Did haplogroup J2a1 originate in Greece?

In A multistep process for the dispersal of a Y chromosomal lineage in the Mediterranean area, Patrizia Malaspina and colleagues identified "Network 1.2", a group of chromosomes identified by a deletion in the DYS413 locus:

Chromosomes grouped into network 1.2 are identified by short CA repeats (<=18) in both PCR fragments at DYS413. All chromosomes within this group can be linked to each other in a network by assuming insertion or deletion of a single CA unit in one of the fragments. By the same criterion, they could not be linked to any other chromosome in a sample of 1801 chromosomes (Malaspina et al. 2000) from Western Eurasia and North Africa.

These chromosomes all belonged to the J2-M172 clade of the Y-chromosome phylogeny, and in the latest phylogenetic revisions, they are now termed as J2a1.

Intriguingly, Malaspina et al. carried out a microsatellite diversity analysis within Network 1.2, which I have not seen repeated on a regional basis since. The results of this analysis:

The largest variances, after averaging across the four loci, are found in Continental Greece, Crete and Romania (>0.40),followed by Continental Turkey (0.36) and Italy (0.32). A super-pool consisting of all typed network 1.2 chromosomes from West Asia, except Turkey, produced the low value of 0.31. Considering that the area from which a population spread is generally characterized by a comparatively higher genetic variance than the areas colonized later (Wooding & Ward, 1997; Barbujani, 2000), these data identify the Balkans, Aegean and Anatolia as the possible homeland harbouring the largest variation within network 1.2, with decreasing values both east/south-east and west of it.

Actually, the microsatellite variance is higher in Greece 0.487, Crete 0.457, the entire Balkans (incl. Greece) 0.478, and Romania 0.4075, all of which are higher than in Anatolia.

This certainly does not seem to be the signature of colonization of the Balkans by pioneer groups of farmers from the east. Moreover, there have been numerous historical attested movements of Balkan peoples into Anatolia, incl. the Phrygians, Thracians, and Greeks. Indeed, by the time that the first Turkic speakers arrived in Anatolia, the peninsula was dominated by Greek and Armenian speakers, both of which had ultimate Balkan origins (the Armenians being Phrygian colonists with ultimate Thraco-Macedonian origins). Obviously these movements affected the genetic composition of the Anatolian population, increasing the diversity of J2a1 lineages there. Hence, the original differential between the Balkans and Anatolia may have been even higher.

However, it could be argued that mobility within the Byzantine and Ottoman Empires may have introduced J2a1 from Anatolia to the Balkans. However, this does not explain the high diversity of J2a1 in Romania and Italy which were little if at all affected by Anatolian populations.

Moreover the idea that J2a1 originated in Greece also explains the coastal distribution of J2 in the Mediterranean, observed by Di Giacomo et al.. It is well-known that Greek colonization was especially maritime.

It also explains why in the Balkans, the western Dinaric regions show little J2: Greeks had few colonies in the Adriatic, whereas colonization of present-day Bulgaria and its Black Sea coast was extensive.

Moreover, Balkan J2 belongs primarily and near-exclusively to clade J2b (old J2e), contrasting greatly with Greeks where both J2b and J2a (mainly J2a1) are present. This, again signifies the differentiation of Greek J2 from Balkan J2, with the former belonging more to the J2a clade.

Furthermore, unlike Slavs of the Balkans that have only a little J2b and almost no J2a, Ukrainians have more J2a than J2b, and more J2 altogether. Unlike the West Balkans, the Ukraine was home to both ancient and more recent Greek colonies and settlements.

The higher frequency of J2 in southern Italy and Sicily compared to northern Italy, is also explained by this theory, as these regions were colonized by Greeks, whereas northern Italy was not.

J2a is also present in Egypt which was conquered by Macedonian Greeks, as well as Iran, but drops to a small frequency in India, and is there limited to the upper castes. This may reflect its presence in the ancient Indo-Aryans and its survival in the Brahmin caste, or alternatively may be the result of intermarriage between the Bactrian Greek aristocracy and high-class Hindus. In any case, if one accepts that the Indo-Aryans of India originated from an ultimate steppe group which was an outgrowth of the Tripolye-Cucuteni culture of the Balkans, the presence of J2a1 among Brahmins ceases to be a mystery.

In all likelihood, J2a1 originated before the ethnogenesis of the Greeks, and may be associated with multiple population movements from the Greek-Balkan region. However, I believe that it makes better sense to view it as a Balkan-Greek clade than a West-Asian one.