investigation of ecotype divergence in Pinus sylvestris vat mongolica
Understanding how ecotypic divergence persists under extensive gene flow is critical for predicting adaptive responses in long-lived conifers. Mongolian Scots pine (Pinus sylvestris var. mongolica) occupies contrasting mountain and sandy-dune habitats in northeastern China, forming two ecotypes with distinct environmental adaptations. Using reference-free SLAF-seq data and genome-wide SNPs, we explored patterns of genomic differentiation and genotype–environment associations to determine whether adaptive divergence is driven by few large-effect loci or polygenic shifts. Despite minimal neutral genetic structure, we identified ~3% of the genome as adaptive outliers with strong between-ecotype differentiation. These loci exhibited significant environmental associations, with LFMM z-scores concentrated in the extreme tail (|z| >3), indicating that both adaptive genomic islands and polygenic shifts are dominated by large-effect variants rather than minor-effect alleles. Furthermore, phenotypic differentiation between ecotypes reflected a dual mechanism: adaptive genetic divergence shaping hydraulic traits and mechanical support, and genotype-by-environment (G×E) interactions enabling phenotypic plasticity in physiological responses, such as water-use efficiency and stress tolerance. This interplay between hard genetic adaptation and plasticity highlights how conifers 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 conifers with high gene flow and demonstrates a novel reference-free approach for dissecting adaptive architectures in non-model genomes.