Discussion: You find that European-African polygenic scores for educational attainment differ by more than 1.5 standard deviations. Some readers may find that strange because the actual difference between black and white Americans today is barely one standard deviation, and differences in educational attainment are even less. 

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Authors have updated the submission to version #14

Good work. Should be accepted after some very minor revisions.

Some specifics:

Abstract, 5^th paragraph:

Substantial Linkage Equilibrium (LD) Decay between Africans and Europeans …

This should be linkage disequilibrium, not linkage equilibrium.

 

Last sentence of abstract:

Finally, it is shown that PGS differences are more sensitive to the significance of GWAS loci than Fst,…

Better: Finally, it is shown that PGS differences are more sensitive than Fst to the significance of GWAS loci

Page 2, last sentence of first complete paragraph: …, which can inflate signals of selection due to co-variance between genes and the environment. Is this current or ancestral environment with which the genes covary?

Table 1: Are these coefficients from regression models with African as the omitted control? This should be mentioned.

Figure 6: I notice that EA polygenic scores for African American and Barbados are almost as low as those of the West African groups, although they have 20% - 25% European admixture. If this is not a fluke, it could mean that most of the admixture-related gains were eaten up by dysgenics. Perhaps something on these lines could be mentioned in the discussion.

Figure 15 is missing a proper heading.

Discussion: You find that European-African polygenic scores for educational attainment differ by more than 1.5 standard deviations. Some readers may find that strange because the actual difference between black and white Americans today is barely one standard deviation, and differences in educational attainment are even less. Such apparent discrepancies could possibly lead people to conclude that therefore there must be something wrong with the genetic results. Can you offer an explanation for this apparent inconsistency? What looks most obvious to me is that the polygenic scores include only the effects of common polymorphisms but not those of rare variants that are mostly subject to mutation-selection balance (aka “genetic garbage”). While polygenic scores reflect the cumulative effect of selection over more than 50,000 years, the genetic garbage is of more recent origin. If recent selection for educational attainment (last few centuries) was the same in different populations, the genetic garbage will be about the same. Therefore, the total genetic difference will be less, and possibly far less, than the 1.5 SD difference in polygenic scores. So, the large size of the PGS difference would indicate that genetic population differences originated through early selection rather than very recent selection.