Urophysa (Ranunculaceae) are plants endemic to the limestone regions of southern China, representing an attractive model for studying species differentiation, endangerment, and adaptive evolution in karst environments. Here, we assembled a chromosome-level genome of U. rockii, and re-sequenced 97 individuals of two Urophysa species. The final genome size was 303.21 Mb with a heterozygosity level of approximately 0.26%. Demographic analyses revealed that U. rockii diverged from U. henryi around 5.95 million years ago, dramatic orogenies and climatic shifts in the Hengduan Mountain (HDM) during the Late Miocene to Pleistocene enhanced population divergence and accelerated allopatric speciation. Extremely low genetic diversity was detected in U. rockii, particularly in the populations CXS and PZ (8.7 × 10^-5 and 9.6 × 10^-5). Long-term bottleneck effects, limited gene flow, habitat specialization and severe inbreeding collectively contributed to its endangerment status. Genomic scan (top 5% F_ST and π ratio) of Urophysa species identified 257 selected genes linked to karst adaptation. Complementary physiological experiments and transcriptome analyses further detected multiple candidate genes under positive selection and expansion (e.g., TPC1, PTR/POT, and CAX3). Maintaining cell wall integrity, regulating ion absorption and excretion, and sequestering excess ions into organelles (e.g., vacuole and mitochondrion) are key survival strategies for Urophysa species in harsh limestone rocky environments. Our findings elucidate the evolutionary patterns and mechanisms underlying species adaptation to karst ecosystems, and identify key drivers of endangerment within such ecologically specialized habitats.

Karst flora confined to isolated ‘habitat islands’ evolve specialized adaptations and unique traits, serving as ideal models for investigating adaptive evolution and species diversification mechanisms. Camellia rubituberculata, endemic to the karst habitats of Guizhou, China, can serve as a model for adaptive evolution and diversity in karst-endemic woody species. However, the lack of a chromosome-level genome for this species has limited in-depth studies on its adaptations to karst and posed a barrier to its genetic improvement. In this study, a chromosome-level genome assembly of C. rubituberculata was generated, with 15 pseudo-chromosomes and a genome size of 2.50 Gb (scaffold N50 = 168.34 Mb, 55,302 protein-coding genes). Comparative genomics revealed two whole-genome duplications (WGDs), namely, an ancient γ-event (～120 Mya) and a subsequent genus-wide event (～86 Mya), after which gene families linked to karst adaptation (e.g., photosynthesis) were significantly expanded. Selective sweep analysis showed that selected genes were associated with phytohormone transmission and metabolism. Genes functionally annotated as involved in stress responses—including SAUR, BSK, NCL, CDPK, and NDPK—participate in calcium homeostasis and ion transport pathways under karst-specific stresses. MYB transcription factors, which are crucial in plant responses to stresses, including drought, may be key for adaptation to the high salinity and drought stress in karst environments. The divergent selection in wild and cultivated groups highlight key adaptations in plant hormone transduction and calcium transport. By elucidating karst adaptation in C. rubituberculata, this work establishes essential genomic resources for advancing genetic evolution research and molecular breeding across Camellia species.

Despite the ecological importance of karst ecosystems, genomic studies on the conservation and adaptation of karst plant species, particularly threatened wild species, remain scarce. Here, we investigate the genetic architecture, demographic history, and adaptive potential of Oreocharis mileensis, a threatened karst-endemic resurrection plant. We generated a high-quality, phased genome assembly of 3.99 Gb covering two haplotypes with a contig N50 of 124 Mb, revealing three lineage-specific whole-genome duplication events following the ancestral γ event. Population resequencing of 107 individuals across 10 localities uncovered strong population structure, low gene flow, and high genetic differentiation, indicating long-term isolation. Core populations exhibited elevated inbreeding, whereas peripheral populations showed reduced runs of homozygosity and fewer deleterious mutations, suggesting historical demographic events and possible purging effects. pRDA analyses on putatively adaptive loci revealed that genetic variation is primarily aligned with pre-existing population structure. Functional annotation of putatively adaptive SNPs identified genes associated with drought tolerance and rapid recovery after rewatering. Gradient Forest models revealed substantial genomic offset in almost all populations, highlighting their increased vulnerability under projected climate scenarios. Based on these findings, we propose conservation strategies that include delineating eight genetically informed management units and facilitating assisted gene flow among compatible populations. For highly isolated populations, ex situ conservation, habitat restoration, and cultivation for horticultural use are recommended to mitigate genetic erosion and enhance adaptive resilience. This study provides critical insights into how historical, demographic, and environmental factors shape genetic diversity and informs conservation efforts for plant species in fragile karst ecosystems.

Asteraceae, the largest family of flowering plants, comprises more than 26,000 species worldwide, many of which serve as crops, medicinal herbs, and ornamentals. While substantial genomic resources are available for nuclear and chloroplast genomes, mitochondrial genomes (mitogenomes) in this family remain poorly explored, limiting an integrated understanding of its genomic evolution. Here, we assembled 38 complete mitogenomes representing 12 subfamilies and 22 tribes. Our analyses revealed substantial size variation, with notably larger mitogenomes in early-diverging lineages. We also observed extensive structural rearrangements across subfamilies and tribes. Although the gene content is largely conserved, we identified notable mutations, horizontal gene transfer events, and losses of RNA editing sites. We reconstructed a comprehensive mitochondrial phylogeny of Asteraceae, which revealed both congruent and conflicting relationships with phylogenies based on plastid and nuclear markers. Furthermore, our fragment analysis of total mitochondrial DNA demonstrated that the differential retention of ancestral sequences significantly influences mitogenome size variation in Asteraceae. This study provides a systematic mitogenomic resource, offering novel insights into the evolutionary dynamics of this major plant family.

Over the past decade, phylogenomics has significantly enhanced our understanding of relationships among numerous angiosperm lineages. However, comprehensive phylogenetic studies combining broad sampling of both genomic sequences and taxa within the nettle family (Urticaceae) are still lacking. Here, we reconstructed the phylogeny of Urticaceae (345 species across 89% of accepted genera) using concatenated and coalescent analyses from plastome and nuclear ribosomal DNA sequences. Different plastid datasets and tree inference methods yielded a consistent phylogenetic backbone, with 98% of nodes achieving > 90% bootstrap support — a significant improvement compared to 54% of nodes in the latest published phylogenetic study of Urticaceae. Plastid and nuclear phylogenetic relationships were largely congruent, with several exceptions that warrant further study. In the context of the updated phylogenetic relationships, we propose dividing the family into seven tribes that correspond to seven major clades or subclades, including a newly established tribe, Sarcochlamydeae stat. nov. Our phylogenetic analysis indicates that Debregeasia and Phenax are non-monophyletic. By combing morphological, molecular and distributional evidence, we describe a new genus Chiajuia gen. nov. Additionally, we propose synonymizing the following genera: Cypholophus (to Boehmeria), Haroldiella (to Pilea), Hemistylus, Neodistemon, Rousselia (all to Pouzolzia), Hesperocnide (to Urtica), and Pellionia (to Elatostema), while recognizing Elatostematoides, Gonostegia, Leptocnide, Margarocarpus, Scepocarpus, and Sceptrocnide as distinct genera. This robust phylogenomic framework and revised classification lays a foundation for future studies on the evolution and ecology of Urticaceae. The approach applied here may also serve as an important reference for other large plant families in angiosperms.

Bignoniaceae, a pantropical family comprising 79 genera and 901 species, exhibits remarkable morphological and ecological diversity, including lianas, shrubs, trees, and high-elevation herbs. Reconstructing the early evolutionary history of Bignoniaceae has been particularly challenging due to ancient hybridization/introgression and incomplete lineage sorting (ILS). In this study, we re-evaluated the deep branching relationships within Bignoniaceae using phylogenomic data from 1275 single/low-copy nuclear genes and the Angiosperms353 dataset, complemented with chloroplast genomes and quantified the roles of hybridization, and ILS in shaping the family’s evolutionary history. Our results robustly resolved Bignoniaceae into ten major clades, with the Argylia clade sister to a clade containing Oroxyleae, the Delostoma clade, Catalpeae, Bignonieae, the Tabebuia alliance, and the Paleotropical clade, while the Delostoma clade and Catalpeae formed a monophyletic lineage. Divergence time estimation revealed a rapid diversification during the early Eocene, coinciding with the Early Eocene Climatic Optimum. Several lines of evidence indicate that the predominant factor underlying phylogenetic conflicts across deep nodes is ILS. Introgression/hybridization also contributed significantly, with at least three ancient events detected: between Tourrettieae and the Delostoma clade, between the Delostoma clade and Bignonieae, and a major introgression from the Argylia clade to the Oroxyleae-Delostoma-Catalpeae-Bignonieae-Tabebuia-Paleotropical clade. This study provides a robust phylogenetic foundation and comprehensive evolutionary synthesis for Bignoniaceae, shedding new light on its early diversification.

Liverworts are an important component of terrestrial ecosystems worldwide. They have adapted to and diversified in a wide variety of environments. Investigating variation in net diversification rate is a major goal of biogeographers and ecologists but such investigation is lacking for liverworts at a global scale. Here, we explore global geographic patterns of mean diversification rate (MDR) within genera of liverworts, which are one of the earliest lineages of the extant land plants, and its relationship with latitude, climatic conditions, and regional species richness. We collated species lists of liverworts for each of 390 geographic units (primarily countries, provinces or states) across the world. We related MDR to geographic and current and historical climatic variables, assessed the relative importance of different sets of climatic variables on MDR, and explored the effect of MDR on species richness after accounting for major climatic factors. We analyzed the data with correlation and regression analyses, and structural equation modeling approach. We find that MDR peaks at tropical latitudes and in humid and hot environments, and that at a global scale current climate, temperature-related variables, and climatic seasonality explained more variation in MDR than Quaternary climate change, precipitation-related variables, and climatic extremes, respectively. In addition, we find a positive relationship between MDR and liverwort species richness, with the latter being directly influenced more strongly by climate than by MDR. Most importantly, we find that tropical regions of high liverwort diversity also have high current diversification rates, suggesting ongoing niche occupation. The above-described patterns are similar between the New World and Old World and between the eastern and western parts of the Old World. Our study highlights that tip diversification rates provide a complementary aspect to understand the evolution of liverwort diversity to that recovered by studying phylogenetic diversity and species richness.

Numerous studies have demonstrated that sampling intensity can significantly influence the detection of richness patterns and the assessment of the importance of driving factors. However, existing research has primarily focused on comparing the influence of sampling intensity across different locations or community types, with less attention paid to its influence across growth forms. Through field surveys on Baima Snow Mountain and bootstrap resampling analyses, we quantified the influence of sampling intensity on plant elevational richness patterns across growth forms (trees, shrubs, and herbs). Our results revealed that with increasing sampling intensity, the error in assessing elevational richness patterns decreased rapidly then stabilized for all growth forms. A similar trend was observed in the estimation of climatic drivers. However, significant variations emerged across different growth forms. The suitable sampling intensity was higher for trees and shrubs than for herbaceous plants. Furthermore, estimation errors for tree richness patterns declined significantly faster with increasing sampling intensity than those for shrubs and herbs. Similarly, the relationship between sampling intensity and error in estimating richness-climate relationships showed significant differences across growth forms. However, these differences were subject to the climate drivers selected. These findings demonstrate that growth-form differences must be considered in elevation-richness surveys. However, our meta-analysis revealed that no current study accounted for this factor in their protocols. Our findings provide empirical evidence for developing growth form-specific sampling protocols, offering practical solutions to improve the accuracy of mountain richness studies and enhance cross-study comparability in elevational gradient research.

The species pool hypothesis argues that local species diversity mainly depends on regional diversity, which is influenced by dispersal, historical and current environmental conditions. We hypothesize that regional factors, such as the size of the regional species pool, current climate, topographical variability, and historical climate stability, also impact local species-abundance patterns, like the rarity of local species, though their specific effects are not yet well understood. Analyzing data from 3307 species across 3923 forest plots in Chinese subtropical and tropical regions, we employed boosted regression trees and structural equation modeling to assess the roles of regional species pool size along with climatic seasonality, topography, and soil factors, in shaping local richness and rarity. We found that local tree species richness declined with increasing latitude, while species rarity decreased from west to east. The factors such as current regional environment, paleoclimate stability, and human disturbance significantly affected local richness and rarity, primarily through their effects on regional species pool size. The impacts of regional mean temperature and elevational range on local richness surpassed local influences. Conversely, local climatic seasonality exerted the strongest influence on species rarity, followed by human activity. Overall, the findings indicate that regions with large regional species pools tend to support diverse communities with high proportions of rare species.

Understanding the mechanisms driving species assembly along elevational gradients in mountains is crucial for biodiversity conservation. However, no consensus has yet been reached on how these mechanisms work. This knowledge gap is particularly pronounced in biodiversity-rich subtropical karst mountains. Integrating multidimensional biodiversity information into research in karst systems will provide new insights into community assembly. Thus, we explored multidimensional forest diversity along an elevational gradient at Jinfo mountain, a karst mountain site, assessing the relative importance of distinct ecological processes in shaping patterns of community diversity and structure. Our results show that different dimensional diversities exhibit similar elevational patterns, with higher diversity observed at low-to-mid elevations than at high elevations. The multidimensional diversity and structure were primarily controlled by climate stress and topographic filtering and were further modulated by soil nutrient limitation and interspecific competition. However, the explanatory weights of these ecological processes were inconsistent among the different dimensions of diversity. The phylogenetic structure was clustered at low and middle elevations, with over-dispersion at high elevations. This indicates that community assembly shifted from being dominated by environmental filtering to being dominated by competitive exclusion as elevation increased. In conclusion, our results demonstrate that combining multidimensional diversity and multiple ecological processes related to community assembly can enhance the understanding of diversity patterns along elevational gradients and the underlying mechanisms maintaining them in subtropical karst mountains.

Ongoing climate change and increasingly frequent extreme precipitation events pose greater threats to plant survival. Plants in the karst environment may face heightened risks because shallow soils and poor water retention amplify drought and temperature stresses, yet their physiological tolerances remain poorly understood. In this study, we aimed to investigate the leaf physiological tolerance strategies to drought and temperature stress in plants from karst versus non-karst forests, and to quantify the relative contributions of lithology and phylogeny to variation in these tolerances. In this study, we measured leaf photosynthetic heat and cold tolerance, leaf turgor loss points, and morphological and anatomical traits in 39 dominant woody species from karst and non-karst forests in Guangxi, China. We used Welch’s t-tests to compare leaf trait differences between forest types, evaluated the trait relationships with Pearson correlation analysis, and partitioned the contributions of lithology and phylogeny to trait variation using phylogenetic eigenvector regression (PVR). Karst species exhibited more negative leaf turgor loss points (π_tlp) and lower heat tolerance (T50_heat) than non-karst species, whereas cold tolerance (T50_cold) did not differ between habitats. Leaf thickness (LT) and leaf mass per area (LMA) were positively correlated with T50_heat, suggesting that higher structural investments enhance heat tolerance, but are not correlated with T50_cold and π_tlp. Phylogeny predominantly explains the variation in T50_cold and the second principal component (PC2), whereas lithology primarily drove variation in π_tlp and T50_heat. Because karst species have lower heat tolerance, they may face a higher risk of thermal damage under future climate warming.

The compositional coupling between aboveground vegetation and soil seed bank is critical for community stability and successional trajectories, but such relationships are highly sensitive to environmental changes. Although nitrogen (N) deposition has been reported to decouple the associations between aboveground vegetation and the soil seed bank in grasslands, it remains unclear whether and how grassland management practices, such as mowing, mediate N deposition effects. We evaluated the impacts of N input and mowing on the diversity and composition of the aboveground vegetation and soil seed bank, as well as their compositional coupling in a decadal grassland experiment. N addition increased the compositional dissimilarity between the soil seed bank and aboveground vegetation by increasing abundance gradient, but only in unmown plots. N addition did not affect the compositional dissimilarity between aboveground vegetation and the soil seed bank in mown plots. Mowing increased the graminoid abundance in the aboveground vegetation, but increased the forb abundance in the soil seed bank, and thus increased the compositional dissimilarity between aboveground vegetation and the soil seed bank by promoting balanced variation in abundance. Our results reveal the importance of context dependence in the consequences of N inputs on the compositional coupling between aboveground vegetation and the soil seed bank in grasslands. The land-use context should be fully considered when evaluating the impacts of global change drivers on grassland community dynamics and succession.

Herbivory plays important roles in forest ecosystems and is thought to be influenced by tree diversity. However, it is unclear whether, and if so how, tree diversity confers associational resistance or associational susceptibility to neighboring trees. In this study, our overall aim is to test whether biodiversity confers associational resistance or associational susceptibility to herbivores in tree species during the early stages of forest development. For this purpose, we examined whether tree species diversity affects herbivore damage in the early stages of forest development and what factors mediate the interaction between tree diversity and herbivory. We found that in some cases herbivory was related to species identity, e.g., Erythrophleum fordii was more susceptible to leaf chewers when surrounded by diverse neighbors. In other cases (i.e., Castanopsis carlesii and Elaeocarpus sylvestris), herbivory was positively associated with tree apparency. Additionally, we found that early-stage damage constrains growth in several species (e.g., C. carlesii and E. sylvestris), highlighting a previously underappreciated pathway through which diversity can shape long-term stand dynamics. Thus, herbivore damage in young subtropical plantations is not only governed by diversity but also by a three-way interplay between the identity of focal tree species, neighborhood diversity, and focal tree apparency, showing signs of associational susceptibility. Our finding that reduced tree apparency contributes to associational resistance in young trees can inform more effective forest management strategies.

Biological invasions threaten biodiversity and ecosystem stability through stage-dependent functional trait mediation. However, the mechanistic linkages between invasion intensity and multidimensional functional traits remain inadequately characterized. To address this gap, we analyzed eight multidimensional functional traits across 290 subtropical herbaceous plots in Jinhua, China. By integrating invasion level, we evaluated how native and invasive species traits differentially regulate community invasibility, a metric quantifying a community’s susceptibility to biological invasion. Functional and taxonomic diversity exhibited hump-shaped patterns, peaking at moderate invasion before declining sharply under heavy invasion, while community invasibility increased markedly with invasion level. Native communities resisted invasion through persistent suppression of canopy height and stage-adaptive strategies: Leaf thickness emerged as a critical resistance trait under heavy invasion, counteracting invasive dominance. In contrast, invasive species initially prioritized rapid canopy occupation via height-mediated advantages, subsequently shifting toward stress tolerance (e.g., thickened leaves) and resource reallocation (e.g., root-shoot ratio adjustments) to consolidate dominance. Native abundance universally suppressed invasibility across all invasion stages, whereas invasive abundance amplified success only at advanced stages. Resistance was governed by stage-dependent trait trade-offs: Native leaf dry weight enhanced invasibility under light invasion but became ineffective as competition intensified. Conversely, invasive aboveground biomass and root-shoot ratio consistently promoted invasibility, reflecting prioritization of rapid resource acquisition. Our findings demonstrate that invasion outcomes depend on the spatiotemporal coordination of multidimensional functional traits. We propose an adaptive management framework for urban ecosystems emphasizing structural preservation (e.g., maintaining native canopy height) combined with stage-specific trait optimization of resistance traits to mitigate invasibility.

Understanding the factors that drive distributional variation in terrestrial vegetation carbon pools (VCPs) is crucial for assessing the potential of carbon sequestration and mitigating climate change. Although previous studies have extensively examined elevational patterns of VCPs and their abiotic drivers, the biotic mechanisms that drive VCPs remain poorly understood, especially in savanna ecosystems. Characterized by a unique “tree-shrub-grass” plant composition, the savannas in the dry-hot valleys have high productivity and carbon storage capacity. In this study, we investigated VCP distribution and the factors that drive these distributions along an elevational gradient (400–1700 m) in the dry-hot valleys of Southwest China. We found no significant elevational pattern in the total VCP, whereas tree and shrub VCPs exhibited divergent distributional patterns. We also found that VCP distribution was more strongly affected by structural diversity than by species diversity, indicating that structural diversity mediates the relationship between species diversity and VCP distribution. These findings suggest that optimized spatial resource use enhances carbon storage. Notably, the total VCP was more influenced by tree structural diversity than by shrub structural diversity, highlighting the dominant role of trees in savanna carbon sequestration. Furthermore, elevation shaped the VCP patterns by regulating both soil and biotic factors. These findings provide valuable insights for carbon-oriented conservation and restoration practices in dryland ecosystems.

Ecological recovery of abandoned mining areas requires developing and implementing effective nature-based solutions. However, ecological processes that underlie the establishment, development, and long-term persistence of plant functional groups within natural plant communities remain poorly understood. Here, we hypothesized that local plant species in abandoned mining areas respond to the harsh environmental conditions of contaminated soils by adjusting their functional traits and survival strategies, thereby enhancing the stability of spontaneous plant communities through the development of distinct plant functional groups. To test this hypothesis, we assessed the responses of plant functional groups to heavy metal contamination and identified both environmental factors and functional traits that influence these plant functional groups. We found that heavy metal pollution induced shifts in plant functional groups and overall community composition. Specifically, stress-tolerant plant abundance fluctuated and declined; ruderal plant abundance initially decreased before increasing; and competitor plant abundance increased. The environmental factors that influenced plant functional group abundance include soil pH, heavy metal concentrations, and nutrient content. Overall, our results specifically indicate that the successional replacement of plant functional groups and the ecological recovery of plant communities in abandoned mining areas depend on soil total nitrogen levels.

Orchid diversity and conservation are tightly linked to the evolution of orchid lifeforms (e.g., epiphytic or terrestrial) as epiphytic species are highly sensitive to environmental changes and includes super-high species diversity. However, the factors that drive the evolution of orchid lifeform remain unclear. Here, we used a global orchid phylogeny (2272 species, all five subfamilies and 302 genera) to evaluate the relative contributions of potential factors (i.e., phylogeny, climate region, pollination traits) that may drive orchid lifeform evolution using partial framework. Conventional correlation results indicated that orchid lifeforms are strongly associated with climate regions and weakly related to pollination traits. In contrast, partial analyses revealed that orchid phylogeny alone accounted for 62% of lifeform variation; pollinator attraction strategies independently explained an additional 23.9% variation, while climate region only further explained 3.4%. The discrepancies arise from variation in phylogenetic conservatism of different orchid traits: both orchid lifeform and climate region are more phylogenetically conserved than pollination traits. Specifically, our findings that species evolution plays a key role in lifeform evolution together with variation in phylogenetic conservatism among key traits provide insights into trait evolution and species conservation in orchids.