Differences in the genetic architecture of cognition?

Tableau III, Piet Mondrian (1872-1944). The polygenic score can provide a measure of innate cognitive ability in various human populations. However, it is less valid for African Americans, apparently because of differences in the genetic architecture of cognition.



When IQ is measured in European Americans and African Americans, the two groups differ on average by about 15 points. Is the difference genetic? Or is it due to different environments?

After years of debate, we are coming close to an answer. The weight of evidence is shifting, especially because of two unrelated developments: 

- We can now easily measure ethnic ancestry by means of genetic data. Previously, we had to rely on self-report or indirect measures like skin color.

- We can now measure the genetic component of cognitive ability: the polygenic score. This score is a summation of alleles associated with high educational attainment. Initially a crude measure, it is getting better and better as we identify more and more of these alleles.

Both research tools were used in a recent study. Lasker et al. (2019) applied them to the Philadelphia Neurodevelopmental Cohort, a sample of 9421 individuals from the Philadelphia area who received medical care from the Children's Hospital of Philadelphia network. They ranged in age from 8 to 21 with a mean of 14.2. They were 51.7% female, 55.8% European American, 32.9% African American, and 11.4% other. All of them were genotyped and given a series of cognitive tests.

This dataset had advantages over those of previous studies:

- All participants came from the same geographic area. 

- Heritabilities of cognitive ability were already estimated by another research team, specifically 0.61 for the African American participants and 0.72 for the European American participants.

- Skin, hair, and eye color could be estimated from the genetic data to control for the effects of "colorism" (discrimination favoring lighter-skinned over darker-skinned African Americans)

- Polygenic scores could be calculated from the genetic data

The main disadvantage was the participants’ young age. Before adulthood the brain is plastic and still developing, so the heritability of cognitive ability is lower. 


IQ results

IQ scores were 100 for European Americans, 98 for self-described biracial Americans, and 85 for African Americans. The three groups were respectively 99% European, 80% European, and 19% European.

African Americans only

European admixture significantly correlated with IQ among the African American participants. The correlation remained significant after controlling for either skin color or socioeconomic status. Interestingly, skin and hair color didn't significantly correlate with IQ independently of European admixture, but eye color did. Brown eyes correlated positively with IQ. No explanation was offered by the authors. Did they get the same finding with European Americans?

Biracial Americans only - smarter than expected

As with African Americans, skin color didn't seem to influence intelligence independently of European admixture. On the other hand, "biracial status had a significant effect independently of European ancestry." In other words, racially mixed individuals who identified equally as African American and European American, and not just as African American, tended to be more intelligent than what their degree of European admixture would predict. 

The term "biracial" as a badge of identity is recent and seems to be most popular among middle-class people: 

Interestingly, many of the respondents here who identify as biracial are middle class, educated in private schools, and raised in predominantly white neighborhoods with mostly white social networks (Rockquemore and Brunsma 2008, p. xxii)

It may be, then, that self-identified "biracial" people have parents who are, on average, of higher quality than other people of the same racial background.

African Americans, Biracial Americans, and European Americans combined

When all three groups were combined, the most important factor was European admixture. Next came socioeconomic status, which correlated with cognitive ability independently of European admixture. Finally, self-identification as a European American had an effect over and above that of European admixture. The last factor suggests that European American culture has a positive influence on cognitive ability.


Polygenic score results

The polygenic scores ran into a problem that others have noted: the genetic architecture of cognition seems to be different in African Americans. This is a problem because researchers have used only Europeans or European Americans to identify genetic variants that are associated with high educational attainment. Those variants did correlate with cognitive ability in the African American sample, but to a much lower degree than in the European American sample. Their validity as a measure of cognitive ability was only 20% of what it was in the European American sample.

The authors used a subset of the same variants to create a polygenic score that would be less sensitive to linkage disequilibrium decay and thus more valid across different human populations. This polygenic score had good validity in both the African- and European-American samples (r = 0.112 and r = 0.227 respectively).

The authors then tried to create an even better polygenic score by excluding variants that are rare in African Americans. There was no effect on the results for either African Americans or European Americans. But what about the reverse? Perhaps cognitive ability is improved by some variants that are rare in European Americans but common in African Americans.


Conclusion

This is an excellent study, on a par with the Minnesota Transracial Adoption Study (Frost 2019). The main problem is the participants’ young age. Had adults been used, there would have been less noise in the data, and the results would have been better.

Another problem is the apparently different genetic architecture of cognition in people of sub-Saharan African origin. Piffer (2019) has noted that polygenic scores underestimate African American IQ. He disagrees, however, with the "different genetic architecture" hypothesis, pointing out that no divergence exists between mean population IQ and the polygenic scores he has calculated for various sub-Saharan African groups (Esan, Gambians, Luhya, Mende, Yoruba). None of them, however, are Igbo, and the Igbo are really the one group that stands out from other West Africans on measures of intellectual and educational attainment (Frost 2015a, 2015b). They also contributed to the gene pool of African Americans: "Many of the enslaved Igbo people in the United States were concentrated in Virginia's lower Tidewater region and at some points in the 18th century they constituted over 30% of the enslaved black population" (Wikipedia 2019).

While the polygenic score is a good measure of raw cognitive ability in most humans, we need to develop a modified version for people whose ancestry comes primarily from sub-Saharan Africa.


References

Frost, P. (2015a). The Jews of West Africa? Evo and Proud, July 4
http://evoandproud.blogspot.ca/2015/07/the-jews-of-west-africa.html 

Frost, P. (2015b). No, blacks aren't all alike. Who said they were? Evo and Proud. October 10.
http://evoandproud.blogspot.com/2015/10/no-blacks-arent-all-alike-who-said-they.html 

Frost, P. (2019). IQ of biracial children and adults. Evo and Proud. March 10.
http://evoandproud.blogspot.com/2019/03/iq-of-biracial-children-and-adults.html

Lasker, J., B.J. Pesta, J.G.R. Fuerst, and E.O.W. Kirkegaard. (2019). Global ancestry and cognitive ability. Psych 1(1)
https://www.mdpi.com/2624-8611/1/1/34 

Piffer, D. (2019). Evidence for Recent Polygenic Selection on Educational Attainment and Intelligence Inferred from Gwas Hits: A Replication of Previous Findings Using Recent Data. Psych 1(1): 55-75
https://www.mdpi.com/2624-8611/1/1/5  

Rockquemore, K.A. and D.L. Brunsma. (2008). Beyond Black. Biracial Identity in America. Lanham: Rowman & Littlefield Publishers.
https://books.google.ca/books?id=Nf0eAAAAQBAJ&printsec=frontcover&hl=fr&source=gbs_ge_summary_r&cad=0#v=onepage&q&f=false

Wikipedia. (2019). Igbo Americans. 
https://en.wikipedia.org/wiki/Igbo_Americans