Fungal incipient local adaptation through allelic and copy-number variation

Human-altered environments can shape the evolution of organisms. Fungi are no exception,
though little is known about how they withstand anthropogenic pollution. Here, we document
incipient polygenic local adaptation in the mycorrhizal fungus Suillus luteus driven by recent soil
heavy metal contamination. Genome scans across individuals from recently polluted and nearby
unpolluted soils in Belgium revealed no evidence of population structure but detected allelic
divergence and gene copy number variation in genes involved in metal exclusion, storage,
immobilization, and reactive oxygen species detoxification. Standing genetic variation included
multiple alleles of small effects contributing to heavy metal tolerance, suggesting the existence
of different strategies to withstand contamination. These variants were shared across the whole
population but under selection in isolates exposed to pollution. Together, our results point to S.
luteus undergoing the initial steps of adaptive divergence and contribute to understanding the
processes underlying local adaptation under strong environmental selection.