Genetic analyses indicate that Pinus densata is a natural homoploid hybrid originating from Pinus tabuliformis and Pinus yunnanensis. Needle morphological and anatomical features show relative species stability and can be used to identify coniferous species. Comparative analyses of these needle characteristics and phenotypic differences between the artificial hybrids, P. densata, and parental species can be used to determine the genetic and phenotypic evolutionary consequences of natural hybridization. Twelve artificial hybrid families, the two parental species, and P. densata were seeded in a high‐altitude habitat in Linzhi, Tibet. The needles of artificial hybrids and the three pine species were collected, and 24 needle morphological and anatomical traits were analyzed. Based on these results, variations in 10 needle traits among artificial hybrid families and 22 traits among species and artificial hybrids were predicted and found to be under moderate genetic control. Nineteen needle traits in artificial hybrids were similar to those in P. densata and between the two parental species, P. tabuliformis and P. yunnanensis. The ratio of plants with three needle clusters in artificial hybrids was 22.92%, which was very similar to P. densata. The eight needle traits (needle length, the mean number of stomata in sections 2 mm in length of the convex and flat sides of the needle, mean stomatal density, mesophyll/vascular bundle area ratio, mesophyll/resin canal area ratio, mesophyll/(resin canals and vascular bundles) area ratio, vascular bundle/resin canal area ratio) relative to physiological adaptability were similar to the artificial hybrids and P. densata. The similar needle features between the artificial hybrids and P. densata could be used to verify the homoploid hybrid origin of P. densata and helps to better understand of the hybridization roles in adaptation and speciation in plants.

The Tabebuia alliance is widely planted in tropical and subtropical countries. However, the lack of accurate taxonomic information for many commercial cultivars leads to commercial disputes. We sought to clarify the background of commercial cultivars in China and to provide a robust basis for patent protection. We collected 82 Tabebuia cultivars and 12 reference individuals, then developed large-scale single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing. We obtained 73,219 SNPs from the test samples, which represented a substantial increase compared with previous studies of Tabebuia species. Based on these SNPs and a clustering analysis, we detected six species among the samples, as well as an uncertain population which may be a hybrid between Handroanthus impetiginosus (Mart. ex DC) Mattos and H. heptaphyllus (Vell.) Mattos. An analysis of genetic diversity to assess germplasm resources indicated that excessive heterozygosity of these cultivars in China, which may explain the genetic basis of “novel-preferred” selection in ornamental plants or a narrow genetic background. After rigorous selection, we identified numerous high-quality molecular markers for cultivar identification, then constructed a concise fingerprint with 54 SNPs. Our work clarifies the background information of commercial cultivars of Tabebuia in China and provides information for cultivar identification. It will serve as an important technical resource for genetic studies, and it will help to protect patents that involve Tabebuia species.

Following its introduction to China, Casuarina equisetifolia 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 C. equisetifolia , 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 C. equisetifolia in natural and other distributions, while 76.7% of individuals showed clear admixture with Casuarina glauca , 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 C. glauca , as well as growth regulation and metabolic processes inherited from C. equisetifolia , offering preliminary insights into adaptive mechanisms during the introduction process. These findings enhance our understanding of the phylogenetic history of Casuarina landraces in China and may contribute to improved efficiency in domestication and breeding programs.

Following its introduction to China, Casuarina equisetifolia 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 C. equisetifolia, 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 the Chinese landrace samples were found to be similar or equivalent to those of C. equisetifolia from Southeast Asia; however, admixed structures between C. equisetifolia and Casuarina glauca were also identified, suggesting that spontaneous and frequent interspecific introgression or hybridization had occurred among the Chinese landraces. Genomic variation associated with pathogen–plant interactions was detected between natural provenances and Chinese founder populations along migration pathways. Furthermore, integrated signals were detected in hybrids, including secondary metabolite synthesis from C. glauca, as well as growth regulation and metabolic processes from C. equisetifolia, providing preliminary insights into adaptive mechanisms during the introduction process. These findings improve our knowledge of the phylogenetic history of Casuarina landraces in China, and may enhance the efficiency of domestication and breeding programs.