Causal inference clarifies the roles of background selection and mutation rate variation in shaping human genetic diversity

Decades of theoretical and empirical work have struggled to reconcile competing views on how evolution shapes patterns of genetic variation. We now understand the genome as a mosaic molded by both neutral and selective forces, but quantifying their relative contributions remains an open challenge. A major obstacle has been the tendency to analyze each evolutionary process in isolation. But different processes may leave similar signatures on genetic variation, making it challenging to draw conclusions from correlations alone. To address this gap, we make predictions of the landscape of diversity based on background selection and mutation rate variation. We then develop structural equation models describing how mutation, recombination and selection jointly shape the genomic landscape of diversity. This approach offers a more realistic representation of biological interactions and enables rigorous evaluation of hypothesized causal structures, marking both conceptual and practical improvements over previous studies. Analyses of human data reveal large variation in the explanatory power of candidate models across chromosomes. We find that previous studies likely overestimated the predictive accuracy of background selection; although it emerges as the overall main driver of diversity, in some chromosomes mutation rate variation has a comparable impact. We also show that recombination increases diversity more strongly through its influence on background selection than through its mutagenic effect, resolving a longstanding debate. This work demonstrates that modeling variation inherent in genome biology substantially improves our ability to explain human genetic diversity. At the same time, evidence for unmodeled covariance between mutation rates and density of constrained sites reinvigorates an ongoing discussion about the evolution of the mutation landscape, although additional work is needed to determine its origins.