal group haplogroup J2, and has been detected as far west as Sicily.
3) The above component is related to the contributor to about half the ancestry among the Yamnaya samples. But, the Yamnaya samples themselves are about half “Eastern Hunter-Gatherer” (EHG), which itself can be decomposed as 25% “Western Hunter-Gatherer” (WHG) and 75% “Ancient North Eurasian” (ANE). This EHG component was lacking entirely in the Minoans of the Bronze Age and is lacking in modern Cypriots (who are mostly ethnically Greek). In contrast, the EHG component begins to increase in the Balkans during the late Neolithic.
4) There seems to have been a further dilution of the steppe component among the Bronze Age Greeks as they moved from the north to the south. The largest component of Greek ancestry then, and now, remains “Early European Farmer” (EFF), related to and descended from “Anatolian Farmer” (AF).
5) Modern Greek samples have more steppe than late Bronze Age samples (Mycenaeans). I am confident this is due to early medieval Slav tribes, who moved as far south as the Peloponnese in large numbers. I’ve looked at a fair number of Greek samples, and some of them have way less steppe ancestry than others, with the latter matching those labeled “northern Greek” by the Estonian Biocentre dataset. I think many of these former are likely island Greeks from the Aegean or Greeks who descend from early 20th century migrants from Anatolia.
All this has to be placed in the context of the broader Indo-European migrations. David Anthony in The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World mentions that there is a lot of circumstantial cultural evidence of contacts between the proto-Greeks and Indo-Iranians in the Proto-Indo-European urheimat. This would make sense if the proto-Greeks migrated from Russia and the Pontic steppe relatively late, rather than being secondary migrants from the post-Corded Ware zone of northeastern Europe. Look up the R1b and R1a ratios of the Greeks. The former outnumber the latter in the south, and the latter the former in the north. I think this is the impact of later Slavic migrants on top of an earlier R1b bearing centum Indo-European population.