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.

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.

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.

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.

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 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.

The formation of pantropical intercontinental disjunction (PID) in plants has generally been attributed to vicariance, boreotropical migration, and long-distance dispersal. However, this pattern has primarily been examined in herbs, shrubs, and trees, and less commonly studied in interlayer plant taxa. Here we examined evolutionary processes that resulted in the PID of a pantropical woody liana, Uncaria (Rubiaceae). We first constructed a comprehensive phylogeny by employing 73 plastid protein-coding sequences from 29 accessions of Uncaria (including 16 newly sequenced) from different continents. We then inferred divergence time, history and ecological niche evolution of this genus. Our results showed that Uncaria consisted of four well-supported clades that belonged to two geographically distinct lineages: the Asia-Oceania lineage and the Afro-Neotropical lineage. Biogeographic reconstruction showed this genus likely originated in Asia during the early Miocene (ca. 19.03 Ma) and the Middle Miocene Climatic Optimum may have triggered the early diversification of Uncaria. Due to its recent origin and small seeds with long wings, wind or water-mediated long-distance dispersal may have contributed to the distribution of Uncaria in tropical Oceania (via stepping-stone dispersal) and tropical Africa and America (by transoceanic dispersal). Our findings also indicate that diversification of Uncaria was primarily driven by ecological niche divergence, particularly climatic factors. Our study emphasizes the dual role of climatic niche divergence and long-distance dispersal in shaping the PID of Uncaria, providing references for many other extant lineages with similar distributions.

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.

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.

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.

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.

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.

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.

Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon (EASM) and subtropical evergreen broad-leaved forests (EBLFs). However, how the genomic insights of EBLFs' species correspond to environmental shifts induced by the EASM remains limited. In this study, we investigated the adaptive mechanisms of evergreen Engelhardia species in response to the EASM through genome sequencing and comparative genomic analyses from the de novo genome assemblies of five closely related Engelhardia taxa and one Rhoiptelea species. Our findings revealed that the divergence of evergreen trees from their sister deciduous species is closely associated with the onset and intensification of the EASM. This genomic transition may have coincided with a significant expansion of the terpene synthase (TPS) gene family in E. fenzelii, driven by four distinct modes of gene duplication. This expansion enhances the biosynthesis of terpene volatiles, providing a defensive mechanism against potential herbivory in EASM affected environments. We also identified a shared whole-genome duplication (WGD) event across Engelhardia, along with substantial differences in transposable element (TE) composition and activity, which contributed to genome size variation between E. fenzelii and E. roxburghiana. In addition, demographic analyses revealed a continuous population decline over the past 10 million years, further exacerbated by recent human disturbance, underscoring the conservation urgency for these species. These results not only provide preliminary insights into the complex evolutionary dynamics within the Engelhardia genus from genomic insights (e.g., the intricate relationships between genomic variations, environmental changes, and adaptive responses driven by significant climatic events such as the EASM), but also provides valuable insights into the conservation significance of EBLFs.

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.

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.

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.

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

Local adaptation is critical for plant survivals and reproductions in the context of global environmental change. Heterogeneous environments impose various selection pressures that influence the fitness of organisms and leave genomic signatures during the process of adaptation to local environments. However, unveiling the genomic signatures of adaptation still poses a major challenge especially for perennials due to limited genomic resources. Here, we utilized Actinidia eriantha, a Chinese endemic liana, as a model case to detect drivers of local adaptation and adaptive signals through landscape genomics for 311 individuals collected from 25 populations. Our results demonstrated precipitation and solar radiation were two crucial factors influencing the patterns of genetic variations and driving adaptive processes. We further uncovered a set of genes involved in adaptation to heterogeneous environments. Among them, AeERF110 showed high genetic differentiation between populations and was confirmed to be involved in local adaptation via changes in allele frequency along with precipitation (Prec_03) and solar radiation (Srad_03) in native habitats separately, implying that adaptive loci frequently exhibited environmental and geographic signals. In addition, we assessed genetic offsets of populations under four future climate models and revealed that populations from middle and east clusters faced higher risks in adapting to future environments, which should address more attentions. Taken together, our study opens new perspectives for understanding the genetic underpinnings of local adaptation in plants to environmental changes in a more comprehensive fashion and offered the guides on applications in conservation efforts.

Invasive alien plant species (IAPS) pose severe threats to global biodiversity conservation. Effective management of IAPS requires mapping their distribution and identifying the environmental factors that drive their spread. The Gaoligong Mountains, a renowned biodiversity hotspot in southwestern China, currently face the dual challenges of IAPS invasion and climate change. However, we know little about the distribution patterns, key environmental drivers, and sensitivity of IAPS to future climate change in this region. In this study, we mapped IAPS richness distribution and identified invasion hotspots throughout the Gaoligong Mountains. In addition, we assessed the relative importance of environmental variables in shaping the spatial distribution of IAPS richness and projected potential shifts in IAPS richness under various climate change scenarios. We identified 161 IAPS, primarily concentrated in the low-elevation tropical and subtropical regions along river valleys, forming belt-like invasion hotspots. The key factors shaping IAPS richness included disturbance complexity, elevation, seasonal precipitation, and vegetation types. Notably, IAPS richness significantly declined with increasing elevation and latitude but increased with higher disturbance complexity. Moreover, IAPS were more prevalent in grasslands and shrublands than in forested areas. Ensemble modeling of future climate scenarios predicted that the distribution of IAPS richness would shift to progressively higher elevations. These findings provide valuable insights for managing IAPS in mountainous regions that play a crucial role in global biodiversity conservation.

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

Predicting whether alien species will invade a native community is a key challenge in invasion ecology. One factor that may help predict invasion success is phylogenetic relatedness. Darwin proposed that closely related species tend to share similar niches, although this relationship may be influenced by various ecological and evolutionary factors. To test this, we classified alien Asteraceae species in China into three categories based on their invasion status and the extent of ecological damage: introduced, naturalized, and invasive. We then compared the genetic relationships and niche overlap between alien and native Asteraceae species. We found that invasive Asteraceae species are more closely related to native Asteraceae species than are introduced and naturalized species. However, alien Asteraceae species (including introduced, naturalized, and invasive species) exhibited relatively low niche overlap with native Asteraceae species. These findings suggest that the main premise underlying Darwin's naturalization conundrum, namely, the universality of phylogenetic niche conservatism, may not hold true. Instead, our findings indicate that alien species are more likely to invade successfully when they are more closely related to native plants, exhibit less niche overlap, and maintain conservative niches during the invasion process. These findings provide new insights into the mechanisms of alien plant invasions, highlight the relationship between alien species invasions and native community vulnerability, and offer important insights into the development of effective biological invasion management strategies.

Managing invasive species requires identifying the factors that determine alien species invasion success. This study investigates how anthropogenic and biogeographical factors influence alien plant invasion in the Sanyang Wetlands, a human-dominated island system in Wenzhou City, China. Specifically, we analyzed whether human activities (e.g., habitat heterogeneity, proportion of road area, and cultivation) and island characteristics (e.g., island area, isolation) affect the diversity of native and invasive plant species similarly. We also assessed the applicability of the equilibrium theory of island biogeography to invasive plant species diversity and examined how these factors affect invasive plant species with different dispersal syndromes (anemochore, zoochore, and autochore). We found that both invasive and native species richness positively correlate with island area, habitat heterogeneity, and proportion of road area. However, although native species richness was negatively correlated with isolation, invasive species richness was not. The diversity and composition of invasive species with different dispersal syndromes were determined by different variables; for example, the composition and diversity of zoochores was increased by habitat heterogeneity, while anemochore species richness was increased by the proportion of road area, whereas anemochore species composition was influenced by distance to the nearest island. We conclude that habitat fragmentation differentially affects invasive and native plant diversity, aligning with the predictions of the equilibrium theory of island biogeography only for native species but not for invasive species. Our findings indicate that tailoring habitat attributes and regulating human activities could be effective strategies for mitigating the spread of invasive species in fragmented landscapes.

Species richness in any area results from the interplay of the processes of speciation, extinction, and dispersal. The relationships between species richness and climate should be considered as an outcome of the effects of climate on speciation, extinction, and dispersal. Diversification rate represents the balance of speciation and extinction rates over time. Here, I explore diversification rates in mosses across geographic and climatic gradients worldwide. Specifically, I investigate latitudinal patterns and climatic associations of the mean diversification rate of mosses at global, hemispheric, and smaller scales. I find that the mean diversification rate of mosses is positively correlated with species richness of mosses, increases with decreasing latitude and increasing mean annual temperature and annual precipitation, and is more strongly associated with mean annual temperature than with annual precipitation. These findings shed light on variation of species richness in mosses across the world. The negative relationship between species richness and latitude and the positive relationship between species richness and mean diversification rate in mosses suggest that higher moss species richness at lower latitudes might have resulted, at least to some degree, from higher moss diversification rates at lower latitudes.

Climate and grazing have a significant effect on vegetation structure and soil organic carbon (SOC) distribution, particularly in mountain ecosystems that are highly susceptible to climate change. However, we lack a systematic understanding of how vegetation structure reacts to long-term grazing disturbances, as well as the processes that influence SOC distribution. This study uses multiple sets of data spanning 20 years from a typical alpine grassland in the Qilian Mountains to investigate the effects of climate and grazing on various root-type grasses as well as the mechanisms that drive SOC distribution. We found that grazing increases the biomass of annual, biennial and perennial taproots while decreasing that of perennial rhizomes. We also found that various root-type grasses have different responses to climate and grazing. Multiple factors jointly control the variation of SOC content (SOCc), and the variation of SOC stock (SOCs) is mainly explained by the interaction between climate and grazing years. Climate and grazing can directly or indirectly affect SOCc through vegetation, and SOCs are mainly dominated by the direct effects of grazing years and grazing gradients. Grazing gradients and root-type grass biomass have a significant effect on SOC, with little effect from climate factors. Therefore, long-term grazing may affect the root-type grass and further affect SOC distribution through differences in nutrient acquisition ability and reproductive pathways. These findings provide important guidance for regulating soil carbon sequestration potential by varying the proportion of different root-type grass in the community via sowing, livestock configuration, or grazing time.

The global burden of cancer, with over 19 million new cases annually, underscores the urgent need for effective therapies. Among the most promising anticancer compounds is camptothecin (CPT), a monoterpene alkaloid predominantly derived from Nothapodytes species. Despite its significant pharmaceutical value, the exploitation of such Threatened Plant Species with Widespread Distribution (TPSWD), particularly driven by the global demand for natural compounds in anticancer therapies, presents a paradox in which their widespread distribution fails to ensure their secure conservation status. Furthermore, the lack of in-depth biogeographic and systematic studies complicates efforts to balance resource utilization with biodiversity preservation. The asymmetric distribution of CPT within plant taxa, along with limited knowledge of its biosynthetic pathways and the enzymes and genes involved, further hampers sustainable production. Here, we review the current knowledge on the production and protection of Nothapodytes, focusing on their plant resources, active ingredients, and natural drug derivatives. We also explore strategies for rescuing and sustainably utilizing Nothapodytes, including biotechnological advancements and integrated conservation practices. Finally, we propose future directions to address conservation challenges, ensuring a sustainable supply of CPT while safeguarding these TPSWD species.

The conversion of forests to pastures is the most important human intervention that has shaped the natural landscape into the Anthropocene environment. The Qinghai-Tibet Plateau (QTP), which has both forest drought-lines and alpine treelines with specific ecotone structures, including isolated trees in treeless plant-covers that represent ever existed forest cover according to ‘Lonely Tooth Hypothesis’, offers an excellent model in which to examine the extent and timing of human activity on the conversion of forest to pasture. The objectives of this paper are to review (1) palaeo-environmental records of the Early Holocene that indicate when forests were first converted to ‘alpine meadows’, and (2) current records of the changing treeline ecotone in the region. ‘Alpine meadows’ of the QTP are part of the largest conversion of mountain forests into pastures worldwide. This change in forest cover is possibly a consequence of the agro-pastoral transition and the dawn of the Anthropocene on the QTP. To date, however, there is an interdisciplinary gap in knowledge of 5000 years between the palaeo-ecological and the archaeolocical and zoo-archaeological records. Rapid changes of the rural economy and the exodus from remote highland villages to down-country cities have diminished the age-old impacts of summer grazing and pasture management by fire; reforestation is obvious, but often seen exclusively as an effect of Anthropocene global warming. We believe that more interdisciplinary collaborations on the QTP are necessary to increase our understanding of the treelines of the Anthropocene in High Asia.

The genus Clematis (Ranunculaceae) comprises over 300 species with remarkable morphological and ecological diversity worldwide. Despite its horticultural, medicinal, and ecological importance, a well-resolved phylogeny and coherent infrageneric classification are still lacking. Here, we reconstruct a robust phylogeny for Clematis using a phylogenomic approach and revise its infrageneric taxonomy. We incorporated 198 samples representing 151 species, two subspecies, and 12 varieties, covering all subgenera and most sections worldwide, obtained from both fresh and herbarium material. Nuclear single nucleotide polymorphisms (SNPs) and complete plastid genomes were assembled for phylogenetic analyses. We also prepared a nuclear ribosomal ITS (nrITS) dataset comprising 171 species, two subspecies, and 12 varieties (217 samples) to include as many species as possible for phylogenetic inference. Phylogenies based on plastid genomes and nrITS exhibited limited resolution and modest support, highlighting challenges in resolving certain relationships. Nuclear SNP analyses yielded a robust phylogenetic tree with 22 well-supported clades corresponding to 22 sections, with most previously recognized subgenera and sections not recovered as monophyletic. Ancestral state reconstruction of 12 key morphological characters revealed multiple independent origins of character states. This study presents the first comprehensive sectional classification for Clematis based on robust phylogenomic evidence, redefines morphological characteristics for each section, and resolves long-standing taxonomic ambiguities. Our results establish a framework for future studies on the evolution, ecology, and horticultural potential of this globally significant genus.

As the highest and largest plateau in the world, the Qinghai-Tibet Plateau (QTP) covers wide geological, topographical and climatic gradients and thus acts as a major center for biodiversity and houses a diverse array of high elevation ecosystems. Together these factors make the QTP a critical ecological shield for Asia. However, the composition, structure and function of plant diversity in QTP has experienced profound changes in recent decades. Long-term on-site monitoring, field experiments, remote sensing, and simulations have led to significant advances in our understanding of how plant diversity on the QTP has responded to climate change and human activity. This review synthesizes findings from previous researches on how climate change and human activity have impacted plant diversity on the QTP. We identify gaps in our knowledge and highlight the need for interdisciplinary studies, long-term monitoring networks, and adaptive management strategies to enhance our knowledge and safeguard the QTP’s biodiversity amid accelerating global climate change.

Prunus spinulosa (2n = 4x = 32) is an evergreen species of significant medicinal usage and ecological value. However, the lacking of a high-quality genome of P. spinulosa has obstructed further exploration of its ecological study and phylogenetic relationship of Prunus. In this study, we present the first haplotype-resolved genome assembly of Prunus s.l. subgenus Laurocerasus, the tetraploid genome of P. spinulosa was phased into 32 pseudochromosomes with 4 haplotypes, the genome size of each haplotype ranged from 249.82 Mb to 259.69 Mb, and N50 fluctuated from 31.35 Mb to 33.25 Mb, the protein-coding genes vary from 21,272 to 22,668. Different evaluation methods showed that the P. spinulosa genome assembly has high quality of completeness, continuity and accuracy. Being the first complete genome of P. spinulosa, it provides a valuable genetic resource for the Prunus tetraploid species database and supports further functional genomic study of this species.

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

Complete plastid genomes have been proposed as potential “super-barcodes” for plant identification and delineation, particularly in cases where standard DNA barcodes may be insufficient. However, few studies have systematically addressed how taxonomic complexity, especially in rapidly radiating lineages with intricate evolutionary histories, might influence the efficacy of plastome-scale barcodes. Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains, and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus. Therefore, Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity. In this study, we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes. Our results revealed that the traditional standard barcode combination (nrITS + matK + rbcL + trnH-psbA) achieved the highest discrimination rates (81.25%), closely followed by the plastid large single copy (LSC) region (80.21%), then by full plastome, the supermatrix of protein-coding genes, and hypervariable regions (79.17%). Notably, the matK and ycf1 gene alone could discriminate 78.13% of species. Key determinants of species discrimination by integrating alignment length (AL) and the proportion of parsimony-informative sites (PPIS), as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity. Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes, this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis’ specific biological habits and potentially reflecting unique evolutionary patterns in the plastid genome.

Deep relationships in the angiosperm tree of life remain highly controversial. To address this, we first assembled the complete mitochondrial genomes for Ceratophyllum demersum and Chloranthus sessilifolius, confirming a well-supported sister relationship that starkly conflicts with nuclear and plastid data. To dissect this classic cyto-nuclear conflict, we developed the ‘PhyloForensics’ framework, a novel diagnostic approach to systematically identify sources of phylogenetic instability. This framework revealed that signal heterogeneity (topological entropy variance) and information content (the proportion of informative sites) are the primary drivers of gene-tree conflict. Empirically validating this, we show that removing a small subset of “loudly conflicted” genes resolves deep-level incongruence, yielding a single, highly-supported topology previously obscured by noise. Finally, complementing this sequence-based resolution, we demonstrate that mitogenome architecture provides powerful phylogenetic signals, revealing predictable, mitogenome-wide evolutionary patterns, such as a significant negative correlation between branch length and both GC content and RNA editing sites. By integrating a validated conflict-resolution framework with architectural genomics, our study provides a comprehensive strategy for navigating the complexities of deep evolutionary histories.

The Qinghai-Tibet Plateau (QTP) has three main grassland types: alpine meadow, alpine steppe, and alpine desert steppe. In this study, we asked how plant productivity and species diversity vary with altitude, longitude and latitude in alpine grasslands of the QTP. We then identified the environmental factors that drive these observed patterns of plant productivity and species diversity. We found that although plant productivity and species diversity varied greatly across large-scale longitudinal and latitudinal gradients, these changes were strongest across the longitudinal gradient. This finding indicates that moisture rather than temperature has the greatest impact on plant productivity and species diversity of the alpine grasslands in the QTP. We also found that besides soil and climate factors, partial pressure of carbon dioxide (pCO₂) also has significant effects on plant productivity, and barometric pressure and partial pressure of oxygen (pO₂) also have significant effects on species diversity. Furthermore, the relationship between the biomass of grassland-dominant species and species diversity was affected by the spatial scale at which these factors were studied. Our study provides new insights into the interconnections between plant productivity and species diversity and the major factors that influence alpine grasslands. It also provides a scientific basis for the maintenance of plant diversity and ecosystem functions in hypoxic (low-oxygen) regions.

Habitat fragmentation dramatically reshapes species richness and community composition. However, most estimates of β-diversity rely on incidence-based metrics, which consider only species presence/absence. Here, we introduce a novel framework that explicitly incorporates species abundance and intraspecific trait variation (ITV) into the quantification of taxonomic, functional, and phylogenetic β-diversity, allowing a more nuanced understanding of community differentiation. To demonstrate the utility of this framework, we quantified the effects of island area and isolation on β-diversity across plant communities in China's Thousand Island Lake. Abundance-weighted taxonomic multiple-site/pairwise β-diversity showed substantially higher nestedness and stronger nestedness-area relationship than incidence-based metrics, indicating that species-poor communities are not only subsets of richer ones but share similar abundance hierarchies, highlighting strong environmental filtering and hierarchical species sorting. We also found that the turnover component was less sensitive to isolation, suggesting limited dispersal effects. Incidence-based functional and phylogenetic distances increased with differences in island area, but these associations weakened or disappeared in abundance-weighted measures, suggesting stronger environmental filtering and functional/phylogenetic clustering among larger islands. Only abundance-weighted standardized effect sizes increased with island area differences. Additionally, ITV further amplified functional nestedness and buffered the influence of isolation on turnover, emphasizing its role in mitigating dispersal limitations. By jointly considering abundance and ITV, two often-overlooked but critical dimensions, this study advances our understanding of how fragmentation shapes β-diversity. These findings highlight the importance of integrating abundance-weighted and trait-based metrics into conservation strategies to better detect functionally important species, prioritize larger habitat patches, and design biodiversity monitoring that captures within-species variation.

Climate warming is reshaping the phenology of plants in recent decades, with potential implications for forest productivity, carbon sequestration, and ecosystem functioning. While the effects of warming on secondary growth phenology is becoming increasingly clear, the influence of environmental factors on different developmental phases of xylem remains to be quantified. In this study, we investigated the temporal dynamics of xylem cell enlargement, wall-thickening, and the interval between these events in twelve temperate tree species from Northeast China over the period 2019–2024. We found that both cell enlargement and wall-thickening advanced significantly in response to climate warming, with species-specific variations in the rate of advancement. Importantly, the advancing rate of wall-thickening was greater than that of cell enlargement, leading to a shortening of the interval between these two events. Linear mixed-effects models revealed that photoperiod, forcing temperature, and precipitation were the primary environmental drivers influencing the timing of both cell enlargement and wall-thickening, with photoperiod emerging as the most important factor. These results suggest that climate warming accelerates the heat accumulation required for the transition from xylem cell enlargement to wall-thickening, thereby shortening the time interval between these two developmental stages. Beyond contributing valuable multi-year xylem phenological data, our results provide mechanistic insights that enhance predictions of wood formation dynamics under future climate scenarios and improve the accuracy of forest carbon models.

A better understanding of the structure and dynamics of disturbed forests is key for forecasting their future successional trajectories. Despite vulnerability of subalpine forests to warming climate, little is known as to how their community composition has responded to disturbances and climate warming over decades. Before the 1970s, subalpine forests on the southeastern Qinghai-Tibet Plateau mainly experienced logging and fire, but afterwards they were more impacted by climate warming. Thus, they provide an excellent setting to test whether disturbances and climate warming led to changes in forest structure. Based on the analysis of 3145 forest inventory plots at 4- to 5-year resolution, we found that spruce-fir forests shifted to pine and broadleaved forests since the early 1970s. Such a turnover in species composition mainly occurred in the 1994–1998 period. By strongly altering site conditions, disturbances in concert with climate warming reshuffle community composition to warm-adapted broadleaf-pine species. Thus, moderate disturbances shifted forest composition through a gradual loss of resilience of spruce-fir forests. Shifts in these foundation species will have profound impacts on ecosystem functions and services. In the future, broadleaved forests could expand more rapidly than evergreen needle-leaved forests under moderate warming scenarios. In addition to climate, the effects of anthropogenic disturbances on subalpine forests should be considered in adaptive forest management and in projections of future forest changes.

Mycorrhizal symbioses are prevalent in terrestrial ecosystems and play essential roles in plant nutrition and health. However, the relative importance of plant evolutionary history, physiology, and eco-geographical factors in shaping mycorrhizal fungal community assembly remains poorly understood. Here, we investigate how plant phylogeny, trophic mode, biogeographic distribution and environmental niche collectively influence the diversity and composition of mycorrhizal fungal communities across the Orchidaceae, spanning broad phylogenetic and ecological scales. By using family-wide orchid-fungal associations and global occurrence data, our analyses showed that the variation in fungal diversity and community structure can be partially explained by orchids’ trophic mode, biogeographic distribution and environmental niche, but not by their overall phylogenetic relatedness. Among trophic modes, partially mycoheterotrophic orchids exhibited the highest level of fungal diversity (the lowest level of fungal specificity) in association with a broad range of phylogenetically dispersed fungal partners. Between biogeographical regions, a significantly higher level of fungal specificity was found for orchid species distributed in Australia than those in Eurasia and Africa. Furthermore, multivariate analyses showed that a small portion of the variation in fungal community structure was significantly related to broad climate, soil and vegetation variables, indicating the existence of large-scale habitat filtering on orchid mycorrhizal communities. Altogether, our findings indicate that mycorrhizal communities in the orchid family are likely shaped by multiple, intertwined factors related to orchid ecophysiology and biogeography on a global scale.

The study of natural hybridization facilitates our understanding of potential adaptive mechanisms in evolution and the process involved in speciation. In this study, we used multiple data types, including morphological traits, ddRAD-seq and ecological niche data, to investigate the differences among Rhododendron×duclouxii hybrid zones and the mechanisms underlying natural hybridization and possible future evolutionary pathways. Our results show that the origins of each hybrid zone are independent, with variations in hybrid formation, structural characteristics, and patterns of genetic components and morphological trait differentiation. There were no significant differences in morphological traits or genetic variation between the F₁ and F₂ generations; however, the range of variation of the F₂ generation was broader than that of the F₁ generation. The distribution and ecological characteristics of R.×duclouxii did not significantly differ from those of the two parental species, indicating weak ecological niche preferences between the hybrid and parental taxa. These results imply that the hybrid zones of R.×duclouxii are characterized by considerable variability, with the magnitude of hybridization in each case likely influenced by unique combinations of biological and ecological factors specific to each hybrid zone. We predict that R.×duclouxii hybrid zones will persist and give rise to complex hybrid swarms, each potentially leading to different evolutionary outcomes.

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

Successful ex situ conservation of plant populations requires a high degree of genetic representativeness. However, spatially biased sampling in ex situ conservation efforts may fail to capture all wild genetic clusters for species with range-wide genetic structure. To investigate the extent of spatially biased sampling in living collections and the coverage of wild genetic clusters in plant populations under ex situ conservation worldwide, we combined a global synthesis of ex situ conservation efforts with a case study of an endangered riparian plant species, Myricaria laxiflora. Our analysis of ex situ conservation worldwide revealed that the majority (82.6%) of ex situ populations fail to cover all wild genetic clusters, largely due to spatially biased sampling with low geographic coverage. Our case study of M. laxiflora showed that genetic diversity differed between the ex situ and upstream populations, while it was comparable between ex situ populations and other wild populations. However, current ex situ populations did not cover all wild genetic clusters, as the upstream genetic cluster was previously uncollected. Our study suggests that the failure to cover all wild genetic clusters in ex situ populations is a widespread issue, and ex situ populations with high genetic diversity can also fail to cover all wild genetic clusters. In future ex situ conservation programs, both the importance of high genetic diversity and the high coverage of wild genetic clusters should be prioritized.

Elucidating the origins and mechanisms of polyploidization requires tracing the evolutionary history of polyploid species, particularly those with complex origins. Agropyron cristatum, traditionally regarded as an autopolyploid, exhibits characteristics indicative of a segmental allopolyploid. Here, we used phylogenetic analysis based on a low-copy nuclear gene (i.e., Pgk1), SLAF-seq, and plastome data from 20 diploid and 120 tetraploid Agropyron individuals to determine whether tetraploid A. cristatum arose from an allopolyploid or autopolyploid event. Phylogenetic analyses based on Pgk1 and SLAF-seq data identified two distinct A. cristatum lineages that corresponded to the two main Agropyron habitats in Central Asia–Europe and East Asia–Qinghai-Tibet Plateau. These findings, taken together with molecular dating and gene flow analyses, suggest that the East Asian tetraploid A. cristatum originated via both autopolyploidy from A. cristatum and hybridization between diploid A. cristatum and A. mongolicum, with each diploid cytotype acting as a maternal donor. Furthermore, the Central Asia–Europe tetraploid A. cristatum originated solely via autopolyploidy of diploid A. cristatum. Our findings also indicate that rapid diversification of Agropyron was likely driven by climate oscillations, geographic isolation, introgressive hybridization, and chloroplast capture. These findings challenge simplistic views of autopolyploids and underscore substantial potential for achieving high levels of genetic and adaptive diversity through recurrent hybridization and reticulate evolution.