A two-step adaptive walk rewires nutrient transport in a challenging edaphic environment

Most well-characterized cases of adaptation involve single genetic loci. Theory suggests that multilocus adaptive walks should be common, but these are challenging to identify in natural populations. Here, we combine trait mapping with population genetic modeling to show that a two-step process rewired nutrient homeostasis in a population of Arabidopsis as it colonized the base of an active stratovolcano characterized by extremely low soil manganese (Mn). First, a variant that disrupted the primary iron (Fe) uptake transporter gene (IRT1) swept quickly to fixation in a hard selective sweep, increasing Mn but limiting Fe in the leaves. Second, multiple independent tandem duplications occurred at NRAMP1 and together rose to near fixation in the island population, compensating the loss of IRT1 by improving Fe homeostasis. This study provides a clear case of a multilocus adaptive walk and reveals how genetic variants reshaped a phenotype and spread over space and time.

Automated summary

This study demonstrates a two-step evolutionary process in which nutrient homeostasis was rewired to adapt to extremely low soil manganese conditions. A variant disrupting the iron uptake transporter gene quickly became fixed in the population, increasing manganese but limiting iron in the leaves. Multiple independent gene duplications then compensated for the loss of the iron transporter gene, improving iron homeostasis. This research provides a clear example of a multilocus adaptive walk and sheds light on how genetic variants reshape phenotypes and spread over space and time.