Ecological factors influence balancing selection on leaf chemical profiles of a wildflower

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Balancing selection is frequently invoked as a mechanism that maintains variation within and across populations. However, there are few examples of balancing selection operating on loci underpinning complex traits, which frequently display high levels of variation. We investigated mechanisms that may maintain variation in a focal polymorphism—leaf chemical profiles of a perennial wildflower (Boechera stricta, Brassicaceae)—explicitly interrogating multiple ecological and genetic processes including spatial variation in selection, antagonistic pleiotropy and frequency-dependent selection. A suite of common garden and greenhouse experiments showed that the alleles underlying variation in chemical profile have contrasting fitness effects across environments, implicating two ecological drivers of selection on chemical profile: herbivory and drought. Phenotype–environment associations and molecular genetic analyses revealed additional evidence of past selection by these drivers. Together, these data are consistent with balancing selection on chemical profile, probably caused by pleiotropic effects of secondary chemical biosynthesis genes on herbivore defence and drought response.


Data availability

The new reference genome assemblies and raw Nanopore reads for the SAD12 and LTM genotypes have been submitted to NCBI (BioProject number PRJNA609209). The short reads of the GBS data for the CFR-NIL families have been submitted to NCBI (BioProject number PRJNA659863). Previously published genomic data are archived with ref. 55. All other data reported in this manuscript are archived in the Dryad digital data repository ( All biological materials are available from the Arabidopsis Biological Resource Center (ABRC) or from the authors.

Code availability

The code used for this manuscript is archived in the Dryad digital repository (