Plant Diversity最新文献

Hybridization and polyploidy are key drivers of species diversity and genome variation in Lycoris, but their cytological and evolutionary consequences remain poorly understood. Here, we investigated chromosome numbers and genome sizes in 64 accessions representing the morphological diversity across the genus. Chromosome numbers ranged from 12 to 33, with seven accessions newly identified, including L. chunxiaoensis (2n = 33), two putative L. guangxiensis (2n = 19), and five natural hybrids (2n = 16, 18, 29, 33). Genome sizes varied from 18.03 Gb (L. wulingensis) to 32.62 Gb (L. caldwellii). Although no significant correlation was found between genome size and chromosome number across all accessions, a strong correlation within ploidy-level groups (i.e., diploid or aneuploid) suggested roles for post-polyploid diploidization, aneuploidy, and dysploidy in speciation. Phylogenetic analyses based on chloroplast genomes and nuclear DNA sequences revealed significant discordance, indicating a complex reticulate evolution and historical hybridization, which may complicate morphological classification. Chromosome number aligned more closely with morphological groups, underscoring the necessity of integrating cytological, molecular, and morphological data for accurate taxonomy, particularly in large-genome taxa. Based on this evidence, we propose a putative speciation pathway involving multiple hybridization and polyploidization events, with allopolyploidy playing a predominant role. Furthermore, our results indicate that the species L. insularis and L. longifolia are geographic populations of L. sprengeri and L. aurea, respectively, and confirmed the distribution of L. traubii and L. albiflora in mainland China. These findings offer new insights into the mechanisms underlying speciation, interspecific relationships, and the evolutionary history of Lycoris.

Preserving genetic diversity is crucial for the long-term survival of wild plant species, yet many remain at risk of genetic erosion due to small population sizes and habitat fragmentation. Here, we present a comparative genomic study of the critically endangered Oreocharis esquirolii (Gesneriaceae) and its widespread congener O. maximowiczii. We assembled and annotated chromosome-level reference genomes for both species and generated whole-genome resequencing data from 28 O. esquirolii and 79 O. maximowiczii individuals. Our analyses reveal substantially lower genetic diversity and higher inbreeding in O. esquirolii, despite its overall reduced mutational burden. Notably, O. esquirolii exhibits an elevated proportion of strongly deleterious mutations relative to O. maximowiczii, suggesting that limited opportunities for purging have allowed these variants to accumulate. These contrasting genomic profiles likely reflect divergent demographic histories, with O. esquirolii having experienced severe bottlenecks and protracted population decline. Collectively, our findings highlight the critically endangered status of O. esquirolii, characterized by diminished genetic diversity, pronounced inbreeding, and reduced ability to eliminate deleterious alleles. This study provides valuable genomic resources for the Gesneriaceae family and underscores the urgent need for targeted conservation measures, including habitat protection and ex situ preservation efforts, to mitigate the extinction risk facing O. esquirolii and potentially other threatened congeners.

The ecological and evolutionary mechanisms underlying montane biodiversity patterns remain unresolved. To understand which factors determined community assembly rules in mountains, biogeographic affinity that represents the biogeographic and evolutionary history of species should incorporate with current environments. We aim to address two following questions: 1) How does plant taxonomic and phylogenetic diversity with disparate biogeographic affinities vary along the subtropical elevational gradient? 2) How do biogeographic affinity and environmental drivers regulate the community assembly? We collected woody plant survey data of 32 forest plots in a subtropical mountain of Mt. Guanshan with typical transitional characteristics, including 250 woody plant species belonging to 56 families and 118 genera. We estimated the effects of biogeographic affinity, climate and soil properties on taxonomic and phylogenetic diversity of plant communities employing linear regression and structural equation models. We found that the richness of temperate-affiliated species increased with elevations, but the evenness decreased, while tropical-affiliated species had no significant patterns. Winter temperature directly or indirectly via biogeographic affinity shaped the assemblage of woody plant communities along elevations. Biogeographic affinity affected what kind of species could colonize higher elevations while local environment determined their fitness to adapt. These results suggest that biogeographic affinity and local environment jointly lead to the dominance of temperate-affiliated species at higher elevations and shape the diversity of woody plant communities along elevational gradients. Our findings highlight the legacy effect of biogeographic affinity on the composition and structure of subtropical montane forests.

Comparative analyses in ecology and evolution often face the challenge of controlling for the effects of shared ancestry (phylogeny) from those of ecological or trait-based predictors on species traits. Phylogenetic Generalized Linear Models (PGLMs) address this issue by integrating phylogenetic relationships into statistical models. However, accurately partitioning explained variance among correlated predictors remains challenging. The phylolm.hp R package tackles this problem by extending the concept of "average shared variance" to PGLMs, enabling nuanced quantification of the relative importance of phylogeny and other predictors. The package calculates individual likelihood-based R² contributions of phylogeny and each predictor, accounting for both unique and shared explained variance. This approach overcomes limitations of traditional partial R² methods, which often fail to sum the total R² due to multicollinearity. We demonstrate the functionality of phylolm.hp through two case studies: one involving continuous trait data (maximum tree height in Californian species) and another focusing on binary trait data (species invasiveness in North American forests). The phylolm.hp package offers researchers a powerful tool to disentangle the contributions of phylogenetic and ecological predictors in comparative analyses.

Hybridization and introgression have long obscured relationships within Adenophora and its relatives, complicating generic delimitation. Leveraging deep genome skimming (DGS) data, we generated a large dataset, including thousands of single-copy nuclear (SCN) genes and plastomes, to untangle this reticulate history. Specifically, 9.89 terabytes (TB) of DGS data from 165 samples-representing 48 species and 13 subspecies of Adenophora (out of ca. 72 species) plus 24 outgroup species-yielded 1506 SCN genes and 77 plastid coding sequences. Tree-like phylogenies inferred with both coalescent- and concatenation-based methods revealed pronounced gene tree heterogeneity. Subsequent analysis showed that incomplete lineage sorting contributed minimally to this discordance; instead, hybridization and introgression were the primary drivers of early diversification. Integrating phylogenomic, morphological, and geographic evidence, we propose a revised generic framework for this group. Adenophora is expanded to include Campanula delavayi and the Korean Peninsula endemic genus Hanabusaya. We also recommend reinstating Hyssaria as a distinct Central Asian genus and introducing two new genera, Boreoasia and Rosomala.

Ca²⁺ signaling plays crucial roles in plant stress responses, including defense against insects. To counteract insect feeding, different parts of a plant deploy systemic signaling to communicate and coordinate defense responses, but little is known about the underlying mechanisms. In this study, micrografting, in vivo imaging of Ca²⁺ and reactive oxygen species (ROS), quantification of jasmonic acid (JA) and defensive metabolites, and bioassay were used to study how Arabidopsis seedlings regulate systemic responses in leaves after hypocotyls are wounded. We show that wounding hypocotyls rapidly activated both Ca²⁺ and ROS signals in leaves. RBOHD, which functions to produce ROS, along with two glutamate receptors GLR3.3 and GLR3.6, but not individually RBOHD or GLR3.3 and GLR3.6, in hypocotyls regulate the dynamics of systemic Ca²⁺ signals in leaves. In line with the systemic Ca²⁺ signals, after wounding hypocotyl, RBOHD, GLR3.3, and GLR3.6 in hypocotyl also cooperatively regulate the transcriptome, hormone jasmonic acid, and defensive secondary metabolites in leaves of Arabidopsis seedlings, thus controlling the systemic resistance to insects. Unlike leaf-to-leaf systemic signaling, this study reveals the unique regulation of wounding-induced hypocotyl-to-leaf systemic signaling and sheds new light on how different plant organs use complex signaling pathways to modulate defense responses.

Tetracentron sinense is a 'living fossil' tree in East Asia. Understanding how this 'living fossil' responds to climate change and adapts to local environments is critical for its conservation. Here, we used re-sequenced genomes to clarify the evolutionary history and adaptive potential of T. sinense. We identified six divergent lineages in T. sinense: three lineages from southwestern China (Yunnan Province) and three lineages from the central subtropical region of China. Additionally, we detected hybridization events between some adjacent lineages. Demographic analysis revealed that over the past 10,000 years the effective population size (Ne) of three T. sinense lineages (i.e., NORTH, SWEST, and YNWEST) increased after their last bottleneck and then remained stable, whereas that of the remaining three lineages (i.e., YSEAST, YC, and EAST) declined steadily. The decline in effective population size in the Yunnan lineages aligned well with the decrease in genome-wide diversity and a significant increase in the frequency of runs of homozygosity. Deleterious variants and positively selected sites were involved in the evolution of different lineages. Further, genotype-environment association (GEA) analyses indicated adaptation to temperature- and precipitation-related factors. Genomic offset analyses found the most vulnerable populations, while SC and SC-yad were predicted to better handle extreme changes. Our findings provide insights into the evolutionary history and conservation of T. sinense and enhance our understanding of the evolution of living fossil species.

Hybridization is a driving force in ecological transitions and speciation, yet direct evidence linking it to adaptive differentiation in natural systems remains limited. This study evaluates the role of hybridization in the speciation of Pinus densata, a keystone forest species on the southeastern Tibetan Plateau. By creating artificial interspecific F1s and a long-term common garden experiment on the plateau, we provide in situ assessments on 44 growth and physiological traits across four seasons, along with RNA sequencing. We found significant phenotypic divergence between P. densata and its putative parental species P. tabuliformis and P. yunnanensis, with P. densata demonstrating superior growth and dynamic balance between photosynthesis and photoprotection. The F1s closely resembled P. densata in most traits. Gene expression revealed 19%-10% of 34,000 examined genes as differentially expressed in P. densata and F1s relative to mid-parent expression values. Both additive (4%) and non-additive gene actions (5%-6% in F1s, 10%-12% in P. densata) were common, while transgressive expression occurred more frequently in the stabilized natural hybrids, illustrating transcriptomic reprogramming brought by hybridization and further divergence by natural selection. We provide compelling evidence for hybridization-derived phenotypic divergence at both physiological and gene expression levels that could have contributed to the adaptation of P. densata to high plateau habitat where both parental species have low fitness. The altered physiology and gene expression in hybrids serve both as a substrate for novel ecological adaptation and as a mechanism for the initiation of reproductive isolation.

The plastid genome (plastome) represents an indispensable molecular resource for studying plant phylogeny and evolution. Although plastome size is much smaller than that of nuclear genomes, accurately and efficiently annotating and utilizing plastome sequences remain challenging. Therefore, a streamlined phylogenomic pipeline spanning plastome annotation, phylogenetic reconstruction and comparative genomics would greatly facilitate research utilizing this important organellar genome. Here, we develop PlastidHub, a novel web application employing innovative tools to analyze plastome sequences. In comparison with existing tools, key novel functionalities in PlastidHub include: (1) standardization of quadripartite structure; (2) improvement of annotation flexibility and consistency; (3) quantitative assessment of annotation completeness; (4) diverse extraction modes for canonical and specialized sequences; (5) intelligent screening of molecular markers for biodiversity studies; (6) gene-level visual comparison of structural variations and annotation completeness. PlastidHub features cloud-based web applications that do not require users to install, update, or maintain tools; detailed help documents including user guides, test examples, a static pop-up prompt box, and dynamic pop-up warning prompts when entering unreasonable parameter values; batch processing capabilities for all tools; intermediate results for secondary use; and easy-to-operate task flows between file upload and download. A key feature of PlastidHub is its interrelated task-based user interface design. Give that PlastidHub is easy to use without specialized computational skills or resources, this new platform should be widely used among botanists and evolutionary biologists, improving and expediting research employing the plastome. PlastidHub is available at https://www.plastidhub.cn.

Over the past century, anthropogenic greenhouse gas emissions have continuously increased global temperature and triggered climate change, significantly impacting species distributions and biodiversity patterns. Understanding how climate-driven shifts in species distributions reshape diversity patterns is crucial for formulating effective future conservation strategies. Based on the distribution data of 314 Rhododendron species in China, along with 16 environmental variables, we examined spatial diversity patterns and assessed regional and biome differences in species responses using ensembled species distribution models. Our results indicated that climatic variables significantly influenced species distributions, with ongoing climate change expected to concentrate Rhododendron distribution patterns and alter species composition. Regional topography played a critical role in shaping species responses to global warming. In the mountainous areas of southwestern China, species exhibited heightened sensitivity to temperature fluctuations, shifting upward as temperature increased. This region also had a higher proportion of threatened species and showed an overall contraction in primary distribution range. Conversely, in southern China, species were more influenced by precipitation, exhibiting a notable northward shift and expansion in primary distribution areas. Notably, alpine species, occurring in habitats above the treeline, may face severe survival risks due to the high degree of habitat loss and fragmentation. We identified seven priority conservation areas, predominantly situated in highly fragmented mountainous regions that were inadequately protected by existing nature reserves. Our findings contribute to a better understanding of changes in Rhododendron diversity patterns under climate change, providing valuable insights for developing comprehensive, flora-wide conservation plans in China.