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The oldest identified J1 sample to date comes from Satsurblia cave (c. 13200 BCE) in Georgia (Jones et al. (2015)), placing the origins of haplogroup J1 in all likelihood in the region around the Caucasus, Zagros, Taurus and eastern Anatolia during the Upper Paleolithic.

Like many other successful lineages from the Middle East, J1 is thought to have undergone a major population expansion during the Neolithic period. Chiaroni et al. (2010) found that the greatest genetic diversity of J1 haplotypes was found in eastern Anatolia, near Lake Van in central Kurdistan. Eastern Anatolia and the Zagros mountains are the region where goats and sheep were first domesticated, some 11,000 years ago. Chiaroni et al. estimated that J1-P58 started expanding 9,000 to 10,000 years ago as pastoralists from the Fertile Crescent. Although they did not analyze the other branches, it is likely that all surviving J1a1b (L136) lineages share the same origin as goat and sheep herders from the Taurus and Zagros mountains.

The mountainous terrain of the Caucasus, Anatolia and modern Iran, which wasn't suitable for early cereal farming, was an ideal ground for goat and sheep herding and catalyzed the propagation of J1 pastoralists. Having colonised most of Anatolia, J1 herders would have settled the mountainous regions of Europe, including the southern Balkans, the Carpathians, central and southern Italy (Apennines, Sicily, Sardinia), southern France (especially Auvergne), and most of the Iberian peninsula. Hotspots of J1 in northern Spain (Cantabria, Asturias) appear to be essentially lineages descended from these Southwest Asian Neolithic herders.

Most J1 Europeans belong to

Most of the J1 in the Caucasus, Anatolia and Europe is of the non-J1-P58 variety. These branches diverged from one another during the Ice Age and have nothing to do with Semitic people. In fact the origins of J1 lie around the Caucasus, which explains that all branches other than P58 are most common in that region, as well as in Anatolia and Europe.

J1a1 (M365.1) has been only found in very low frequencies in Western Europe (Western Iberia, French Pyrenees, Belgium and England), in northern Iran and Qatar. It may have come to Europe during the Mesolithic period, or as a very minor Neolithic lineage.

J1a1b1 (P56) is a minor Arabic cluster found on the Red Sea coast of Saudi Arabia, Yemen and Ethiopia. It can be identified by the STR value DYS641=11.

J1a2a (Z1828) is defined by the STR values DYS436=11 and DYS388<15. It is the second most common top level subclade after J1-P58. It is particularly frequent around the Taurus and Zagros mountains and all over the Caucasus region, but has also been found at low frequencies in western Turkey, Greece, Ukraine, South Italy, Central Europe, France, and the British Isles. The L1189 subclade seems to be mostly northern European (+ a few samples in Greece and the Arabian peninsula). Under Z1842, the CTS1460 subclade is geographically restricted to the Caucasus, Zagros and Taurus, while ZS3089 is found mainly around Armenia and Azerbaijan.