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Notes -
once you analyzed lots of phenotype-genotypes for moderns you can apply these models for ancient, and analyzing population averages is simpler in some aspects than getting a good score for individual: for individual, a trait would depend on non-linear combinations and rare alleles; for comparing between populations, these aren't significant, because a population cannot reliably continue lucky non-linear combinations (we however do in in agriculture with f1 seeds and cloning).
How verifiable is it, though? Where are we getting DNA from, are they outliers trapped in peat bog pits or something? The article says they just found basically anonymous DNA samples from across Eurasia, over thousands and thousands of years. We can't know that this is a balanced sample.
What if they have X genetics and we accurately capture that but some epigenetics are activated/deactivated at the time? As far as I can determine, the methylation pattern is more easily lost (and they didn't cover it anyway).
I like my science as concrete and provable as possible. This is dangerously abstract. Abstraction is fine if we had some real Indo-European farmers or Neolithics to talk to but since we don't, standards for validity should be kept high.
Not much verifiable. There should be much more work comparing new data (hopefully more detailed and nuanced than this) to see whether there shifts make sense with what we know from other means. There is no expectation why samples would be unbiased but this is problem for all archeology, not just DNA.
How then do you like hypothesis that we are smarter than Homo erectus? It's not something that can be tested. It's pure speculation, right? Heck, how we can be even be sure Indo-Europeans existed? It's just deep extrapolation from existing languages on much murkier ground.
Skull size is a pretty clear signal for Erectus, I'm happy with skull size variations implying intelligence difference, ceteris paribus. I'm happy with a broad trend of rising intelligence under selection pressure. I do believe in evolution and genetics. But I don't believe that we can precisely chart IQ rising and falling over thousands of years like OP's charts suggest. The level of confidence is too high.
DNA methylation is absolutely relevant to working out which genes are expressed, it's a way of determining epigenetics.
The human body is a very complex piece of machinery that we don't fully understand. This article suggests that the heart can store memories (which are transferred with transplants) which I didn't believe in at all prior to this: https://www.sciencedirect.com/science/article/abs/pii/S0306987719307145
When dealing with such a complex system, with many facets barely known to us, we should be cautious before reaching conclusions - especially if there's no way to test them.
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