The Short Version
Improved analysis of rare types of ancient Y-DNA from the Neolithic era in Europe confirms that there were two genetically distinct populations that brought farming with them in a mass migration replacing prior European hunter-gatherers in Europe, one by a Danubian route associated with the LBK culture, and one by a Northern Mediterranean route associated with the CP culture.
The analysis also provides a good example of more general processes in how the populations genetics of a large region changes in a punctuated manner driven by cultural divisions between genetically distinct groups (in this case, basically, by racism of the steppe people directed towards Europe's first farmers).
The Long Version
A new method called YMCA allows for more precise characterization of Y-DNA found in ancient DNA samples.
This has been used to reanalyze the rare (in Europe) Y-DNA H2 samples from the Neolithic era to shed more light on how farmers dispersed through Europe, supporting the archaeologically supported hypothesis that the expansion involved a distinct Daunbian Linear Pottery (LBK) culture and a Northern Mediterranean Cardial Pottery (CP) culture. Each migration group was a genetically distinct population that contained a small number of individuals with distinct rare Y-DNA H2 haplotypes that serve as markers of distinct populations following each route.
Haplogroup H is believed to have emerged in South Asia around 48,000 years ago. Its three branches H1-M69, H2-P96 and H3-Z5857 then appeared rapidly between 44,000 and 45,000 years ago. H1 and H3 are found today at frequencies of up to 20% in South Asia, but at very low frequency in Europe.
In particular H1 is associated with the arrival of Roma populations about 900 years ago.
The H2 branch has been present in Europe for much longer since it arrives with the first farmers of the Neolithic. It is thus found at frequencies of 1.5 to 9% depending on the archaeological sites. Today, however, it is present at frequencies below 0.2% in Europe.The authors therefore applied the new YMCA method to 58 European Neolithic haplogroup H2 samples. Until now the H2 haplogroup has been divided into three sub-branches: H2a, H2b and H2c obtained from contemporary genomes.
Analysis of the ancient genomes of the European Neolithic revealed two new sub-branches: H2d and H2m both further divided into two sub-branches: H2d1, H2d2, H2m1 and H2m2. . . .Interestingly all H2d haplogroup samples are located on the Danubian route of the European Neolithic, while all H2m haplogroup samples are located on the Mediterranean route, all the way to the Iberian Peninsula and beyond into Ireland. A sample threshold H2m is found in Central Germany, but it is dated to the end of the Neolithic.The authors then dated the common ancestor of the H2 branch to approximately 24,100 years, the H2d and H2m sub-branches to approximately 15,400 years, the H2m1 and H2m2 sub-branches to approximately 13,300 years and the H2d1 and H2d2 sub-branches to about 11,900 years old.
The dates at which the subclades emerged are in the Mesolithic era, appropriately prior to the Fertile Crescent Neolithic revolution and its expansion into Europe around 8,000 years ago.
The fairly high, although minority percentage of Y-DNA H in the first farmer wave of Europe is also a notable fact in and of itself that would not obviously be suspected and does not have a full explanation.
Why Did Y-DNA H Decline In Frequency So Dramatically?
The decay in the fraction of Y-DNA H in Europe is partially due to direct decline by dilution from the expansion of steppe people with horses and metal into Europe in the late Neolithic and early Bronze Age. But more than simple dilution was at work.
Y-DNA haplogroups are particularly prone to changes in frequency in societies organized on a patrilineal basis when one culture displaces another in a leadership role.
This is in part because men of the defeated culture are massacred.
It is in part, because men of the defeated culture have a harder time obtaining wives.
And, it is in part, because men of the defeated culture are deprived on a relative basis of resources like food. Malnutrition reduces the chances their children have of survival not only directly from starvation. It also reduces their chance of survival indirectly due to their children's increased vulnerability to disease, and their wives' vulnerability to miscarriage and stillbirth, when malnourished.
Also, not all Neolithic Y-DNA groups declined in the same proportion. This is because lower frequency Y-DNA haplogroups in a population are disproportionately lost in a period of declining frequency, such as the experienced by men with patrilineal descent from the first farmers of Europe rather than from subsequent steppe people, relative to higher frequency Y-DNA haplogroups.