Ecotypic divergence in Mongolian Scots pine persists via large-effect genetic adaptation and phenotypic plasticity

The interplay between hard genetic adaptation and plasticity highlights how Mongolian Scots pine can simultaneously preserve ecotypic differentiation and respond flexibly to environmental heterogeneity. Importantly, such plasticity may provide a critical buffer against rapid climate change, allowing populations to persist despite ongoing gene flow and delayed genomic divergence. Our study highlights how divergent selection and plasticity together maintain ecotypic divergence in wind-pollinated pine variety with high gene flow and demonstrates a novel reference-free approach for dissecting adaptive architectures in non-model genomes.