Scientist Steve Hsu writes:

GCTA (Genome-wide Complex Trait Analysis)…allows an estimation of heritability due to common SNPs using relatively small sample sizes (e.g., a few thousand genotype-phenotype pairs). The new method is independent of, but delivers results consistent with, “classical” methods such as twin and adoption studies. To oversimplify, it examines pairs of unrelated individuals and computes the correlation between pairwise phenotype similarity and genotype similarity (relatedness). It has been applied to height,intelligence, and many medical and psychiatric conditions.

Apparently this technique has been used to show that (fluid) IQ has a narrow sense of heritability of at least 51%.  Not quite the 80% heritability found in twin studies but keep in mind, the latter measures broad sense heritability.

Of course as commenter chartreuse has noted, all of these studies are based on local populations so they don’t prove that high IQ folks are truly genetically smarter than low IQ folks; rather they may only show that high IQ folks have genes that are compatible with a specific environment.  If their genes were planted in a different time and place,  low IQ people might have higher IQs than high IQ people.

In order to show independent genetic effects (geneotypes that are smarter in virtually every environment), charteruse feels you would need a study of people, preferably of similar genetic background, living in different countries.  He recomends a sample taken from the entire developed World.

On the other hand, I would recommend doing a study comparing unmixed African Americans (whose ancestors had been in the United States for centuries) with unmixed West Africans living in the same part of West Africa.  Despite having the same genetic background, the latter score much lower on IQ tests than the former, presumably because of the extreme deprivation of the Third World compared to the First World.

If you had a 1000 pairs of such unrelated individuals (with one member of each pair being an unmixed African American, and the other being a West African) and you found a high correlation between IQ similarity and genetic similarity among coethnics living in such radically different environments, then this should be convincing evidence of independent genetic effects on IQ