The basic idea is simple: first build a map of Oetzi's ancestry with a tool that distinguishes between the Near East and Europe. I did this with my West Eurasian cline (weac2) calculator. The output of this procedure is to calculate admixture proportions for Oetzi across the genome. In some windows along his chromosomes, he will appear to be 100% Atlantic_Baltic (European-centered component), in others 100% Near_East, and in some intermediate, or possessing some other component. At each window we have an Atlantic_Baltic and a Near_East admixture score.
Secondly, we need to calculate a score of Oetzi-Neandertal (Vindija) similarity in the same window. I used the Neandertal data from the Harvard HGDP, and my own copy of the Oetzi genome which I've created by intersecting a SNP file provided by Andreas Keller with the Stanford HGDP set of SNPs. In the end I combined Oetzi and Vindija in a common set of 37,320 SNPs, removing all SNPs with missing alleles. One could get more SNPs by not taking these various intersections and working with full genomes, but this set of SNPs suffices for my purposes.
In any case, I used 0/1/2 coding and took the absolute value of the Oetzi minus the Vindija value, normalizing by dividing with the number of SNPs in each window. That was my Score variable, and the lower the value the more Oetzi matches Vindija.
The idea is simple: does Oetzi tend to appear "Near_East" or "Atlantic_Baltic" in places along his genome where he is close to Neandertals?
I limited myself to windows where there were at least 10 SNPs common between Oetzi and Vindija, as well as windows where the sum of Atlantic_Baltic and Near_East was at least 95%, so there was good evidence that these two components were responsible for the whole diploid pair of segments. A total of 1,128 windows remained. The results are as follows:
Cor("Near_East", Score) = +0.082
Cor("Atlantic_Baltic", Score) = -0.079
These are small, but significant, and we should remember that relative levels of Near_East and Atlantic_Baltic vary for reasons unrelated to Neandertal ancestry in most of the genome. Here is a plot of the Score variable for the 1,128 windows, ordered from high-to-low:
In any case, the median Atlantic_Baltic for all windows is 46.48%, and the median Near_East one is 52.78%. But, let's see how these numbers look when we consider the lowest quantiles of Score (=more Neandertal matching):
These numbers kinda speak for themselves. Of course, it is wrong to equate Near_East = Neolithic and Atlantic_Baltic = Paleolithic. On the other hand, the assumption that these two components possess a greater relationship with the Neolithic farmers and the Paleolithic Europeans respectively, seems justified.
So, it seems that in regions where Oetzi matches the Vindija genome, he tends to be "Atlantic_Baltic". The implication is that Paleolithic Europeans were more Vindija-like than incoming Neolithic ones from the Near East. Oetzi may have been more Neolithic farmer than Paleolithic hunter-gatherer across his whole genome, but the situation is reversed for regions suggestive of Neandertal ancestry.
figure on the left is from one of his most recent works, showing a Copper Age European male (top) sharing features with La Chapelle Neandertal (middle) at the exclusion of Herto (an archaic H. sapiens from Ethiopia), indicating a degree of continuity from Neandertals to more recent Europeans.)
Just how Neandertal-admixed were the Paleolithic Europeans? If Hawks is correct in his claim that Oetzi was ~5.5% Neandertal, and given that Oetzi appears to have been overall more than 50% incoming farmer and less than 50% local hunter-gatherer (conservatively), then it is easy to conclude that even ~10% Neandertal for Paleolithic Europeans may not be too far from the truth. We'll have to see what their actual ancient DNA looks like to confirm the hypothesis found in this post.
Finally, since it's my custom to resuscitate old physical anthropology when it matches modern observation, here's Carleton Coon's 1939 Races of Europe, from his "Statement of Aims and Proposals":
At any rate, the main conclusion of this study will be that the present races of Europe are derived from a blend of (A), food-producing peoples from Asia and Africa, of basically Mediterranean racial form, with (B), the descendants of interglacial and glacial food-gatherers, produced in turn by a blending of basic Homo sapiens, related to the remote ancestor of the Mediterraneans, with some non-sapiens species of general Neanderthaloid form. The actions and interactions of environment, selection, migration, and human culture upon the various entities within this amalgam, have produced the white race in its present complexity.I'd say that if these results are confirmed by subsequent research, then "bullseye" is a good way to describe the above passage.
(But, I will not refrain from spoiling the fun a little bit, by pointing out that the potential high similarity of UP Europeans with the Vindija genome may be due, at least in part, to gene flow from UP Europeans-to-European Neandertals in that particular specimen. Now, it may be that such gene flow may have gradually made the European Neandertals more modern-like, and thus facilitated their eventual full absorption into the gene pool of subsequent Europeans. But, we don't know that for sure. A second Neandertal genome, preferably a pre-contact one will be the decisive factor in determining the direction of gene flow conclusively.)