The angiosperm family Elaeagnaceae comprises three genera and . 100 species distributed mainly in Eurasia and North America. Little family-wide phylogenetic and biogeographic research on Elaeagnaceae has been conducted, limiting the application and preservation of natural genetic resources. Here, we reconstructed a strongly supported phylogenetic framework of Elaeagnaceae to better understand inter- and intrageneric relationships, as well as the origin and biogeographical history of the family. For this purpose, we used both nuclear and plastid sequences from Hyb-Seq and genome skimming approaches to reconstruct a well-supported phylogeny and, along with current distributional data, infer historical biogeographical processes. Our phylogenetic analyses of both nuclear and plastid data strongly support the monophyly of Elaeagnaceae and each of the three genera. was resolved as sister to the well-supported clade of and . The intrageneric relationships of and were also well resolved. High levels of nuclear gene tree conflict and cytonuclear discordance were detected within , and our analyses suggest putative ancient and recent hybridization. We inferred that Elaeagnaceae originated at . 90.48 Ma (95% CI = 89.91-91.05 Ma), and long-distance dispersal likely played a major role in shaping its intercontinentally disjunct distribution. This work presents the most comprehensive phylogenetic framework for Elaeagnaceae to date, offers new insights into previously unresolved relationships in , and provides a foundation for further studies on classification, evolution, biogeography, and conservation of Elaeagnaceae.

Phylogenetic niche conservatism posits that species tend to retain ancestral ecological traits and distributions, which has been broadly tested for lineages originating in tropical climates but has been rarely tested for lineages that originated and diversified in temperate climates. Liverworts are thought to originate in temperate climates. Mean lineage age reflects evolutionary history of biological communities. Here, using regional liverwort floras across a long latitudinal gradient from tropical to arctic climates in North America, we test the age-component of the temperate niche conservatism hypothesis. Mean genus age (MGA) was estimated for each of 76 regional floras of liverworts. We related MGA to climatic variables for North America as a whole and for its eastern and western parts separately, and used variation partitioning analysis to assess the relative importance of temperature- versus precipitation-related variables and of climate extremes versus seasonality on MGA. We found that older genera of liverworts tend to concentrate in humid regions of intermediate temperatures in the range of 10 °C-20 °C, from which liverworts have adapted to and diversified into more arid, colder, and hotter regions, supporting the temperate niche conservatism hypothesis. We also found that across North America the MGA of liverwort assemblages is more strongly affected by precipitation-related variables than by temperature-related variables, and is more strongly affected by climate extremes than by climate seasonality. Geographic patterns of the MGA of liverworts are consistent with the temperate niche conservatism hypothesis, rather than the tropical niche conservatism hypothesis, the latter of which is broadly supported by angiosperms.

The Indo-Burma Biodiversity Hotspot is renowned for its rich biodiversity, including that of vascular plants. However, the fern diversity and its endemism in this hotspot have not been well understood and so far, the diversity of very few groups of ferns in this region has been explored using combined molecular and morphological approaches. Here, we updated the plastid phylogeny of the Java fern genus with 226 (115% increase of the latest sampling) samples across the distribution range, specifically those of three phylogenetically significant species, , . , and . . We also reconstructed the first nuclear phylogeny of the genus based on gene data. Based on molecular and morphological evidence, we identified three new major clades and six new subclades, redefined three existing species, discovered a number of cryptic species of the genus, and elucidated the evolution of the three most variable characters. Our divergence time analyses and ancestral area reconstruction showed that originated in the Oligocene and diversified from early Miocene and 15 dispersal events from lower to higher latitudes are identified. The evolution of three most important morphological characters is analyzed in a context of the new phylogeny. Our analysis showed that 30 (59% of total 51) species of occur in Indo-Burma hotspot, 24 (80% of the 30 species) of which are endemic to this hotspot. We argue that the Indo-Burma hotspot should be recognized as a diversity hotspot for ferns.

Genome skimming has dramatically extended DNA barcoding from short DNA fragments to next generation barcodes in plants. However, conserved DNA barcoding markers, including complete plastid genome and nuclear ribosomal DNA (nrDNA) sequences, are inadequate for accurate species identification. Skmer, a recently proposed approach that estimates genetic distances among species based on unassembled genome skims, has been proposed to effectively improve species discrimination rate. In this study, we used Skmer to identify species based on genomic skims of 47 individuals representing 10 out of 13 species of (Theaceae) from China. The unassembled reads identified six species, with a species identification rate of 60%, twice as high as previous efforts that used plastid genomes (27.27%). In addition, Skmer was able to identify species with only 0.5× sequencing depth, as six species were well-supported with unassembled data sizes as small as 0.5 Gb. These findings demonstrate the potential for Skmer approach in species identification, where nuclear genomic data plays a crucial role. For taxonomically difficult taxa such as , which have diverged recently and have low levels of genetic variation, Skmer is a promising alternative to next generation barcodes.

Functional diversity (FD) reflects within- and between-site variation of species traits (α- and β-FD, respectively). Understanding how much data types (occurrence-based vs. abundance-weighted) and spatial scales (sites vs. regions) change FD and ultimately interfere with the detection of underlying geoclimatic filters is still debated. To contribute to this debate, we explored the occurrence of 1690 species in 690 sites, abundances of 1198 species in 343 sites, and seven functional traits of the Atlantic Forest woody flora in South America. All FD indices were sensitive and dependent on the data type at both scales, with occurrence particularly increasing α richness and dispersion (occurrence > abundance in 80% of the sites) while abundance increased β total, β replacement, and α evenness (abundance > occurrence in 60% of the sites). Furthermore, detecting the effect of geoclimatic filters depended on the data type and was scale-dependent. At the site scale, precipitation seasonality and soil depth had weak effects on α- and β-FD (max. R = 0.11). However, regional-scale patterns of α richness, dispersion, and evenness strongly mirrored the variation in precipitation seasonality, soil depth, forest stability over the last 120 kyr, and cation exchange capacity (correlations > 0.80), suggesting that geoclimatic filters manifest stronger effects at the regional scale. Also, the role of edaphic gradients expands the idea of biogeographical filters beyond climate. Our findings caution functional biogeographic studies to consider the effect of data type and spatial scale before designing and reaching ecological conclusions about the complex nature of FD.

Leaf nitrogen (N) and phosphorus (P) levels provide critical strategies for plant adaptions to changing environments. However, it is unclear whether leaf N and P levels of different plant functional groups (e.g., monocots and dicots) respond to environmental gradients in a generalizable pattern. Here, we used a global database of leaf N and P to determine whether monocots and dicots might have evolved contrasting strategies to balance N and P in response to changes in climate and soil nutrient availability. Specifically, we characterized global patterns of leaf N, P and N/P ratio in monocots and dicots, and explored the sensitivity of stoichiometry to environment factors in these plants. Our results indicate that leaf N and P levels responded to environmental factors differently in monocots than in dicots. In dicots, variations of leaf N, P and N/P ratio were significantly correlated to temperature and precipitation. In monocots, leaf N/P ratio was not significantly affected by temperature or precipitation. This indicates that leaf N, P and N/P ratio are less sensitive to environmental dynamics in monocots. We also found that in both monocots and dicots N/P ratios are associated with the availability of soil total P rather than soil total N, indicating that P limitation on plant growth is pervasive globally. In addition, there were significant phylogenetic signals for leaf N (λ = 0.65), P (λ = 0.57) and N/P ratio (λ = 0.46) in dicots, however, only significant phylogenetic signals for leaf P in monocots. Taken together, our findings indicate that monocots exhibit a "conservative" strategy (high stoichiometric homeostasis and weak phylogenetic signals in stoichiometry) to maintain their growth in stressful conditions with lower water and soil nutrients. In contrast, dicots exhibit lower stoichiometric homeostasis in changing environments because of their wide climate-soil niches and significant phylogenetic signals in stoichiometry.

As the core of leaf functional traits, the trade-off relationship between the petiole and lamina expresses the plant's adaptability to the environment in terms of support structure and photosynthesis. We investigated the proportions of allometric growth in the relationship between the petiole and the lamina of broadleaf woody plants in temperate highland Tianshan Mountains montane forests through three dimensions (length, area, and mass), including the length of the lamina (LL) and the length of the petiole (PL), and the area of the lamina (LA) and petiole cross sectional area (PCA) versus the mass of the lamina (LM) and the mass of the petiole (PM), as well as exploring the characteristics of the variance in response to seasonal changes. We found that the functional traits in all three dimensions showed a clear convergent evolution as the seasons progressed, that is, a "seasonal effect" of increasing and then decreasing. The effect of the petiole-lamina relationship under spring was minimal in the area dimension; the effects of the three-dimensional relationships of the traits were all highest in summer, and the effect of the petiole-lamina relationship was lower in autumn. We also found that petiole traits are simultaneously and multiply affected by lamina traits, with LA and LM having additional effects on the length/mass and area dimensions, respectively. Compared to tree species, shrub species significantly require more light intensity and support capacity. Compound-leaved plants would invest more in photoluminescence, increasing leaf light capture efficiency and static load and dynamic resistance. Our results suggest that plants have rather complex trade-off mechanisms at the leaf level influencing their ability to adapt to the environment, emphasize the need for leaf-level studies on the relationships between functional traits in plants, and illustrate the importance of the season as a distinct time scale for plant trade-off mechanisms.

•Three types of from the late Oligocene and Miocene of Guangxi showcase the diversity of during this time.•Earliest Asian megafossils of are from the late Oligocene of Nanning Basin, Guangxi, China.•Fossils and modeling reveal was quite diverse and has persisted at low latitudes within Asia since late Oligocene.•Climate probably plays a crucial role in driving the diversification of in low latitudes of Asia.

Grasslands account for about a quarter of the Earth's land area and are one of the major terrestrial ecosystems, with significant ecological and economic values. The influence of environmental factors and management types on grassland biodiversity has garnered considerable attention. This study investigated how patterns of species richness are influenced by geographical distance, environmental gradients, and management type in the moist mountain grasslands of northeastern Yunnan, China. We used structural equation modeling to disentangle the impacts of environment and management on phylogenetic community structure, and using partial Mantel tests estimated the roles of dispersal limitation and environmental filtering on taxonomic and phylogenetic beta diversity of three types of grasslands. Our results show that taxonomic alpha diversity increased in grazed grasslands and decreased in mowed grasslands, compared with protected grasslands. However, the phylogenetic structure of both grazed and mowed grassland communities was clustered, whereas that of protected communities was random. Moreover, both grazing and mowing significantly reduced the taxonomic and phylogenetic beta diversity of grasslands, with the lowest values observed in mowed grasslands. Both taxonomic and phylogenetic beta diversity were dominated by species turnover under different management types. The taxonomic and phylogenetic beta diversities of protected and grazed grasslands were simultaneously affected by environmental filtering and dispersal limitation, with the later playing a stronger role. In addition, mowing and following management measures had a stronger filtering effect on grassland community structure, as reflected by changes in community composition.

Salinity is a severe abiotic stress that affects plant growth and yield. Salinity stress activates jasmonate (JA) signaling in , but the underlying molecular mechanism remains to be elucidated. In this study, we confirmed the activation of JA signaling under saline conditions and demonstrated the importance of the CORONATINE INSENSITIVE1 (COI1)-mediated JA signaling for this process. Phenotypic analyses reflected the negative regulation of JASMONATE ZIM-DOMAIN (JAZ) repressors during salinity stress-enhanced JA signaling. Mechanistic analyses revealed that JAZ proteins physically interact with ABSCISIC ACID-RESPONSIVE ELEMENT BINDING FACTOR1 (ABF1), AREB1/ABF2, ABF3, and AREB2/ABF4, which belong to the basic leucine zipper (bZIP) transcription factor family and respond to salinity stress. Analyses on the overexpression plants and mutants indicated the positive role of ABF3 in regulating JA signaling under saline condition. Furthermore, overexpression partially recovered the JA-related phenotypes of plants. Moreover, ABF3 was observed to indirectly activate () transcription, but this activation was inhibited by JAZ1. In addition, ABF3 competitively bind to JAZ1, thereby decreasing the interaction between JAZ1 and MYC2, which is the master transcription factor controlling JA signaling. Collectively, our findings have clarified the regulatory effects of ABF3 on JA signaling and provide new insights into how JA signaling is enhanced following an exposure to salinity stress.

Medicinal plants have long been used to treat various diseases in both indigenous and non-indigenous populations of Mindanao, Philippines. Here, we extracted data from ethnobotanical studies to compile a comprehensive list of these medicinal plants and identify how and for what purpose they are most commonly used. We identified 530 verified medicinal plant species across 372 genera in 118 families. The two most frequently cited species were and . The most represented family was Fabaceae and the most represented genus was . A total of 28 medicinal plant species are designated as threatened at the national or global level; of these, 11 are endemic to the Philippines. Medicinal plant preparations most commonly use leaves for oral administration to treat various diseases such as digestive issues, including diarrhea. This study underscores the need for further ethnobotanical investigations, particularly in areas lacking records. It also emphasizes the need for conservation of threatened and endemic medicinal plants to ensure sustainable utilization of this valuable resource.

Tropical regions have provided new insights into how ecological communities are assembled. In dry coastal communities, water stress has been hypothesized to determine plant assembly structure by favoring preadapted lineages from neighboring ecosystems, consistent with functional clustering. However, it is unclear whether this hypothesis is sufficient to explain how coastal communities in tropical ecosystems are assembled. Here, we test whether water stress or other factors drive community assembly in woody plant communities across the coastal zone of Brazil, a tropical ecosystem. We characterized functional and phylogenetic structures of these communities and determined the underlying environmental factors (e.g., water stress, historical climate stability, edaphic constraints, and habitat heterogeneity) that drive their community assembly. Assemblages of coastal woody species show geographically varied patterns, including stochastic arrangements, clustering, and overdispersion of species relative to their traits and phylogenetic relatedness. Topographic complexity, water vapor pressure, and soil nutrient availability best explained the gradient in the functional structure. Water deficit, water vapor pressure, and soil organic carbon were the best predictors of variation in phylogenetic structure. Our results support the water-stress conservatism hypothesis on functional and phylogenetic structure, as well as the effect of habitat heterogeneity on functional structure and edaphic constraints on functional and phylogenetic structure. These effects are associated with increased phenotypic and phylogenetic divergence of woody plant assemblages, which is likely mediated by abiotic filtering and niche opportunities, suggesting a complex pattern of ecological assembly.

The common walnut () is one of the most economically important nut trees cultivated worldwide. Despite its importance, no comprehensive evaluation of walnut tree population genetics has been undertaken across the range where it originated, Central Asia. In this study, we investigated the genetic diversity and population structure of 1082 individuals from 46 populations across Central Asia. We found moderate genetic diversity of across Central Asia, with 46 populations clustered into three groups with a weak relationship between genetic and geographic distance. Our findings reveal that the western Himalaya might be the core region of common walnut genetic diversity in Central Asia and that, except for two populations in Gongliu Wild Walnut Valley, humans might have introduced walnut populations to Xinjiang, China. The observed distribution of the genetic landscape has probably been affected by historical climate fluctuation, breeding system, and prolonged anthropogenic activity. We propose the conservation of the core genetic diversity resources in the western Himalaya and pay special attention to populations from Gongliu in Xinjiang. These findings enhance our understanding of the genetic variation throughout the distribution range of . in Central Asia, which will provide a key prerequisite for evidence-based conservation and management.

We used 11 years of census data from 450 seedling quadrats established in a 20-ha forest dynamics plot to study seedling dynamics in tree species of a tropical seasonal rainforest in Xishuangbanna, southwestern China. We found that overall seedling recruitment rate and relative growth rate were higher in the rainy season than in the dry season. Both the recruitment rate of seedlings from canopy tree species (two species) and the relative growth rate of seedlings from understory species (nine species) were higher in the rainy season than in the dry season. However, in the rainy season, the recruitment rate of seedlings was higher for canopy tree species than for understory tree species. In addition, relative growth rate of seedlings was higher in the canopy species than in understory seedlings in the dry season. We also observed that, in both rainy and dry seasons, mortality rate of seedlings was higher for canopy species than for understory species. Overall, canopy tree species appear to have evolved a flexible strategy to adapt to the seasonal changes of a monsoon climate. In contrast, understory tree species seem to have adopted a conservative strategy. Specifically, these species mainly release seedlings in the rainy season and maintain relatively stable populations with a lower mortality rate and recruitment rate in both dry and rainy seasons. Our study suggests that canopy and understory seedling populations growing in forest understory may respond to future climate change scenarios with distinct regeneration strategies.

Understanding genome-wide diversity, inbreeding, and the burden of accumulated deleterious mutations in small and isolated populations is essential for predicting and enhancing population persistence and resilience. However, these effects are rarely studied in limestone karst plants. Here, we re-sequenced the nuclear genomes of 62 individuals of the complex (, , and ) and investigated genomic divergence and genetic load for these four species. Our analyses revealed four distinct clusters corresponding to each species within the complex. Notably, there was only limited admixture between and occurring in overlapping geographic regions. All species experienced historical bottlenecks during the Pleistocene, which were likely caused by glacial climate fluctuations. We detected an asymmetric historical gene flow between group pairs within this timeframe, highlighting a distinctive pattern of interspecific divergence attributable to karst geographic isolation. We found that isolated populations of have limited gene flow, the smallest recent population size, the highest inbreeding coefficients, and the greatest accumulation of recessive deleterious mutations. These findings underscore the urgency to prioritize conservation efforts for these isolated population. This study is among the first to disentangle the genetic differentiation and specific demographic history of karst plants at the whole-genome level, shedding light on the potential risks associated with the accumulation of deleterious mutations over generations of inbreeding. Moreover, our findings may facilitate conservation planning by providing critical baseline genetic data and a better understanding of the historical events that have shaped current population structure of rare and endangered karst plants.

Relict subtropical coniferous forests in China face severe fragmentation, resulting in declining populations, and some are under significant threat from invasive alien species. Despite the crucial importance of understanding forest dynamics, knowledge gaps persist, particularly regarding the impact of invasive plants on vulnerable natives like . In this study, we investigated the impact of invasive plants on the regeneration of forests dominated by . , a subtropical relict species in southwestern China. For this purpose, we characterized forest dynamics of 160 forest plots featuring as the primary dominant species and determined whether the presence of invasive plants was correlated with regeneration of . We identified four distinct forest types in which was dominant. We found that radial growth of trees is faster in younger age-classes today than it was for older trees at the same age. The population structure of in each forest type exhibited a multimodal age-class distribution. However, three forest types lacked established saplings younger than 10 years old, a situation attributed to the dense coverage of the invasive alien . This invasive species resulted in a reduction of understory species diversity. Additionally, our analysis uncovered a significant negative correlation in phylogenetic relatedness (net relatedness index) between native and invasive alien plant species in eastern Yunnan. This suggests closely related invasive species face heightened competition, hindering successful invasion. Taken together, our findings indicate that successful establishment and habitat restoration of seedling/saplings require effective measures to control invasive plants.

Alien plant invasion success can be inhibited by two key biotic factors: native herbivores and plant diversity. However, few studies have experimentally tested whether these factors interact to synergistically resist invasion success, especially factoring in changing global environments (e.g. nutrient enrichment). Here we tested how the synergy between native herbivores and plant diversity affects alien plant invasion success in various nutrient conditions. For this purpose, we exposed alien plant species in pot-mesocosms to different levels of native plant diversity (4 . 8 species), native generalist herbivores, and high and low soil nutrient levels. We found that generalist herbivores preferred alien plants to native plants, inhibiting invasion success in a native community. This inhibition was amplified by highly diverse native communities. Further, the amplified effect between herbivory and native plant diversity was independent of nutrient conditions. Our results suggest that a higher diversity of native communities can strengthen the resistance of native generalist herbivores to alien plant invasions by enhancing herbivory tolerance. The synergistic effect remains in force in nutrient-enriched habitats that are always invaded by alien plant species. Our results shed light on the effective control of plant invasions using multi-trophic means, even in the face of future global changes.

Reproductive strategies of sexually dimorphic plants vary in response to the environment. Here, we ask whether the sexual systems of species (i.e., selfing homostylous and out-crossing distylous) represent distinct adaptive strategies to increase reproductive success in changing alpine environments. To answer this question, we determined how spatial and temporal factors (e.g., elevation and peak flowering time) affect reproductive success (i.e., stigmatic pollen load) in nine wild species (seven distylous and two homostylous) among 28 populations along an elevation gradient of 1299-3315 m in the Hengduan Mountains, southwestern China. We also observed pollinators and conducted hundreds of hand pollinations to investigate inter/intra-morph compatibility, self-compatibility and pollen limitation in four species (two distylous and two homostylous). We found that species at higher elevation generally had bigger flowers and more stigmatic pollen loads; late-flowering individuals had smaller flowers and lower pollen deposition. Stigmatic pollen deposition was more variable in distylous species than in homostylous species. Although seed set was not pollen-limited in all species, we found that fruit set was much lower in distylous species, which rely on frequent pollinator visits, than in homostylous species capable of autonomous self-pollination. Our findings that pollination success increases at high elevations and decreases during the flowering season suggest that distylous and homostylous species have spatially and temporally distinct reproductive strategies related to environment-dependent pollinator activity.

Leaf economics spectrum (LES) describes the fundamental trade-offs between leaf structural, chemical, and physiological investments. Generally, structurally robust thick leaves with high leaf dry mass per unit area (LMA) exhibit lower photosynthetic capacity per dry mass ( ). Paradoxically, "soft and thin-leaved" mosses and spikemosses have very low , but due to minute-size foliage elements, their LMA and its components, leaf thickness (LT) and density (LD), have not been systematically estimated. Here, we characterized LES and associated traits in cryptogams in unprecedented details, covering five evolutionarily different lineages. We found that mosses and spikemosses had the lowest LMA and LT values ever measured for terrestrial plants. Across a broad range of species from different lineages, and LD were negatively correlated. In contrast, was only related to LMA when LMA was greater than 14 g cm . In fact, low reflected high LD and cell wall thickness in the studied cryptogams. We conclude that evolutionarily old plant lineages attained poorly differentiated, ultrathin mesophyll by increasing LD. Across plant lineages, LD, not LMA, is the trait that represents the trade-off between leaf robustness and physiology in the LES.

China is a hotspot of relict plant species that were once widespread throughout the Northern Hemisphere. Recent research has demonstrated that the occurrence of long-term stable refugia in the mountainous regions of central and south-western China allowed their persistence through the late Neogene climate fluctuations. One of these relict lineages is , an oligotypic tree genus with a fossil record extending to the Paleocene. Here, we investigated the genetic variability, demographic dynamics and diversification patterns of the two currently recognized species ( and ). Molecular data were obtained from 45 populations of by genotyping three cpDNA regions, two single copy nuclear genes and 15 simple sequence repeat loci. The genetic study was combined with niche comparison analyses on the environmental space, ecological niche modeling, and landscape connectivity analysis. We found that the two species have highly diverged both in genetic and ecological terms. Despite the incipient speciation processes that can be observed in , the occurrence of long-term stable refugia and, particularly, a dispersal corridor along Daba Shan-west Qinling, likely ensured its genetic and ecological integrity to date. Our study will not only help us to understand how populations of species responded to the tectonic and climatic changes of the Cenozoic, but also provide insight into how Arcto-Tertiary relict plants in East Asia survived, evolved, and diversified.

Mountain biodiversity is of great importance to biogeography and ecology. However, it is unclear what ecological and evolutionary processes best explain the generation and maintenance of its high levels of species diversity. In this study, we determined which of six common hypotheses (e.g., climate hypotheses, habitat heterogeneity hypothesis and island biogeography theory) best explain global patterns of species diversity in . We found that diversity patterns were most strongly explained by proxies of island biogeography theory (i.e., mountain area) and habitat heterogeneity (i.e., elevation range). When we examined other relationships important to island biogeography theory, we found that the planimetric area and the volume of mountains were positively correlated with the diversity, whereas the 'mountains-to-mainland' distance was negatively correlated with diversity and shared species. Our findings demonstrate that diversity can be explained by island biogeography theory and habitat heterogeneity, and mountains can be regarded as islands which supported island biogeography theory.