Background & Aims: As one of the mega-biodiverse countries in the world, China has implemented in situ and ex situ biodiversity conservation programs through the national parks and the national botanic gardens system respectively to responsibly study and conserve this diversity. We aimed to provide a baseline reference for the current national botanic garden system program.

Methods: We assessed the ex situ conservation profile in Chinese botanic gardens of plants from three categories: National Key Protected Wild Plants (NKPWP), threatened species, and endemic species. Statistical and comparative analyses of integrated data sets show that there are 7,141 species of vascular plants that have been conserved ex situ in botanic gardens of China. These species span 1,271 genera and 265 families, accounting for 76% of families, 42% of genera, and 23% of species of vascular plants in China.

Results: Among the 7,141 species, 743 species are National Key Protected Wild Plants, 2,095 species are threatened, and 5,957 species are endemic to China, accounting for 72%, 59% and 37% of the total number of species catalogued for these categories in China, respectively. These species include 2,555 trees, 1,025 shrubs, 3,117 herbs, 419 climbers, and 25 aquatic plants. The phylogenetic diversity is variable among these gardens, with a low proportion of shared species across gardens.

Background: Research techniques in molecular biology, cell biology, microbiology and genetics have been accelerated by rapid development of modern genomic technologies. These advances have rapidly evolved the field of biodiversity research, once a branch of natural history focusing on morphology, into an integrated life science. Modern biodiversity studies can now investigate and link element of ecological systems, the species within them, and their genetic diversity. DNA related technologies, among other omics techniques, have continued to develop and launch new sequencing platforms, leading to a reduction of DNA sequencing costs that has already outstripped Moore’s Law, which also facilitates a series of breakthroughs in the research fields of biodiversity.
Prospects: Here, we introduce emerging trends in DNA-based omics techniques applied in biodiversity research, including species-level genomics as well as genetic diversity and community-levels species diversity. The former includes genomes obtained based on single individuals and genetic diversity of focal populations in both spatial and temporal dimensions, while the latter includes molecular identification approaches, such as metabarcoding, eDNA, iDNA etc. These new methods can be applied in biodiversity estimation for various communities, as well as in monitoring and conservation of flagship species and interspecific interactions.

Background: The formation of ecological communities has occurred through a long process of evolution. The current community composition we have observed is not only determined by the ecological traits of the species itself but also affected by environmental changes, human activities, and various random events. Time scales and experimental constraints mean we cannot fully observe the process of community assembly, and can only speculate on this process through fragmented data. Simulations can be used to test aspects of community assembly thanks to their relative efficiency, controllability, and traceability.
Aim: We review efforts to simulate of community assembly and the approaches taken to combine different explanations for assembly. We note advantages, disadvantages, and prospects of simulation for study of community assembly. To introduce numerical simulation into the study of community assembly, it is necessary to extract the factors and rules that affect the assembly pathways and that can be modeled within the requirements of a chosen simulation model.
Process: Robert Paine used virtual species to build community food web structure, and discussed the relationship between food web complexity and species diversity from a purely mathematical perspective approximately 50 years ago. Many subsequent studies, such as exploring the impact of isolation and sub-networks in complex food webs, and evaluating the impact of network isolation on ecological stability through food web complexity and other related theories, are typical cases of using numerical simulation at to consider the impact of interspecific interactions and the complexity-stability relationship. At the cross-community scale, May et al. modelled the abundance and distribution of individuals of different species in a spatially defined landscape, defining key attributes of multiple communities (total individuals, population density, and intraspecific degree of spatial aggregation, etc.), deducing the relevant indicators of biodiversity and comparing the performance of the biodiversity-related indicators of multiple community structures under different sampling modes and intensities. For protected area planning, numerical simulations can use artificial intelligence to prioritize protected areas, and quantify the trade-offs between the costs and benefits of regional and biodiversity conservation. On regional or global scales, the relationship between species niche breadth, dispersal capacity, environmental change rate and each of species extinction and new species formation was analyzed. We confirmed that topography and climate drive the evolution of species and the formation of species diversity along the latitudinal gradient of niche breadth and species diversity for bird communities in South America over the past 800,000 years. We also modelled the formation of species in the Ordovician, late Pliocene and Pleistocene, and the discussion of the impact of topographic factors on species extinction.
Prospect: The change of biodiversity can be a long-term and complex process. Understanding how these processes change over time requires the integration of multidisciplinary theories and research methods such as macroevolution, paleontology, biogeography, and community ecology. The study of large-scale biodiversity patterns has reached a global scale, and it is becoming harder and harder to find the drivers of biodiversity patterns via simple correlation analysis. In fact, macroecology is now shifting its focus from finding correlations between ecological phenomena and environmental factors to understanding, explaining, and predicting observed patterns of biodiversity from a causal perspective. Simulation provides an opportunity to observe community assembly.

Aims: The origin and evolution of biodiversity is one of the most important scientific questions in the field of life sciences. The accumulation of multi-omics data and the development of related analytical techniques have greatly promoted our understanding and research on the origin and evolution of biodiversity, thereby making it possible to clarify the processes and reveal the mechanisms of biological evolution events. On the occasion of the 30th Anniversary of the inaugural of Biodiversity Science, this paper briefly retrospects the important research progress of the origin and evolution of biodiversity in recent years, aiming to help the readers comprehend the present development on this topic.
Progresses: In the past decade, research on the origin and evolution of biodiversity has made many significant advancements, including the reconstruction of the tree of life, the spatiotemporal distribution pattern of biodiversity, the concepts of species, speciation, and adaptive evolution, and the origin and diversification of new characters. Based on these advancements, phylogenetic relationships among many taxa were clarified; some historical causes of biodiversity distribution patterns were revealed; some new species concepts and speciation models were proposed; and some molecular mechanisms of new characters and functions were revealed.
Prospect: We believe that the more accurate reconstruction of the tree of life, in-depth mining of genomic data, and the multidisciplinary integration would be the main trends in biodiversity research.

Background & Aims: Biodiversity is a key feature of ecosystem complexity. Understanding the origination and maintenance of biodiversity has been a major task of theoretical ecology research. Here we reviewed recent advances in theoretical studies on biodiversity.
Progresses: We first summarized recent progress in modern coexistence theory and process-based community assembly theory. We then synthetized different approaches for inferring the presence and strengths of species interactions. Lastly, we introduced the general framework of eco-evolutionary models and their applications in biodiversity research.
Prospects: We ended with a brief discussion on future developments of biodiversity theory, particularly in integrating processes across scales and predicting biodiversity responses to global changes.

Aims: Studies on plant systematics and evolution aim to elucidate the origin and diversification of plants and to elucidate the factors that affect the patterns of plant diversity temporally and spatially. As the largest and most highly attended conference on plant sciences, the International Botanical Congress (IBC) came to China in 2017 (IBC 2017) and attracted nearly 7,000 participants from around the globe. The success of holding IBC 2017 in China has profound influence on plant sciences in China both because it was an important forum to demonstrate the achievements and progresses of Chinese scientists and because it strengthened the link and collaboration of scientists between China and abroad.
Progresses: On the occasion of the fifth anniversary of IBC 2017, I reviewed the achievements and breakthroughs in the field of plant systematics and evolution in China, including the origin and diversification of early plants, taxonomy and phylogenetic reconstruction of major plant lineages, plant speciation and adaptive evolution, species interaction and concerted evolution, origin and underlying mechanisms of innovation characters, plant polyploidy and polyploid evolution, species endangerment and protection, as well as origin and domestication of cultivated plants. All the progresses highlighted here have contributed greatly to our better understanding of plant biodiversity across the world, which embodies the growing impacts of Chinese scientists on global research and development in plant sciences.
Prospect: I pointed out the opportunities and challenges that plant scientists have faced, including fast development of genome sequencing and ‘-omic’ studies, the interdisciplinary and multi-level investigations and cooperation, management of big data, and the practical applications of plant systematics and evolutionary studies in resource utilization, species conservation, agriculture and horticulture, medicine and plant trade, etc.

Background: Lycophytes and ferns are the second largest group of vascular plants, dating back as far as 400 million years ago. Before the domination of angiosperms, lycophytes and ferns were the key component of ancient terrestrial ecosystems, and are still important to modern ecosystems today. Since the 1940s, the study of lycophytes and ferns in China has attracted worldwide attention. In the past five years since the 19th International Botanical Congress (IBC) held in Shenzhen in 2017, research on lycophytes and ferns in China has expanded internationally and focuses on a wider range of scientific issues. A series of important advances have been made on plant diversity, conservation, phylogeny, and ecological adaptation.
Results: From 2017 to 2022, the tree of life for lycophytes and ferns in the world has been reconstructed by the family level, and a new evolutionary model for the sporangium was proposed. Some of the phylogenetic and taxonomic problems of order, family, genus and species of lycophytes and ferns were solved, meanwhile 106 new taxa were published. A large number of floristic collections and studies have been conducted, and six Chinese plus one worldwide monographs on the diversity of lycophytes and ferns have been published. In addition, 65 species of lycophytes and ferns under state priority conservation have been ex situ protected, and spore reproduction has been achieved in priority conservation groups such as Cyatheaceae, Ceratopteris, Angiopteris and Platycerium wallichiia. The ecological restoration and adaptive evolution of lycophytes and ferns were studied under the phylogeny.
Perspectives: After literature survey on the research of lycophytes and ferns in China from 2017 to 2022, we make the following suggestions for future studies: (1) Focus future research on Chinese oligotypic families/genera and the worldwide mega-diverse families/genera. (2) Prioritize research in under-studied areas, such as Tibet and Sichuan, and utilize new technologies (e.g., DNA barcoding) to improve the efficiency and accuracy of species identification. (3) When clarifying the systematic relationship between families, genera, and species by using multi-disciplinary approaches, it is necessary to conduct research on plant evolutionary history and adaptation mechanisms. (4) Research efforts should focus on the common scientific conjecture of the systematic position of lycophytes and fern as the origin for the evolution of terrestrial vascular plants. (5) Pay more attention to the cooperation among the phylogenetics, ecology, phytochemistry, conservation biology and other subjects of lycophytes and ferns.

Aims: The angiosperm sexual system is a critical trait closely related to mutation accumulation and genetic diversity resulting from sexual reproduction, which could further significantly affect the evolution of extant angiosperm diversity and ecosystem stability. There is growing recognition that the sexual system plays an important role at various levels including population, community, and ecosystem and can also reflect the response of vegetation to environmental change.
Progresses: We reviewed key research progress over the last three decades addressing important ecological issues based on the angiosperm sexual system, including evolution of sexual system diversity, the relationship between sexual system and phylogeny, ecological correlation of dioecy in angiosperms, mechanisms of community assembly and dynamics regarding sexual systems, variation of sexual system distribution along environmental gradients, and the effect and response of functional traits to ecosystem functions and disturbance. In addition, we also provided future recommendations, including research directions, methods and applications based on functional traits in plant science.
Prospect: Sexual systems are not only a genetically determined trait but may also be an environmentally adaptive strategy to enhance plant fitness. We thus propose that sexual systems can also be used as an indicator or reference for biodiversity conservation and management of ecosystems under global climate change.

Aims: Uncovering the assembly mechanism that shapes the large-scale biodiversity patterns is a key challenge in ecology. Numerous previous studies have demonstrated that multiple ecological processes can simultaneously regulate plant community assembly. However, how they shape the plant taxonomic, functional, and phylogenetic β-diversity of gobi deserts remains unclear, hindering the understanding of gobi plant assembly processes and diversity maintenance.
Methods: We selected 61 sites from major gobi desert habitat types across northern Qinghai-Tibet Plateau. Plant species abundance, molecular phylogeny, as well as eight functional traits including: leaf nitrogen concentrations (LNC), leaf phosphorus concentrations (LPC), leaf area (LA), specific leaf area (SLA), fine root nitrogen concentrations (RNC), fine root phosphorus concentrations (RPC), root length (RL), specific root length (SRL), and associated environmental variables were measured. We then tested the relative effects of different assembly processes on taxonomic, functional and phylogenetic diversity using null model and variation partitioning analyses.
Results: Plant taxonomic, functional, and phylogenetic β-diversity all significantly increased with geographic distance, whereas taxonomic and functional β-diversity were more strongly related to geographic distance. Null model analysis revealed that three facets of plant β-diversity exhibited a non-random pattern, indicating niche processes may dominate the gobi desert plant community assembly. Plant functional β-diversity exhibited clustering patterns, while phylogenetic β-diversity displayed dispersion patterns. Among eight traits, only LA and RL demonstrated significant but weak phylogenetic signals, suggesting gobi plant functional traits were not conserved throughout evolution. Variation partitioning analysis further indicated that compared with geographic distance, environmental distance could better explain the variation in all three facets of plant β-diversity. More importantly, local habitat factors, such as soil moisture content and gravel coverage, drove the variation in both three facets of plant β-diversity rather than climatic factors.
Conclusions: These results demonstrated that niche processes, such as habitat filtering, may determine the different facets of plant β-diversity in the gobi desert, and the distribution patterns of plant functional and phylogenetic β-diversity were significantly different. In addition, the mismatch between functional and phylogenetic β-diversity patterns may be partly caused by functional traits that were not conserved along the phylogeny. Taken together, our findings provide new understanding for plant assembly mechanism in extremely harsh environment regime.

Background & Aims Understanding the mechanisms underlying the formation of species is a major task of ecological and evolutionary studies. Aided by the rapid development of sequencing technologies during the last two decades, a growing body of research has revealed a heterogeneous genomic landscape of divergence with the existence of genomic islands of divergence between closely related taxa. This pattern was interpreted as evidence for the speciation-with-gene-flow model, and genomic islands in divergence landscape were hypothesized to be caused by divergent selection in the face of gene flow. However, genomic islands can also arise from other evolutionary processes, such as introgression, divergent sorting of ancient polymorphisms, and linked selection. Previous empirical studies often focused on part of evolutionary processes when discerning the mechanism governing the formation of genomic islands. Therefore, this paper aims to clarify genomic island of divergence and related concepts, summarize the pros and cons of different methods of identifying genomic islands, compare the predicted properties of genomic islands of divergence under different evolutionary processes, and propose a research route for discerning the mechanism contributing to genomic islands during speciation. This paper may provide a guide for future studies on genomic islands and their underlying mechanisms.

Progress In recent years, various empirical and model-based approaches have been proposed to identify genomic islands. After comparing the pros and cons of these approaches, we think the significance test on observed F_ST using the null distribution of F_ST under different recombination rate according to the inferred best-fitting demographic model is the most reasonable. Based on similarities and differences of the predicted properties of genomic islands of divergence under different evolutionary processes, we point out the necessity of exploiting multiple indicators, such as introgression level, absolute divergence (d_XY), relative node depth (RND), and recombination rate, when discerning the mechanism contributing to genomic islands during speciation.

Prospects We suggest more attention should be paid to the ecological and genetic basis of reproductive isolation after discerning the mechanism underlying the formation of genomic islands. Meanwhile, future researches should be standardized to facilitate integrative analysis in a comparative framework, thus improving our understandings of the frequency of speciation with gene flow in the natural world.

Background & Aim: Speciation is a constant theme in the study of evolutionary biology. The nature of the dynamics and continuity of population evolution makes it hard to define the concept of species. Understanding the mechanisms of speciation remains crucial in the fields of evolutionary biology, taxonomy, conservation biology and biodiversity. Here we revisited the existent theories of speciation and reviewed the recent advances in empirical study.

Progresses: We discussed three geographical patterns of speciation (sympatric, parapatric, and allopatric speciation) and reviewed the corresponding empirical evidence from recent studies, based on the classical concept of biological species coined in terms of reproduction isolation. We further discussed the molecular genetics basis of postzygotic reproductive isolation and the evidence derived from analyses of applying population genomic data, including BDMI (Bateson-Dobzhansky-Muller incompatibility), QTLs (quantitative trait loci) analysis, Haldane’s rule and the large X-chromosome effects. We finally discussed the relationship between mating system, one of the pre-zygotic isolation barriers, and speciation. We inferred that selfing or inbreeding could drive speciation via either increasing population genetic differentiation or impeding gene flow between populations of different mating systems, or both.

Prospects: More evidence is needed to verify speciation theories. In addition, given the more frequent transitions to selfing from outcrossing in plant species, both flower characters and genomic differentiation could drive the so-called selfing syndromes. It is significant to clarify the role of mating system as a driver or as a reinforcer in plant speciation.

Aims One of the determinants of water availability in drylands, groundwater plays a fundamental role in regulating plant traits, phylogeny, and community assemblage. However, considerable uncertainties exist regarding how groundwater depth influences the relative importance of community assembly process in plant communities, as well as how the influence differs among the above- and belowground components.

Methods By using the leaf and root functional traits, in addition to associated environmental factors in 230 plant communities in the lower reaches of an arid inland river basin, we attempted to uncover how the pattern of the community assembly process varied along a depth gradient of groundwater and the key drivers of this variation.

Results (1) Across all study sites, we found that the standard effect size of Rao’s quadratic entropy (SES.RaoQ) of leaf and root functional diversity determined using the plant individual species, mean functional traits and phylogenetic information was significantly less than zero. Functional clustering was pervasive among plant communities (90% of the traits). (2) Groundwater depth and soil variables together explained 13%-39% and 14%-48% of the variation in SES.RaoQ determined using leaf and root traits, respectively, and groundwater depth individually explained 13%-22% and 14%-36% of the variation. (3) The SES.RaoQ determined using leaf and root traits decreased as mean groundwater depth decreased, but it increased with increased groundwater depth seasonality. Root traits showed a faster shift in SES.RaoQ along groundwater depth gradients than leaf traits.

Conclusion Plant communities in an arid inland river basin are primarily affected by deterministic processes, which supports the niche theory. Most plant communities exhibited functional clustering. Groundwater depth is the key factor determining the relative importance of the community assembly process of plant communities. With the decrease of groundwater depths, the functional structure changes from a pattern of mostly overdispersion to a pattern of clustering. The variation in aboveground functional structure along groundwater gradients is highly consistent with that of the belowground functional structure, but the belowground component of plant communities may be more sensitive to changes in groundwater depth.

Aims: During the first two decades of the 21st century, China has made remarkable progress in desertification control. The area of desertified and degraded grassland has been decreasing and the amount of vegetation has been increasing. However, it remains unclear how plant diversity varies during vegetation restoration. This knowledge gap hinders a full assessment of the effectiveness of desertification control efforts. Our goal was to quantify species diversity, functional diversity, and phylogenetic diversity in plant communities at different phases of vegetation restoration (semi-fixed dunes, fixed dunes, fixed dunes covered with biological soil crusts, fixed dunes with abundant herbaceous plants) in the Mu Us sandy grassland.

Methods: We conducted field investigations and leaf trait measurements (leaf thickness, leaf dry matter content, leaf density, and specific leaf area) during the mid-growing season of 2020 in Yanchi, Ningxia. Based on this, we further used one-way ANOVA and Pearson correlation analysis to explore the differences and relationships among diversity indices at different phases of vegetation restoration.

Results: Our results indicated that: (1) Most leaf traits exhibited no significant phylogenetic signal, implying that leaf functional traits were primarily driven by environmental factors. (2) For α-diversity, Shannon-Wiener diversity (H), species richness (S), functional richness (FRic), and phylogenetic diversity (PD) were the lowest in plant communities at the phase of fixed dunes covered with biological soil crusts. Each of these α-diversity parameters were not significantly different among plant communities during the other three restoration phases. Furthermore, these biodiversity indices were positively correlated with each other, suggesting coordinated changes in species diversity, functional diversity, and phylogenetic diversity during vegetation restoration. (3) All β-diversity indices increased with the number of transitions between phases, indicating that species composition, leaf traits, and phylogeny were consistently changing during vegetation restoration. Species composition, leaf traits, and phylogeny all changed dramatically during the transition from semi-fixed to fixed dunes, resulting in a large dissimilarity between communities during the two phases. (4) The phylogenetic structure of plant communities tended to diverge on fixed dunes, fixed dunes covered with biological soil crusts, and fixed dunes with abundant herbaceous plants, indicating that competitive exclusion was the key factor driving community organization. However, the phylogenetic structure of plant communities on semi-fixed dunes did not exhibit any consistent patterns, implying that community organization was affected by the combined effects of habitat filtering and competitive exclusion.

Conclusion: Although plant diversity did not demonstrate a monotonic increasing trend during vegetation restoration in the Mu Us sandy grassland, different indices of diversity varied coordinately. Therefore, species diversity can be regarded as a reasonable proxy of functional and phylogenetic diversity in this system. The results of this study can provide reference for vegetation construction and management whilst implementing desertification controls, as well as provide scientific basis for the ecological conservation and biodiversity protection of the Mu Us sandy grassland.

Background & Aims: Natural selection assumes that there is an expected fitness advantage (or aim) for any selection of gene mutations or phenotypic characteristics. However, the fitness of the selected gene mutation/phenotypic characteristic might vary as it spreads throughout a population or might vary with changing living environments over both evolutionary and ecological scales. This may result in a “paradox of stationary fitness landscape” in which an expected fitness advantage of a selected gene mutation/phenotypic characteristic might therefore not exist. Based on a dynamic state but not a stationary fitness landscape, we propose that natural selection might exhibit path-dependent selection.

Summary: In path-dependent selection, the gene mutation or phenotypic characteristics are produced completely at random, but some might meet a specific condition which could generate positive feedback as they spread. Such positive feedback might also be that such matched conditions could further facilitate the occurrence of a genetic trait/phenotypic characteristic. The positive feedback effect will therefore increase the probability of a genetic trait or phenotypic characteristic in specific conditions, meaning natural selection will depend on the probability of path, but not fitness value. Analogy to that many paths lead to a bus stop near your office building, the path-dependent selection argues that the quickest path might be mostly selected, especially when the bus stop is at a fixed location and selection pressure is strong. However, the other paths may also be selected especially when the bus stop could change location or selection pressure is weak. In path-dependent selection, both evolutionary history and distribution of ecological characteristics will greatly affect the evolution of any path. Using this understanding, different pathways can be understood as different points of speciation, where the distribution of species is similar to the peaks of a mountain in which the paths with a high probability will shape peaks, while many other species with low path probability will not separate into other peaks, creating sister species, cryptic species, or redundant species.

Prospects: Path-dependent selection can be described by the complex function, a mathematical skill widely used in modern physics. Through complex function, we can describe how multiple factors shape a probability of path-dependent selection in speciation peaks and the oscillation of species peaks. Different pathways, which could also be understood as different dimensional viewpoints, will demonstrate a different understanding of the evolutionary aim of a gene mutation, phenotypic characteristic.

Aims: Populus euphratica is a rare tree species in the extremely arid desert area of northwest China. The research on the germplasm genetic resources within the natural populations and the construction of a germplasm bank are helpful to protect the gene resources of P. euphratica.
Methods: In this study, according to the Nei’s genetic similarity among populations by using SNPs from 120 DNA fragments, the gradual clustering priority sampling method was used and t-test was performed to compare the genetic diversity within populations, the conservation units and the rest populations. A total of 58 natural P. euphratica populations from northwest China, including Xinjiang, Qinghai, Gansu, Ningxia, and Inner Mongolia, were used to obtain the different natural conservation units.
Results: The P. euphratica populations were divided into four distinct clades that demonstrated strong geographical distribution patterns (NX, SX, QH and GNM, with the GNM clade containing individuals from Gansu, Ningxia and Inner Mongolia individuals). PCA analysis confirmed the differentiation of populations, similar to population structure. Southern Xinjiang holds the major distribution of P. euphratica in China, and the higher genetic diversity than other distribution areas, and the analysis of molecular variance (AMOVA) showed that most of the variation within P. euphratica was distributed within population compared to the variation among populations. The primary core conservation units (CU3) contained three populations, and the secondary core conservation units (CU33) contained 33 populations. There may be natural ancient P. euphratica resources with putative resistance to stress in southern Xinjiang, and the average genetic diversity in southern Xinjiang was higher than that in northern Xinjiang.
Conclusion: The overall genetic diversity of P. euphratica and the number of ancient trees in southern Xinjiang were higher than those in northern Xinjiang. The priority protection of the first and second core conservation units was constructed. Combining comprehensively with habitat information, such as the severity of drought index in Xinjiang, it was recommended to increase the conservation of ancient P. euphratica trees in southern Xinjiang, and to pay more attentions to the regeneration of P. euphratica forests in northern Xinjiang.

Aims As a constructive shrub species widely distributed across the temperate deserts of arid Central Asia, Reaumuria soongarica (Tamaricaceae) had undergone divergence and hybridization during its evolutionary history, which make it an ideal model for understanding the molecular basis of biodiversity of desert ecosystems and plant hybrid speciation. However, the ploidy level of different populations of R. soongarica is still unclear, which confines the further study on its speciation mechanism.
Methods To clarify the ploidy level and variation patterns of genome size of different R. soongarica lineages, we investigated the DNA 1C-value of eight R. soongarica populations from the northern lineage (distributed in northern Xinjiang) and its putative parental lineages (the eastern and western lineages) by flow cytometry. The young roots of R. soongarica were selected as the experimental material, and Solanum pimpinellifolium was used as an internal standard species.
Results Our data showed that the DNA 1C-value of the eastern lineage (1.149 ± 0.012 pg) was slightly smaller than that of the western lineage (1.195 ± 0.031 pg), and the DNA 1C-value of the Fukang (FW) and Shawan (SW) populations in the northern lineage was intermediate between that of its parental lineages. However, the DNA 1C-values of the Huoshaoshan (HSS) and Wucaicheng (WCC) populations from the northern lineage were closely twice as those from the eastern and western populations.
Conclusion Considering to the previous results of molecular markers, we infer that the FW and SW populations belong to the homoploid hybrid populations from the eastern and western lineages, while the HSS and WCC populations are allopolyploid hybrid populations. The populations with different ploidy levels in the northern lineage could originate from different hybrid events, which could be classified into different species.

Aim: Whole-genome duplication (WGD) plays a positive role in speciation in vascular plants and is considered to be an important mechanism for species adaptation to the extreme environments. Dating whole-genome duplication events in different species is essential for understanding the adaptive evolution of organisms. However, the role that these mechanisms play in vascular plants, especially ferns, is still poorly understood.

Method: Based on the synonymous substitution rates (Ks) and absolute dating of the WGD event, this study used three different transcriptome sequences of Angiopteris fokiensis to analyze the contribution of polyploidy to the evolution of plants, and the silent substitution rate. Gene annotation and functional enrichment were carried out to elucidate the biological processes, molecular function, and cellular component for the genes retained after the WGD.

Results: We found that there was at least one WGD event in A. fokiensis at 159-165 Mya, and most duplicated genes were often related to nutrient metabolism, signal transduction, adaptive regulation and anatomical structure development. The silent substitution rate of A. fokiensis is 1.66 × 10^‒9 synonymous substitutions per site per year. Based on the above results, we speculate that the WGD event was associated with gymnosperms flourishing and the emergence of core angiosperms, or the Toarcian extinction event. The retention of particular genes after the WGD may have promoted genetic and morphological innovation in Angiopteris, thus helping it adapt to the drastic changes in environmental conditions. At present, A. fokiensisis the slowest evolving group of land plants except gymnosperms, which may relate to the long generation time, large genome and stable living habitat.

Conclusion: In this study, we analyzed the whole-genome duplication history and the patterns of retention of duplicated genes in A. fokiensis, suggesting that WGD events are of great influence in promoting the adaptation to extreme environmental changes of plants with slower evolutionary rates. These results provide more inspiration for understanding the adaptive evolution of other land plants.

Aims: Environmental heterogeneity of forest gaps leads to variation in taxonomic and phylogenetic diversity of trees in these areas. Studying tree diversity in different sizes of forest gap communities can help to reveal the mechanisms that drive the formation and maintenance of biodiversity. This study took Castanopsis kawakamiigaps as the research object, and aimed to reveal the relationship between the taxonomic and phylogenetic diversity of plants and its environmental influence factors.

Methods: We examined different sizes of forest gaps in a Castanopsis kawakamii natural forest as to study the taxonomic and phylogenetic diversity of plants, and used a generalized linear model (GLM) to explore the environmental factors driving the community assembly.

Results: We found that the plant species and plant abundance in large gaps (> 200 m²) were higher than those of medium gaps ([50 m², 100 m²)), small gaps ([30 m², 50 m²)) and non-gaps (100 m²). The phylogenetic community structure of the large gaps tends to diverge, while that of the medium gaps, small gaps and non-gaps were affected by the combined effect of habitat filtering and competitive exclusion. The phylogenetic community diversity index (PD) was significantly positively correlated with species richness (SR), Margalef index and Shannon-Wiener index, which is related to the higher species composition of sparse species than dense species in forest gaps. Overall, forest gap size had a significantly positive effect on species diversity, and the soil total nitrogen content had a significantly positive effect on community phylogenetic diversity and phylogenetic structure.

Conclusion: The formation of forest gaps increase the taxonomic and phylogenetic diversity of trees in natural forests, with gap size and soil total nitrogen jointly driving tree diversity in these natural forest gaps.

Aim: Almost all the research in biology relies on a species concept as the basis for biodiversity. However, all of the existing species definitions are imprinted with artificial factors or difficult to observe in practical applications, which brings negative impacts on the species classification. Here, we introduce an “evolutionary path” using a path integral to provide a rule for species classification. We aim to show the speciation process and define the species concept with a mathematical form.
Methods: In this species definition, we assumed that uncertain environmental changes and random drift in the population might simultaneously lead to a change in the fitness expectation. Therefore, a constant fitness expectation for any biological characteristic might not be reliable when considering how characteristics vary through time and space. We introduce the concept of “evolutionary path” which is formed by repeating a short-time transfer process. In this process, a species evolves to different states at different probabilities over time based on the instantaneous fitness landscape at any current moment. In this framework, evolution moves in the direction of increased fitness on the varying fitness landscape, and speciation will be of path dependence on the varying fitness landscape. Different individuals with the same or different biological characteristics (e.g. phenotype, genotype, etc.) will interact with another one at random, similar to the process of gambling among them. In a simulation, under the framework of evolutionary game theory, species differentiation will be similar to the evolution of the peaks on a mountain. Every peak after differentiation may represent a species, a cryptic species, or a sympatric species. The picture of species peaks within a mountain is determined by the relationship between the distance and the width of two adjacent peaks and by the dimensionality that characteristics differentiation satisfied.
Results: We found a more practicable concept to define species, i.e, based on statistical analysis applicable for multiple types of traits like genetics, morphological characteristics, or ecological process between two populations. Once the respective discontinuities of two or more dimensional variables between populations are all greater than the difference of variables within the population, the individuals with corresponding variables belong to different species.
Conclusions: The path-dependent evolutionary mechanism in this model demonstrated that species can coexist with different probabilities when environmental pressures are limited. A new species, cryptic species, sympatric species may occur in a path-dependent evolution process. This model also showed that species survival in an ecosystem is not determined by its fitness directly, but dependent on the probability of its evolutionary path.

Plant-microbe mutualism, a special form of cooperation, has been crucial throughout the evolutionary history of life and terrestrial ecosystems. With human activities changing the condition of Earth’s surface at an unprecedented rate and scale, we expect this ancient bond between plants and microbes to continue to play a key role. Yet, despite its importance, there has been a historical bias towards cooperation/mutualism in biology, and a general underrepresentation in mathematical biology/theoretical ecology. Moreover, even though theoretical representation of mutualism has come a long way, there exists multiple disparate perspectives with diverse associated scientific communities, among which interaction has been limited. This review focuses on two seemingly opposite schools of perspectives: microbiologists’ perspective that zooms in for the microscale mechanisms vs. ecosystem ecologists’ perspective that zooms out for the macroscale consequences. Macroscale models often start with a simple set of naive assumptions. But over time microscale mechanisms (once understood well) will eventually be incorporated into newer-generation process-based large models, greatly enhancing our ability to quantitatively predict our future. I hope this review can facilitate this process, a process that will only become more important against the backdrop of rapid global change. Lastly, but perhaps more broadly, I hope this review will attract more attention to the important role of cooperation/mutualism, a concept that we can maybe leverage to solve a range of other broader problems in ecology and our society.

Benthic macroinvertebrates serve as important indicator organisms for water environment monitoring, and the study of their community structure and biodiversity can effectively reflect the health of the water body. From 2015 to 2019, we investigated the community structure and biodiversity of benthic macroinvertebrates in the Baoying Lake, Yangzhou, Jiangsu Province. Using both morphological traits and DNA barcoding, we identified a total of 57 species. Assigned to three phyla and five classes, these species included: 23 molluscs (15 gastropods and 8 bivalves); 12 oligochaetes; and 22 arthropods (5 malacostracans and 17 insects). Gastropods constituted the most dominant group, accounting for more than 65% of density ratio during five years. The three most abundant gastropods were Bithynia fuchsiana, B. misella, and Alocinma longicornis. Surveys on the annual variation of species diversity and community structure showed mean values of the Margalef abundance index, Simpson dominance index and Pielou evenness index at 2.27 ± 0.28, 0.82 ± 0.02, and 0.78 ± 0.08, respectively. Biotic assessments of water quality based on both the Shannon-Wiener index (H') and the biotic index (BI) suggested varying intensities of pollutants in the Baoying Lake between 2016 and 2019. This variation is likely related to anthropogenic eutrophication, notably overstocking during barrier net aquaculture.

In the 60-year development of invasion ecology, many hypotheses have been proposed to explain the mechanisms behind biological invasion. However, it remains difficult to integrate these hypotheses into a unified framework. In particular, whether exotics ecologically differ from natives, and how ecological differences between exotic and native species could determine invasion outcome, have been hotly debated. By categorizing exotic-native ecological differences into niche differences and fitness differences, modern coexistence theory provides a framework to place different invasion hypotheses and mechanisms into a common context. This framework emphasizes that invasion success depends on either a niche difference between exotics and natives, or that exotics have fitness advantage over natives. By reviewing the leading invasion hypotheses, we found that most invasion hypotheses can be incorporated into this framework, as they considered different aspects of exotic-native niche and fitness differences. This framework can well explain why exotic-native phylogenetic distance and trait difference have complex influences on invasion, and therefore may help to reconcile the long-standing Darwin’s naturalization conundrum and the debate regarding the value of native versus exotic trait comparisons. Together, this framework provides a new opportunity to better understand the mechanisms of ecological invasion.

Digital sequence information (DSI) on genetic resources is a product of unprecedented improvements in genetic sequencing technology in recent years. The application of genetic DSI can help to explain the molecular basis and evolutionary theory of life and provide new technical methods for the conservation and sustainable utilization of biodiversity. With the implementation of the Nagoya Protocol, the Conference of the Parties (COP) has gradually deepened their understanding of benefit-sharing and adopted effective legislative and administrative measures to control their biological genetic resources. As a special kind of “non-physical” information resource, the application of genetic digital sequence information will bring challenges to access systems and benefit sharing. In recent years, genetic digital sequence information has become the focus of negotiations for CBD. China, as a large country with rich biodiversity, a contracting party of Nagoya Protocol, and also one of the countries with rapid development in biotechnology in recent years, should strive to participate in relevant research on this topic and actively respond to the challenges arising therewithin.

Species are not static, but in the process of continuous differentiation and evolution. In this context, reproductive isolation is considered the key to most speciation events. However, species that may be only partially reproductively isolated may disturb our understanding of a species, as stated by ‘The integrative species concept’. In the Flora of China, Chinese Sphaeropteris contains two species, S. brunoniana and S. lepifera. S. brunoniana is thought to be the same species as a Hainan native, S. hainanensis, however, S. hainanensis seems to have differentiated morphologically. This study further explores the genetic relationship between S. brunoniana and its related species by collecting 21 samples from 9 populations for GBS reduced-representation genome sequencing for phylogenetic analysis. Using both genetic and morphological data, our results indicate that S. hainanensis differs genetically from S. brunoniana, but is also morphologically distinct based on leaf characteristics and spore ornamentation. Although the reproductive isolation of the two populations is weak, hybrids are formed in the coastal areas of Guangxi and leaves mimic intermediate morphology between parents. Therefore, our results suggest that S. hainanensis is in the process of speciation due to geographic isolation and suggests to restore its species status. S. brunoniana × hainanensis which the sample from Guangxi should be considered an independent natural hybrid taxon.

Spore morphology is diverse and complex in ferns, thus serving as an important indicator of taxonomy. In conjunction, morphological traits and phylogeny are used to study taxonomy and recent character evolution. This study analyzes the evolution of spore ornamentation in once-pinnate maidenhair ferns (Adiantum) using scanning electron microscopy and ancestral state reconstruction. Our results show that there are five ornamental types in once-pinnate maidenhair ferns: psilate, scabrate, granulate, verrucate and tuberculate. The ancestral state of spore ornamentation in Adiantum is probably tuberculate, with verrucate ornamentation possibly deriving from tuberculate. We suggest that spore ornamentation evolved from simple to complex in Adiantum. In other words, the more evolutionary species, will with a more complex spore ornamentation.

In 1859, Charles Darwin put forward the concept of the tree of life (TOL), a metaphor for charting relationships between organisms in space and time in his The Origin of Species. The TOL is a cornerstone in evolutionary theory and makes sense of all biology. Decades of research in plant molecular systematics has led to substantial progress in understanding many aspects of the plant TOL. Here, we summarized five major aspects of reconstructing the plant TOL, which are being studied at the present day and will continue to be goals moving forward. These include: (1) constructing genus- and species-level phylogenies for plant groups; (2) resolving deep-time and/or rapidly divergent phylogenetic relationships using genomic approaches; (3) updating classification systems by combining morphological and molecular data; (4) integrating fossil taxa into phylogenies derived from extant taxa; and (5) building big trees using supermatrix methods. We then outlined the current state of plant molecular systematics and highlight existing problems in the field, specifically in regard to China. Finally, we propose the corresponding guidelines and policy suggestions for the continued study of China’s reconstruction of the plant TOL.

Genetic diversity is an important component of biodiversity. However, the overexploitation of natural resources and habitat fragmentation have severely degraded the genetic diversity of many affected species. Wild Plant with Extremely Small Populations (WPESP) are in urgent need of rescue, their genetic diversity are of great significance for studying the endangerment mechanism and providing conservation strategies. Habitat fragmentation might reduce genetic diversity, increase genetic differentiation among populations or limit gene flow. However, biological and ecological factors of threatened species, such as the reproductive characteristic and the demographic history, may also impact the genetic effects of recent habitat fragmentation. For gymnosperms, genetic composition can be quite stable when facing habitat fragmentation because of their lengthy generation time. However, in the long term, the loss of genetic diversity will be unrecoverable. In this review paper, we survey genetic studies of threatened gymnosperms, summarize endangerment mechanisms under habitat fragmentation, and finally recommend conservation strategies for gymnosperms. The findings of this paper indicate that a comprehensive understanding of the endangerment mechanisms through genetic diversity studies is important for effective and efficient conservation of Wild Plant with Extremely Small Populations.

The Loess Plateau is home to various vegetation types as it contains famous transitional forests, grasslands, and deserts. Due to natural resource limitation and intensive human activities, this natural environment faces serious conservation challenges. In order to effectively conserve this natural environment, spatial mapping of species diversity is key to conservation efforts. In this study, we first modeled the potential distribution of 293 woody species based on specimen records and climate data and then calculated the spatial patterns of species richness and weighted endemism. Secondly, we calculated phylogenetic diversity and phylogenetic endemism and identified environmental drivers of the observed spatial patterns. Finally, we analyzed endemism types and tested their significance. Our results suggest that biodiversity hotspots are distributed on the southern edge of the Loess Plateau and are highly related to the flora of Qinling Mountains. The biodiversity patterns of this transitional region are driven by annual precipitation and minimum temperature of coldest month. Endemism hotspots were found on the southern edge of the Loess Plateau, which contain paleo-endemism and mixed-endemism, but no neo-endemism. We concluded that most woody species of the Loess Plateau originated in tropical or subtropical regions, and the species richness patterns of this region are maintained by dispersal rather than speciation. Our study indicated the importance of incorporating the evolutionary history in biodiversity conservation.

Lycophyte and fern genetic research has accumulated over recent years due to sequencing technology advancement, making nuclear, plastid, and mitochondrial genomes accessible. While early plastid genome research focused on reporting genome structures and sequence characteristics, our current understanding spans comprehensively over structural evolution and phylogenomic analyses. These studies provide us with important insight for understanding the early evolution of vascular plants. Although lycophyte and fern plastid genomes are relatively well understood, this paper summarizes the current understanding of lycophyte and fern plastid genome structure and its variation. Such variation includes large inversions, boundary shifts of repeat regions, gene and intron loss, and some of which could be recognized as synapomorphies of higher taxonomic ranks. We also review RNA editing and long noncoding sequence inserts in plastid genomes, which are prevalent in lycophytes and ferns. However, the origin, mechanism and function of such remain unclear. We also comment on the application, merit and future of plastid phylogenomics.

DNA barcoding has been growing exponentially in terms of the number of barcode generated as well as its applications, e.g. as conservation tools in: species identification for damaged specimens, diet analysis from gut content and feces, biodiversity assessment from environmental DNA (eDNA), bulk arthropod samples or invertebrate-derived DNA (iDNA). These applications often require coupling with high throughput sequencing (HTS) technologies, and when done so are referred to as metabarcoding. Here, we discuss the methods used to generate reference barcodes using cost-efficient HTS platforms, and introduce several rules-of-thumb and some widely-used tools to conduct data quality control, denoising, and Operational Taxonomic Units (OTUs) clustering. We hope this review will help readers better understand how these emerging technologies can be implemented alongside existing technologies to accelerate biodiversity assessments in an accurate and efficient way.

Large carnivores play an important role in the regulation of food-web structure and ecosystem functioning. However, large carnivores face serious threats that have caused declines in their populations and geographic ranges due to habitat loss and degradation, hunting, human disturbance and pathogen transmission. Conservation of large carnivore species richness and population size has become a pressing issue and an important research focus of conservation biology. The western Sichuan Plateau, located at the intersection of the mountains of southwest China and the eastern margin of the Tibetan Plateau, is a global biodiversity hotspot and has high carnivore species richness. However, increasing human activities may exacerbate the destruction of local flora and fauna, thereby threatening the survival of wild carnivores. Information on species composition and dietary habits can improve our understanding of the structure and function of the ecosystem and food-web relationships in the study area. In addition, species composition and dietary habits are of great significance for understanding multi-species coexistence mechanisms and preserving biodiversity. This study collected carnivore fecal samples from Xinlong and Shiqu counties in the Ganzi Tibetan Autonomous Prefecture, Sichuan Province. DNA was then extracted from the samples and the species was identified based on DNA sequences and DNA barcoding techniques. Seven carnivores were identified, including five large carnivores (Canis lupus, Ursus arctos, Panthera pardus, P. uncia and Canis lupus familiaris) and two medium and small-sized carnivores (Prionailurus bengalensis and Vulpes vulpes). Using fecal DNA, high-throughput sequencing and metabarcoding, we conducted diet analysis for the seven carnivores and found 28 different food molecular operational taxonomic units (MOTUs), including 19 mammals, eight birds and one fish species. The predominant prey categories of wolves, dogs and brown bears were ungulates. The domestic yak (Bos grunniens) was the most frequently identified prey species. Small mammals such as rodents and lagomorphs accounted for a significant proportion in the diets of leopard cats and red foxes, The most frequent prey of this category of carnivore were the Chinese scrub vole (Neodon irene) and plateau pika (Ochotona curzoniae). In addition, leopards and snow leopards mainly fed on the Chinese goral (Naemorhedus griseus) and blue sheep (Pseudois nayaur), respectively. Our study highlights the utility of fecal DNA and metabarcoding technique in fast carnivore surveys and high-throughput diet analysis, and provides a technical reference and guidance for future biodiversity surveys and food-web studies.

Phylogeography seeks to identify the historical ecological and evolutionary processes underlying modern-day phylogenetic relationships across a spatial gradient. Owing to the characteristics of uniparental inheritance, low mutation rates and haploid, chloroplast DNA (cpDNA) markers record the events occurring in historical long-term evolutionary processes to different extents, and hence aid in understanding the mechanisms for phylogeographic variation. Here we discuss how these characteristics affect cpDNA marker selection, how they increase or reduce population genetic differentiation, how they lengthen or shorten the average gene coalescent times, how they promote or impede gene introgression among species and how the process of lineage sorting functions from polyphyly to paraphyly to monophyly. We reviewed the theoretical bases of these mechanisms, as well as the progress made in empirical studies regarding the theories of phylogeographic variation. Because of the heterogeneity of DNA sites in mutation rate, selection strength and interactions with genetic drift effects, one study to examine the genome-wide pattern of phylogeography will be necessary in the future. This must include the analysis of differential gene introgression and gene flow among sites, as well as the distribution of the differential phases of lineage sorting along the chloroplast genome.

Recently, numerous studies have used functional trait or phylogeny to infer the mechanisms of community assembly. However, different processes may lead to similar patterns of diversity. In an alpine meadow plant community in Gannan, we compared the dynamical changes in species diversity, functional diversity and phylogenetic diversity with experimental removal of plant functional groups. We assessed how colonization and extinction affected diversity dynamics after removing functional groups. We found that for communities receiving removals of different number of functional groups, species richness (SR), Shannon-Wiener index (H°), Simpson index (D), and evenness index (J) rapidly converged to the levels for natural communities. Moreover, functional diversity (FD) and phylogenetic diversity (PD) showed the similar trends as species diversity, while the mean pairwise distances (MPD/MPDa and MFD/MFDa) converged to medium levels. Next, species and functional group compositions recovered to the levels of natural communities within a short period. Finally, we found that functional patterns of species colonization and extinction was the main driver of the community recovery. This study indicates that the diversity of species, functions, and phylogeny of plant communities in alpine meadows can recover quickly from functional group removal at small scales when close to natural alpine meadows.

The agricultural civilization that originated in the Yangtze River Basin is an important part of Chinese civilization. Being one of the world-famous crop origin centers, the Yangtze River Basin is rich in biodiversity, and has bred many cultivated plants. This review has collected data of crops that originated in the Yangtze River Basin and information of plant remains found in Neolithic archaeological sites. By summarizing the environmental features and tracking the changes of vegetation since the Holocene in the Yangtze River Basin, we attempt to dissect the dynamics of plant use in this area and investigate the relationship between local cultivated plants and biodiversity. Our results indicate the agricultural civilization in the Yangtze River Basin greatly relied on rice production, and domesticated a large amount of fruit and aquatic vegetable crops, which reflects the adaptation and dependence to local subtropical evergreen broad-leaved forests and wetlands. When compared to other basins, the Yangtze River Basin is advantageous in allocation of ecological factors, and the characteristic of domesticated crops shows a typical feature of subtropical humid forest vegetation areas. Studying the natural and human factors related to crop domestication can help us to better understand the origin of agriculture civilization in the Yangtze River Basin. This work not only provides a reference for the conservation and utilization of plant genetic resources, but also plays a guiding role in promoting the construction of ecological civilization and sustainable development in the Yangtze River Basin.

The Yangtze River Basin is key distribution area involved in the origin and evolution of kiwifruit as it possesses more important resources of wild kiwifruit species and populations of Actinidia chinensis-A. deliciosa species complex in the world. The seeds of kiwifruit were brought from Yichang, Hubei to Shanghai along the Yangtze River and reached New Zealand more than 100 years ago. Through cultivation and domestication, the initial seedlings gradually developed as a new fruit crop industry. In recent decades, great progress has been made on kiwifruit studies in China including genomic sequencing for diploid Actinidia chinensis cv. Hongyang, resequencing for interspecific relationships among the Actinidia species, molecular phylogeny and infrageneric classification of the genus Actinidia, and population genetic structure of certain species. However, more results are still needed to understand the origin, domestication and speciation of the kiwifruit species. Resource assessment on the base of the latest research is still lacking. It is of great importance to strengthen the protection and sustainable utilization of wild kiwifruit resources. Here we review the domestication history of cultivated kiwifruit, advances of systematics and classification in Actinidia, analyze the potential value and the present situation of wild kiwifruit resources in the Yangtze River Basin, and summarize distribution characteristics and threats to the endangered species of Actinidia in the basin. Finally, corresponding protection strategies for the existing problems are suggested, including the establishment of long-term protection mechanisms, the enhancement of basic scientific research and systematic evaluation of genetic resources, and the improvement of conservation standards of the germplasm resources for the sustainable utilization of wild kiwifruit resources.

Pollinators serve key ecological functions, ensuring stable ecosystems and high agricultural yields. Hence, assessing ecosystem health and effects of agricultural management would benefit from understanding and monitoring pollination networks, which involves identifications of pollinators and pollinated plants. Classic approaches of morphology-based identification of plants and pollinators can be time-consuming, labor-intensive and costly, and require highly specialized taxonomic expertise. In comparison, DNA barcoding and high-throughput sequencing technologies can provide efficient and accurate identifications of plants and their pollinators, which may facilitate construction of pollination networks. Here we propose using sequencing technologies with a PCR-free genome-skimming work frame, using "super DNA barcode" as a new method to assess plant-pollinator networks. We expect this technique to improve resolution and accuracy of taxonomic identification to help gain quantitative information for bulk samples of pollinators or pollens. Although there are technical challenges to be resolved, the robustness of the new methodology has been validated in relevant biodiversity studies, suggesting promise in constructing pollination networks.

Halo-tolerant plants compose a huge group of plants with unique ecological and economical value. Little is known about their DNA barcoding speciality. In this study, 562 samples of coastal halo-tolerant plants (including 53 families, 97 genera and 116 species) were collected from 10 coastal provinces, ranging from Liaoning to Hainan. Three chloroplast DNA markers (matK, rbcL and trnH-psbA) and one nuclear DNA marker (ITS) were amplified and sequenced. Primer universality and sequence availability of each locus were examined and species resolution rates were tested. When considering sequence availability, matK and trnH- psbA were among the best. But the primer universality of ITS was marginally worse than expected. The all-to-all BLASTn searches indicated that the species resolution rate of ITS was the highest (73.36%), followed by those of matK (64.03%), trnH-psbA (61.21%) and rbcL (46.41%). Phylogenetic trees (NJ trees) indicated that the species resolution rate of matK was the highest (82.3%), but no reliable NJ tree based on trnH-psbA could be acquired because of unequal sequence length. NMDS and PCoA results demonstrated that both chloroplast DNA markers and nuclear DNA markers should be considered when conducting coastal plant DNA barcoding studies. Based on the above results, we suggest that the combination of ITS + matK should be regarded as the barcode for halo-tolerant plants in Chinese coastal regions. In total, the 1939 newly acquired sequences in this study lay the foundation for a DNA barcode database of costal halo-tolerant plants.