Data from: DNA methylation site loss for plasticity-led novel trait genetic fixation

Phenotypic plasticity allows organisms to adapt traits in response to
environmental changes, yet the molecular basis by which such plastic
traits become genetically fixed remains unclear. Here, we investigated gut
length plasticity in medaka fish (Oryzias latipes) through genome-wide
methylation profiling, CRISPR/Cas9-mediated deletion, and population
genomic analyses. We found that seasonal methylation of CpG sites upstream
of the Plxnb3 is correlated with gut length plasticity, and deletion of
this region abolishes plasticity. Additionally, standing variation in
Ppp3r1 is associated with genetically fixed longer gut length in
populations lacking plasticity. These results suggest that loss of
epigenetic regulation via CpG site reduction triggers the genetic fixation
of novel traits. Our findings provide molecular evidence linking
epigenetic plasticity and genetic assimilation, advancing understanding of
plasticity-led evolution in natural populations.