There is something I don't understand in the admixture analysis from the paper. Modern Greeks from Thessaloniki are shown as having 20% of red EHG, 20% of pink CHG, 59% of blue ENF and 1% of dark green Natufian, but they completely lack the purple admixture that makes up 35-100% of Neolithic Greeks, 15-30% of Minoans and 25-45% of Mycenaeans. It's also missing from other modern Greeks and Cypriots. What happened to that admixture? It couldn't simply have vanished like that. Is that because they didn't re-run those samples using the same K17 parameters? If so that would be highly unprofessional of them for a published peer-reviewed paper. If not, that raises a lot of questions.
I also disagree with Lazaridis and al. when they say that "
Modern Greeks resemble the Mycenaeans, but with some additional dilution of the Early Neolithic ancestry". Mycenaeans are much closer to the Minoans than to Modern Greeks. Modern Greeks have 3x more EHG (about 20%) than Mycenaeans (7%), but they also have WHG (3% according to D-stat). This suggests that numerous waves of European invaders (Dorians, Celts, Romans, Goths, Slavs) contributed to a large share of modern Greek DNA. Since obviously no invader to Greece were pure EHG, and none had more than 50% of EHG in average (30-35% might be more realistic as the Romans had comparatively low EHG), to increase from 7% to 20% of EHG, the percentage of post-Mycenaean DNA from European invaders must be comprised between 25% and 40%. Most of it will be blue ENF and pink CHG that won't be identifiable using these relatively simple admixtures. What we see is only the clear increase in EHG, which is only one third to half of the new invaders' DNA.
In other words modern Greeks are nothing like Mycenaean Greeks, and even less Minoan Greeks. Modern Greeks have much more European ancestry. Y-DNA alone suggests 40 to 45% of European lineages (as opposed to Near Eastern), and over 60% if we included E-V13 (E1b1b came from the Near East but E-V13 clearly emerged in Europe). Greeks possess lineages that are clearly Germanic (3.5% of I1, so about 10% of Germanic overall with I2a2-L801, R1b-U106 and R1a-L664), Slavic (11% of R1a, which is overwhelmingly M458 and CTS1211) and Italo-Celtic (about 7% of R1b-U152 and 1% of G2a-L497).