Incomplete lineage sorting (ILS) and introgression/hybridization (IH) are prevalent in nature and thus frequently result in discrepancies within phylogenetic tree topologies, leading to misinterpretation of phylogenomic data. Despite the availability of numerous tools for detecting ILS and IH among species, many of these tools lack effective visualization, or are time-consuming, or require prior predetermination. Here, we addressed these shortcomings by developing a fast-running, user-friendly tool called Phytop. By defining ILS and IH indices to quantify ILS and IH, this tool can detect the extent of ILS and IH among lineages with high reliability, and can visualize them based on the gene tree topology patterns constructed using ASTRAL. We tested Phytop extensively using both simulated and real data, and found that it enables users to quickly and conveniently estimate the extent of ILS and IH, thus clarifying the phylogenetic uncertainty. Phytop is available at https://github.com/zhangrengang/phytop and is expected to contribute to the intuitive and convenient inference of genetic relationships among lineages in future research.

Sapium sebiferum (L.) Roxb. is an economically important tree in eastern Asia, and it exhibits many traits associated with good forestation species in coastal land. However, scarce research has been conducted to elucidate the effects of rhizosphere bacterial diversity on the adaptability and viability of S. sebiferum trees grown in the coastal environment. Field trials were conducted, and rhizosphere soil samples were collected from typical coastal and forestry nursery environments. Rhizosphere bacterial communities were evaluated using 16S rRNA pyrosequencing. A total of 43 bacterial phyla were detected in all the coastal and nursery rhizospheric soil samples. Relatively higher rhizosphere community diversity was found in coastal field-grown trees. Proteobacteria, Acidobacteriota, Bacteroidota, Chloroflex, and Gemmatimonadota were dominant bacterial phyla in rhizosphere communities of tallow trees. However, the rare groups in the coastal rhizosphere soils, with a relative abundance lower than 1%, including Latescibacterota, Methylomirabilota, NB1-j, and Nitrospirota, were largely absent in the nursery field-grown tree’s rhizosphere soils. LEfSe analysis identified a total of 43 bacterial groups that were more significantly abundant in the coastal rhizosphere environment than in that of forestry nursery grown trees. Further, our cladogram analysis identified Nitrospirota, Methylomirabilota, NB1-j, and Latescibacterota as biomarkers for the coastal environment at the phylum taxonomic level. These results suggested that the adaptability of S. sebiferum trees in coastal environment might be promoted by rhizosphere microbial interactions. Complex tree–microbe interactions might enhance the resistance of the trees to coastal environment, partially by recruiting certain bacterial microbiome species, which is of high saline-alkali resistance.

The study provides quantitative evidence refuting the traditional tripartite infraspecific classification of Cryptotaenia japonica complex (Apiaceae) in East Asia, whose taxonomic status is controversial because its leaf‑shape variation has historically been divided into three infraspecific forms (f. japonica, f. dissecta, f. pinnatisecta) based on qualitative assessments, and it is unclear if these forms represent discrete lineages or a continuous response to environmental gradients. The authors analyzed 1,061 leaf specimens from 72 East Asian populations and 9 North American C. canadensis samples using geometric morphometrics and fractal dimension analysis. Unsupervised multivariate approaches (PCA, hierarchical clustering, silhouette analysis) were applied to assess the intrinsic structure of the data without any a priori taxonomic assignment. The results revealed a continuous morphological gradient, with PCA capturing 68.63% of the total variance. The low Adjusted Rand Index (ARI = 0.088) statistically refuted the three‑form classification. Generalized additive modelling (GAM) identified a significant nonlinear relationship between leaf complexity (PC1) and altitude (adj. R²= 0.0559, P < 0.001), with an inflection point occurring at 850 m s.l.m. These findings demonstrate that the three traditional infraspecific forms are not discrete taxa, but rather arbitrary segments along a continuous altitudinal phenotypic cline. Multivariate analyses statistically reject the tripartite classification, leaf complexity increases non‑linearly with elevation (threshold ~850 m s.l.m), and the phenotypic contrasts between East Asian C. japonica and North American C. canadensis suggest divergent evolutionary strategies. Consequently, we propose reducing f. dissecta and f. pinnatisecta to synonyms under C. japonica, reflecting altitudinal morphological variation within a single, polymorphic taxon.

Introduction: The soils of subtropical forests are generally limited by P availability, and over time the P limitation experienced by the tree species becomes increasingly severe. The plasticity of leaf traits and the reprogramming of metabolites are strategies for plants to adapt to environmental stress, including P limitation. However, research that link the plasticity of leaf traits, gene regulation, and metabolism to reveal the adaptive survival mechanisms to P limitation is still relatively scarce. Methods: The structural and chemical traits, transcriptomics, and metabolomics of the leaves of an endemic species, Carpinus oblongifolia (Betulaceae), naturally growing in a P-limited subtropical forest of eastern China, were investigated. Results and Discussion: P limitation and pH was the predominant soil factor driving the variation in leaf traits of C. oblongifolia . The plasticity of leaf thickness (LT) was the core ecological strategy for this species to adapt to P-limited habitats and leaf thickening was closely related to the accumulation of secondary metabolites. Further, through integrated analysis of transcriptomics and metabolomics, the regulatory network involving four hub genes and five metabolites was constructed to mediate leaf thickening. The coordinated adaptation in leaf structure and metabolism achieves a balance between resource utilization efficiency and stress tolerance, which were the adaptive survival mechanisms of C. oblongifolia in P-limited subtropical forest ecosystems. This study has for the first time revealed the adaptive survival mechanisms of C. oblongifolia , providing a new perspective on ecological restoration, conservation planning, and genetic resource management of a species with small population under global climate change.

Glehnia littoralis, a critically endangered coastal plant endemic to sandy beach habitats, plays a unique role in the ecology of fragile coastal ecosystems. Its genome was characterized using an integrated approach combining flow cytometry, high-throughput sequencing, k-mer analysis, Smudgeplot, and cytogenetic validation. Flow cytometry estimated the genome size at ~2,913 Mb, while k-mer analysis under a diploid model (p = 2) revealed low heterozygosity (1.15%) and a high repeat content (80.87%), reflecting a relatively homogeneous yet highly repetitive genome shaped by historical whole-genome duplication events and transposon expansion. Smudgeplot patterns and cytogenetic analysis further confirmed the diploid status (2n = 22, x = 11) with a karyotype of 2n = 2x = 18m + 4sm (type 2A). These findings not only illuminate the evolutionary history and genomic architecture of this rare Apiaceae species but also offer critical insights into its adaptation to extreme coastal environments, providing valuable information for conservation strategies aimed at preserving this highly vulnerable, ecologically significant plant.