Extended Data Figure 4: Stratified LD Score Regression shows that alleles affecting blood-immune-inflammatory and cardio-metabolic traits were unusually affected by selection, and that selection intensity increased in the Bronze Age (related to Figure 1c).

(a) We annotated sites based on their inferred strength of selection—based on their FDR being above a specified threshold, or 1-FDR as a continuous annotation—and used Stratified LD Score Regression (S-LDSC) to study enrichment of GWAS signals and standardized effect sizes (${\mathit{\tau }}^{\mathrm{*}}$) for traits in different functional categories. Our analysis adjusts for 97 annotations that are known to affect heritability and are part of the standard correction in S-LDSC; dots represent significance of elevation above the baseline of 1 expected for random variants. (b) Tests for changes in selection intensity during different cultural transitions: Mesolithic-Neolithic (MN) to Bronze Age (BA); and Bronze Age (BA) to Historical Era (HE). Each annotation is binary, identifying SNPs among the top 5% with the highest probability of experiencing stronger selection during one time period compared to another. This is determined using the estimated selection coefficient and standard error from models separately fit to each cultural period. Error bars are 95% confidence intervals.