What about Rootsi?

The 2012 Rootsi study Distinguishing the co-ancestries of haplogroup G Y-chromosomes in the populations of Europe and the Caucasus was a defining analysis of the G Haplogroup in Europe.  It has set the stage and framed thinking regarding G in Europe for the past decade.  It has also given us an initial backbone in regard to frequencies of certain the G Haplogroup and it's subclades in Europe and other areas.  However, these frequencies are based on STR estimates and not SNPs which can be problematic in some situations but does not seem to overly undermine the data.  In addition, when it comes to G-M406 and many other subclades much has been learned regarding TMRCAs from SNP analysis in the interim.  So how does the conclusions of Rootsi in regard to G-M406 stack up to what we know now?

https://www.nature.com/articles/ejhg201286?fbclid=IwAR1NAQ034WsNcRHD7lNiTnIKRblTsFX3CjQj8M5qMMDk-VgsuCaplCRGKfA

"Another frequent sub-clade of the G2a3-M485 lineage is G2a3a-M406 (Figure 2e). In contrast to its widely dispersed sister clade defined by P303, hg G-M406 has a peak frequency in Cappadocia, Mediterranean Anatolia and Central Anatolia (6–7%) and it is not detected in most other regions with considerable P303 frequency." 

This information is still fairly accurate except to say that Sicily and Southern Italy also have fairly high percentages of G-M406 (3-5%).

"The expansion time of G-M406 in Anatolia is 12 800 years ago, which corresponds to climatic improvement at the beginning of the Holocene and the commencement of sedentary hunter-forager settlements at locations, such as Gobekli Tepi in Southeast Anatolia, thought to be critical for the domestication of crops (wheat and barley) that propelled the development of the Neolithic."

M406 expansion according to the newest Yfull estimates is 12200 years ago (10200 BCE) which is ins line with climactic improvements.  However, 99% of G-M406 is also G-M3317 which expands at 9,000 (7,000 BCE).  Also G-M406 has not been found in the first settlements of Anatolia such as Gobekli Tepe and may have missed out on the population expansion experiences by other G2a clades such as G-P303, who have been shown to give rise to the Early European Farmers.

"G2a3a-M406 has a modest presence in Thessaly and the Peloponnese (4%),10 areas of the initial Greek Neolithic settlements. More distantly, G2a3a-M406 occurs in Italy (3%) with a Td of 8100 years ago, consistent with the model of maritime Neolithic colonization of the Italian peninsula from coastal Anatolia and/or the Levant.

Finally, to the east, G2a3a-M406 has an expansion time of 8800 years ago in Iran, a time horizon that corresponds to the first Neolithic settlements of the Zagros Mountains of Iran. Thus, G2a3a-M406, along with other lineages, such as J2a3b1-M92 and J2a4h2-DYS445=616, may track the expansion of the Neolithic from Central/Mediterranean Anatolia to Greece/Italy and Iran."

This paper was written at a time when STR (Short Tandem Repeat) analysis was the preeminent way of analyzing and assigning haplogroups and sub haplogroups.  STR markers change over time and scientists can use them to make certain Haplogroup associations.  However, sometimes STR markers randomly change in a way that mimics common identifiers of other clades or are so similar to other clades that one can not be certain to which set an individual or group belongs.

SNPs (Single Nucleotide Polymorphisms), one the other hand, are a variation in a single base pair in a DNA sequence (mutation) that is passed down and inherited by all males descended from an individual.  Therefore, one can track SNP mutations in YDNA and establish a precisely accurate tree of common descent.

Rootsi et al., 2012 makes the mistake of assuming that G-M406 was planted in certain geographical areas and grew in isolation.  Hence it assigned an average marker to the G-M406 Italian and assumed this progenitor lived 8100 years ago (6100 BCE).  Or that a G-M406 man existed 8,800 years ago (6,800 BCE) and is the father of all Iranian G. 

Therefore, the scientists pointed to a Neolithic expansion for G-M406.  But in reality, what they were seeing was regional expansion times in line with the overall expansion times of G-M3317.  However, unlike the Rootsi study's assumptions, this group was clearly in one place at the time.  All available evidence suggests that place was Anatolia.  As the G-M406 SNP tree has expanded we see sub-haplogroups with TMRCAs from 6,000 to 5,000 years ago (4,000-3,000) with members stretching from at home in Anatolia to the Middle East, Europe, and even parts of Asia (see Y-Full tree) .  This suggests a post Neolithic Expansion of G-M406 into other areas outside of Anatolia.  It also casts doubts about any G-M406 ties to the Neolithic Cardium Ware (Impressed) Expansion which almost DID include other G Haplogroups associated with the First Farmers.