Natural selection and recombination interact to structure genome-wide variation in pines

Genetic differentiation among populations often varies significantly across the genome due to factors such as selection and recombination, resulting in a heterogeneous genomic landscape. However, variation in low-differentiation regions-genomic valleys-remains poorly understood. Moreover, most insights into plant genomic landscapes come from flowering plants, while comparable genome-wide studies in other taxa, such as conifers, remain limited. We analyzed whole-genome sequencing data from 100 individuals of three pine species-Pinus banksiana, Pinus contorta, and Pinus nigra. We found substantial genome-wide variation in recombination rates, with intergenic regions exhibiting higher recombination than genic regions, and rates decreasing with increasing distance from genes. Recombination rate was negatively correlated with gene length, driven primarily by intron length, suggesting that long introns in conifers may promote the retention of exceptionally long genes by maintaining low recombination in these regions. Genomic scans further revealed that genomic valleys are maintained through either balancing, background, or parallel selection. Additionally, multiple forms of selection were strongly associated with local recombination rate variation, highlighting the significant role of recombination in shaping patterns of genomic differentiation. Our findings provide new insight into the evolution and maintenance of extremely long genes in conifers. Moreover, the results indicate that allopatric selection in regions of low recombination is a major force structuring genomic variation in these species.