Phylogenetic History and Adaptation Mechanisms of <scp> <i>Casuarina equisetifolia</i> </scp> Landraces in China

Following its introduction to China, <i>Casuarina equisetifolia</i> rapidly adapted to its new habitat and was extensively cultivated as a crucial tree species for coastal shelterbelts. However, the systematic classification of Chinese landraces remains controversial and the mechanism underlying the rapid adaptation of this species in China remains unknown. To understand more fully the phylogenetic history and adaptation mechanisms of <i>C. equisetifolia</i>, 66 samples were collected from Chinese landraces and five from other potentially related provenances. Single nucleotide polymorphisms were detected through genotyping by sequencing and used for genetic structural analysis and genome comparison. The genetic structures of Chinese landraces were largely consistent with that of <i>C. equisetifolia</i> in natural and other distributions, while 76.7% of individuals showed clear admixture with <i>Casuarina glauca</i>, indicating frequent spontaneous interspecific introgression or hybridization. Phylogenetic and gene flow analyses further support a distinct local origin involving unique parental combinations. Genomic variation associated with pathogen-plant interactions was observed between natural provenances and founder populations along migration pathways. Moreover, integrated genomic signals were identified in hybrids, including secondary metabolite synthesis derived from <i>C. glauca</i>, as well as growth regulation and metabolic processes inherited from <i>C. equisetifolia</i>, offering preliminary insights into adaptive mechanisms during the introduction process. These findings enhance our understanding of the phylogenetic history of <i>Casuarina</i> landraces in China and may contribute to improved efficiency in domestication and breeding programs.