Wednesday, September 25, 2019

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.


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.


Frost, P. (2015a). The Jews of West Africa? Evo and Proud, July 4 

Frost, P. (2015b). No, blacks aren't all alike. Who said they were? Evo and Proud. October 10. 

Frost, P. (2019). IQ of biracial children and adults. Evo and Proud. March 10.

Lasker, J., B.J. Pesta, J.G.R. Fuerst, and E.O.W. Kirkegaard. (2019). Global ancestry and cognitive ability. Psych 1(1) 

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  

Rockquemore, K.A. and D.L. Brunsma. (2008). Beyond Black. Biracial Identity in America. Lanham: Rowman & Littlefield Publishers.

Wikipedia. (2019). Igbo Americans


Sid said...

Direct evidence for genetic differences in intelligence is emerging. As time passes and African genetics are better explored, I expect the direct evidence will become ever more incontrovertible.

Thing is, James Flynn, the best challenger of IQ hereditarianism of all time, can't even get a book about free speech published in the UK. Even he! The new evidence will be harder to contradict, but can be ignored.

Peter Frost said...

He probably could get it published. At the very least, it would be an interesting test case, and the publisher should have the gonadic fortitude to push ahead. I suspect the publisher has come under pressure from individuals or groups behind the scenes. That's the real reason.

It's a bit of a surprise that James Flynn should be targeted for this special treatment. He's an anti-hereditarian!

Dietz said...

We need more studies of this type. I have always suspected that the contribution of genes to IQ is not race-linear, but rather "threshold" in nature. Like yeast in bread. People should be tested over time to watch how cognition changes.

Anonymous said...

Would be interesting to conduct the same tests on similar reference populations within the UK; that country carries similar results with functionally no difference in IQ test scores between white and biracial populations as well:

Santo said...

Just follow humankind macro-evolutionary path. Seems, aboriginals [more genetically distant] would have a more differentiated cognitive archicteture, i wonder.

Peter Frost said...


That was the purpose of the Minnesota Transracial Adoption Study. Cognitive ability seems to be more malleable when we're young, so it's possible to boost it at younger ages. Unfortunately, that improvement tends to wash out over time.


The problem is that people of self-identified "mixed" ancestry tend to be more European than African. In the Philadelphia study, self-identified "biracials" were 80% European. There also seems to be a middle-class bias: people of mixed background are more likely to acknowledge their mixed background if they're middle class. Otherwise, they call themselves "black."


The deepest genetic split is between Africans and non-Africans. Of course, the most important factor is natural selection (or rather differences in natural selection). Two population can be separated from each other for a long time and still be remarkably similar.

Mike-SMO said...

Way late to the party and it is way late almost to dawn.

There is anecdotal evidence that the Afro-American population is "bimodal", i.e. coming from two distinct sub-populations due to selection. One group are "kidnap victims" the other are "culls" who lost their freedom due to debt, incompetence, and/or criminal behavior in West Africa.

Individuals could "loose their freedom" due to bad luck or common error (e.g. crop choice) but do well with their "asigned" family/clan and then remain in a life-long position. Those who were lazy, dim and/or criminal would be more likely to end as part of a trade with Arab or European slave traders wherethhey were exchanged for merchandise or cash. The export slave population would include some portion of "typicals" who were kidnapped but would be "enriched" in culls who were lazy, dim and/or criminal and uncooperative.

There does not seem to be an obvious way to differentiate the descendents of the typicals and the culls in the founder population in the Western Hemisphere, but the typicals in the Afro-American population may amount to as few as 30% as guesstimated from the low crime portion of the Afro-American population that remained in Compton (California) after the violent Hispanic gang purge of the criminal, Black gang members and their families.

It maybe worth noting that the "woke" Afro-American students at Cornell University, several years ago, were well aware of the different success rates of Immigrant African students compared to those of domestic Afro-American students. This difference was attributed to the Afro-American experience of "slavery" without any consideration of the different selection process involved for the two groups.

The possible existance of two sub-populations of African descendents in the Western hemisphere might complicate the interpretation of genetic and IQ findings.