Seed dispersal modes play a crucial role in angiosperm migration, adaptation, and responses to climate change, yet their global spatiotemporal patterns and underlying drivers remain largely unexplored. Here, using a global dataset on seed dispersal modes (zoochory, anemochory, hydrochory, and autochory) of 35 131 angiosperm species, we provide a large-scale assessment of their evolutionary dynamics, diversification impact, and geographic variation. We found that the increase in zoochorous lineages began after c. 105 Ma, and the transition rate from abiotic-to-biotic dispersal strongly correlated with paleotemperature, being positive from 105 to 90 Ma and negative thereafter. However, contrary to previous hypotheses, we found no significant effect of seed dispersal mode on diversification rates across angiosperms. Spatially, the prevalence of zoochory declined, and that of autochory increased with latitude, both closely linked to contemporary temperature. Meanwhile, the frequency of zoochory and anemochory was positively associated with temperature anomalies since the Last Glacial Maximum, suggesting that dispersal modes facilitating long-distance dispersal are favored in climatically unstable regions. These findings highlight the key role of climate fluctuations in shaping the spatiotemporal patterns of angiosperm seed dispersal modes and suggest a more complex relationship between dispersal modes and angiosperm diversification than previously assumed.

The Guangdong-Hong Kong-Macao Greater Bay Area (GBA) is a critical region in the Pearl River Delta along the South China coast and has a remarkably diverse seed plant species. However, factors such as rapid urbanization and climate change are increasingly impacting the resilience of the Greater Bay Area’s ecosystems. While morphology identification has many drawbacks such as slow process, incorrect identifications, and unreliable for distinguishing species at the growth stage; DNA barcoding has become a valuable tool in plant taxonomy by effectively overcoming many limitations of traditional methods. In this study, we constructed a comprehensive DNA barcoding database for native seed plants in the GBA using three barcodes (matK, rbcL, and ITS2). A total of 2864 native species from 1117 genera and 192 families were represented, of which 695 individuals from 516 species that were newly generated. This study enhances sustainable management and accurate identification of species, facilitates research on plant evolution and ecology, and supporting biodiversity monitoring and conservation efforts within the Greater Bay Area.

Approximately 6.6 million km2 of China’s territory consists of drylands at high desertification risk. Despite ecological vulnerability, these regions remain understudied in biodiversity research. DNA barcoding provides an efficient tool for rapid species identification, offering significant potential for biodiversity conservation and ecological surveys in drylands. However, comprehensive reference data for China’s drylands are currently lacking, underscoring the urgent need for a reliable, extensive, and traceable DNA barcode reference library. To address this gap, we systematically surveyed plant diversity across nearly all Chinese drylands from 2013 to 2021. Our study documented 1,140 species, representing 434 genera, 76 families, and 29 orders. Based on this effort, we constructed the most comprehensive DNA barcode reference library for native dryland seed plants in China, comprising 13,246 sequences across five markers: rbcL (3,056), matK (3,332), ITS (3,358), psbA-trnH (1,770), and trnL-F (1,730). This resource establishes a critical foundation for integrated taxonomic research, biodiversity monitoring, and environmental impact assessments. Moreover, it supports initiatives in desertification control, plant conservation, and sustainable development in China’s dryland regions.

Abiotic environments and biotic neighbourhoods interact to influence plant growth and community assembly. However, the nature of this interaction depends very much on how biotic neighbourhoods are measured, including their relatedness to focal plants. In a tropical seasonal rainforest, we examine the growth of a dominant canopy species in response to environmental factors, the densities and relatedness of conspecific and heterospecific neighbours, and their interactions. We find significant environmental effects and conspecific negative density dependence on growth. Furthermore, conspecific neighbour density has stronger negative effects on growth under high light and soil water resource levels, but weaker negative effects under low light and soil water resource levels. In addition, more closely related heterospecifics in the neighbourhood have negative effects on growth under high soil phosphorus availability, but positive effects under low soil phosphorus availability. In contrast, more closely related conspecifics in the neighbourhood have negative effects on growth under low soil potassium availability, but positive effects under high soil potassium availability. Our study emphasizes the importance of both intra- and interspecific neighbourhood composition and their interactions with resource levels for understanding tree growth. This enhances our understanding of the complex processes in community assembly and species coexistence within forest communities.

Several species in the genus Oxalis occupy Peruvian fog oases (Lomas) with a significant habitat-adapted and endemic diversity. Acknowledging this aspect, the genus Oxalis is a conceivable group for evolutionary and biogeographic hypothesis testing; however, molecular resources for the genus still need improvement. We conducted a genome skimming approach to assemble new plastomes from 18 accessions (six species) of Oxalis collected in Lomas locations in Peru. These complete plastomes of Oxalis species (several reported for the first time) present a highly conserved composition. Our phylogenetic results were congruent with previous section-based backbone phylogenies of Oxalis; however, a closer look at the phylogeny of sect. Carnosae revealed nonmonophyletic arrangements involving Oxalis megalorrhiza and Oxalis bulbocastanum individuals. We also propose a set of three hypervariable plastid regions as potential molecular markers. Likewise, an array of primers for nuclear simple sequence repeat markers based on the most widely distributed species, O. megalorrhiza, were listed and evaluated for their transferability to the other species under examination. These new genomic resources represent a significant development for future population, phylogenetic, and biogeographic studies in Oxalis.

Background Acer is a taxonomically intractable and speciose genus that contains over 150 species. It is challenging to distinguish Acer species only by morphological method due to their abundant variations. Plastome and nuclear ribosomal DNA (nrDNA) sequences are recommended as powerful next-generation DNA barcodes for species discrimination. However, their efficacies were still poorly studied. The current study will evaluate the application of plastome and nrDNA in species identification and perform phylogenetic analyses for Acer. Result Based on a collection of 83 individuals representing 55 species (c. 55% of Chinese species) from 13 sections, our barcoding analyses demonstrated that plastomes exhibited the highest (90.47%) species discriminatory power among all plastid DNA markers, such as the standard plastid barcodes matK + rbcL + trnH-psbA (61.90%) and ycf1 (76.19%). And the nrDNA (80.95%) revealed higher species resolution than ITS (71.43%). Acer plastomes show abundant interspecific variations, however, species identification failure may be due to the incomplete lineage sorting (ILS) and chloroplast capture resulting from hybridization. We found that the usage of nrDNA contributed to identifying those species that were unidentified by plastomes, implying its capability to some extent to mitigate the impact of hybridization and ILS on species discrimination. However, combining plastome and nrDNA is not recommended given the cytonuclear conflict caused by potential hybridization. Our phylogenetic analysis covering 19 sections (95% sections of Acer) and 128 species (over 80% species of this genus) revealed pervasive inter- and intra-section cytonuclear discordances, hinting that hybridization has played an important role in the evolution of Acer. Conclusion Plastomes and nrDNA can significantly improve the species resolution in Acer. Our phylogenetic analysis uncovered the scope and depth of cytonuclear conflict in Acer, providing important insights into its evolution.

Aim: The equator-to-poles decline in the number of species, namely the latitudinal diversity gradient (LDG), is the most conspicuous pattern in biology, yet the underlying mechanisms of this pattern remain controversial. Species dispersal could have strong effects on large-scale species distributions but has rarely been considered in understanding the LDG. Here we sought to examine how dispersal ability may influence the latitudinal phylogenetic patterns of woody angiosperm assemblages.Location: China.Taxon: Woody angiosperms.Methods: Based on a highly supported mega-phylogeny constructed from plastid genomes, we assessed the patterns of phylogenetic relatedness and dissimilarity of 1184 trees with three different seed dispersal modes (i.e. zoochory, anemochory and autochory) in 12 permanent forest dynamic plots covering tropical, subtropical and temperate zones in China.Results: We found that, compared with zoochorous and anemochorous species, the less vagile autochorous trees exhibited a much weaker latitudinal pattern in phylogenetic relatedness and higher phylogenetic dissimilarity among plots. The phylogenetic dissimilarity pattern of autochorous trees was explained more by geographic distance than environmental factors, consistent with a dominant role for dispersal limitation.Main Conclusions: Our study, for the first time, demonstrates that seed dispersal mode strongly influences the latitudinal phylogenetic patterns of woody angiosperm assemblages in China and highlights the importance of interaction between dispersal limitation and environmental filtering in determining the large-scale distribution of forest biodiversity.

Hyperdominant trees in Amazonia account for half of the individual trees (>10 cm dbh) in the forest, and thus play a crucial role in ecosystem dynamics. However, several of these widespread hyperdominant species may be complexes hiding cryptic diversity that can affect species richness estimates and conservation priorities. Here, we study the intraspecific variation of Astrocaryum murumuru (Arecaceae), a keystone and hyperdominant species in Amazonia, also known as Astrocaryum sect. Huicungo, a complex of 15 understory to subcanopy palm species. Using chloroplast DNA from genome skimming (>66 kbp alignment) in a Bayesian framework, we present evidence that A. sect. Huicungo represents three separately evolving lineages, suggesting that the section is not a single hyperdominant species, and that the 15 morphology-based species may be an over-representation. Genome skimming chloroplast data did not fully resolve the species-level phylogenetic relationships in A. sect. Huicungo mostly because of gene discordance and the paraphyly of most species. Contrary to a previous nuclear-based phylogenetic analysis, the chloroplast genomic data did not recover A. sect. Huicungo monophyletic, but yielded monophyly in an increased number of species (six) in the complex. Interspecific phylogenetic relationships showed a geographic pattern, and the traditional morphology-based classification was not supported. Our phylogenomic results are discussed in light of earlier phylogeographical studies using Sanger sequencing. Our findings show the utility of genome skimming data in species delimitation analyses to uncover intraspecific variation of hyperdominant species in Amazonia, the largest evergreen tropical forest.

DNA barcoding is a well-established tool for rapid species identification and biodiversity monitoring. A reliable and traceable DNA barcode reference library with extensive coverage is necessary but unavailable for many geographical regions. The arid region in northwestern China, a vast area of about 2.5 million km(2), is ecologically fragile and often overlooked in biodiversity studies. In particular, DNA barcode data from the arid region in China are lacking. We develop and evaluate the efficacy of an extensive DNA barcode library for native flowering plants in the arid region of northwestern China. Plant specimens were collected, identified and vouchered for this purpose. The database utilized four DNA barcode markers, namely rbcL, matK, ITS and ITS2, for 1816 accessions (representing 890 species from 385 genera and 72 families), and consisted of 5196 barcode sequences. Individual barcodes varied in resolution rates: species- and genus-level rates for rbcL, matK, ITS and ITS2 were 79.9%-51.1%/76.1%, 79.9%-67.2%/88.9%, 85.0%-72.0%/88.2% and 81.0%-67.4%/84.9%, respectively. The three-barcode combination of rbcL + matK + ITS (RMI) revealed a higher species- and genus-level resolution (75.5%/92.1%, respectively). A total of 110 plastomes were newly generated as super-barcodes to increase species resolution for seven species-rich genera, namely Astragalus, Caragana, Lactuca, Lappula, Lepidium, Silene and Zygophyllum. Plastomes revealed higher species resolution compared to standard DNA barcodes and their combination. We suggest future databases include super-barcodes, especially for species-rich and complex genera. The plant DNA barcode library in the current study provides a valuable resource for future biological investigations in the arid regions of China.

Metabolomics provides an unprecedented window on diverse plant secondary metabolites that represent a potentially critical niche dimension in tropical forests underlying co-existence. Here, we used untargeted metabolomics to evaluate the chemical composition of 358 tree species and its relationship to phylogeny and variation in light environment, soil nutrients, and insect-herbivore leaf damage in a tropical rain forest plot. We found that tree species that co-occur locally are less chemically similar than random, and that local chemical dispersion and metabolite diversity reduce herbivory, especially that of specialist insect herbivores. Our results suggest that plant secondary metabolites have the potential to mediate plant-herbivore interactions in a manner consistent with diversity maintenance at the community scale.

Metabolomics provides an unprecedented window into diverse plant secondary metabolites that represent a potentially critical niche dimension in tropical forests underlying species coexistence. Here, we used untargeted metabolomics to evaluate chemical composition of 358 tree species and its relationship with phylogeny and variation in light environment, soil nutrients, and insect herbivore leaf damage in a tropical rainforest plot. We report no phylogenetic signal in most compound classes, indicating rapid diversification in tree metabolomes. We found that locally co-occurring species were more chemically dissimilar than random and that local chemical dispersion and metabolite diversity were associated with lower herbivory, especially that of specialist insect herbivores. Our results highlight the role of secondary metabolites in mediating plant-herbivore interactions and their potential to facilitate niche differentiation in a manner that contributes to species coexistence. Furthermore, our findings suggest that specialist herbivore pressure is an important mechanism promoting phytochemical diversity in tropical forests.

Global environmental changes drive biodiversity loss and community compositional change. Yet whether and how both factors simultaneously impact biomass dynamics in natural ecosystems remains elusive, especially considering their multidimensional effects (e.g., taxonomic, functional, and phylogenetic) over spatial scales. To fill this knowledge gap, we generated an experimental spatial gradient using circular quadrats that vary in radius (2–30 m) in a subtropical forest on Dinghushan Mountain, China. Within each quadrat over 10 years, we calculated the changes in aboveground biomass (i.e., net Δbiomass), biodiversity (i.e., Δbiodiversity for richness, Shannon diversity, functional, phylogenetic), and community composition (i.e., β-diversity for taxonomic, functional, phylogenetic). Based on multi-model inference, we determined the most parsimonious relationships of Δbiomass as a function of Δbiodiversity and β-diversity and then quantified their standardized coefficients in response to the spatial gradient. Our results showed that Δbiomass, Δbiodiversity, and β-diversity decreased with quadrat size; the former at an accelerating rate and the latter at decelerating rates. While Δbiomass as a function of Δbiodiversity and β-diversity had low occurrences across the gradient, Δbiomass was strongly related to the change in functional dispersion (i.e., ΔFDis) and taxonomic β-diversity at larger spatial scales. Our results suggest scale-dependent influences of biodiversity loss and community compositional change on biomass dynamics in natural ecosystems. Further, our results highlight that multiple dimensions of biodiversity should be considered when predicting biomass dynamics at large spatial scales.

The application of DNA barcoding has been significantly limited by the scarcity of reliable specimens and inadequate coverage and replication across all species. The deficiency of DNA barcode reference coverage is particularly striking for highly biodiverse subtropical and tropical regions. In this study, we present a comprehensive barcode library for woody plants in tropical and subtropical China. Our dataset includes a standard barcode library comprising the four most widely used barcodes (rbcL, matK, ITS, and ITS2) for 2,520 species from 4,654 samples across 49 orders, 144 families, and 693 genera, along with 79 samples identified at the genus level. This dataset also provides a super-barcode library consisting of 1,239 samples from 1,139 species, 411 genera, 113 families, and 40 orders. This newly developed library will serve as a valuable resource for DNA barcoding research in tropical and subtropical China and bordering countries, enable more accurate species identification, and contribute to the conservation and management of tropical and subtropical forests.

Metabolomics provides an unprecedented window on diverse plant secondary metabolites that represent a potentially critical niche dimension in tropical forests underlying co-existence. Here, we used untargeted metabolomics to evaluate the chemical composition of 358 tree species and its relationship to phylogeny and variation in light environment, soil nutrients, and insect-herbivore leaf damage in a tropical rain forest plot. We found that tree species that co-occur locally are less chemically similar than random, and that local chemical dispersion and metabolite diversity reduce herbivory, especially that of specialist insect herbivores. Our results suggest that plant secondary metabolites have the potential to mediate plant-herbivore interactions in a manner consistent with diversity maintenance at the community scale.

Phylogenetic trees have been extensively used in community ecology. However, how the phylogeny construction affects ecological inferences is poorly understood. In this study, we constructed three different types of phylogenetic trees (a synthetic-tree generated using V.PhyloMaker, a barcode-tree generated using rbcL+matK+trnH-psbA, and a plastome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six forest dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the plastome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith's PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the plastome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and plastome-tree detected phylogenetic signal in maximum height, but only the plastome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the improvement of plastome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.

Climate warming and atmospheric nitrogen deposition threaten plant biodiversity in mountain ecosystems; however, their influences on soil microbial diversity and community composition remain poorly understood. We conducted randomized block factorial experiments in three mountain meadows of different elevations on Yulong Snow Mountain, China. These include open-top chambers and urea fertilization to simulate climate warming and nitrogen deposition, respectively. Using Next-generation sequencing (NGS) technology, we measured soil microbial diversity and community composition for archaea, bacteria, and fungi. In addition, we measured plant diversity, plant aboveground biomass, soil chemical characteristics, air temperature, and rainfall as quantitative predictors. We determined the most parsimonious relationships with soil microbial diversity and community composition for each predictor based on generalized linear mixed-effect models and distance-based redundancy analyses, respectively. Elevation explained the majority of the variation associated with microbial diversity under short-term warming and fertilization. Microbial diversity decreased with increasing elevation, and the tendency was strongest for bacteria. Fertilization decreased bacterial diversity at the highest elevation but increased fungal diversity across the elevational gradient; microbial community composition was weakly affected by elevation. Climatic factors, especially air temperature, were the most important determinants of soil microbial diversity and composition. Taken together, the results presented here contribute to our understanding of how future global climate change may impact the belowground diversity of mountain ecosystems.

The complete chloroplast genome of Isatis minima, a typical ephemeral plant of Brassicaceae in the Central Asia desert, was sequenced and characterized in this study. The genome 153,642 bp in size, contains a typical quadripartite genome organization including LSC and SSC regions of 83,423 bp and 17,709 bp, and two copies of the IR regions of 26,255 bp. It has 113 unique genes, including 79 protein-coding, 30 tRNA, and four rRNA genes. Phylogenetic analysis fully resolved I. minima in a monophyletic clade with I. tinctoria. This bioinformatic data contributes to the phylogenetics systematics and evolutionary history of Brassicaceae.

Phylogenetic trees have been extensively used in community ecology. However, how the phylogenetic reconstruction affects ecological inferences is poorly understood. In this study, we reconstructed three different types of phylogenetic trees (a synthetic-tree generated using VPhylomaker, a barcode-tree generated using rbcL+matK+trnH-psbA and a genome-tree generated from plastid genomes) that represented an increasing level of phylogenetic resolution among 580 woody plant species from six dynamic plots in subtropical evergreen broadleaved forests of China. We then evaluated the performance of each phylogeny in estimations of community phylogenetic structure, turnover and phylogenetic signal in functional traits. As expected, the genome-tree was most resolved and most supported for relationships among species. For local phylogenetic structure, the three trees showed consistent results with Faith’s PD and MPD; however, only the synthetic-tree produced significant clustering patterns using MNTD for some plots. For phylogenetic turnover, contrasting results between the molecular trees and the synthetic-tree occurred only with nearest neighbor distance. The barcode-tree agreed more with the genome-tree than the synthetic-tree for both phylogenetic structure and turnover. For functional traits, both the barcode-tree and genome-tree detected phylogenetic signal in maximum height, but only the genome-tree detected signal in leaf width. This is the first study that uses plastid genomes in large-scale community phylogenetics. Our results highlight the outperformance of genome-trees over barcode-trees and synthetic-trees for the analyses studied here. Our results also point to the possibility of Type I and II errors in estimation of phylogenetic structure and turnover and detection of phylogenetic signal when using synthetic-trees.

Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single unit, and tree discordance among these loci has seldom been examined. Using samples of Laureae (Lauraceae) plastomes, we explored plastome variation among the tribe, examined the influence of non-coding regions on tree topology, and quantified intra-plastome conflict. Results We found that the plastomes of Laureae have low inter-specific variation and are highly similar in structure, size, and gene content. Laureae was divided into three groups, subclades I, II and III. The inclusion of non-coding regions changed the phylogenetic relationship among the three subclades. Topologies based on coding and non-coding regions were largely congruent except for the relationship among subclades I, II and III. By measuring the distribution of phylogenetic signal across loci that supported different topologies, we found that nine loci (two coding regions, two introns and five intergenic spacers) played a critical role at the contentious node. Conclusions Our results suggest that subclade III and subclade II are successively sister to subclade I. Conflicting phylogenetic signals exist between coding and non-coding regions of Laureae plastomes. Our study highlights the importance of evaluating the influence of non-coding regions on tree topology and emphasizes the necessity of examining discordance among different plastid loci in phylogenetic studies.