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Haplogroup G from the Levant (early farmer), R1b & J (herders) from East Anatolia
Here is a new hypothesis. I, like most of the population genetics community, have assumed until now that haplogroup G originated in Anatolia or in the Caucasus, because this haplogroup is the most common there. A few elements make me think that haplogroup G could have expanded from the Levant instead.
1) Agriculture expanded from the Levant to Greece, then to the Balkans and the Mediterranean. Most of the early farmers tested so far being members of hg G2a, it would make sense that they originated where agriculture started, i.e. the Levant.
2) Haplogroup G has a fairly high frequency in Egypt (9%). There is so far no explanation as to how it got there. Either hg G was already in Egypt since the late Paleolithic, or it came with the spread of agriculture from the Levant. If Anatolian G people learned to farm from their Levantine neighbours (so far assumed to be E1b1b or J2 people) then expanded to Europe, there is no reason to find any G in Egypt. If G was absorbed by E1b1b an/or J2 farmers, then these two haplogroups should be found among early farmers in Europe, but so far it hasn't been the case.
3) What's more, hg G is found (at low frequencies) as far south as East Africa, Yemen and Oman, and as far east as India and Central Asia. So I think that the most reasonable assumption is that agriculture started with G people in the Levant, then expanded to Egypt, East Africa, all the Middle East, South Asia, Central Asia, and of course Europe. However they would probably have been outnumbered by local hunter-gatherers as G is a minority haplogroup almost everywhere.
If farming started with G in the Levant, then domestication started in East Anatolia/North Mesopotamia, and the prime candidates for spreading the new herder/stockbreeder lifestyle must have been haplogroups J and R1b1b, which both seem to have originated in that region in the Mesolithic. I see a stronger association of R1b1b with cattle and sheep, and J with goats.
As I have stated many times before, I believe that R1b1b crossed the Caucasus and settled in the Pontic Steppes, becoming one branch of the Proto-Indo-European speakers, a language that they probably spread to their R1a1a neighbours to the north and east.
As for haplogroup J, both J1 and J2 and found all over the Middle East, North Africa, Europe, and Central Asia. I really don't think that the medieval Arabic expansion is responsible for spreading all of it in North Africa and Central Asia. J2 being found among Hindus in India, was almost certainly in South Asia since the Neolithic. Dry, mountainous regions like the Maghreb, the Caucasus, most of Iran and Central Asia are also better adapted to herding than to agriculture, which may be why there is more haplogroup J than G in these regions. The same is true within Greece; Thessaly is better suited to agriculture and has a lot of hg G, while Crete is better suited to (goat) herding and has a lot of hg J2. In Iberia, hg G is more common in the wetter Northwest, while J1 and J2 are both more common in dryer Andalusia and Castilla-La Mancha.