Over 50,000 years ago, a group of hunter gatherers, whose male members bore the Y chromosome mutation G-M201, began a migration that would ultimately see its descendants out of Africa.  The group, likely pushed by extreme climactic events and the availability of food, reached the fertile land of the Levant around 40,000 BC.  There they would have found an advantageous area where fish, animal life, and wild grains were prevalent.  A range of wild barley and wild emmer wheat stretched from the southern levant, northward in an arch towards Anatolia and then west towards the Zagros mountains.  Climactic factors may have pressured G peoples north out of the Levant and into the valleys of Northern Syria beginning around 18,000 BC in the area known as the "Golden Triangle".  As these groups migrated, they followed the arch of Emmer Wheat and Barley and thus were able to continue their pre-farming lifestyles which relied on harvesting on the reliable growth of certain grains as well as hunting and gathering.

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At the dawn of the Neolithic Period, the men of Haplogroup G likely expanded out of an area in Northern Syria staying within range of native wheat and adapting to domesticate goats, pigs, and sheep.  While many men of Haplogroup G are credited with spreading farming to Europe during the Neolithic Age, G-M406 (and G-M3302 for that matter) has not been found among the many ancient sequences brought to us via the remains of Neolithic European Farmers.  The First Farmers penetrated Europe, traveling up the Danube and establishing what is called the Linear Pottery Culture.  Others seemed to have gradually made their way along the shore lines in what is known as the Cardium Pottery or Impressed Ware Culture.  The male lines of the First Farmers were very nearly wiped out in Europe with the arrival of the Indo-Europeans (mainly Haplogroup R).  Again, G-M406 and its downstream clades do not seem to have been in Europe when this occurred.  Instead, they likely settled in Central Anatolia and along the Black Sea coast, perhaps remaining semi-sedentary  and transitioning to farming later than their other G2a peers.  Therefore, while G men are credited with spreading farming west into Europe and possibly east into Iran, the men of G-M406 likely remained in Anatolia during this period.

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At the dawn of the Bronze Age, men bearing the G-M406 (G-FGC5089 & G-M3302) signature have been found amongst the Native Anatolians living along the bend of the Halys (Kızılırmak) River as well as the southern coast of the Black Sea in Central Anatolia. These people may have received the Neolithic package later than their cousins to the south. In those days the now less forgiving landscape of Central Anatolia was in part covered by dense forest.  Due to its deposits of Copper, the region played an important role in the advancement of metallurgy that led to the Bronze Age.  One city, Ḫattuša, became the focal point of what would become known as the Hattic civilization. The Hatti were a non-Indo-European indigenous people and almost certainly G-M406 (G-FGC5089 & G-M3302) made up a sizable percentage of it's male lines.  Following the Indo-European invasion of the Hittites around 1700 BCE, a majority of the Hattic peoples were incorporated into the lower ranks of Hittite society.  However, some of the Hittite's most persistent enemies, the wild Kaška peoples who dominated the mountainous passes along the Black Sea coast, and the Azzi-Hayassa confederation possibly stretching from the Eastern Black Sea to Lake Van, likely represented a continued Native Anatolian presence into the Iron Age

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