This is an important new paper about Y chromosomes in Greece. The authors studied Cretans as well as Greek populations from early Neolithic sites in Macedonia, Thessaly, and the Peloponnese.
My main gripe -which is a general one and not limited to this paper- is for researchers to consider prehistorical explanations, related to "hot topics" in archaeology, such as the origin of the Neolithic, rather than more mundane historical ones.
It would be interesting to include a discussion of the post-Neolithic population settlement history of the studied areas: the idea that the current gene pools preserve a strong signal of the Neolithic inhabitants of the same areas seems rather arbitrary to me.
I will add more comments as I read the paper and supplementary information more closely, but one of the certain conclusions from the paper is that it places the final tombstone to the whole Bernal/Black Athena (or alternatively Poe/Black Spark, White Fire) theory of Aegean prehistory. The complete dissimilarity of E3b related lineages between Greece and Crete on the one hand and Egypt on the other, makes any type of Bronze Age colonization of the Aegean by Egyptians an impossibility.
Annals of Human Genetics, Volume 72 Issue 2 Page 205-214, March 2008
Differential Y-chromosome Anatolian Influences on the Greek and Cretan Neolithic
R. J. King et al.
The earliest Neolithic sites of Europe are located in Crete and mainland Greece. A debate persists concerning whether these farmers originated in neighboring Anatolia and the role of maritime colonization. To address these issues 171 samples were collected from areas near three known early Neolithic settlements in Greece together with 193 samples from Crete. An analysis of Y-chromosome haplogroups determined that the samples from the Greek Neolithic sites showed strong affinity to Balkan data, while Crete shows affinity with central/Mediterranean Anatolia. Haplogroup J2b-M12 was frequent in Thessaly and Greek Macedonia while haplogroup J2a-M410 was scarce. Alternatively, Crete, like Anatolia showed a high frequency of J2a-M410 and a low frequency of J2b-M12. This dichotomy parallels archaeobotanical evidence, specifically that while bread wheat (Triticum aestivum) is known from Neolithic Anatolia, Crete and southern Italy; it is absent from earliest Neolithic Greece. The expansion time of YSTR variation for haplogroup E3b1a2-V13, in the Peloponnese was consistent with an indigenous Mesolithic presence. In turn, two distinctive haplogroups, J2a1h-M319 and J2a1b1-M92, have demographic properties consistent with Bronze Age expansions in Crete, arguably from NW/W Anatolia and Syro-Palestine, while a later mainland (Mycenaean) contribution to Crete is indicated by relative frequencies of V13.