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Even historically isolated populations have had significant selection pressure and intermixture with Eurasian peoples. The average age of the most common past ancestor has been put at between 5,000 and 15,000 years ago, so in biodiversity terms human beings are closer to Cheetahs than they are to Chimpanzees. There isn't a significant amount of 'diversity' within the population to start with.
It also acts as a proxy for environmental and sociocultural factors as well. Melanin levels as far as I am aware have little to know direct impact on brain development, but it still has a clear and measurable effect on social and cultural factors.
I.Q. tests are designed for instance to give men and women the same I.Qs on average -- 100. Recent 'gains' by women that raised their relative I.Q. compared to men, IIRC 100 vs 104, would that indicate that women as a group are smarter than men on average, or does in indicate that the factors that lowered women's I.Q. in the past were removed and the test's adjustment hasn't taken that into account yet?
Not quite plausible, though getting much closer. The oldest American sites are from right around 15000 years ago. I wouldn't expect too many people to have Native American ancestry. (Yes, if I remember correctly, Athabaskans and Inuit etc. peoples are later, but I don't think that's enough to matter.)
Humans have much, much more diversity than cheetahs*, though also quite a bit less than chimpanzees. Cheetahs are extremely low in genetic diversity. It's silly to say that there isn't a significant amount of diversity when it's obvious that humans vary substantially among many traits that we might consider significant, and when many traits are heritable.
Yes, of course. Disambiguating would take some care, investigation into what effects environmental/sociocultural factors have, etc. It would be odd not to recognize the possibility (and I would expect it would have some effect). And as pointed out, race can act as a proxy for genetic ancestry, since non-exceptional subsaharan africans will, I believe, look genetically more like each other than they do like non-subsaharan africans. It would also be odd not to recognize that genes could play a factor.
Assuming that IQ tests match sufficiently well on to our usual concepts of smartness (probably, but with only a 4 point difference, and IQ tests evened by construction, I'm less confident than usual), then yes, it would follow that women would be smarter than men; the tests said so. We could investigate causes, sure, to see whether they're innately smarter or due to the environment, but that wouldn't change that there'd be a difference.
You could investigate to what extent groups differing in whatever factors might be lowering IQ would differ in IQ. (Adoption studies could be one avenue to pick up on some sources of variation, different countries, etc.)
*the graph on page 91
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