Widespread natural selection on metabolite levels in humans

Natural selection acts ubiquitously on complex human traits, predominantly constraining the occurrence of extreme phenotypes (stabilizing selection). These constraints propagate to DNA sequence variants associated with traits under selection. The genetic imprints of such evolutionary events can thus be detected via combining effect size estimates from genetic association studies and the corresponding allele frequencies. While this approach has been successfully applied to high-level traits, the prevalence and mode of selection acting on molecular traits remains poorly understood. Here, we estimate the action of natural selection on genetic variants associated with metabolite levels, an important layer of molecular traits. By leveraging summary statistics of published genome-wide association studies with large sample sizes, we find strong evidence of stabilizing selection for 15 out of 97 plasma metabolites. Mendelian randomization analysis revealed that metabolites under stronger stabilizing selection display larger effects on a range of clinically relevant complex traits, suggesting that maintaining a disease-free profile may be an important source of selective constraints on the metabolome. Metabolites under strong stabilizing selection in humans are also more conserved in their concentrations among diverse mammalian species, suggesting shared selective forces across micro and macroevolutionary time scales. Finally, we also found evidence for both disruptive and directional selection on specific lipid metabolites, potentially indicating ongoing evolutionary adaptation in humans. Overall, this study demonstrates that variation in metabolite levels among humans is frequently shaped by natural selection and this may act through their causal impact on disease susceptibility.