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It would be strange if ancient northern italians were really so southern genetically considering that in the Bronze Age North Italy was almost a prolongation of the Danube valley (Beaker, Polada, Wieselburg-Gàta in Friuli, Terramare, Canegrate/Golasecca all show influences from the north of the Alps)..not to mention the later Gaulish invasion
Yes, it surprised me too, so I combed through not only the paper, but the supplementary text, and it seems that the authors conducted a rather exhaustive analysis not only of the archaeological context, kinship networks based on genetic analysis, and precise dating of the remains, but a more than exhaustive isotope analysis of each sample. Indeed, as Razib Khan pointed out, the paper is in that way an excellent example of multi-disciplinary analysis. I wouldn't expect anything less of Johannes Krause.
This is what they concluded:
""In contrast, in Collegno it was notable that the five individuals with major southern ancestry are primarily assigned to Italy using PAA, exhibited local strontium signatures. When examining the two major kindred, we observe the striking general pattern that earlier generations had strontium isotope values that diverged from the local range more than later generations (Fig 3D, Figure S15.3). This appears to fit a model of individuals of central/northern European ancestry migrating and settling in Collegno amongst a set of local individuals of primarily Italian origin. "
Again, in another part of the study:
""At Collegno it has been possible to identify first-generation migrants with ‘northern’ ancestry, who were followed by two or three generations of stable settlement. They settled among individuals with high percentages of ‘southern’ ancestry."
That seems pretty clear, yes?
To contest the conclusion you would have to be able to show that they're wrong about the isotope analysis, or they compared samples from vastly different dates, etc.
Now, this doesn't mean that every site in Italy is going to be the same. It means this was the case here.
Perhaps, as I was speculating above, there was indeed an influx of Indo-European speaking people into Italy. We may find graves in other parts of Italy which are pretty "northern". However, we always have this problem in archaeology, and therefore in genetics, that we usually only find elite graves. The mass of the people weren't buried with that kind of care. This analysis is unique in that they recovered the remains not only of the "elite", but of those who weren't "elite".
That's also why I mentioned above the disparity between the Thracian remains. It took a long time for these groups to admix thoroughly. Look at the hunter-gatherers and the Neolithic farmers. It took two thousand years.