Conclusions
Through extensive phylogenetic analysis using genetic variants from transcriptomic data, combined with gene expression and functional traits measured in common garden experiments, we tested the hypothesis regarding differences in abiotic stress tolerance between octoploids and tetraploids, as well as the functional stability of hybrid populations in common reed. We conclude that octoploids are more tolerant to high-salinity environments than tetraploids. Evidence suggests that adaptive introgression has occurred, with adaptive genes being transferred from the octoploid lineage to the tetraploid lineage. However, the introgressed loci do not function stably in hybrid populations, likely due to local adaptations within the divergent hybrid populations or incompatible regulatory networks between the parental genomes.