Justin’s Notes

The Same Polygenic Scores That Prove Rapid Selection Warn Against Reading Group Differences

2026-07-21 · AI-generated insight

Put these two notes side by side and they lean on the same instrument while pulling it in opposite directions.

The ancient DNA paper offers Warne something he wants: proof that trait-relevant allele frequencies can shift fast. Over just ten millennia, hundreds of alleles underwent strong directional selection in West Eurasians, producing standard-deviation-scale changes in the polygenic predictors of complex traits—including, the authors note, increases in "measures of cognitive performance." That establishes the biological plausibility Warne needs: selection acting on standing variation can, in principle, move populations apart on polygenic traits within evolutionary eyeblinks. It undercuts any claim that group-level genetic differences in a polygenic trait are impossible on timescales this short.

But the same paper carries a caveat that lands squarely on Warne's fourth line of evidence—polygenic scores applied to diverse samples. Reich and colleagues are careful: these effects "were measured in industrialized societies, and it remains unclear how these relate to phenotypes that were adaptive in the past." The score is not the trait; it is a correlational shadow calibrated in one environment, whose meaning outside that environment is genuinely uncertain. That is precisely the portability problem that makes cross-group polygenic comparison treacherous. GWAS effect sizes are estimated within a population and confounded with its structure; carrying them across populations or across environments is the contested move, not a settled one.

So the geneticists whose method most vividly demonstrates that populations can diverge under selection are also the ones flagging why the polygenic-score readout can't be taken at face value across contexts. Warne's admixture and Spearman's-hypothesis arguments don't depend on this, but his genomic line does—and the ancient DNA authors, working the same data with far larger samples, treat the industrialized-society calibration as a live limitation rather than a footnote.

The honest synthesis: mechanism is plausible, measurement is not yet trustworthy. The tool that best shows selection is real is the same tool that isn't ready to tell us where any given group sits.

Woven from these notes

Ancient DNA has transformed our understanding of population history, but its potential to reveal as much about human evolutionary biology has not been realized because of limited sample sizes and the difficulty of distinguishing sustained rises in allele frequency increasing fitness—directional selection—from shifts due to migrations, population structure, or non-adaptive purifying or stabilizing selection. Here we present a method for detecting directional selection in ancient DNA time-series data that tests for consistent trends in allele frequency change over time, and apply it to 15,836 West Eurasians (10,016 with new data). Previous work has shown that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution8,9. By contrast, in the past ten millennia, we find that many hundreds of alleles have been affected by strong directional selection. We also document one-standard-deviation changes on the scale of modern variation in combinations of alleles that today predict complex traits. This includes decreases in predicted body fat and schizophrenia, and increases in measures of cognitive performance. These effects were measured in industrialized societies, and it remains unclear how these relate to phenotypes that were adaptive in the past. We estimate selection coefficients at 9.7 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.
Ancient DNA reveals pervasive directional selection across West Eurasia
The past 30 years of research in intelligence has produced a wealth of knowledge about the causes and consequences of differences in intelligence between individuals, and today mainstream opinion is that individual differences in intelligence are caused by both genetic and environmental influences. Much more contentious is the discussion over the cause of mean intelligence differences between racial or ethnic groups. In contrast to the general consensus that interindividual differences are both genetic and environmental in origin, some claim that mean intelligence differences between racial groups are completely environmental in origin, whereas others postulate a mix of genetic and environmental causes. In this article I discuss 5 lines of research that provide evidence that mean differences in intelligence between racial and ethnic groups are partially genetic. These lines of evidence are findings in support of Spearman’s hypothesis, consistent results from tests of measurement invariance across American racial groups, the mathematical relationship that exists for between-group and within-group sources of heritability, genomic data derived from genome-wide association studies of intelligence and polygenic scores applied to diverse samples, and admixture studies. I also discuss future potential lines of evidence regarding the causes of average group differences across racial groups. However, the data are not fully conclusive, and the exact degree to which genes influence intergroup mean differences in intelligence is not known. This discussion applies only to native English speakers born in the United States and not necessarily to any other human populations.
— Russell Warne Between-Group Mean Differences in Intelligence in the United States Are >0% Genetically Caused: Five Converging Lines of Evidence