Over the past two decades, our understanding of Lauraceae, a large family of woody plants, has undergone significant advances in phylogeny, taxonomy, and biogeography. Molecular systematic studies have elucidated the basic relationships within the family with plastid phylogenomic analyses providing robust support for deep-level relationships between Lauraceae lineages, leading to the recognition of nine tribes: Hypodaphnideae, Cryptocaryeae, Cassytheae, Neocinnamomeae, Caryodaphnopsideae, Mezilaureae, Perseeae, Laureae, and Cinnamomeae, with Mezilaureae validated here. Nuclear genomes and comparative genomics studies have also clarified aspects of the family’s evolutionary history and metabolic diversity. Taxonomic studies have focused mainly on the most diverse regions, e.g., tropical Asia, tropical America, and Africa (Madagascar), with six new genera described and five reinstated since the last major overview of the family. The extensive fossil record suggests that Lauraceae diversified globally during the Late Cretaceous and Early Cenozoic. Biogeographic studies indicate that different lineages of the family are sorted into Gondwanan and Laurasian lineages, with patterns resulting from the disruption of boreotropical flora and multiple long-distance dispersal events. Phylogeographic studies, predominantly from East Asia, have shown patterns of in situ survival and demographic stability or expansion during the Quaternary. Nevertheless, many systematic relationships within the family remain unresolved and further research is needed into the complex biogeographic history and ecological roles of Lauraceae. A multifaceted approach integrating genomic studies, field work, morphological and ecological investigations is therefore needed to understand the evolution and diversity of this ecologically and economically significant plant family.

Evergreen broad-leaved forests (EBLFs) are widely distributed in East Asia and play a vital role in ecosystem stability. The occurrence of these forests in East Asia has been a subject of debate across various disciplines. In this study, we explored the occurrence of East Asian EBLFs from a paleobotanical perspective. By collecting plant fossils from four regions in East Asia, we have established the evolutionary history of EBLFs. Through floral similarity analysis and paleoclimatic reconstruction, we have revealed a diverse spatio-temporal pattern for the occurrence of EBLFs in East Asia. The earliest occurrence of EBLFs in southern China can be traced back to the middle Eocene, followed by southwestern China during the late Eocene-early Oligocene. Subsequently, EBLFs emerged in Japan during the early Oligocene and eventually appeared in central-eastern China around the Miocene. Paleoclimate simulation results suggest that the precipitation of wettest quarter (PWetQ, mm) exceeding 600 mm is crucial for the occurrence of EBLFs. Furthermore, the heterogeneous occurrence of EBLFs in East Asia is closely associated with the evolution of the Asian Monsoon. This study provides new insights into the occurrence of EBLFs in East Asia.

Intraspecific genetic variance and gene flow can support the adaptive evolution of species challenged by climate shifts or novel environmental conditions. Less well understood is how genome organization and gene flow interact in closely related species during evolutionary divergence and differentiation. Here we conducted genomic footprint analyses to determine how three species of Pterocarya (P. stenoptera, P. hupehensis, and P. macroptera), which are sympatric but occupy different elevational niches, adapted to the heterogeneous environment of the Qinling-Daba Mountains, China. We identified candidate genes for environmental adaptation (i.e., PIEZO1, WRKY39, VDAC3, CBL1, and RAF), and also identified regions of gene introgression between P. hupehensis and P. macroptera that show lower genetic load and higher genetic diversity than the rest of their genomes. The same introgressed regions are notably situated in areas of minimal genetic divergence yet they are characterized by elevated recombination rates. We also identified candidate genes within these introgressed regions related to environmental adaptation (TPLC2, CYCH;1, LUH, bHLH112, GLX1, TLP-3, and ABC1). Our findings have thus clarified the important role of gene flow in ecological adaptation and revealed genomic signatures of past introgression. Together, these findings provide a stronger theoretical basis for understanding the ecological adaptation and conservation of Quaternary relict woody plants in East Asia.

The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value. However, taxonomy and systematics of Salix is extremely difficult and relationships between main lineages, especially deep phylogenies, remain largely unresolved. In this study, we used genome-skimming, plastome assembly, and single-copy orthologs (SCOs) from 66 Salix accessions, along with publicly available plastome and sequence read archive (SRA) datasets to obtain a robust backbone phylogeny of Salix, clarify relationships between its main lineages, and gain a more precise understanding of the origin and diversification of this species-rich genus. The plastome and SCO datasets resolved Salix into two robust clades, with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies. Our results support the classification of Salix into five subgenera: Salix, Urbaniana, Triandrae, Longifoliae and Vetrix. We observed a significant acceleration in the diversification rate within the Chamaetia-Vetrix clade, while Salix exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene. These changes coincided with contemporaneous tectonic and climate change events. Our results provide a foundation for future systematic and evolutionary studies of Salix. Additionally, we showed that genome skimming data is an efficient, rapid, and reliable approach for obtaining extensive genomic data for phylogenomic studies, enabling the comprehensive elucidation of Salix relationships.

Mimetic seeds attract birds to disperse seeds mainly by mimicking fleshy fruits or arillate seeds, however, they provide little nutritive reward for bird dispersers. The key characteristics of mimetic seeds are conspicuous seed color, hard seed coat, certain toxic secondary metabolites, and perhaps smooth waxy layer. In this review, we discuss the global distribution of mimetic seeds, the interaction of mimetic seeds with bird dispersers, and secondary metabolites that underlie key characteristics of mimetic seeds. Mimetic-seed species mainly occur in the tropics, with large numbers distributed along coastal areas. The interaction between mimetic-seed species and bird dispersers can be antagonistic, mutualistic, or both. These interactions are generally established by conspicuous visual cues and hard tactile cues from mimetic seeds. The formation and variation of key characteristics of mimetic seeds may contribute to the metabolism of several kind of secondary compounds. Here, we also discuss mimetic-seed dispersal in the context of an evolutionary game, and propose several aspects of mimetic-seed dispersal that remain unstudied. While this review is based on preliminary findings and does not account for other potential influencing factors such as climate, it is expected to contribute to an improved understanding of mimetic-seed dispersal.

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.

Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change. Quercus is a keystone genus in Northern Hemisphere forests, and its wide distribution in diverse ecosystems and long evolutionary history make it an ideal model for studying the genomic basis of ecological adaptations. Here we used a newly sequenced genome of Quercus gilva, an evergreen oak species from East Asia, with 18 published Fagales genomes to determine how Fagaceae genomes have evolved, identify genomic footprints of ecological adaptability in oaks in general, as well as between evergreen and deciduous oaks. We found that oak species exhibited a higher degree of genomic conservation and stability, as indicated by the absence of large-scale chromosomal structural variations or additional whole-genome duplication events. In addition, we identified expansion and tandem repetitions within gene families that contribute to plant physical and chemical defense (e.g., cuticle biosynthesis and oxidosqualene cyclase genes), which may represent the foundation for the ecological adaptation of oak species. Circadian rhythm and hormone-related genes may regulate the habits of evergreen and deciduous oaks. This study provides a comprehensive perspective on the ecological adaptations of tree species based on phylogenetic, genome evolutionary, and functional genomic analyses.

Dryopteridaceae are the largest fern family and include nearly 20% of extant fern diversity, with 24 currently recognized genera. Recognition and delineation of genera within this family have varied greatly. The three-subfamily classification of Dryopteridaceae was based primarily on molecular phylogenetic relationships but lacked morphological evidence, and the phylogenetic relationships of the subfamilies and genera of Dryopteridaceae are only partially resolved. A comprehensive and robust phylogeny is urgently needed. The heterogeneous morphology of the current members of Dryopteridaceae makes the family and its subfamilies difficult to define by single morphological characteristics or even character combinations. We carried out phylogenetic analyses to reconstruct a highly supported phylogeny of Dryopteridaceae. Our analyses recovered 24 strongly supported clades grouped into seven major clades of Dryopteridaceae. Seven morphological characters including habit, rhizome shape, frond morphology, rachis-costae architecture, appendages on stipe base and lamina, and soral arrangement were found to be informative for identifying different major clades and clades in Dryopteridaceae. Based on phylogenetic reconstruction and morphological analysis, we presented an updated infra-familial classification of Dryopteridaceae with seven subfamilies and 24 genera including four newly proposed subfamilies (Ctenitidoideae, Lastreopsidoideae, Pleocnemioideae, and Polystichopsidoideae). Morphological character combinations of each subfamily are summarized, and a key is provided. Most genera sensu PPG I are recognized, with Stigmatopetris reclassified into Dryopteridoideae and Arthrobotrya considered a synonym of Teratophyllum. A new genus Pseudarachniodes is introduced. This revised classification will serve as a foundational framework for future investigations on taxonomy, biogeography, and diversification of the most species-rich Dryopteridaceae in ferns.

Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress, while hexaploid wild Camellia oleifera shows strong freezing tolerance. As a valuable genetic resource of woody oil crop C. oleifera, wild C. oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress. Here, 47 wild C. oleifera from 11 natural distribution sites in China and 4 relative species of C. oleifera were selected for genome sequencing. “Min Temperature of Coldest Month” (BIO6) had the highest comprehensive contribution to wild C. oleifera distribution. The population genetic structure of wild C. oleifera could be divided into two groups: in cold winter (BIO6 ≤ 0 °C) and warm winter (BIO6 > 0 °C) areas. Wild C. oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N_e than those in warm winter areas. 155 single-nucleotide polymorphisms (SNPs) were significantly correlated with the key bioclimatic variables (106 SNPs significantly correlated with BIO6). Twenty key SNPs and 15 key copy number variation regions (CNVRs) were found with genotype differentiation > 50% between the two groups of wild C. oleifera. Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance, and they were also found within a CNVR suggesting interactions between them. Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress. The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.

The black wolfberry (Lycium ruthenicum; 2n = 2x = 24) is an important medicinal plant with ecological and economic value. Its fruits have numerous beneficial pharmacological activities, especially those of anthocyanins, polysaccharides, and alkaloids, and have high nutritional value. However, the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms. In this study, we developed the telomere-to-telomere (T2T) nearly gapless genome of L. ruthenicum (2.26 Gb) by integrating PacBio HiFi, Nanopore Ultra-Long, and Hi-C technologies. The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated. Approximately 80% of the repetitive sequences were identified, of which long terminal repeats (LTRs) were the most abundant, accounting for 73.01%. The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species. The species-specific genes of L. ruthenicum were related to defense mechanisms, salt tolerance, drought resistance, and oxidative stress, further demonstrating their superior adaptability to arid environments. Based on the assembled genome and fruit transcriptome data, we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L. ruthenicum, most of which were highly expressed at a later stage in fruit development. Furthermore, 154 potential disease resistance-related nucleotide-binding genes have been identified in the L. ruthenicum genome. The whole-genome and proximal, dispersed, and tandem duplication genes in the L. ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways. These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.

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.

The future distribution of invading species depends on the climate space available and certain life history traits that facilitate invasion. Here, to predict the spread potential of plant species introduced in North America north of Mexico (NAM), we compiled distribution and life history data (i.e., seed size, life form, and photosynthetic pathways) for 3021 exotic plant species introduced to NAM. We comparatively examined the species’ range size and climate space in both native and exotic regions and the role of key life history traits. We found that large climate space for most exotic plants is still available in NAM. The range sizes in global exotic regions could better predict the current range sizes in NAM than those in global native regions or global native plus exotic regions. C3 species had larger ranges on average than C4 and CAM plants, and herbaceous species consistently showed stronger relationships in range size between native and exotic regions than woody species, as was the case within the C3 species group. Seed size was negatively related to range size both in native regions and in NAM. However, seed size surprisingly showed a positive correlation with global exotic range size and no correlation with the current actual global (native plus exotic) range size. Our findings underline the importance of species’ native distribution and life history traits in predicting the spread of exotic species. Future studies should continue to identify potential climate space and use underappreciated species traits to better predict species invasions under changing climate.

Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades. Debregeasia (Urticaceae), an economically important genus, presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments. Here, we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in Debregeasia. We also used a universal set of 353 nuclear genes to explore reticulate evolution and biogeographic history of Debregeasia. Plastomes of Debregeasia exhibited the typical quadripartite structure with conserved gene content and marginal independent variations in the SC/IR boundary at inter- and intra-specific levels. Three Debregeasia species were non-monophyletic and could not be discerned by any barcode; however, ultra-barcodes identified the remaining six (67%), outperforming standard barcodes (56%). Our phylogenetic analyses placed Debregeasia wallichiana outside the genus and suggested six monophyletic clades in Debregeasia, although the placement between Debregeasia hekouensis and Debregeasia libera varied. There was extensive trait overlap in key morphologically diagnostic characters, with reticulation analysis showing potentially pervasive hybridization, likely influenced by speciation patterns and overlaps between species ranges. We inferred that Debregeasia crown diversification began at ca. 12.82 Ma (95% HPD: 11.54-14.63 Ma) in the mid-Miocene within Australia, followed by vicariance and later long-distance dispersal, mainly out of southern China. Our findings highlight the utility of genomic data with integrative lines of evidence to refine species delimitation and explore evolutionary relationships in complex plant lineages.

Angiosperms experienced one of the most remarkable radiations of land plants and are now the dominant autotrophs in terrestrial ecosystems. Recent phylogenomic studies based on large-scale data from plastid, mitochondrial, or nuclear transcriptomes/genomes and increased taxon sampling have provided unprecedent resolution into the phylogeny of flowering plants. However, owing to ancient rapid radiations, the interrelationships among the five lineages of Mesangiospermae, the vast majority of angiosperms, remain contentious. Here we show that, although plastid and mitochondrial genomes lack sufficient phylogenetic signal for resolving deeper phylogeny, the relationships among five mesangiosperm lineages can be confidently resolved under better-fitting models using genome-scale data. According to our Bayesian cross-validation and model test in a maximum likelihood framework, site-heterogeneous models (e.g., CAT-GTR + G4, LG + C20 + F + G) outperform site-homogeneous or partition models often used in previous studies. Under site-heterogeneous models, the approximately unbiased test favored our preferred tree recovered from various datasets: Ceratophyllales (coontails) are robustly recovered as sister to monocots, and they together are sister to the clade comprising magnoliids, Chloranthales, and eudicots. Our phylogenomic analyses resolve the last enigma of the deeper phylogeny of angiosperms and emphasize the efficacy of modeling compositional heterogeneity in resolving rapid radiations of plants.

Biological collections are critical for the understanding of species distributions and for formulating biodiversity conservation strategies. However, biological collections are susceptible to various biases, including the “road-map effect”, meaning that the geography of biological collections can be influenced by road networks. Here, using species occurrence records derived from 921,233 plant specimens, we quantified the intensity of the “road-map effect” on floristic collections of China, and investigated its relationships with various environmental and socio-economic variables. Species occurrence records mainly distributed in major mountain ranges, while lowlands were underrepresented. The distance of species occurrence records to the nearest road decreased from 19.54 km in 1960s to 3.58 km in 2010s. These records showed significant clustering within 5 km and 10 km buffer zones of roads. The road density surrounding these records was significantly higher than that in random patterns. Collectively, our results confirmed a significant “road-map effect” in the floristic collections of China, and this effect has substantially intensified from the 1960s to the 2010s, even after controlling for the impact of road network expansion. Topographic, climatic and socio-economic variables that determine regional species diversity, vegetation cover and human impact on vegetation played crucial roles in predicting the intensity of the “road-map effect”. Our findings indicate that biological surveys have become increasingly dependent on road networks, a trend rarely reported in published studies. Future floristic surveys in China should prioritize the lowland areas that have experienced stronger human disturbances, as well as remote areas that may harbor more unique and rare species.

Studies on plant diversity are usually based on the total number of species in a community. However, few studies have examined species richness (SR) of different plant life forms in a community along large-scale environmental gradients. Particularly, the relative importance (RIV) of different plant life forms in a community and how they vary with environmental variables are still unclear. To fill these gaps, we determined plant diversity of ephemeral plants, annual herbs, perennial herbs, and woody plants from 187 sites across drylands in China. The SR patterns of herbaceous plants, especially perennial herbs, and their RIV in plant communities increased with increasing precipitation and soil nutrient content; however, the RIV of annual herbs was not altered along these gradients. The SR and RIV of ephemeral plants were affected mainly by precipitation seasonality. The SR of woody plants had a unimodal relationship with air temperature and exhibited the highest RIV and SR percentage in plant communities under the harshest environments. An obvious shift emerged in plant community composition, SR and their critical impact factors at 238.5 mm of mean annual precipitation (MAP). In mesic regions (> 238.5 mm), herbs were the dominant species, and the SR displayed a relatively slow decreasing rate with increasing aridity, which was mediated mainly by MAP and soil nutrients. In arid regions (< 238.5 mm), woody plants were the dominant species, and the SR displayed a relatively fast decreasing rate with increasing aridity, which was mediated mainly by climate variables, especially precipitation. Our findings highlight the importance of comparative life form studies in community structure and biodiversity, as their responses to gradients differed substantially on a large scale.

Saussurea is one of the largest and most rapidly evolving genera within the Asteraceae, comprising approximately 520 species from the Northern Hemisphere. A comprehensive infrageneric classification, supported by robust phylogenetic trees and corroborated by morphological and other data, has not yet been published. For the first time, we recovered a well-resolved nuclear phylogeny of Saussurea consisting of four main clades, which was also supported by morphological data. Our analyses show that ancient hybridization is the most likely source of deep cytoplasmic-nuclear conflict in Saussurea, and a phylogeny based on nuclear data is more suitable than one based on chloroplast data for exploring the infrageneric classification of Saussurea. Based on the nuclear phylogeny obtained and morphological characters, we proposed a revised infrageneric taxonomy of Saussurea, which includes four subgenera and 13 sections. Specifically, 1) S. sect. Cincta, S. sect. Gymnocline, S. sect. Lagurostemon, and S. sect. Strictae were moved from S. subg. Saussurea to S. subg. Amphilaena, 2) S. sect. Pseudoeriocoryne was moved from S. subg. Eriocoryne to S. subg. Amphilaena, and 3) S. sect. Laguranthera was moved from S. subg. Saussurea to S. subg. Theodorea.

Alpine plants possess unique traits to adapt alpine environments. Whether leaf trait relationships of alpine plants can be captured by the two trait dimensions of organ size and resource economics is unknown. We hypothesized that, beyond the trait dimensions of leaf size and resource economics, non-structured carbohydrates (NSC) would reflect a dimension of cold-tolerance in alpine plants. To test this hypothesis, we measured 12 leaf traits critical to leaf construction and growth in 143 species across 7 sites ranging from alpine steppes to alpine meadows along an environmental gradient on the Tibetan Plateau. Furthermore, a cold resistance experiment was conducted at one of these sites to estimate the lethal temperature causing 50% frost damage (LT₅₀) of 11 alpine species. The majority of variations in 12 leaf traits of alpine plants were captured by three trait axes, in which leaf carbon (LCC) and NSC (including leaf starch; LSC and leaf soluble sugars; LSS) were clustered in a new dimension (PC3) beyond leaf size and structure, and resource economics. Although LCC, LSC and LSS all showed negative correlations with mean annual temperature, a significant negative correlation was only found between LSS and LT₅₀. It indicated that PC3 was able to reflect the cold-tolerance of alpine plants to some extent, in which LSS was the most critical trait. The storage and transformation of NSC under stressful conditions could reflect a dimension of long-term metabolic adaptation and cold-tolerance, which is an extension of the resource-utilization strategy beyond construction cost and growth.

Understanding how and why assemblage dissimilarity changes along spatial gradient is a great challenge in ecology, because answers to these questions depend on the analytical types, dimensions, and components of beta diversity we concerned. To obtain a comprehensive understanding of assemblage dissimilarity and its implications for biodiversity conservation in the Himalayas, we explored the elevational patterns and determinants of beta diversity and its turnover and nestedness components of pairwise and multiple types and taxonomic and phylogenetic dimensions simultaneously. Patterns of beta diversity and their components of different types and dimensions were calculated based on 96 sampling quadrats along an 1800-5400 m elevational gradient. We examined whether and how these patterns differed from random expectations using null models. Furthermore, we used random forest methods to quantify the role of environmental variables representing climate, topography, and human disturbance in determining these patterns. We found that beta diversity and its turnover component, regardless of its types and dimensions, shown a hump-shaped elevational patterns. Both pairwise and multiple phylogenetic beta diversity were remarkably lower than their taxonomic counterpart. These patterns were significantly less than random expectation and were mostly associated with climate variables. In summary, our results suggested that assemblage dissimilarity of seed plants was mostly originate from the replacement of closely related species determined by climate-driven environmental filtering. Accordingly, conservation efforts should better cover elevations with different climate types to maximalize biodiversity conservation, rather than only focus on elevations with highest species richness. Our study demonstrated that comparisons of beta diversity of different types, dimensions, and components could be conductive to consensus on the origin and mechanism of assemblage dissimilarity.

Root anatomical traits play an important role in understanding the link between root physiological function and ecological process. To determine how plants change root anatomical traits to adapt to distinct environments, we measured four key root anatomical traits—stele diameter (SD), cortex thickness (CT), root diameter (RD), and the stele to root diameter ratio (SDRD)—of first-order roots of 82 species collected from different vegetation zones along a 2000 m altitudinal gradient on the northern slope of Taibai Mountain. Compared with other altitudes, plants located in temperate birch and fir forests had thinner SD, CT, RD, and SDRD. We found that elevational variation in root anatomical traits could largely be explained by phylogenetic taxonomy (clade). In addition, changes in SD were driven by soil bulk density, whereas variations in CT and RD were influenced by soil available nitrogen. When phylogenetic factors were removed from our analysis, allometric relationships between RD and root anatomical traits (SD and CT) were observed across different altitudes. Our study reveals the influence of phylogeny and environment on the elevational variation in root anatomical traits and further supports the allometric relationship between root anatomical traits (SD and CT) and RD. These findings enhance our understanding of the evolutionary and adaptive mechanisms of root anatomical structures, providing a basis for predicting how root anatomical traits respond to global changes.

The utilization of palynological data for plant diversity reconstructions offers notable advantages in addressing the discontinuity of plant fossils in the stratigraphic record. However, additional studies of modern processes are required to validate or refine the accuracy of diversity results obtained from palynological data. In this study, we used a modern pollen dataset of China to compare the accuracy of plant diversity reconstructions using five different palynological diversity indices (i.e., the pollen species number, Berger–Parker index, Simpson diversity index, Hill index, and Shannon–Wiener index) over a large spatial scale. We then identified climate factors that are most strongly correlated with these patterns of plant diversity. We found that the index that most accurately reflects plant diversity is the Shannon–Wiener index. Our analyses indicated that the most effective indices at reflecting plant diversity are the Shannon–Wiener index and Berger–Parker index. Numerical analysis revealed that palynological diversity (measured using the Shannon–Wiener index) was strongly correlated with climatic parameters, in particular average temperature in the coldest month and annual precipitation, suggesting these factors may be primary determinants of plant diversity distribution. We also found that a threshold value of the normalized Shannon–Wiener index (NH = 0.4) approximately aligns with the contour line specifying 400 mm annual precipitation, serving as a rudimentary indicator for assessing plant diversity in arid versus humid climates. This study suggests that pollen diversity indices have remarkable potential for quantitatively reconstructing paleoclimatic parameters.

Exploring the worldwide patterns of endemism and the processes that lead to the formation of high-endemism centers is crucial in biogeography. This study examines the geographic distribution and ecological influences on the endemism of liverworts across 390 regions worldwide. We assess phylogenetic endemism and relative phylogenetic endemism in relation to eleven environmental factors, which represent current and Quaternary climate variations, as well as topographic and environmental heterogeneity. Areas with higher endemism in liverworts tend to have higher temperatures, precipitation, and environmental heterogeneity, but lower temperature seasonality and lesser impacts from Quaternary climate changes. Regions exhibiting notably high endemism are predominantly found in tropical Asia, Madagascar, eastern Australia, and the Andes, while those with notably low endemism are generally in temperate Eurasia and North America, parts of Africa, and eastern South America. Centers of neo-endemism are mainly in southern Africa, whereas centers of paleo-endemism are in southern South America, tropical Asia, and New Zealand. Environment variability is a more significant predictor of phylogenetic endemism than current climate conditions, which are themselves more predictive than variables related to Quaternary climate changes. Nevertheless, these three types of explanatory variables combined explain only about one-third of the variance in phylogenetic endemism.

DNA barcoding has been extensively used for species identification. However, species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods. In this study, we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification (AFRAID) method of species identification, a novel approach for precise species identification in plants. Specifically, we determined (1) the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae, (2) the minimum size of chloroplast dataset for species discrimination, and (3) minimum amount of next generation sequencing (NGS) data required for species identification. We found that species identification rates were highest when whole chloroplast genomes were used, followed by taxon-specific DNA barcodes, and then universal DNA barcodes. Species identification of 100% was achieved when chloroplast genome sequence coverage reached 20% and the original sequencing data reached 500,000 reads. AFRAID accurately identified species for all samples tested after 500,000 clean reads, with far less computing time than common approaches. These results provide a new approach to accurately identify species, overcoming limitations of traditional DNA barcodes. Our method, which uses next generation sequencing to generate partial chloroplast genomes, reveals that DNA barcode regions are not necessarily fixed, accelerating the process of species identification.

The sugarcane subtribe Saccharinae (Andropogoneae, Poaceae) was established in 1846, but its delimitation has long been debated. Moreover, the relationships among the genera of Saccharinae remain unclear, and there is no consensus on whether Pseudosorghum, a small genus in tropical Asia with only two species, should be included. Here, we performed phylogenomic analyses using whole plastomes (69 of them newly sequenced) from 132 individuals, representing 65 species in 19 related genera. We also built trees with nuclear ribosomal DNA sequences. Our results justify the inclusion of Pseudosorghum, likely also the Eulalia Clade III, in Saccharinae. Furthermore, both morphological and molecular analyses support merging the two Pseudosorghum species. The backbone relationships of the Saccharinae phylogeny were highly supported with four polyphyletic clades of Miscanthus and the inclusion of Narenga and Tripidium rufipilum in Saccharum. Pseudosorghum is moderately supported as sister to the Miscanthus Clade I, while the remaining Tripidium species could be excluded from the subtribe. Saccharinae is estimated to have originated ~3.73 million years ago in East Asia, followed by intercontinental dispersals. Our study provides a comprehensive phylogenetic framework for future taxonomic revisions of this economically important subtribe.

Understanding the underlying mechanisms driving species assembly along elevational gradients is of great interest in ecology and biogeography. The Himalaya is one of the world’s hotspots of biodiversity, and the elevational gradient of the central Himalaya in Nepal is one of the longest elevational gradients in the world. Mosses are important constituents of vegetation in the Himalaya, and knowledge of geographic patterns and ecological causes of phylogenetic structure of mosses along elevational gradients in the Himalaya is critical to understanding the assembly of plant diversity in general, and moss diversity in particular, in the Himalaya. Here, we investigate the relationships of phylogenetic structure metrics reflecting different evolutionary depths with elevation and climatic variables representing mean temperature and precipitation conditions, climate extremes, and climate seasonality for mosses distributed along an elevational gradient spanning about 5000 m in the central Himalaya, Nepal. For a given climatic variable, different metrics of phylogenetic structure show different spatial and climatic patterns, but all phylogenetic metrics standardized for species richness show that phylogenetic dispersion in moss assemblages tend to increase with increasing elevation and decreasing temperature. The standardized effect size of mean pairwise distance of moss assemblages shows a triphasic (zig-zag) pattern, which is generally consistent with the triphasic patterns previously found in angiosperms and ferns along the same elevational gradient. Our study shows that temperature-related variables and climate seasonality variables are more important drivers of phylogenetic dispersion in mosses in Nepal, compared with precipitation-related variables and climate extreme variables, respectively.

Herbaceous plants are an essential component of forest diversity and driver of ecosystem processes. However, because the growth forms and life-history strategies of herbaceous plants differ from those of woody plants, it is unclear whether the mechanisms that drive patterns plant diversity and community structure in these two plant groups are the same. In this study, we determined whether herb and woody plant communities have similar patterns and drivers of alpha- and beta-diversity. We compared species richness, distribution, and abundance of herbs to woody seedlings in a 20-ha Donglingshan warm-temperate forest (Donglingshan FDP), China. We also determined whether variation in patterns of species richness and composition are better explained by environmental or spatial variables. Herbaceous plants accounted for 72% of all species (81 herbaceous, 31 woody) recorded. Alpha- and beta-diversity were higher in herbs than in woody seedlings. Although alpha-diversity of herbs and woody seedlings was not correlated across the site, the local-site contributions to beta-diversity for herbs and woody seedlings were negatively correlated. Habitat type explained slightly more variation in herb community composition than in woody seedling composition, with the highest diversity in the low-elevation slope. Environmental variables explained the variation in species richness and composition more in herbaceous plants than in woody seedlings. Our results indicate that different mechanisms drive variation in the herb and woody seedling communities, with herbs exhibiting greater environmental sensitivity and habitat dependence. These findings contribute to the better understanding of herbaceous plant diversity and composition in forest communities.

The island rule, a general pattern of dwarfism in large species to gigantism in small species on islands relative to mainland, is typically seen as a macroevolutionary phenomenon. However, whether the ecological processes associated with abiotic and biotic factors generate a pattern of plant size variation similar to the island rule remains unknown. We measured plant height for 29,623 individuals of 50 common woody plant species across 43 islands in the Zhoushan Archipelago (8500 years old and yet to undergo major evolutionary adaptation) and the adjacent mainlands in China. We found pronounced variations in plant height, similar to those of the island rule. Interestingly, islands with low resource availability, such as low soil organic matter content and low precipitation, had a high degree of dwarfism; islands experiencing high environmental stress, such as high soil pH, had a high degree of dwarfism; and islands experiencing less plant–plant competition had a high degree of gigantism. The magnitude of plant dwarfism was higher on small and remote islands than on larger and nearer islands. These results highlight the importance of ecological processes associated with abiotic and biotic conditions in shaping the island rule-like patterns of plant size variation. Since our studied archipelago is too young to undergo major evolution, ecological processes likely played a prominent role in generating the observed pattern, challenging the notion that the evolutionary process is the dominant factor underlying the island rule. Future studies on the island rule need to perform experiments to disentangle evolutionary from ecological mechanisms.

The presence of heterozygous individuals in a population is crucial for maintaining genetic diversity, which can positively affect fitness and adaptability to environmental changes. While inbreeding generally reduces the proportion of heterozygous individuals in a population, polyploidy tends to increase the proportion. North American Populus tremuloides is one of the most widely distributed and ecologically important tree species in the Northern Hemisphere. However, genetic variation in Mexican populations of P. tremuloides, including the genetic signatures of their adaptation to a variety of environments, remains largely uncharacterized. The aim of this study was to analyze how inbreeding coefficient (F_IS) and ploidy are associated with clonal richness, population cover, climate and soil traits in 91 marginal to small, isolated populations of this tree species throughout its entire distribution in Mexico. Genetic variables were determined using 36,810 filtered SNPs derived from genome re-sequencing. We found that F_IS was approximately between 0 and -1, indicating an extreme heterozygosity excess. One key contributor to the observed extreme heterozygosity excess was asexual reproduction, although ploidy levels cannot explain this excess. Analysis of all neutral SNPs showed that asexual reproduction was positively correlated with observed heterozygosity (H_o) but negatively correlated with expected heterozygosity (H_e). Analysis of outlier SNPs also showed that asexual reproduction was positively correlated with H_o and negatively correlated with H_e, although this latter correlation was not significant. These findings support the presence of a Meselson effect.

Single-stranded DNA-binding proteins (SSBs) play essential roles in the replication, recombination and repair processes of organellar DNA molecules. In Arabidopsis thaliana, SSBs are encoded by a small family of two genes (SSB1 and SSB2). However, the functional divergence of these two SSB copies in plants remains largely unknown, and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete. In this study, phylogenetic, gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants. Based on accurate long-read sequencing results, ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA (mtDNA) and plastid DNA (ptDNA), accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes. Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.

Pollination niches, which encompass the factors influencing pollen exchange among angiosperms, are fundamental to understanding reproductive success and the intricate eco-evolutionary dynamics of plants. In this study, we investigated pollination niche shift among four sympatric Eriosyce cacti with restricted distributions in the South American Mediterranean region. Utilizing a comprehensive approach—including pollination niche analysis, pollinator color perception studies, reproductive output assessments, molecular phylogenetics, gene flow analyses, and species distribution modeling—we revealed a significant pollination niche displacement in E. chilensis and its variety, E. chilensis var. albidiflora. These taxa transitioned from a hummingbird-pollinated system prevalent in the Eriosyce sect. Neoporteria, characteristic of their sister species E. litoralis, to a bee-pollination strategy akin to that of the co-occurring species E. mutabilis. This shift highlights a simultaneous convergence of E. chilensis toward E. mutabilis and divergence from E. litoralis in pollination strategies, providing adaptive advantages by reducing pollen limitation and enhancing seed production. The morphological and flowering phenological similarities between E. chilensis and E. mutabilis suggest the evolution of a shared advertising display, potentially indicative of floral mimicry, wherein both species benefit from attracting shared bee pollinators. Genomic analyses reveal distinct pollinator-driven selection pressures, with E. chilensis/E. albidiflora exhibiting traits that promote reproductive isolation from E. litoralis, supporting a scenario of rapid speciation occurring within the past half of million years in the absence of geographic barriers. These findings underscore the pivotal role of pollinator interactions in shaping angiosperm speciation and biodiversity, highlighting their dynamic influence on ecological and evolutionary processes.

Latitudinal patterns of tree β-diversity reveal important insights into the biogeographical processes that influence forest ecosystems. Although previous studies have extensively documented β-diversity within relatively small spatial extents, the potential drivers of β-diversity along latitudinal gradients are still not well understood at larger spatial extents. In this study, we determined whether tree β-diversity is correlated with latitude in forests of southeastern China, and if so, what ecological processes contribute to these patterns of tree β-diversity. We specifically aimed to disentangle the relative contributions from interspecific aggregation and environmental filtering across various spatial extents. We delineated regional communities comprising multiple nearby national forest inventory (NFI) plots around random focal plots. The number of NFI plots in a regional community served as a surrogate for spatial extent. We also used a null model to simulate randomly assembled communities and quantify the deviation (β-deviation) between observed and expected β-diversity. We found that β-diversity decreased along a latitudinal gradient and that this pattern was clearer at larger spatial extents. In addition, latitudinal patterns of β-deviation were explained by the degree of species spatial aggregation. We also identified environmental factors that drive β-deviation in these forests, including precipitation, seasonality, and temperature variation. At larger spatial extents, these environmental variables explained up to 84% of the β-deviation. Our results reinforce that ecological processes are scale-dependent and collectively contribute to the β-gradient in subtropical forests. We recommend that conservation efforts maintain diverse forests and heterogeneous environments at multiple spatial extents to mitigate the adverse effects of climate change.

The global rise in animal protein consumption has significantly amplified the demand for fodder. A comprehensive understanding of the diversity and characteristics of existing fodder resources is essential for balanced nutritional fodder production. This study investigates the diversity and composition of fodder plants and identifies key species for cattle in Zhaotong City, Yunnan, China, while documenting indigenous knowledge on their usage and selection criteria. Ethnobotanical surveys were conducted in 19 villages across seven townships with 140 informants. Data were collected through semi-structured interviews, free listing, and participatory observation, and analyzed using Relative Frequency Citation. A total of 125 taxa (including 106 wild and 19 cultivated) were reported. The most cited family is Poaceae (27 taxa, 21.43%), followed by Asteraceae (17 taxa, 13.49%), Fabaceae (14 taxa, 11.11%), Polygonaceae (9 taxa, 7.14%) and Lamiaceae (4 taxa, 3.17%). The whole plant (66.04%) and herbaceous plants (84.80%) were the most used parts and life forms. The most cited species were Zea mays, Brassica rapa, Solanum tuberosum, Eragrostis nigra, and Artemisia dubia. Usage of diverse fodder resources reflects local wisdom in managing resource availability and achieving balanced nutrition while coping with environmental and climatic risks. Preferences for certain taxonomic groups are due to their quality as premier fodder resources. To promote integrated crop-livestock farming, we suggest further research into highly preferred fodder species, focusing on nutritional assessment, digestibility, meat quality impacts, and potential as antibiotic alternatives. Establishing germplasm and gene banks for fodder resources is also recommended.

The expansion of road networks in recent decades has drawn considerable attention due to its impact on biodiversity in high-altitude ecosystems. Here, we conducted a comprehensive field survey to investigate the effects of road disturbance on plant diversity in alpine grasslands on the Tibetan Plateau. Our results indicate that road disturbance caused no significant changes in species richness, Shannon-Wiener’s diversity, or Simpson’s diversity, and the alteration in species composition was limited. These findings demonstrate the robust resistance of alpine grassland plant diversity to road disturbance. Plant diversity exhibited more resistance to road disturbance in regions with more hostile environments, such as plateau sub-frigid regions and alpine steppes. Our study suggests that road construction in the Tibetan Plateau poses limited risk to plant biodiversity.

Species boundaries are dynamic and constantly challenged by gene flow. Understanding the strategies different lineages adopt to maintain ecological and genetic distinctiveness requires employing an integrative species concept that incorporates data from a variety of sources. In this study, we incorporated genetic, ecological, and environmental evidence to assess the extent of speciation or evolutionary divergence within a monophyletic yet dimorphic group (i.e., clade Leucolirion consisting of six species) within the genus Lilium. This clade consists of two lineages that exhibit unexpectedly distinct perianth appearances: whitish trumpet (funnel form, encompassing four species) and orange recurved (reflex form, including two species), respectively, which are separated by completely different pollination syndromes. Transcriptome-based nuclear and plastome datasets indicate that these two lineages are isolated, with only weak ancient gene flow between them. Within each lineage, several taxa with incomplete isolation have diverged, as indicated by weak genetic structure, strong gene flow, and conflicts between nuclear and chloroplast phylogenies, especially in the trumpet lineage. Although these taxa are not entirely independent, our evidence indicates that they are diverging, with recent gene flow disappearing and multiple isolation strategies emerging, such as differences in flowering time and niche specialization. Taken together, our findings suggest that species divergence and maintenance in Lilium are driven by a combination of adaptive and non-adaptive processes, highlighting the complex interplay of historical climate changes, ecological adaptation, and gene flow in shaping biodiversity within this genus.

Evolutionary transitions from sexual to asexual reproduction should have significant influences on genetic divergence and polymorphism at the genome level. Plant lineages with diverse reproductive systems provide opportunities to investigate this question using comparative approaches and studies of molecular evolution. We investigated evidence for differences among the transcriptomes of 19 Dioscorea species (wild yams) with diverse reproductive systems. These included sexual species, those that propagate primarily by bulbils, and those with mixed sexual and asexual reproductive modes. We examined how transitions between these reproductive systems affected between-species divergence and within-species polymorphism. Primarily asexual species exhibited a reduced efficacy of natural selection and accumulation of deleterious mutations for both divergence and polymorphism. In contrast, species with mixed reproductive strategies involving both seed and clonal reproduction showed no evidence of an increased fixation of harmful mutations at the divergence level, while an accumulation of genetic load present in polymorphism was evident. Our study indicates that the genetic consequences of evolutionary transitions from sexual to predominantly clonal reproduction is likely to depend on both the duration and extent of asexuality occurring in populations.

The parasitic dodder (Cuscuta, Convolvulaceae) species have wide ranges of hosts. However, some plants, including the cultivated tomato (Solanum lycopersicum), have different degrees of resistance to Cuscuta. The cultivated tomato plants activate a strong hypersensitive response (HR) where Cuscuta haustoria penetrate stems of cultivated tomato, but the underlying mechanisms by which the cultivated tomato perceives Cuscuta and activates resistance remain unclear. In this study, we show that the phytohormones jasmonic acid (JA) and salicylic acid (SA) in cultivated tomato stems were highly induced by Cuscuta australis parasitization. Genetic analyses and experiments of supplementation of JA or SA indicated that the JA and SA pathway not only are both required for activation of HR against Cuscuta parasitization but also function in non-HR-based resistance. The Cuscuta Receptor 1 (CuRe1), which is a leucine-rich repeat receptor-like protein, and suppressor of BAK1-interacting receptor kinase (SOBIR1) and SOBIR1-like, two adaptor kinases, are also important for HR-based and non-HR-based resistance. Importantly, we found that the JA and SA pathway both transcriptionally regulate CuRe1. However, in the cure1 mutants, JA and SA levels were still normally induced by C. australis parasitization. We propose a linear model that an unknown receptor perceives Cuscuta parasitization and thus triggers accumulation of JA and SA, which in turn induce the transcription of CuRe1, and CuRe1 and SOBIR1/SOBIR1-like thereby activate HR-based and non-HR-based resistance to Cuscuta. This study underscores the important roles of hormone signaling and resistance (R) genes in host plant-parasitic plant interactions.

Rivers are crucial in the spread of invasive plants. Invasive plants alter their seed traits to adapt to environmental changes and promote invasion. Studying the trait changes in invasive plant seeds may improve the understanding of their propagation mechanisms along the river and provide appropriate control measures. In this study, seven Ambrosia trifida populations along the Liaohe River were used as study subjects. The results showed that the seven A. trifida populations were closely related and exhibited a certain gene exchange, but the absence of evidence of directed gene flow among populations did not confirm that rivers were the medium of seed dispersal of A. trifida. Along the Liaohe River, from top to bottom, the positive view area, length, width, perimeter, and thousand seed weight of A. trifida seeds showed an increasing trend. The total nitrogen and phosphorus contents in the river water of the A. trifida population in the lower reaches of the Liaohe River were higher than those at the other sites. Furthermore, along the river, from top to bottom, the available nitrogen, total nitrogen, total potassium, available potassium, and organic matter contents in the soil in which A. trifida populations grew showed significant increasing trends. River structure, water quality, and soil nutrients had direct and indirect effects on seed morphology. Soil total nitrogen, available potassium, and organic matter had significant positive effects on seed positive view area and perimeter, suggesting that the maternal effect played a critical role in shaping seed morphology. Our analysis showed that soil nutrients along the river may be the primary driver that governs changes in A. trifida seed traits.

Change of flower color can readily lead to a shift in pollinators, potentially causing pollinator mediated reproductive isolation or even speciation. Here, we examined the ecological and evolutionary consequences of flower color polymorphism in Roscoea cautleoides, an alpine ginger with sympatric distribution of purple- and yellow-flowered plants. Variations in pollinator visitation and specialization to the flower color contributed greatly to pre-zygotic reproductive isolation, with post-zygotic isolation also observed in reciprocal pollination. Yellow-flowered plants evolved independently from purple-flowered plants in two populations due to the absence of anthocyanins, as supported by metabolic, expression, and genetic analysis. Despite early genetic divergence between the two-flower-colored plants, highly differentiated genes were associated with reproduction and stress, while highly selective genes were enriched in stress. Our results suggest that parallel loss of anthocyanins leads to flower color polymorphism in different populations of R. cautleoides, with pollinator preference contributing to reproductive isolation and subsequent genetic differentiation, indicating the process of incipient speciation triggered by flower color changes with sympatric distribution.

The primary mechanism driving plant species loss after nitrogen (N) addition has been often hypothesized to be asymmetric competition for light, resulting from increased aboveground biomass. However, it is largely unknown whether plants’ access to soil water at different depths would affect their responses, fate, and community composition under nitrogen addition. In a semiarid grassland exposed to 8-years of N addition, we measured plant aboveground biomass and diversity under four nitrogen addition rates (0, 4, 10, and 16 g m^-2 year^-1), and evaluated plant use of water across the soil profile using oxygen isotope. Aboveground biomass increased significantly, but diversity and shallow soil-water content decreased, with increasing rate of nitrogen addition. The water isotopic signature for both plant and soil water at the high N rate indicated that Leymus secalinus (a perennial grass) absorbed 7% more water from the subsurface soil layer (20-100 cm) compared to Elymus dahuricus (a perennial grass) and Artemisia annua (an annual forb). L. secalinus thus had a significantly larger biomass and was more abundant than the other two species at the high N rate but did not differ significantly from the other two species under ambient and the low N rate. Species that could use water from deeper soil layers became dominant when water in the shallow layers was insufficient to meet the demands of increased aboveground plant biomass. Our study highlights the importance of water across soil depths as key driver of plant growth and dominance in grasslands under N addition.

Patterns and drivers of species-genetic diversity correlations (SGDCs) have been broadly examined across taxa and ecosystems and greatly deepen our understanding of how biodiversity is maintained. However, few studies have examined the role of canopy structural heterogeneity, which is a defining feature of forests, in shaping SGDCs. Here, we determine what factors contribute to α- and β-species-genetic diversity correlations (i.e., α- and β-SGDCs) in a Chinese subtropical forest. For this purpose, we used neutral molecular markers to assess genetic variation in almost all adult individuals of the dominant tree species, Lithocarpus xylocarpus, across plots in the Ailaoshan National Natural Reserve. We also quantified microhabitat variation by quantifying canopy structure heterogeneity with airborne laser scanning on 20 1-ha subtropical forest plots. We found that species α-diversity was negatively correlated with genetic α-diversity. Canopy structural heterogeneity was positively correlated with species α-diversity but negatively correlated with genetic α-diversity. These contrasting effects contributed to the formation of a negative α-SGDC. Further, we found that canopy structural heterogeneity increases species α-diversity and decreases genetic α-diversity by reducing the population size of target species. Species β-diversity, in contrast, was positively correlated with genetic β-diversity. Differences in canopy structural heterogeneity between plots had non-linear parallel effects on the two levels of β-diversity, while geographic distance had a relatively weak effect on β-SGDC. Our study indicates that canopy structural heterogeneity simultaneously affects plot-level community species diversity and population genetic diversity, and species and genetic turnover across plots, thus driving α- and β-SGDCs.

Co-flowering species may have evolved strategies to avoid or tolerate the adverse effects of heterospecific pollen deposition. However, the precondition for this evolutionary response is spatial-temporal stability, an aspect currently understudied. Here, we examined the spatial-temporal stability in conspecific and heterospecific pollen loads on stigmas across 19 co-flowering species in six sub-alpine meadow communities over four consecutive years. We found that, although conspecific and heterospecific pollen loads, as well as proportions of heterospecific pollen, differed significantly among species, with heterospecific pollen proportion ranging from 0.1% to 41.8%, variation in heterospecific pollen proportion among species was stable across different years and communities. The most important predictor of variation in both conspecific and heterospecific pollen loads, as well as heterospecific pollen proportions, was species identity; furthermore, this factor was independent of phylogenetic relationship. The proportion of heterospecific pollen varied less within species that had high proportions of heterospecific pollen. Furthermore, both the proportion of heterospecific pollen and its coefficient of variation were more strongly driven by heterospecific pollen than by conspecific pollen. Our study suggests that variation in stigmatic pollen load among co-flowering species is spatially and temporally consistent, a precondition for the tolerance-avoidance strategy. This study provides new insights into how different plant species respond to heterospecific pollen deposition.

The karst forest in southwestern China is characterized by thin soil layers, numerous fissures and holes, resulting in low soil water availability and poor water retention, making it challenging for plant growth and survival. While the relationship between plant functional traits and tree growth performance has been extensively studied, the links between tree seasonal growth and drought-tolerant traits in tree species with different leaf habit remains poorly understood. This study evaluated the associations between four-year averaged rainy season stem diameter growth rate and 17 branch and leaf traits across evergreen and deciduous species in a tropical karst forest in southwest China. The cross-species variations in tree growth rates were related to plant hydraulic traits (e.g., vessel lumen diameter, xylem vessel density, stomatal density, and stomatal size) and leaf anatomical traits (e.g., total leaf thickness, lower/upper epidermis thickness, and spongy thickness). The growth of evergreen trees exhibited lower hydraulic efficiency but greater drought tolerance than deciduous tree, which enabled them to maintain higher persistence under low soil water availability and consequently a relatively longer growing season. In contrast, deciduous species showed no correlation between their functional traits and growth rate. The distinct water use strategies of evergreen and deciduous trees may offer a potential explanation for their co-existence in the tropical karst forests.

Plants and their interaction partners offer unparalleled views of evolutionary ecology. Nectar larceny, entailing nectar extraction without pollinating, is thought to be an example of a harmful, antagonistic behavior, but the precise consequences of floral larceny on plant reproductive success remain contentious. We conducted a comprehensive meta-analysis of 153 studies across 120 plant species, using 14 moderators to assess the effects of floral larceny on plant reproductive success and examine the key moderators. We found that floral larceny negatively impacts flower traits, pollinator visitation, pollen deposition, and fruit set, while having a neutral effect on critical female fitness indicators, such as seed set and seed quality, as well as on male fitness. By altering pollinator behavior, floral larceny may reduce geitonogamy, potentially enhancing genetic diversity. Additionally, factors such as pollinator type, plant mating system, and pollen limitation were identified as key moderators of these effects. Our analysis reveals an ultimately neutral effect of floral larceny on plant reproductive success, with potential benefits in certain contexts. These findings suggest that floral larceny plays a complex and multifaceted role within plant-pollinator interactions, facilitating the evolutionary stability and coexistence of floral larcenists and host plants.

Rapid growth is an innovative trait of woody bamboos that has been widely studied. However, the genetic basis and evolution of this trait are poorly understood. Taking advantage of genomic resources of 11 representative bamboos at different ploidal levels, we integrated morphological, physiological, and transcriptomic datasets to investigate rapid growth. In particular, these bamboos include two large-sized and a small-sized woody species, compared with a diploid herbaceous species. Our results showed that gibberellin A1 was important for the rapid shoot growth of the world's largest bamboo, Dendrocalamus sinicus, and indicated that two gibberellins (GAs)-related genes, KAO and SLRL1, were key to the rapid shoot growth and culm size in woody bamboos. The expression of GAs-related genes exhibited significant subgenome asymmetry with subgenomes A and C demonstrating expression dominance in the large-sized woody bamboos while the generally submissive subgenomes B and D dominating in the small-sized species. The subgenome asymmetry was found to be correlated with the subgenome-specific gene structure, particularly UTRs and core promoters. Our study provides novel insights into the molecular mechanism and evolution of rapid shoot growth following allopolyploidization in woody bamboos, particularly via subgenome asymmetry. These findings are helpful for understanding of how polyploidization in general and subgenome asymmetry in particular contributed to the origin of innovative traits in plants.

Mating patterns in angiosperms are typically nonrandom, yet the mechanisms driving nonrandom mating remain unclear, especially regarding the effects of quantitative floral traits on plant mating success across male and female functions. In this study, we investigated how variation in spur length and flower number per plant influences mating patterns in Aquilegia rockii within a natural population. Using marker-based paternity analyses and manipulative experiments, we assessed the role of these traits in mating success across both sexual functions. We found significant variation in the mate composition between male and female function, with spur-length frequency positively associated with female outcrossing rate and mate number, but not with male outcrossing or mate number. Most mating events occurred within 10 m, and spur-length frequency positively correlated with mating distance. Regardless of selfing, there was evidence for assortative mating for spur length. Although spur length did not correlate with pollinator visitation, plants with mid-length spurs had higher seed set than those with shorter or longer spurs when autonomous selfing was excluded. Flowers number per plant was only associated with mating distance and female outcrossing rate. Our results suggest that spur length plays a key role in nonrandom mating by frequency-dependent mating, with implications for stabilizing selection and maintenance of genetic diversity. This study advances our understanding of floral diversity by dissecting the role of quantitative floral traits in plant mating through both female and male functions.

Nutrient acquisition through symbiotic ectomycorrhizal fungi is carbon (C) costly but fundamental for plant growth, community, and ecosystem functioning. Here, we examined the functions of roots and mycorrhiza with respect to nutrient uptake after artificially inducing C limitation-seven months after girdling of an ectomycorrhizal tree, Pinus taeda. Root physiological activity (measured as root nitrogen content and root exudation) declined after girdling and was accompanied with 110% and 340% increases in mycorrhizal colonization and extramatrical hyphal length, respectively. Fungi colonizing roots switched to a community characterized by higher C efficiency (lower C cost) of nutrient acquisition (CENA, the amount of nutrient acquisition per unit C cost) and lower network complexity, indicating a tradeoff between CENA and stability of the fungal community. Root transcriptome analysis suggested a shift in metabolic pathways from a tricarboxylic acid cycle decomposition of carbohydrate to lipid biosynthesis to maintain closer associations with mycorrhiza for nutrient cycling after the girdling. By integrating multi-level evidence, including root transcriptome, fungal composition, and network complexity data, we demonstrate an increased dependence on mycorrhiza for nutrient acquisition under the C limitation condition, which is likely due to a shift to fungal community with higher CENA at the cost of lower stability.