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There was an almost total replacement of the EEF y dna in central Europe. As you say there is more than one possible explanation for that of course but one of those possible explanations is the EEF farmers were over-run. Taking that possibility as a premise then leads to the question of how could the EEF percentage be high if the farmers were over-run? One possibility is the surviving EEF females had beneficial genes which were strongly selected for. Is there evidence for strong selection on those genes, yes. Is there evidence for farmer mtdna increasing over time, yes. If you work the logic backwards from those two points then it hints at the farmers being over-run.
This is where I have my strongest disagreement with your position. The beneficial genes to which you're referring are only partly located on the mtdna. Many of them, the pigmentation genes, for example, are part of autosomal variation. Additionally, even when combined, we would be talking about a very small percentage of genomic variation.
This *can't* have been a case where a large Bronze Age group of peoples migrated into Europe and mated with a few females of the prior population and then beneficial alleles just surfaced among a mostly newcomer population, or where just certain mtDNA lines were the subject of positive selection. Prior to Lazaridis et al, and even the prior Reich lab papers, it might have been possible to hold that position, but it is completely unsupported as things now stand.
You would never wind up with 50% EEF levels in northern Europeans in that way. When Lazaridis et al says 50% of the genome of the Germans is EEF, to take one example, they mean that the computer scanned the
total genome of the three ancient samples and the
total genome of modern samples, and in terms of the
total autosomal make up of a population like the Germans, not just a few percentage points that could be attributable to certain beneficial alleles or to the mtDNA, it turns out that there is a 50% overlap between this modern population and the Stuttgart woman.
Even assuming that the Bronze Age populations were very large in number, and without taking into consideration the fact that even, as just one example, a slight increase of the ability to father males of the R1b and R1a lines might over thousands of years result in a dramatic shift in frequency of certain yDNA lines, the only way that such high levels of EEF could appear in northern Europeans is if these Bronze Age migrations were mostly male mediated. I think that's also a conclusion that can be drawn from the ancient mtDNA paper to which I linked upthread. A very small percentage of "new" mtDNA appears in the cultures most likely to have experienced gene flow from the east.
I don't know how to explain my thinking on this any better than I have...I just don't think admixture works in the way you envision if I am understanding you correctly.
Ed.I also think it's important to note that the "Kurgan" archaeological trail which most people link to the "Indo-Europeans" ends in Hungary. I'm not aware of any paper that claims to find evidence of
large scale migration into western Europe from that point. There is also zero archaeological evidence found to date of any large scale massacre of the prior Neolithic populations of central and northern Europe, which is what you seem to be be envisaging.
Should that evidence surface, I would, of course, have to change my position. Speaking personally, I would, however, find that disturbing...I prefer not to think, absent some convincing evidence, that some of my ancestors were homicidal maniacs who virtually committed a holocaust on another set of my ancestors. It's bad enough having to accept the behavior of my Roman ancestors against my Celt-Ligurian ancestors, even if we're talking about a different level of inhumanity.
That's emotion, and my moral consciousness speaking, of course, but still...
