Species classification and identification is the basis of biodiversity monitoring, and is critical to deal with almost all ecological questions. In this paper, we aim to understand the current status and existing problems in plant species classification and identification using multi-source remote sensing data. We summarized the studies in this field since the year 2000, and found that most of these studies focus on temperate or boreal forests in Europe and North America, or African savanna. Airborne hyperspectral data is the most widely used remote sensing data source, and the LiDAR, as a supplementary data, significantly improves the classification accuracy through the information of single tree segmentation and three-dimensional vertical structure. Support vector machine and random forest are the most widely used non-parametric classification algorithms with an average classification accuracy of 80%. With the development of computer technology and machine learning, artificial neural network has developed rapidly in species identification. Based on the literature-based analysis, we propose that the current research in this field is still facing some challenges, including the complexity of classification objects, the effective integration of multi-source remote sensing data, the integration of plant phenology and texture characteristics, and the improvement in plant classification algorithm. The accuracy of plant classification and identification could be greatly improved by using the high-frequency data collection over time, the integration of hyperspectral and LiDAR data, the use of specific spectral information such as short-wave infrared imagery, and the development of novel deep learning techniques.

The construction of natural protected area system is a biodiversity conservation strategy which has been highly emphasized by international communities. In recent years, China expresses its concerns about the overlapping and intersection of natural protected area and proposed Guidance on Establishing a Natural Protected Area System Dominated by National Parks. To implement the proposed strategy, it is important to conduct a systematic study on the relationship and spatial distribution of the natural protected areas. This study collected data from 8,572 natural protected areas in different categories and administrative levels, including coordinates, types of ecosystems, administrative regions and boundaries. Among them, 1,532 natural protected areas with spatial overlapping and cross-jurisdictions were selected. Geographic concentration index (G) was calculated, and ArcGIS software was adopted for Kernel density estimation. Finally, the spatial distribution patterns, overlap of protected areas in ecological and geographic zones, ecosystem types, agencies with crossing jurisdiction and province locations were obtained. The results showed that: (1) Natural protected areas were concentrated in mountainous areas in central Shandong, Taihang Mountain, Dabie Mountain, Tianmu-Huaiyu Mountain and Wanjiang region, across multiple wetlands and forest ecosystems (Mean > 6, Max > 8). Among 10 pilot national parks, only Giant panda, Nanshan and Qianjiangyuan were located in areas with high density of overlapping; (2) The former State Administration of Forestry and the Ministry of Housing and Urban-rural Development had the largest number of sites under cross-jurisdiction among all the former agencies; (3) The number of overlapping natural protected areas in Heilongjiang, Anhui, Shandong, Henan, Hubei and Hunan provinces are significantly higher than other provinces. The overlap between Shanxi-Hebei-Henan and Anhui-Hubei-Jiangxi provinces is higher, and there is moderate overlap in other provinces. The areas studied above could become key priority areas for reassembling and optimizing China’s protected area system. Based on overlap hot zones, priority zones for biodiversity conservation, and cultural ecosystem services, this paper proposes a framework for reassembling and optimizing overlapped protected areas. According to 3 new protected area categories including national parks, nature reserves and natural parks, suggestions are given prioritizing reassembling and associating the area with a new category, which would provide a reference scheme to the urgent needs of ongoing reform of China’s natural protected areas system.

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 that many current studies include and that we believe 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.

Tea (Camellia sinensis) is an important crop and is sensitive to climate change. Evaluating the impact of climate change on tea distribution and production is not only important for the global economy but also the livelihoods of farmers in many countries. Here we compiled data from 858 global occurrences of C. sinensis and six climatic variables, and used species distribution model (SDM) to predict the current potential distribution and possible range shifts in response to climate change in 2070 under Representative Concentration Pathway 2.6 and 8.5 (RCP2.6 and RCP8.5). The results indicate that the current potential distribution of tea is mainly confined to Asia, Africa and South America, and distribution is limited by mean temperature of coldest quarter (MTCQ) and precipitation of warmest quarter (PWQ). Under future climate change scenarios, by 2070 suitable habitat for tea could significantly shrink at low latitudes, but expand at middle latitudes, leading to a northward shift of the distribution. However, the influence of future climate change on tea distribution differed across regions. The climatically suitable areas in Argentina, Myanmar, and Vietnam are projected to decrease by 57.8%-95.8%, whereas those in China and Japan are projected to increase by 2.7%-31.5%. Moreover, 68% of the new suitable habitat for tea cultivation under future climate change are predicted to lie within areas of natural vegetation cover. Therefore, the establishment of new tea gardens in these areas may lead to conflicts between tea cultivation and conservation of natural vegetation and biodiversity.

Earth is experiencing its sixth mass extinction, and in response to the severity of accelerated biodiversity loss, the 10th meeting of the Conference of the Parties to the Convention on Biological Diversity (CBD) adopted the Strategic Plan for Biodiversity 2011-2020, including Aichi Biodiversity Targets. However, the IPBES global assessment showed that most of the Aichi Biodiversity Targets for 2020 will possibly be missed, because of which the IPBES called for transformative changes in nature conservation in its global assessment report. China has made significant progress in biodiversity conservation, put forward with completed eco-civilization system, try to develop a protected area system, stress the importance of biodiversity conservation by inspection and “Green Shield” action. In addition, up to 18% of territory has been designated as protected area. However, biodiversity is still declining at an accelerated rate, more species are threatened. Although a series of reforms to eco-civilization has started the transformative changes, such as mainstreaming biodiversity in central government, managing all the protected areas in one department, emphasizing the importance of biodiversity in national spatial planning and China Ecological Conservation Red Line (ECRL) designation, systematic strategies and actions are still in need for biodiversity conservation. It is important to further implement “mainstreaming” at different levels, establish a systematic legal system and effective conservation mechanism, guarantee enough funds, clarify the status of biodiversity in production and living space, and make ecosystem service possible to become economic benefits. Therefore, it is necessary for China to achieve transformative changes in terms of conservation awareness, spatial planning, and conservation actions by promoting balanced economic, political, cultural, social, and ecological progress. It is possible to mainstream conservation awareness, coordinate between conservation and utilization, and promote citizen-based conservation actions if China combines the forces of law, governance, market, technology, and society. This approach world form an efficient and integrated mechanism to achieve the ideal state of biodiversity conservation, “living in harmony with nature”.

The 18 ^th Conference of the Parties of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) was held in Geneva, Switzerland from August 17 to 28, 2019. The Parties discussed 56 proposals for amendment of the Appendix of the Convention and 140 working documents, continuing the trend of the amendment of the Appendix in recent years. However, the trend of including more species in the Appendix slowed down at this Convention. The Parties clarified the annotations, application, interpretation and implementation of the Appendix, established new regulatory resolutions and adopted the CITES Strategic Vision post-2020. At the meeting, China established a positive image as a responsible country that attaches importance to the construction of ecological civilization, and all five proposals for amendments of the CITES Appendix proposed or jointly proposed by China have been adopted by the Parties.

China’s key protected species lists include the List of State Key Protected Wild Animals (LSKPWA), the List of Terrestrial Wildlife with Important Ecological, Scientific and Social Values, and the lists of local key protected wild animals. After the amendment and implementation of the Wild Animal Protection Law of the People’s Republic of China in 2017, the revision of the LSKPWA is on the agenda. In order to revise the list of the state key protected species, the relationship between these lists should be delineated to reflect the priority of protection and to facilitate administration and to divide the responsibility of protection between the central and local governments. It is recommended to determine the level of key protected wildlife species according to their attributes of endangerment, endemism, rareness, preciousness and management requirement. By adopting the Principle of Clump Listing, related species or the higher taxa such as a whole genus even a whole family should be included in the lists of protected species as far as possible. It is also practical to list a subspecies or a population as a management unit on the species protection list. In addition, to reflect the new provisions of the amended Wild Animal Protection Law of the People’s Republic of China, it is necessary to distinguish domesticated and wild populations, those populations which have been artificially successfully bred with mature technology and stable production traits should be exempted from the listing. Thus, using the Principle of Splitting Listing to solve the real problems in conservation. In addition, taxonomic changes should be closely tracked and species list should be updated in time. It is also necessary to formulate criteria for protection levels, to develop guidelines for species recovery plan after their listing and to design amendment procedure for the list. It is important to formulate populations and habitats recovery plan for each key protected species. Through periodic evaluation of the listed species, the listed species are upgraded, downgraded, deleted or maintain its status for the needs of dynamic management of rare and endangered wild animals.

Microbes are ubiquitous in human life. In years past, the study of microbes has only focused on single-bacteria cultures and qualitative analyses. The development of sequencing technology has greatly enhanced progress in microbiology research and more and more evidence shows that human symbiotic microbes, especially intestinal microbes, are closely related to human health. Second-generation sequencing technology is currently mainstream in microbiology research because of its high throughput, high accuracy and low cost. However, with the deepening complexity of research, the disadvantages of second-generation technology, i.e. short read length (< 450 bp), lead to subsequent challenges in data analysis and genome assembly, and limit the applicability to future research. In this context, the third-generation sequencing technology comes into being. The third-generation of sequencing (TGS) technology is also called single molecule sequencing. It directly carries out real-time sequencing of single DNA molecules without PCR amplifications. TGS technology significantly increases read length up to 2-10 kb or even 2.2 Mb. Because of its advantages of long read and no preference for GC, TGS provides a new method for full-length gene sequencing that facilitates the assembly of complete and reliable genome maps in microbes and that further reveals the diversity of microbial structures and functions. This review summarizes the technical characteristics and principles of TGS, and then mainly analyzes its applications and progress in 16S/18S rRNA gene sequencing, complete bacterial genome mapping and metagenomics research.

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.

From May 2014 to April 2019, we conducted camera-trapping surveys in the Qianjiangyuan National Park, Zhejiang Province. We divided the park into a grid containing 267 1 km × 1 km plots, with 3 fixed survey stations (> 300 m apart from each other) in each plot. One camera trap was set up in each plot and rotated among the stations within the plot every four months. In the Gutianshan section of the park, the cameras were running for 14 rotations from 2014-2019. The survey started in Hetian, Qixi and Changhong in 2018, and the cameras were rotated once in Qixi and twice in Hetian and Changhong. With a survey effort of 140,413 camera-days from 741 stations in 253 grids, we obtained 268,833 pictures/videos resulting in 74,368 independent detections. The survey recorded 21 wild mammalian and 72 avian species, as well as 5 domestic animal species. Among the species, two (black muntjac Muntiacus crinifrons and Elliot’s pheasant Syrmaticus ellioti) are Class I, and seventeen are Class II national protected animals, accounting for 20.4% of total recorded wild species. Five species are red-listed by the IUCN as Vulnerable and four as Near Threatened, accounting for 9.7% of the total recorded wild species. One species is red-listed as Endangered, nine as Vulnerable and ten as Near Threatened by Red list of China’s vertebrates, accounting for 21.5% of the total recorded wild species. The most detected mammal species was Reeve’s muntjac Muntiacus reevesi, and the most detected bird species was silver pheasant Lophura nycthemera. Our results provide reliable baseline information on the species composition, their spatial distribution, and relative abundance of mammals and birds in the Qianjiangyuan National Park.

Biological invasion is a major threat to multiple ecosystems across the globe, causing severe damages to ecological integrity, loss of biodiversity, economic and social development and even human health. With the rapid development in aquaculture, shipping and aquarium and ornamental trades in the past several decades, China has become one of the countries most influenced by invasive species. Studies have clearly shown that the development and application of robust early monitoring and warning is one of the most effective ways to prevent and possibly control invasive species in aquatic ecosystems. Compared to terrestrial ecosystems, there remain several technical difficulties for developing early monitoring and warning in aquatic habitats. The technical challenges are mainly due to several features of aquatic biological communities such as high biodiversity and complex structure, a large number of microscopic species, extremely low population density and lack of available taxonomic keys for species identification. With the rapid development of high-throughput sequencing techniques, environmental DNA (eDNA)-metabarcoding has become the top priority method for developing the early monitoring and warning programs in aquatic ecosystems. In this review, we aim to synthesize the research progress on eDNA-metabarcoding and its application to early monitoring and warning of invasive species in aquatic ecosystems. In addition, we briefly discuss the technological advantages of eDNA-metabarcoding for the early monitoring and warning programs. Finally, we propose research perspectives for solutions to technical issues for false positive and false negative errors in the eDNA-metabarcoding process.

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.

The Lancang-Mekong River is the longest river in Southeast Asia, and is one of the richest areas of freshwater biodiversity in the world. Because it is an international river through six countries and holds extremely high fish biodiversity, there is a lack of systematic understanding of freshwater fish diversity. Over the past two decades, this team systematically compiled a list of freshwater fish species in 32 sub-basins or tributaries in the upper and middle reaches of the Lancang-Mekong River. Now in this paper, the species composition and distribution of fish have been analyzed, and the species diversity of the upper and middle reaches of the Lancang-Mekong River has been evaluated using the taxonomic diversity index. The results showed that 745 species of freshwater fish were recorded in the middle and upper reaches of the Lancang-Mekong River. These fish belong to 229 genera, 63 families, 17 orders and 2 classes. Of these, 451 species of Cypriniformes fish accounted for 60.5% of the species. The taxonomic diversity index showed that, from the source to the middle reaches of the river, the taxonomic distribution of freshwater fish became increasingly more even, the relationships were increasingly further apart, and the fish diversity gradually increased. Cluster analysis (CA) and multi-dimensional scaling analysis (MDS) results showed that the 32 sub-basins could be divided into three groups (Jaccard similarity coefficient=8.69), and the analysis of similarity (ANOSIM) indicated that the composition of freshwater fish differed significantly between the groups (R = 0.877, P = 0.001). Similarity percentage analysis (SIMPER) results indicated that Cypriniformes and Siluriformes were the main fish that differed among the three groups, and the species composition of groups presented distinctive changes at the family and species levels with the altitude rising. With the rapid population growth and economic development of the countries in the river basin in recent decades, the fish diversity and fishery resources of the Lancang-Mekong River face serious threats. Thus, it is urgent that countries in the river basin cooperate and formulate a scientific protection plan at the basin scale.

In the 1970s, the intuition that complex communities are more stable than simple ones was challenged by mathematical models which gave diametrically opposing conclusions. Since then, this “paradox” has been heavily researched making the complexity-stability relationship of continued interest. Here, we analyzed the concepts of “complexity” and “stability” and classified the half-century of mathematical models generated by this field into linear approach and nonlinear approaches. The former is also referred to as community matrix, while the latter could be further classified into interaction matrix, numerical simulation of complex network, and food web module dynamics. Based on different community construction methods and adopting different stability criteria, together they provide a rich knowledge of how species interact and coexist, enabling us to reveal the vain of the paradox. In general, species diversity and connectivity play a negative role in the stability of randomly constructed community models. However, in models that mimic natural, empirical communities, several characteristics (including network topology, interaction intensity distribution, and interaction mode) provide mechanisms for maintaining stability, enabling these communities to reach higher levels of complexity. The study of complexity-stability is far from over. The complex interactions in natural communities is still beyond the reach of current models, and the concept of stability also needs to be expanded. The in-depth study of this topic will contribute both ecological theory and ecosystem management practice profoundly.

The Tibetan sacred nature sites (SNS) encompass culturally significant, ritually protected sites in the Baima National Nature Reserve. Animistic and Tibetan Buddhist custodians of these sites have used traditional knowledge to conserve these sites for generations. Here, we assess how the Tibetan traditional eco-conservation culture conserves biodiversity, promotes community-based conservation, and restores forest ecosystems using methods of applied ethnobotany and ethnoecology. In particular, we applied strengths, weaknesses, opportunities, and threats (SWOT) analyses and community participatory approaches in three Tibetan SNS: Bazhu, Kegong, and Zhuida in Baima National Nature Reserve and its surrounding area in Shangrila County of Deqin Tibetan Autonomous Prefecture of Yunnan Province.Our results show that the driving force for community conservation of biodiversity comes from the established, traditional cultures and the dependence of community livelihoods on biodiversity. We conclude that community conservation on Sacred Nature Sites is an important way to protect biological and cultural diversity, as well as livelihood development at the community level. The Tibetan community's long-term compliance with, and practice of, SNS conservation has been a significant contribution to biodiversity conservation throughout the region.

Community structure plays a fundamental role in forest ecosystems as one of the basic mechanisms underlying community assembly. Community structure includes both horizontal and vertical structure. We stratified the vertical structure of a lower subtropical evergreen broad-leaved forest at Dinghushan in Guangdong Province, China by surveying each individual with DBH ≥ 1 cm via a canopy crane, and then explored α diversity within each layer, as well as β diversity between layers. We found that: (1) The vertical structure of the forest was stratified into five layers; from bottom to top, the shrub, sub-canopy, lower canopy, middle canopy, and upper canopy correspond to the traditionally defined vertical levels of a forest community. (2) Layer α diversity decreased with height, and the Pielou evenness index was largest in the lower canopy. (3) The β diversity of layers relative to the shrub layer increased with height. Using the POD framework, the differences between layer community compositions were mainly attributed to differences in species richness. However, the lower canopy showed increased species replacement and decreased richness difference relative to the middle canopy layer when compared with other neighbouring layers. (4) Air temperature, light intensity and relative humidity increased with layer height, and the most dramatic change in light occurred in the middle canopy. These microenvironmental features may play an important role in the formation of vertical hierarchy in the forest, with light intensity as the largest factor.

Understanding key species and their roles and impacts within communities plays a vital role in protecting key species within communities. Species relationship indicators, i.e., betweenness centrality (BC), closeness centrality (CC), and degree centrality (DC) measured food web connectivity among a community of 49 species. Once indicators were calculated, a clustering analysis analyzed species influences on connectivity robustness among different species classes. In addition to clustering analysis, node removal was tested to measure connectivity robustness under removal modes. Based off of clustering results, species were divided into three food web classes: (1) Class I species have relatively higher BC, CC, and DC values. (2) Class II species have relatively lower BC, CC, and DC values while (3) Class III species are intermediate between Class I and Class II species. In our analyses, it appeared that Class I species are more important for food web processes and are therefore considered key species, contributing to our understanding of how to quantify key food web species. Besides, the connectivity robustness decreased along with the increase in removed nodes under the ascending order removal mode. In the descending order and random removal modes, the connectivity robustness slightly increased after a continuous decrease along with the increase in removed nodes. It indicates that removal modes significantly affect the connectivity robustness. Moreover, under the three removal methods, the significant change in the connectivity robustness corresponds to almost the same number of removed nodes. It suggests key species play an essential role in maintaining the connectivity robustness of the food web.

LiDAR (light detection and ranging), a fairly new active remote sensing technology, is being widely used in the field of animal ecology by more and more scholars due to the recent development where forest parameters can be extracted and inverted from LiDAR. In this paper, we review the advances in forest parameter extraction from LiDAR and its many applications in studying wildlife habitat. We also analyze current research on forest parameter inversion algorithms based on LiDAR, mainly in forestry research, though we lack quantitative parameters related to the ecological significance of animals. Because few studies have applied LiDAR technology to animal ecology research in China, we consider foreign research in this field in three categories: (1) The relationship between species habitat selection and three-dimensional forest structure; (2) Three-dimensional habitat mapping; (3) Biodiversity assessment and species distribution model prediction. Compared with traditional methods, the high-precision three-dimensional structure information provided by LiDAR can significantly improve the efficacy of monitoring animal habitat quality and biodiversity and the modelling accuracy of species distribution models. These advancements contribute to deeper understanding of species habitat selection and the clustering process mechanism. However, the studies that utilize LiDAR to date have mainly focused on previously known ecological relationships, especially the relationship between canopy structure and species diversity. These studies fail to account for either forest understory habitat quality or biodiversity monitoring and evaluation. In short, the relationship between wildlife and its three-dimensional habitat needs to be further explored through analysis of LiDAR data. Future studies should focus on extracting three-dimensional structures of forest understories to improve the efficacy of monitoring habitat quality and biodiversity in the understory, and to provide standard quantitative indicators for the evaluation of animal ecology.

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.

Based on historical accounts and the latest research on the taxonomy and phylogeny of amphibians, we provide an updated species list of the diversity and distribution of amphibian and reptile species in the Anhui Province, China. As of 30 November 2018, we recorded 44 amphibian species, representing 2 orders, 9 families and 26 genera, and 72 reptile species, representing 3 orders, 11 families and 48 genera in Anhui. Among these, 3 amphibian species and 1 reptile species are endemic to Anhui. When compared to amphibian and reptile species records in The Amphibian and Reptilian Fauna of Anhui, our census added 12 species, excluded 1 species, and renamed 29 species in this revised species list. According to the animal geographical regions of China, 91 species belong to the Oriental Realm, 10 species are classified in the Palaearctic Realm, and the remaining species are considered widespread. Four recorded species are listed in the National Key Protected Wild Animal List, and 112 species are ranked in the Red List of China’s Vertebrates.

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.

Populus yunnanensis is an endemic tree species to Southwestern China. It is a typical southern Populus species that is fast-growing species with easy to clone propagules and is highly adaptable. It is important to research the genetic diversity and population structure of P. yunnanensis for the collection, preservation and utilization of the germplasm resources. In this study, 64 individuals were collected from six populations, spaning the main distribution areas of P. yunnanensis, including Zhaotong (ZT), Huize (HZ), Songming (SM), Eryuan (EY), Lashihai (LS) and Sichuan Meigu (MG). A total of 34 pairs of SSR primers and three pairs of cpDNA primers were used to determine out the genetic diversity and genetic structure. A total of 154 alleles were detected by SSR primers in P. yunnanensis. The average number of alleles was 4.529. The observed heterozygosity (Ho) and expected heterozygosity (He) were 0.552 and 0.472, respectively. And the average genetic differentiation coefficient (Fst) was 0.238. The average polymorphism information content (PIC) was 0.421 and the gene flow (Nm) was 0.806. The results of the DAPC, PCoA and UPGMA analyses showed that the six populations can be divided into three sub-categories: Group І included ZT, HZ and four individuals of SM. Group II included EY, LS and the six remaining individuals of SM; and group III included MG; SM population include mixed genetic components from І and ІІ. A total of 35 variable sites were detected in the three cpDNA combinations, forming 13 haplotypes. Among them, haplotype H5 was the most widely distributed in the population, while the remaining ones were of private haplotypes. Analysis of molecular variance (AMOVA) showed that genetic variation within the population was greater than between populations. The study clarifies that P. yunnanensis has geographical distribution characteristics and is suited to in situ conservation. As ZT population has the highest geneticdiversity and contains seven chloroplast haplotypes, it should be given protection priority.

Endangered species conservation is an important part of biodiversity conservation, heavily helped by threatened species assessment guides. The assessment of threatened level has gradually evolved from being qualitative to quantitative with qualitative supplement. This paper reviews the research progress of the domestic threatened plant species quantitative assessment system, and introduces the mature IUCN Red List Assessment System, CITES Assessment System, and the National Natural Conservation Association Assessment System. Through this, we propose future development requirements of quantitative assessment criteria for threatened species should have the following characteristics: (1) a clear, unified, and reasonable definition of category setting, (2) quantitative, objective, and non-redundant criteria for endangered categories, (3) adaptation to different geographical range while simultaneously expressing threatened category over different ranges, (4) evaluation indicators contain the dynamic information of the species which can quantitatively analyze the change of the species through time. In addition, the domestic quantitative assessment system for threatened species should form a standardized outline with increased publicity to combine theoretical research with specific conservation actions. Lastly, China should adopt the widely-used endangered rating systems to assess species threatened level and integrate domestic biodiversity conservation work into the global scale.

Environmental DNA (eDNA) refers to DNA fragments that organisms leave behind in their surrounding environment (such as soil, sediment and water). eDNA technology sequences these DNA fragments and can provide information on taxonomic composition of benthic macroinvertebrate communities. Compared with traditional biological survey methods, eDNA technology is more sensitive, efficient and noninvasive. As a novel method for surveying aquatic organisms, eDNA techniques have been widely used in biodiversity assessments of aquatic organisms, including monitoring of endangered, rare and invasive species. In this review, we summarize recent developments in eDNA technology and focus primarily on the operational procedure and its application for freshwater benthic macroinvertebrate analyses. Finally, we discuss the advantages and potential caveats of current eDNA practices.

Exploring how functional traits vary along environmental gradients has always been one of the core issues of trait-based community ecology. While functional traits vary both among species and within species, little is known about how intraspecific variation changes along environmental gradients. We explored how intraspecific trait variations of four leaf functional traits (specific leaf area, leaf dry matter content, leaf thickness, leaf area) varied along vertical layer within community using data for 2,820 individuals belonging to 16 species in a 1.44-ha plot in the south subtropical evergreen broad-leaved forest in Dinghushan. First, we quantified the relative importance of intra- and interspecific trait variation within the canopy crane plot using linear random effect model. Trees were classified into three categories: shrub, subcanopy, canopy using the Kmeans method and investigated the patterns of intraspecific trait variation in different vertical layer using regression models. Finally, we explored whether intraspecific trait variation in different vertical layers depended on species differences using linear mixed effect models and a one-way analysis of variance. Results suggest that general intraspecific trait variation was lower than interspecific variation in the local community. Moreover, the pattern of intraspecific trait variation differed significantly among different vertical layer, and intraspecific trait variation was positively correlated with the vertical range. Intraspecific variation of leaf functional traits strongly depended on species differences, so species differences were relatively more important than microenvironment in explaining trait variation. In addition, intraspecific variation of different leaf functional traits showed different trends along vertical layer. Our study found the important role of intraspecific trait variation in species coexistence.

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.

Due to the small area and the cascaded structure formed by surface water, alpine micro-waterbodies are often considered to have similar habitats to alpine streams. However, due to the differences between the environmental factors and the benthic diversity, the functions of these two habitats in the ecosystem may be completely different. Northwest Yunnan hosts one of the richest global biodiversity hotspots where alpine micro-waterbodies and streams are densely concentrated. These two fresh water ecosystems have important functions in regional benthic biodiversity maintenance, however, these peculiar freshwater ecosystems have barely received research attention. In order to compare the similarities and differences of environmental factors and biodiversity between these two habitats and their maintenance effects on benthic diversity, in this study, benthic biodiversity and the environmental factors of 27 alpine micro-waterbodies and a stream in the same region (9 sample sites within an altitude gradient of 500 m) were investigated in an alpine valley of Gongshan County, Nujiang, Yunnan Province in June of 2015. Results showed that: (1) The common characteristics of benthic communities in alpine micro-waterbodies and the stream were that the dominant taxa have large population size, while, the rare taxa had higher richness but small population size. (2) However, the environmental factors, species diversity, functional diversity and community structures were quite different between the alpine micro-waterbodies and the stream, the alpine stream had higher species richness, species diversity and functional diversity than alpine micro-waterbodies. (3) the benthic biodiversity and formation of community structure in alpine stream were related to the elevation and aquatic environmental factors relating to flow rate regulation, while, the aquatic environmental factors of alpine micro-waterbodies did not act as the drivers for the distribution of benthic biodiversity. Therefore, these findings suggest that alpine micro-waterbodies and streams are distinct ecosystems that each feature has very different characteristics, they cannot be regarded as similar ecosystem types. Both of them play an important role in the maintenance of regional benthic biodiversity and ecosystem functions.

Species cataloguing is the basis for understanding their biodiversity. In the study, the diversity and geographical distribution of lycophytes and ferns in the Loess Plateau have been analyzed by utilizing published monographs, the current literature, and Herbaria specimens’ information. Following the order system from Flora of China, families and genera are classified relying on the latest research update on molecular taxonomy in this paper. Data analysis shows that the Loess Plateau is diverse with 165 species, 2 subspecies, 5 varieties, 42 genera and 18 families of lycophytes and ferns, which including 35 species endemic to China (20.35% of total species). The top five families are Pteridaceae (29 species, including subspecies and varieties), Dryopteridaceae (28 species), Polypodiaceae (19 species), Athyriaceae (16 species), and Aspleniaceae (16 species). The top six genera are Asplenium (16 species), Dryopteris (15 species), Polystichum (12 species), Woodsia (11 species), Selaginella (10 species), and Lepisorus (10 species). No rare and endangered plants, or endemic genera to China are contained. According to the ecological type, lycophytes and ferns are divided into 4 categories in the Loess Plateau, including terrestrial (112 species), lithophytes (75 species), epiphytes (18 species), and hydrophytes (3 species). The species of terrestrial or lithophytes are rich to 89.53% of the total species in this area. While the lycophytes and ferns of the Loess Plateau are located at the current geographical distribution edge, the distributions found in this study are consistent with our current understanding of lycophytes and ferns in China.

The Vegetation Map of the People’s Republic of China (1:1,000,000) is the most important dataset for vegetation studies in China. However, some vegetation formations were not included in the Vegetation Map of China due to limitations of data and mapping techniques in the last century. In order to update the dataset, we collected data of vegetation formations and their distributions from the literature (1950-present). Based on the phytocoenology-ecology principle, formations with the same dominant species were classified as the same formation. Compared to formations in the Vegetation Map of the People’s Republic of China (1:1,000,000), we added 1,475 new vegetation formations of forests and scrubs.

As the apex predator of plateau ecosystems in Central Asia and the Qinghai-Tibet Plateau, the snow leopard (Panthera uncia) plays an essential role in maintaining food-web structure and ecosystem stability. Learning the diet composition and dynamics of the snow leopard is important for understanding its role in ecosystem functioning and interspecific interactions. Previous diet analyses of the snow leopard have been based mainly on morphological identification of food debris in the feces, though the accuracy of this practice has been broadly debated. The Qionglai Mountains are located at the southeast edge of the snow leopard range, harboring a small and relatively isolated population of snow leopards that are barely studied. Using non-invasive sampling, we collected 38 putative snow leopard fecal samples in the Wolong National Nature Reserve in the Qionglai Mountains. To identify the fecal origin, we extracted the fecal DNA and amplified the mitochondrial DNA 16S rRNA gene fragment. Twenty-two fecal samples were identified as originating from snow leopards. Subsequently, vertebrate universal primers and a snow leopard-specific blocking oligo were used to amplify the food components in the fecal DNA, and then high-throughput sequencing was performed to analyze the diet composition of snow leopards. The blue sheep (Pseudois nayaur) was detected in 67% of the samples and was found to be the main staple food of snow leopards’ diet. The domestic yak (Bos grunniens) appeared in 33% of the fecal samples, also accounting for a high proportion of the snow leopard diet. In addition, pikas (Ochotona spp.) and birds were found in a small number of fecal samples. Therefore, wild prey was found to be the main food source for snow leopards in Wolong. However, livestock (yak) also accounted for a relatively large proportion of their diet.

Aristolochia (s. l.) is widely distributed in tropical, subtropical and temperate regions of the world, with monochlamydeous and tubular flowers, gynostemia, inferior ovaries, axile placentations, pluriovulate capsules, and others as the main characters. It is the largest genus in Aristolochiaceae, which consists of about 600 species. According to Flora of China, there are 45 species in China, 33 of which are endemic. In recent years, many new species have been discovered in China, especially in Yunnan and Guangxi. Additionally, some taxa were confirmed, reinstated, republished and revised. Isotrema, previously treated as a subgenus of Aristolochia, was recently reinstated as an independent genus based on molecular and morphological evidences. This genus has strongly curved calyxes, 3-lobed gynostemia with paired anthers on the outer surface of each gynostemium segment, and basipetally dehiscent capsules. Through extensive field work, careful examination of many specimens, digital photos and related literatures, an updated checklist and identification key of Aristolochia (s. s.) and Isotrema in China are presented here. Relevant discussions and distribution for the 17 species of Aristolochia, 58 species and one subspecies of Isotrema are also provided. Among them, I. mollis and I. neolongifolia are reinstated and illustrated, the relationship among A. gentilis, A. chuandianensis and A. gracillima, and the relationship between I. kunmingense and A. bonatii are discussed, knotty taxa, such as I. ovatifolium complex, I. cucurbitoides complex, I. griffithii complex, I. versicolor complex, I. dabieshanensis complex and suspected species I. saccata, are also discussed.

To maximize species conservation outcomes and effectively allocate limited resources, the first step in conservation planning is to define conservation priority areas and migration pathways between them. Based on field survey and high-resolution satellite data, we used species distribution models, conservation planning tools and connectivity analysis tools to define the core habitat area and potential corridors for snow leopards (Panthera uncia) in the Sanjiangyuan Region. With potential threats identified, we proposed differentiated conservation strategies for different parts of the Sanjiangyuan Region: (1) In the western region, snow leopard core habitats are mostly small and fragmented but with widespread migration pathways and no obvious bottlenecks. However, the Qinghai-Tibet Railway is a potential barrier for snow leopard populations in the western region and needs further investigation. (2) The central region contains the largest core habitat which also has highest centrality in the connectivity analysis. To maintain the function of these source populations, we recommend long-term monitoring, anti-poaching patrol and supervision on development projects for this region. (3) For the eastern region, which has the highest human density, it is important to safeguard two core habitats (Anemaqen and Nanpo Yutze) and maintain the narrow corridors in between them. The provincial highway in Gande County may be a potential barrier for snow leopard migration and deserves further monitoring. As the epicenter for snow leopard conservation in China, the habitat quality in the Sanjiangyuan Region remains good overall. The goal of snow leopard landscape conservation in Sanjiangyuan should be to maintain core source populations while keeping migration routes unblocked. Integrated space-ground monitoring approaches should be implemented in the future for assessments and early warning signs of habitat degradation for these important protected species, especially in non-protected areas in core habitat at risk for development.

Aspergillus flavus is commonly regarded as a kind of saprophytic fungi with a wide distribution. It is the major aflatoxin B (AFB) and cyclopiazonic acid (CPA) producing species, as well as a pathogen to humans and animals. In the world, huge amounts of corns, peanuts and cotton seeds are vulnerable to be contaminated by A. flavus and aflatoxin each year. There is much variance in morphological, genetic and toxin-producing characters among isolates of A. flavus, resulting in its ambiguous population structure. In this paper, we analyzed 88 isolates of A. flavus from different environments of 26 provinces (including the Greater and Lesser Khinggan Mountains) in China, as well as nine ex-types and authentic strains based on CaM and benA sequences to infer their sequence types (STs) using multi-locus sequence typing (MLST), and their phylogenetic relationships and population structures employing MEGA 6.0 and Structure 2.3.4 softwares, together with their toxin-producing features (AFB and CPA). Our results showed that the 88 Chinese isolates and nine ex-type and authentic strains were distributed in three populations, i.e. A. flavus population I, A. flavus population II and population A. oryzae. There were 17 STs among the 97 isolates, among which the 88 strains from China were distributed in 15 STs. All isolates of population A. oryzae did not produce AFB, but most isolates of the A. flavus populations I and II produced AFB and CPA. The toxin-producing features were strain-specific, but not correlated to sequence types or populations. Some correlations between toxin-producing characters and geographical environments or crop types were recognized. The isolates of A. flavus populations I and II from the northeast areas planting corns, the arid northwest planting cottons and the south areas growing peanuts all produced AFB and CPA. The isolates from Hoh Xil of Qinghai and Aba of Sichuan did not produce AFB, though with the production of CPA. The isolates of A. oryzae population without AFB production were almost from North China with diverse climates and geographical environments, where the traditional Chinese soybean paste is made in the rural areas.

Fabaceae (= Leguminosae) is the third largest plant family after Asteraceae and Orchidaceae. It contains ca. 791 genera and 19,325-19,560 species. Many taxa possess great economic and ecological significance. Since the publication of Flora Republicae Popularis Sinicae in 1998, molecular systematics has continued to develop, and thus the classification categories of many genera have changed tremendously. In this paper, we summarize recent research results from both home and abroad (including 32 treatments and 4 newly recorded genera), compare these new changes with the treatment of legume genera in Flora Republicae Popularis Sinicae and provide a reference for future taxonomic research into native Chinese legumes.

Spatial patterns of species richness and mechanism are vital to biodiversity conservation. Based on the distribution of beetles and combined the climate and habitat heterogeneity, we explored the distribution patterns and effect factors of beetle species richness of overall and six dominant families in Helan Mountain of northern China. The results showed that species richness and fauna differentiation intensity of beetles were the highest in the middle of Helan Mountain, the southern section was higher than the northern section, and the western section was higher than the eastern section. After clustering analysis of species distributed in 183 grids, the distribution of beetles could be classified into three groups (xerophilic landscape beetle groups in the northern section, semi-hygric landscape beetle groups in the middle-western section, and semi-xerophytic beetle groups in the middle-east and south section). The mean annual temperature and precipitation were the most significant factors on beetle distribution by analyzing of RDA. Meanwhile, water and energy factors together explained 57.1% of the spatial variation in overall beetle species richness, only 5.9% and 7.1% separately, followed by habitat heterogeneity (35.2%) and only 1.8% separately. The relative effect of dominant species richness were inconsistent with climatic and habitat heterogeneity, but water and habitat heterogeneity have significant effect on beetle species richness in southern and northern of Helan Mountain. Water and energy factors dominantly impacted beetle spatial distribution, and habitat heterogeneity increased the species richness. Therefore, we suggested that topographic and soil factors may also have an important influence on beetle species richness in Helan Mountain according to the unexplained proportion.

Pollinator bees are providers of an important ecosystem service, and their survival relies completely on the landscape. Now with the landscape dominated by agriculture, bee diversity has been significantly reduced. Studies suggest that bee populations decline as agricultural land-use increases due to increased exposure to detrimental pesticides. Further, the protein content of pollen is highly important for the growth and development of a bee, and different landscapes provide distinct sources of nutrition. Although many studies have demonstrated the apparent impacts of landscape change on the population dynamics and individual survival of the bees, the underpinning mechanisms remain largely unknown. On the other hand, an increasing body of literature has shown that bee gut symbionts are of great importance to the health of the host bees in absorbing nutrients and resisting pathogens. When foraging, pollinator bees are exposed to particular microbes from pollen and nectar which have been suggested to be a source of some bee gut symbionts and could be either probiotics or pathogens. Together with landscape-related nutrition and pesticides, environmental microbes have been reported to affect bee microbiomes significantly. A number of pilot studies suggest that landscape change could affect bee microbiota, thereby influencing host health. An important linkage, however, is missing between environmental microbiota, especially those associated with the flowers, and that of the bee gut in a changing habitat. It is worth exploring how gut microbiomes respond to landscape changes. This will hopefully help us identify landscape types that are friendly to bees, so proper land-use can be implemented to protect the bees.