Seeds with different desiccation tolerance and their foraging animals present unique strategies for ensuring population growth and ecological fitness in the natural environment. While some seeds minimize physical injuries by having lignified thick coats or defensive compounds, others tolerate a certain degree of mass loss, with larger seeds enduring partial animal consumption better than smaller seeds, consistent with the reserve effect hypothesis, regardless of their desiccation tolerance. In endozoochory, aerial, terrestrial and aquatic fauna with appropriate gape sizes that consume whole fruits with mostly orthodox seeds are important for longer-distance seed dispersal as long as seed viability suffers little impairment following defecation. Some seeds even gain benefits from animal consumption when physical dormancy is overcome and germination occurs earlier. Dung beetles perform secondary spread and burial of seeds, reducing plant aggregation. On the other hand, highly nutritious recalcitrant seeds of a limited number of plant species show sprouting despite partial loss of embryonic axes to browsing animals, often with damage to radicles being less critical than to plumules. Some recalcitrant seeds even possess the unique ability to regenerate roots and shoots from the cotyledonary tissues devoid of embryonic axes. Such embryonic cell development, or ‘stemness’, from seed tissue fraction is rare in the plant kingdom, but evidently present in at least four families. Plant regeneration despite seed predation is a multi-trait adaptation that ensures species survival and fosters resilient natural ecosystems.

The impact of key traits on lineage diversity remains a central focus in macroevolutionary research. Seeds, encapsulated within fruits, carry the complete genetic blueprint of their species, and the capacity of their adaptive evolution to diverse environmental conditions shapes species origination and extinction dynamics. However, the role of specific traits in driving species diversification under changing environmental conditions remains poorly understood, particularly among taxa that produce desiccation-sensitive seeds. In this study, we reconstructed the phylogenetic relationships of Quercus section Cyclobalanopsis based on whole-genome resequencing data from 52 species, covering approximately 50% of the section. We investigated six fruit traits—fruit volume, shape, maturation period, cotyledonary petiole, embryonic axis position and dormancy type—through experimental observations and data collection. The influence of these traits, climatic variables, and phylogenetic signal on diversification rates, along with the effects of climatic variables on these traits were analysed. Our findings reveal substantial diversity in fruit trait states within the section Cyclobalanopsis. Climates characterized by hot summers and wet-cold winters provide favorable habitat conditions that promote speciation. Furthermore, ancestral fruit traits, such as small acorns, oblong ellipsoid shapes, normal cotyledonary petioles, and embryonic axes near the apex, along with the derived trait of annual fruit maturation, were associated with increased net diversification rates. These ancestral fruit traits, adapted to the subtropical evergreen broad-leaved forests of East Asia, facilitated rapid evolutionary radiation during the Miocene through climatic niche innovation. In contrast, species inhabiting tropical landscapes appear to adapt to local environmental changes through fruit trait innovations, such as larger fruits and rapid germination.

Cryopreservation of partially dried embryonic axes represents the primary approach for long-term preservation of recalcitrant seeds. However, while many seed traits and responses relate to either pre- or post-dispersal climate, little is known about whether axis responses to cryopreservation relate to climate. For 13 Quercus species from subalpine, subtropical and temperate forests in China, we tested the hypothesis that axis responses to desiccation and cold stress co-vary and relate to climate. There were strong relationships between axis desiccation sensitivity, responses to cryopreservation and climate. Subalpine oak axes were highly desiccation-sensitive, but had high survival of freezing, even at high water contents. Temperate species were less desiccation-sensitive. However, only those from the coldest locations survived freezing when dried to lower water contents. While subtropical species had a similarly high level of desiccation-sensitivity as subalpine species, most species died under all cryo-exposure conditions. Our findings underscore the essential role of climate in shaping diverse, cold stress mitigation strategies among different Quercus groups. The paradoxical cryopreservation tolerance of highly desiccation-sensitive subalpine species, likely traits acquired during their shift to colder habitats since the mid-Miocene Himalaya-Hengduan uplift, reveals broader cold stress tolerance strategies in Quercus than previously reported, suggesting this group is suitable for long-term storage. For temperate and subtropical species, surviving cryo-exposure represented a balance between the risk of ice crystal formation and desiccation. However, the limited survival of subtropical species, many of which are threatened, highlights the need for further research to develop long-term conservation strategies.

Fruit volume is a pivotal reproductive trait that influences dispersal, seed predation, and offspring establishment, yet its large-scale drivers remain poorly understood. Here, we compiled phylogenetic, functional, and climatic data for 2668 angiosperm species sampled from 22 ecological stations across China to disentangle the relative contributions of evolutionary history, plant traits, and climate to interspecific fruit volume variation. We quantified phylogenetic signal, fitted phylogenetic generalized linear models and mixed-effects models, and conducted hierarchical variance partitioning to evaluate predictor importance. Fruit volume exhibited a strong phylogenetic signal (Pagel’s λ = 0.916), with phylogenetic relationships explaining 64.71% of the variance. Functional traits, particularly plant height (11.99%) and growth form (9.97%), also contributed significantly. Importantly, the explanatory power of phylogenetic relationships declined in warmer environments, where the effects of plant height and leaf area increased, indicating that phylogenetic niche conservatism is context dependent. These findings highlight that this phylogenetic pattern reflects the dominant role of evolutionary history in shaping fruit volume while revealing how climate modulates the relative importance of phylogenetic history and functional traits during community assembly. By integrating macroevolutionary patterns with ecological filtering, this study provides new insights into the evolutionary ecology of plant reproduction under environmental change.

Although the phylogenetic backbone of Moraceae, an ecologically important angiosperm family in tropical rainforests, has been significantly improved, phylogenetic discordance among nuclear genes and between nuclear and plastid genomes remains common at various phylogenetic depths. However, the patterns and causes of this discordance across the entire family have not been systematically investigated. Here, we reconstructed a comprehensive phylogeny of 319 species of Moraceae using sequences from nuclear and plastid gene datasets to investigate family-wide phylogenetic conflict, identify the evolutionary drivers of conflict, and inform taxonomic revision. Phylogenetic analyses showed general congruence at the section level and above in nuclear datasets, but notable conflicts occurred at several nodes (e.g., Chlorophoreae, Bagassa, and Sloetiopsis). Discordance between nuclear and plastid trees was widespread, especially within the tribes Antiarideae, Artocarpeae, Dorstenieae, and Ficeae. Coalescent simulations and phylogenetic network analyses suggest that the observed discordance arises from a combination of incomplete lineage sorting and ancient hybridization. Based on integrated phylogenetic and morphological evidence, we propose several taxonomic revisions for the family. Overall, this work elucidates the evolutionary history of Moraceae, emphasizing the role of hybridization in its diversification, and provides a robust phylogenetic framework for future research on its classification, biogeography, and diversification.

Global patterns of species diversity are highly heterogeneous, and even within the same evolutionary lineage, species richness can differ markedly. Understanding the mechanisms underlying such disparities remains a central question in evolutionary biology and biogeography. Here, we investigate the evolutionary drivers of asymmetric diversity and distribution patterns in Ulmaceae by integrating molecular phylogenetics, fossil evidence, climatic niche analyses, and biogeographic reconstructions. We reconstructed a time-calibrated, species-level phylogeny encompassing 86.21% of extant Ulmaceae species and incorporating 61 fossil taxa. Phylogenetic analyses supported the division of Ulmaceae into a temperate clade and a tropical clade, which differ substantially in species richness, climatic niche characteristics, and geographic distributions. The temperate clade exhibited strong climatic niche conservatism combined with a broader niche breadth, enabling repeated intercontinental dispersal and geographic expansion across the Northern Hemisphere since the Late Cretaceous. In contrast, the tropical clade shows more constrained niche evolution and limited dispersal capacity, remaining largely restricted to low-latitude tropical regions and exhibiting lower species richness. Fossil-integrated analyses suggest that Ulmaceae originated in northern temperate regions during the Late Cretaceous and experienced extensive intercontinental exchanges during the Paleogene, particularly via the Bering and North Atlantic land bridges. Diversification-rate analyses indicated that net diversification rates in both clades remained relatively stable through time. This pattern suggested that long-term differences in species richness were better explained by early climatic niche divergence and contrasting biogeographic histories, rather than by temporal shifts in diversification rates. Our study highlights the critical role of fossil integration in revealing deep-time evolutionary processes that shape modern plant diversity under long-term climatic change, and provides a framework applicable to many other extant lineages with similar distribution patterns.

The Tianshan Mountains constitute a major biogeographic barrier in Arid Central Asia, yet their impact on plant genomic divergence and adaptation remains poorly understood. Using Typha laxmannii, a wetland species distributed across this range, we generated a chromosome-scale genome and performed integrated population genomic and environmental analyses of 126 individuals from 31 sites. Our results revealed a clear north-south genetic split demarcated by the Tianshan Mountains, with gene flow restricted since divergence approximately 88.1 thousand years ago (Kya), a pattern further reinforced by post-Pleistocene demographic contraction. Northern and southern populations evolved distinct adaptive signatures in response to their local environments, including differentiation in genes associated with stress response, transcriptional regulation, and flowering time. Beyond single loci, adaptation also acts on large genomic blocks: a ∼2.5 Mb parallel sweep (∼91 Kya) contains a linked block of stress-response genes shared across the species, suggesting a range-wide response to intensified continentality and repeated glacial-interglacial aridification following population decline (∼100 Kya) but preceding the north-south split. In contrast, a ∼3 Mb divergent sweep (∼85 Kya) harbours northern-specific alleles related to glutathione metabolism, zeatin biosynthesis, and transcriptional regulation, likely enhancing tolerance to extreme winter cooling and freeze-thaw cycles under a strengthened Siberian High after divergence. Together, our findings establish a “spatio-temporal environmental sorting” model of biodiversity, providing a critical framework for understanding how the topography and climate of the Arid Central Asian mountains promote evolutionary novelty and safeguard genetic resilience in the face of ongoing global climate change.

Understanding how natural selection sustains genetic differentiation despite ongoing hybridization remains a central question in evolutionary biology. Here, we integrated range-wide whole-genome resequencing data and ecological niche modeling to elucidate the evolutionary history, local adaptation, and hybridization patterns of Juglans cathayensis, a walnut species widely distributed across subtropical China. Our analyses revealed that Chinese walnut comprised two genetic clusters corresponding to its two recognized varieties, which were further subdivided into three lineages: the East lineage, consisting exclusively of J. cathayensis var. formosana individuals; and the West and Admixed lineages, comprising genetically pure and admixed individuals of J. cathayensis var. cathayensis, respectively. The admixed populations formed a hybrid zone in the ecotone between the East and West lineages. Divergence between the East and West lineages dates to the Middle Pliocene, with persistent bidirectional gene flow until the mid-Pleistocene, likely driven by long-term local adaptation to niche differences between eastern and western China. Genomic regions of differentiation may result from divergent selection under gene flow and divergent sorting of ancient polymorphisms. Moreover, we identified positively selected genes and environment-associated loci involved in ecological adaptation, underscoring their role in promoting intraspecific differentiation. Bayesian genomic cline analysis detected limited introgression of adaptive loci in the hybrid zone, suggesting that natural selection sustains divergence in genomic regions associated with local adaptation, while neutral loci are homogenized through hybridization. Together, these findings provide novel insights into the evolutionary mechanisms shaping plant diversity in subtropical China, a region recognized as an evolutionary cradle.

The genus Lycium is of considerable medicinal and economic importance and has a discontinuous intercontinental distribution. However, its evolutionary history remains obscured by morphological convergence, hybridization, and incomplete lineage sorting (ILS). Here, we conducted the first phylogenomic study of Lycium, integrating three independent genomic compartments, single-copy nuclear genes, mitochondrial genomes, and published plastid data to reconstruct its history and dissect the roles of incomplete lineage sorting, hybridization, and long-distance dispersal in its evolution. Both concatenation and coalescence methods based on nuclear genes yielded a congruent, well-resolved phylogeny, strongly supporting the monophyly of Lycium and recovering five major clades with a North American lineage as sisters to all the others. This phylogeny reveals significant conflicts with the traditional morphology. Our analyses clarify the primary cause of two distinct types of conflict. First, the pervasive tripartite (nuclear-plastid-mitochondrial) topological discordance is primarily linked to historical hybridization and introgression events, as demonstrated by strong gene-flow signals and detailed network models. In contrast, the discordance observed among gene trees appears to be predominantly influenced by incomplete lineage sorting, with some nodes exhibiting peaks exceeding 60%, indicative of rapid radiation during the Miocene epoch. Divergence dating and ancestral area reconstruction support a North American origin in the early Miocene (∼21.84 Ma), followed by sequential long-distance dispersal to South America across the Pacific, Africa, and Eurasia. Collectively, our results establish a process-based framework for Lycium’s complex evolutionary history, highlighting the interplay of rapid radiation, quantified ILS, modeled hybridization, and bird-mediated dispersal in shaping its intercontinental distribution.

Dryland biodiversity-productivity relationships remain poorly resolved. Specifically, the environmental conditions governing the shift between complementarity and mass ratio mechanisms remain unclear, limiting the effectiveness of restoration and management strategies. To address this gap, the aim of this study was to investigate the geographical patterns of diversity and biomass production in herbaceous communities along a 2100-km precipitation gradient in North China. We studied how α- and β-diversity affect community-wide productivity using linear mixed-effects models and piecewise structural equation models, along with rolling-window change-point analyses. In arid regions, biomass productivity was primarily driven by interspecific niche complementarity, where higher functional diversity (FD(α)) enhanced resource-use efficiency. However, in semi-arid regions, productivity was regulated by the mass ratio effect, specifically through the traits of dominant species, including community weighted mean height and specific leaf area, as these species exploited broader resource spectra with increasing water availability. A critical mechanistic shift occurred at a mean annual precipitation (MAP) threshold of ∼168 mm (95% CI: 152-171 mm; p < 0.001). Below this threshold, productivity was driven by diversity-mediated complementarity and stress tolerant strategies. Conversely, as MAP surpassed 168 mm, the system transitioned to mass ratio control, coincident with a shift toward competitive strategies. Overall, our study provides empirical evidence to guide dryland management: prioritising the maintenance of functional diversity in arid communities, while emphasising dominant-trait optimisation (plant height and specific leaf area) in semi-arid communities to maximise aboveground biomass.

Nitrogen (N) and phosphorus (P) play crucial roles in early seedling establishment, influencing germination, survival, and overall performance. However, large-scale multispecies seed element survey data are extremely scarce, and studies on the N, P concentrations and N:P ratios as well as scaling relationships of N and P in seeds remain limited. To examine the N versus P scaling relationship and N:P stoichiometry in seeds, we conducted a large-scale survey and collected 1652 seed samples from 446 species in 51 families spanning 236 sites across the Chinese grasslands, including typical steppe, desert steppe, and alpine meadow. We found that the arithmetic means of seed N and P concentrations and N:P ratios were 28.95 ± 0.32 mg/g, 4.26 ± 0.05 mg/g, and 7.24 ± 0.07, respectively. Seed N, P concentrations and N:P ratios varied across different plant groups and grassland types. For example, N-fixers had the highest N, P concentrations and N:P ratios across plant groups. Among the grassland types, alpine meadow displayed the highest N and P concentrations but the lowest N:P ratios. Using a recent bootstrapping approach to resolve data imbalance, the overall seed N vs. P scaling exponent was 0.75, supporting the growth rate hypothesis. We also detected strong phylogenetic signals in these traits. After accounting for phylogeny, the scaling exponent in independently evolving lineages was 0.66. These findings highlight how both environment and evolutionary history regulate seed nutrient allocation, advancing our understanding of plant reproductive strategies and providing key parameters for modelling early plant growth.

Crown architectural traits are critical adaptations that balance light capture with mechanical stability. Given that light availability plays a fundamental role in shaping forest community structure, co-occurring tree species of different shade tolerance guilds exhibit distinct resource acquisition strategies. However, how shade tolerance governs multidimensional crown architecture and mediates neighborhood interactions remains unclear. In a subtropical Chinese forest, we monitored 5-year growth and measured six individual-level crown traits for 3589 trees. We quantified trade-offs among crown traits and evaluated the relative effects of tree size, spatial structure, neighborhood density, and crown trait dissimilarity on growth across shade tolerance guilds. Principal component analysis revealed two major axes: crown shape (PC1, narrow-deep vs. broad-shallow) and crown size (PC2, height and apical dominance). Light-demanding species exhibited higher scores along the crown size axis, consistent with a strategy of rapid vertical growth, whereas shade-tolerant species showed more plastic crown forms, advantageous for persistence under low light conditions. The influence of crown trait-mediated neighborhood interactions on growth also diverged between shade tolerance guilds. Growth of light-demanding species was suppressed by dissimilarity in apical dominance ratio and crown shape (PC1), yet enhanced by dissimilarity in crown projection area, reflecting both environmental filtering and niche differentiation. In contrast, shade-tolerant species were mainly constrained by conspecific density, consistent with density dependent effects potentially linked to natural enemies. These findings demonstrate that shade tolerance structures crown trait trade-offs and determines how crown traits mediate neighborhood interactions, thereby improving our understanding of crown architecture-driven demography and coexistence in forest ecosystems under global change.

The degradation of alpine cushion plants is known to disrupt soil microbial networks. To explore the mechanisms behind this, we collected soils across a degradation sequence on the Qinghai-Xizang Plateau and, using a microcosm approach, simulated the effects of three global change factors: warming (T), nitrogen addition (N), and dry-wet cycling (D). Our findings indicated that fungal and bacterial networks exhibited contrasting structures and response patterns. Fungal networks displayed hub-dependent structure: they maintained complexity and enhanced robustness under T, N, and D, yet showed vulnerability when keystone nodes were preferentially removed. Bacterial networks exhibited connector-mediated redundancy that conferred high baseline robustness but limited adaptive capacity; their robustness did not increase under T or N, though assortativity rose under N. Network complexity showed nonlinear shifts across degradation stages. At two thresholds—individual-level Stage 3-4 and community-level balanced-to-stable transition—fungal networks reorganized while bacterial networks simplified. Both abiotic and biotic factors predicted network dynamics. Abiotic predictors included microbial biomass, nutrients, pH, and polyphenol oxidase (PPO) activity. Beyond these, keystone taxa abundance emerged as a biotic driver strongly correlated with bacterial network complexity, though this relationship was attenuated under warming. We propose a management framework that prioritizes protecting bacterial network integrity through mitigating warming and nitrogen deposition, targets pre-threshold stages as intervention windows, and integrates soil-microbial indicators for early warning. This study provides a practical basis for predicting and managing microbial network dynamics in alpine tundra under global change.

Extreme climate scenarios threaten the ecological stability of grassland ecosystems. Plant litter plays a critical role in regulating ecosystem structure and function, therefore its accumulation must be carefully managed and manipulated. However, little is known about whether plant litter addition mitigates the effects of extreme weather events (e.g., heavy rainfall) on the ecological stability of grasslands. Here, we determined whether and, if so, how plant litter increases the ecological stability (i.e., resistance, resilience, and recovery) after extreme rainfall events in alpine grasslands on the Qinghai-Tibet Plateau. We found that plant litter addition increased resilience and recovery of alpine grassland following extreme rainfall, but did not increase resistance. The ecological stability of plant functional groups, plant asynchrony, and changes in plant community compositional dynamics contributed to the resistance, resilience, and recovery of plant communities following extreme rainfall in the alpine grassland. Our findings indicate that the addition of plant litter could improve the ecological stability of alpine grassland following extreme rainfall event. Mainly through changing the ecological stability of certain plant functional groups within the community. These findings highlight the important role of plant litter accumulation in maintaining ecosystem stability of grassland in response to extreme weather events.

Plant height is critical for crops in agricultural research and practice. Optimizing plant height helps to increase yield and lodging resistance. The green revolution gene semi-dwarf 1 (SD1) encoding GA 20-oxidase 2 (GA20ox2) has been widely used in modern rice breeding. However, the molecular mechanism of how SD1 is transcriptionally regulated remains elusive. TCP proteins, one family of the plant-specific transcription factors (TFs), have been proved to widely distribute in plants and play important roles in plant growth and development. Here, we report a TCP TF OsTCP4, which belongs to class I clade TCP, plays critical roles in regulating plant height of rice through acting as a transcriptional repressor of SD1. OsTCP4 is a nuclear-localized TF, which has a preferential transcriptional accumulation in stem nodes and tiller bases. ostcp4 knock-out mutants displayed higher plant height compared with WT, while overexpression of OsTCP4 reduced plant height compared with WT, which was confirmed by two cultivars on four planting sites of Yunnan under three-year investigation. The expression of SD1 was upregulated in ostcp4 mutants and reduced in OsTCP4-overexpression plants. Moreover, OsTCP4 protein directly binds to the promoter region of SD1. The genetic regulation between OsTCP4 and SD1 was further verified with ossd1 tcp4 double mutant. Moreover, distinction of plant height in ostcp4 lines and OsTCP4-OE lines is caused by different concentrations of GA₁. Taken together, OsTCP4 acts as a transcriptional repressor of SD1 and it may play a critical role in rice growth and development through the fine-tuning of GA₁ biosynthesis.

Soybean (Glycine max) is a key source of plant protein and oil, yet genomic resources for male-sterile germplasms remain scarce. This study addresses this gap by presenting the first telomere-to-telomere (T2T) genome assembly of the landrace soybean 88-428BY, a Chinese photoperiod-sensitive genic male sterility (PGMS) germplasm with photoperiod-dependent fertility. Using a hybrid strategy combining PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C scaffolding, we generated a high-quality reference genome of 1.01 Gb (N50 = 52.05 Mb), achieving 99.88% BUSCO completeness and assembling telomeres at both ends of 80% of the chromosomes. Annotation revealed 55,292 protein-coding genes and a high repetitive content (63.03%), which was dominated by LTR retrotransposons. Comparative genomics identified 35,236 structural variations (SVs), with hotspot regions harboring genes showing suppressed expression. Transcriptomic analysis under long-day and short-day conditions uncovered co-expression modules enriched in flavonoid biosynthesis and protease inhibitors, alongside key transcription factors (e.g., NAC25, ERF113) potentially associated with fertility regulation. This T2T genome provides a critical resource for elucidating the molecular basis of photoperiod-sensitive male sterility and advancing functional genomics and molecular breeding in soybean.