How species coexist locally is a fundamental question in community ecology. Classical coexistence theory underscores the importance of niche differentiation between species and focuses on specific coexistence mechanisms. Studies on these specific coexistence mechanisms have profoundly contributed to understanding species coexistence at the local scale and inspired ecologists to create a more general contemporary coexistence theory. Under the contemporary coexistence theory, species differences are categorized into two groups: niche differences and average fitness differences. Niche differences serve as stabilizing mechanisms that promote species coexistence, whereas average fitness differences are related to equalizing mechanisms that drive competitive exclusion. In this paper we provide a detailed review of contemporary coexistence theory, including its definition and theoretical models, empirical tests of these models and their applications to biodiversity studies. Coexistence theory has applications in a number of other areas including biodiversity conservation and management in a changing world beyond the basic concept of how communities are structured. We show how contemporary coexistence theory has advanced the niche-based classic coexistence theory, helping us to better understand the underlying mechanisms of community assembly and biodiversity maintenance.

High-quality biodiversity data are the scientific basis for understanding the origin and maintenance of biodiversity and dealing with its extinction risk. Currently, we identify at least seven knowledge shortfalls or gaps in biodiversity science, including the lack of knowledge on species descriptions, species geographic distributions, species abundance and population dynamics, evolutional history, functional traits, interactions between species and the abiotic environment, and biotic interactions. The arrival of the current era of big data offers a potential solution to address these shortfalls. Big data mining and its applications have recently become the frontier of biodiversity science and macroecology. It is a challenge for ecologists to utilize and effectively analyze the ever-growing quantity of biodiversity data. In this paper, I review several biodiversity-related studies over global, continental, and regional scales, and demonstrate how big data approaches are used to address biodiversity questions. These examples include forest cover changes, conservation ecology, biodiversity and ecosystem functioning, and the effect of climate change on biodiversity. Furthermore, I summarize the current challenges facing biodiversity data collection, data processing and data analysis, and discuss potential applications of big data approaches in the fields of biodiversity science and macroecology.

With the rise of plant molecular systematics, tremendous progress has been made in understanding phylogenetic relationships within angiosperms. With the basic phylogenetic framework of angiosperms established, a DNA phylogeny-based angiosperm classification system at the order and familial levels was proposed by the Angiosperm Phylogeny Group (APG) in 1998 and has been updated three times. In this paper, we summarize the major achievements of the APG system as follows: (1) testing the repeatability and predictability of the APG system for angiosperms; (2) resolving the systematic positions of some segregate taxa which were not placed based on morphological characters; (3) proving that it is not reasonable to first divide angiosperms based on cotyledon character; (4) demonstrating the importance of tricolpate/tricolporate pollen and derivatives for angiosperm classification; (5) finding that the centrifugal development of stamens in polyandrous groups have evolved independently many times and should not be used to delimit class or subclass of angiosperms; (6) supporting that most of the families delimited by broad morphological characters are natural; and (7) separating some families which are traditionally regarded as natural. We then point out potential problems that need to be resolved in the future, including: (1) how to harmonize the APG system and the morphology-based systems; (2) establishing new morphological evolution theories on the basis of the APG system; (3) determining whether it is enough to only use “monophyly” as a criterion to circumscribe orders and families; (4) determining morphological synapormorphies of those orders in the APG system; and (5) how to best compile a key to distinguish the orders and families of the APG system and to list their diagnostic characters for orders and families. In addition, we propose suggestions for the phylogenetic relationships and taxonomic status of some taxa mainly distributed in Asia, specifically East Asia, including Illiciaceae, Acanthochlamydaceae, Tetracentraceae, Leeaceae, Rhoipteiaceae, Hippocastenaceae, Aceraceae, Bretschneideraceae as familial status, and dividing Cornaceae sensu lato into Cornaceae sensu stricto and Nyssaceae sensu lato.

The evolution and maintenance of biodiversity is largely determined by the interaction of genetics and environmental factors. Geological and climatic histories, which played pivotal roles in the evolution and maintenance of plant diversity in the Qinghai-Tibet Plateau (QTP) and adjacent regions, are the most important environmental aspects. We review the major effects of QTP environmental changes associated with geological uplift, Asian monsoon evolution, and Pleistocene climatic oscillation on the origin, evolution, population demography, and maintenance mechanisms of plant diversity in the QTP and adjacent regions across spatiotemporal scales. Furthermore, we summarize the current progress and knowledge gaps on mechanisms of diversification and maintenance of plant diversity, and outline the effect of climate change on plant genetic diversity, hybrid zone dynamics, plant diversity patterns, the effect of Asian Monsoon evolution on plant diversity maintenance, and mechanisms of community assembly, the five additional future research hotspots.

This paper summarizes the research status, existing issues, and trends in floristic geography. There is now a wealth of research accumulation on floristic investigations, distribution types of genera, floristic regions, and regional floristic analysis. It is also noted that most of these studies utilize simple statistical analyses, comparative studies, traditional methods, and single subjects, to provide a basic understanding and description of the floristic phenomenon, which is lacking spatial pattern formation processes and detailed exploration of formation mechanisms. Additionally, there are still some weak and non-existent areas of botanical investigation. Many existing specimens lack detailed or accurate information and the precise identification of plant species also needs to be much improved. At the same time, when analyzing the development trends of floristic geography, with the rapid development of related disciplines, including the development of biogeography and analysis methods and improvements, floristic geography research is an area of multidisciplinary integration, comprehensive research, and analysis. On the one hand, using database information, and combining ecology, paleobotany, and geology can allow us to probe into spatial pattern formation. On the other hand, combining phylogenetics, the tree of life, and molecular biogeography allow us to reveal floristic origins and evolution. The rapid development of various disciplines has given rise to a large amount of data, meanwhile, the emergence and application of new analytical methods and theories incorporate big data into floristic geography research, which will enhance qualitative understanding and description, and allow us to further explore the mechanisms of formation quantitatively.

Beta diversity describes the variation in species composition among communities within a region and it is determined by two antithetic processes: species turnover (or species replacement), and nestedness (or difference in richness). Beta-diversity partitioning aims to separate these two processes when examining species composition among communities, and to reveal their underlying mechanisms. Since 2010, the partitioning methods were proposed following two dominant frameworks: the BAS method proposed by Andrés Baselga in 2010 (partitioning overall beta diversity into turnover and nestedness components) and the POD method proposed by János Podani and Dénes Schmera in 2011 and José C. Carvalho et al. in 2012 (partitioning overall beta diversity into species replacement and richness difference components). With the continuous debate on the nature of the BAS and POD methods, studies on beta-diversity partitioning have developed rapidly worldwide. We reviewed journal articles in the field of beta-diversity partitioning since 2010. Results showed that the number of publications and citations using the BAS method were greater than those using the POD method (75% vs. 20%). In those publications, most of study sites were located in Europe (45%) and research taxa were dominated by animals (64%). Here, we introduce the history and development of beta-diversity partitioning, potential applications in studying biodiversity distributions across spatial-temporal scales (latitudinal/altitudinal gradients, habitat fragmentation, seasonal and annual dynamics), multiple-faceted diversity (taxonomic, functional and phylogenetic diversity), and comparisons among various biological taxa. We point out the following directions in the field of beta-diversity partitioning in the future: (1) the synthesis and comparative analysis of the methods of beta-diversity partitioning; (2) examining patterns of overall beta diversity and its components by incorporating species abundance; and (3) testing the generality of results yielded from beta-diversity partitioning across large scales.

Soil microbial diversity has not been extensively observed due to technique limitations. With the development of the high-throughput sequencing technique and bioinformatics, much progress has been made in observations of microbial diversity. Currently, international microbiome initiatives have been founded (including the Earth Microbial Project). However, problems in these projects include a lack of dynamic observations, differences in observational methods, and data integration. The soil microbial observation network (SMON) is an important part of the Chinese Biodiversity Monitoring and Research Network (Sino BON). The observational network initially selected field observation sites in forest ecosystems along a temperature and precipitation gradient from south to north, in grassland ecosystems along a precipitation transect from east to west, and in typical wetland and agricultural ecosystems in China. Field ecological observation stations have been established in these selected ecosystems. Key tasks for the SMON are to observe spatial and temporal dynamics of soil microbial communities and functional genes in various ecosystems, including bacteria, archaea, fungi, and lichens. Observational data will be published periodically in the format of database, annals, and illustrated handbooks. Key methods used in the SMON are high- throughput sequencing, metagenomics, and bioinformatics. A soil biota database is currently being constructed to store observational data for public inquiry and analysis. Through the efforts of SMON, we plan to explore the driving mechanisms of spatial and temporal variations of soil microbial communities and their functional genes, and understand the relationships between microbial diversity and ecosystem function, in order to predict microbial dynamics under global environmental change scenarios, and to design strategies to protect soil microbial diversity and properly utilize microbial resources.

Camellia oleifera is the dominant woody oil crop in China, and wild C. oleifera is a valuable genetic resource for C. oleifera breeding. Using distribution data of wild C. oleifera from the Chinese Virtual Herbarium (CVH, http://www.cvh.org.cn/), together with climate and soil data, ecological niche models were constructed with MaxEnt and genetic algorithm for rule-set prediction (GARP) models to predict the potential distribution of wild C. oleifera, and the major environmental factors affecting the distribution of wild C. oleifera were analyzed. Based on the presence probability of wild C. oleifera predicted by the models, the distribution regions of wild C. oleifera were divided into different suitable growing categories, which were then compared with actual distribution data of major C. oleifera production fields to evaluate reliability. Results indicated that the predictions of both MaxEnt and GARP models represented the distributions of C. oleifera well. The potential distribution range predicted by the GARP model was wider, while that predicted by the MaxEnt model was more accurate. Predictions of both the MaxEnt and GARP models showed that the potential distribution regions of wild C. oleifera were located mainly in China and partly in the Indo-China Peninsula. According to predictions of the MaxEnt model, the potential distribution regions of wild C. oleifera in China were matched with the distribution regions of subtropical evergreen broad-leaved forests, and the highly suitable growing regions could be divided into three large regions: (1) northeastern-southwestern trending Wuyi Mountain and adjacent mountainous regions; (2) eastern-western trending Nanling Mountain and adjacent mountainous regions; (3) northeastern-southwestern trending Wuling Mountain and adjacent mountainous regions. The analysis of the MaxEnt model showed that the major environmental factors affecting the distribution of wild C. oleifera were mean monthly diurnal temperature range, precipitation during the driest quarter, and precipitation during the warmest quarter. The vast majority of the regions with large growing areas of C. oleifera were located in the medium to highly suitable growing regions predicted by the MaxEnt model, suggesting that the division of suitable growing regions was reliable. The field investigations showed that the model predictions had high reference values for finding wild C. oleifera resources. Additionally, the study shows that using the plant distribution data from CVH and related environmental data to construct an ecological niche model can help to understand the geographic distribution of crop wild relatives.

China is one of the world’s richest countries in terms of biodiversity, which has been seriously threatened. In 2010, to effectively protect biodiversity, the State Council of China authorized the Protection Strategy and Action Plan of China Biological Diversity (Year 2010-2030), in which 32 terrestrial Biodiversity Priority Areas were delineated as preferential areas, and background surveys of biodiversity in these areas were also discussed. To protect biodiversity, the Ministry of Environmental Protection of the People’s Republic of China, alongside various research institutions such as Chinese Academy of Sciences and universities, conducted biodiversity background surveys at the county level in 18 counties in Northwest Yunnan of the southern section of the Hengduan Mountains Area from 2010 to 2011. The survey included ecosystems and species. At the ecosystem level, the survey investigated the diversity of vegetation formations within each county. At the species level, the survey investigated diversity of species composition, quantity, and usage of higher plants, vertebrates, and macro-fungi, analyzed the quantities of endemic, rare, and endangered species. The survey culminated in a species inventory at the county level. Based on the survey results, a comparative analysis of biodiversity composition among different counties was conducted. Among the 18 investigated counties, Yulong County, Jianchuan County, Gucheng District, Shangri-La County, and Eryuan County have relatively abundant ecosystem types. While all of these counties have more than 48 formations, Yulong County has the largest number of formations (108 formations). The formations of other counties ranged from 20 to 40. Yulong County not only has the richest vegetation formations, it also has the most abundant number of species (including 4,550 higher plants, 625 vertebrates, and 222 macro-fungi). The region also has a high proportion of endemic species. With respect to higher plants, the ratio of endemic species in most of the counties is about 20%, however, the ratio can approach or exceed 50%. With respect to animal species, the ratio of endemic species in most of the counties is about 10%, with the highest ratio in Heqing County, where 46 endemic species account for 17% of the total species. The authors hold that a comprehensive biodiversity survey is a necessary basis and hence suggest that this study be taken as a case for large-scale biodiversity investigations in the future.

Conservation effectiveness of protected areas indicates the status of main protected objects, and achievements in maintaining biodiversity and ecosystem function. Evaluation of conservation effectiveness is becoming a popular issue surrounding protected areas. From multiple spatial scales, subjects, methods and indicators, we reviewed advances in evaluating conservation effectiveness of protected areas. Recent studies have represented global, regional, national, and individual scales. Evaluated projects include the most common ecosystems (forests, wetlands, grasslands, deserts) and wild species. Evaluation methods have been moving from traditional direct before-and-after or inside-outside comparisons to “matching” techniques, which allows one to control for known landscape or environmental biases when determining the impacts of protection. Some researchers have explored indicator systems to make systematic evaluations of the effectiveness of protected areas, meanwhile others have tested indicators using case studies. In China, nature reserve is the backbone of the country’s protected areas system. Different ministries and state-level authorities have initiated evaluation of conservation effectiveness of nature reserves. We suggest that future studies should explore the following issues to improve the quality of nature reserves: (1) conservation effectiveness of nature reserve networks; (2) conservation effectiveness of different types of reserves; (3) integration of conservation effectiveness and management evaluation; and (4) potential impacts on nature reserves.

In order to provide a scientific basis for upgrading the level of a nature reserve (NR) and selecting the appropriate management type, the conservation priority of NRs should be identified. How to objectively identify conservation priorities has become a key problem. We propose a mathematical method to comprehensively assess species diversity conservation values by comparing existing evaluation indexes and methods, consulting experts and processing indexes quantitatively. This evaluation method includes the following indices: the wild plant diversity conservation value index; wild animal diversity conservation value index; rare and endangered wild plant diversity conservation value index; and the rare and endangered wild animal diversity conservation value index of a NR. Meanwhile, 39 NRs in North China Warm Temperate Region and 67 NRs in Northeast China Temperate Region were selected as case studies to verify methods, based on species diversity data of the NRs. The evaluation results revealed that some provincial NRs could be recommended for an upgrade to national NRs, due to high species diversity conservation values, including the Nandagang Wetland and Liaohe River Source NRs of Hebei, Wuling Mountain NR of Beijing in the North China Warm Temperate Region, the Jingpo Lake, Dajia River, and Cuibei Wetland NRs of Heilongjiang in the Northeast China Temperate Region. The computation method showed a great advantage in comparing species (various groups) diversity conservation values for different NRs and determining the conservation priority sequence. Moreover, there were significant differences in the species diversity conservation value of NR among different natural conservation geographical areas, and types of NRs.

Due to recent modifications of mammalian taxonomy, discoveries of mammalogy in China, and conservation needs of the country, China’s mammal diversity inventory is in urgent need of an update. We collected new species and records of mammal species in China from the literature since March 2015, adopted the new taxonomy, incorporated our own research, and added mammalian species of the Zangnan Region, to renew the inventory of mammal diversity in the country. The major changes in the new version of the inventory are the elevation of the order Cetartiodactyla to the super order Cetartiodactyla and the split of the order Cetartiodactyla in Jiang et al (2015) into orders Cetacea and Artiodactyla, respectively. Chodsigoa hoffmanni C. furva and Mesechinus sp. were added to the order Eulipotyphla. In the order Chiroptera, Murina fanjingshanensis, Myotis rufoniger and Rhinolophus subbadius were added, while Myotis hirsutus and Miniopterus fuscus were deleted from the inventory. In the order Primates, Hoolock tianxing, Trachypithecus pileatus, Nycticebus coucang and Hoolock hoolock were added to the inventory. In the order Carnivora, Melursus ursinus, Canis aureus, Vulpes bengakensis, Herpestes edwardsii, and Felis viverrinus were added. We reclassified the species in the order Artiodactyla according to the taxonomy of the Handbook of the Mammals of the World, Vol. 2, Ungulates. Ovis ammon, O. collium, Budorcas taxicolor, and Muntiacus muntjak were added to the order. All sika deer in the country were grouped as a single species, Cervus nippon, and all moose were grouped as a single species, Alces alces. Cervus alashanicus and C. macneilli as well as the dwarf blue sheep, Psuodois sharferi, were deleted, and the species of the Tragulus in Xishuangbanna was listed as Tragulus sp. In the order Cetacea, Platanista gangetica was added while Delphinus capensis was deleted. In the order Rodentia, new species, Typhlomys nanus, Neodon medogensis and N. nyalamensis, Bandicota bengalensis as well as Myospalax cansus, Biswamoyopterus biswasi, Niviventer niviventer, Mus booduga; and one species, Typhlomys daloushanensis, which was elevated from the status of subspecies, were added to the inventory, however, Hadromys humei was deleted from the inventory. The taxonomy of Arvicolini of Cricetidae was renewed. Caprolagus hispidus and Lepus nigricollis were added to the order Lagomorpha and the taxonomy of Ochotona was renewed, with 5 species downgraded from the status of species to subspecies while 4 were elevated from subspecies to species. Altogether there are 29 pika species in China. However, O. princeps, O. collaris, O. hoffinanni, O. rufescens and O. pusilla are not found in the country. The new inventory of China’s mammals has 13 orders, 56 families, 248 genera and 693 species. Compared with that reported by Jiang et al (2015), there is now an additional order, family, three genera and 20 species in the new mammalian diversity inventory. Of the mammalian species in country, the statuses of 18 species, mostly rodents, are still in dispute amongst mammalogists. There are 146 endemic mammalian species in China, which accounted for 21% of the total mammal species in the country. Of those endemic species by order, the highest endemic rate is found in Lagomorpha (37%), followed by Eulipotyphla (35%) and Artiodactyla (25%). Overall, China has the richest mammal diversity in the world.

Spruce-fir forests are one of the best protected areas of forest vegetation occurring on the eastern slope of the Yulongxueshan (Jade Dragon Snow Mountains). To further understand the spruce-fir species composition and community structure, a 25 ha (500 m × 500 m) forest dynamics plot was established in the Yulongxueshan Provincial Nature Reserve by the Kunming Institute of Botany, Chinese Academy of Sciences and Administration Bureau of Yulongxueshan Provincial Nature Reserve from 2012 to 2014, according to the standards from the Center for Tropical Forest Science (CTFS). In this study, we analyzed the flora, community composition, structure, DBH size-classes and spatial distribution based data collected from all woody (excluding bamboo) plants with DBH ≥ 1 cm. Our results demonstrated that a total of 47,751 free-standing individuals with DBH ≥ 1 cm were recorded, belonging to 62 species, 41 genera and 26 families. The north temperate distribution plant contributed to the most significant floristic characteristics. In the plot, the 18 species with importance value (IV) ≥ 1 contributed 90.24% to the IV of the community. Based on the vertical structure of plant heights, the community was divided into four layers. The dominant species in the canopy layer were Abies forrestii, Picea likiangensis and Quercus guajavifolia, which exhibited a pattern of ridge type and a reverse-J shape in DBH size-classes structure and strong regenerating capacity. Gamblea ciliata var. evodiifolia, Acer pectinatum and Padus brachypoda occupied the sub-canopy layer, and could be the constructive community species in some fragmented habitats. These species were lacking small DBH trees, so their populations are predicted to decline in the future. Sorbus prattii, Viburnum betulifolium and Rhododendron yunnanense dominated the sub-tree layer. In the shrub layer, Berberis fallax consisted of the largest number of individuals and accounting for 59.51% of the total number of individuals; together with the highest importance value, accounting for 22.75% of the total IV, and DBH size-class distribution in a “L” shape.

During the past decade, unmanned aerial vehicle (UAV) based remote sensing has been increasingly used in the fields of vegetation inventory, natural resource management, and biodiversity conservation, due to its low cost and high flexibility. In this study, we present a reference for the selection of UAV platforms and remote sensing sensors, by introducing a UAV classification system and summarizing applicability in biodiversity monitoring using remote sensing techniques. For each UAV platform category, we also introduce the characteristics and capabilities of different remote sensing sensors that can be supported. Moreover, through the combination of a case study which collected high-fidelity UAV-based remotely sensed data, we discuss current research progress using UAV-borne remote sensing data to derive direct and indirect biodiversity parameters. Finally, we discuss the current limitations of UAV-based remote sensing platforms for biodiversity monitoring, such as the existing gap between hardware and software, the high cost of certain components (e.g. the initial measurement unit), incomplete laws and regulations, and the disconnect with traditional biodiversity monitoring methods. In summary, we believe that UAV-based remote sensing platforms can greatly help to fill the gaps between terrestrial measurements and aerial/spaceborne measurements, and can increase the accuracy and reliability of upscaling point-based terrestrial measurements to the regional scale. There is a need to launch more projects that address building a UAV-based biodiversity monitoring network, and therefore improve our capability to analyze and forecast biodiversity changes in hotspots.

World Natural Heritage site is recognized globally as the pinnacle of natural protected areas that are the cornerstones of biodiversity conservation. The World Natural Heritage of Shennongjia represents one of the worldwide biodiversity hotspots. But, until now, it has not been clear how outstanding the universal value of Shennongjia is worldwide, and this study presents one of the most compelling challenges to conservation efforts. Here, we compiled literature and conducted additional field surveys in the Shennongjia region to illustrate the outstanding universal value of Shennongjia World Natural Heritage Site using World Heritage criteria (ix) and (x), following the operational guidelines for the implementation of the World Heritage Convention. Results show that the heritage of Shennongjia offers an outstanding example of the ongoing ecological processes occurring in the development of intact subtropical mixed broad-leaved evergreen and deciduous forests in the Northern Hemisphere. This region presents a typical example of mountain altitudinal biological zones in the Oriental Deciduous Forest Biogeographical Province. Shennongjia is also a vital origin location for global temperate flora, and harbors the highest concentration of global temperate genera of trees. Moreover, the heritage of Shennongjia displays exceptional biodiversity and is a key habitat for numerous relic, rare, endangered and endemic species. The richness of deciduous woody species in Shennongjia is the highest in the world. Our study provides great insight into protecting, monitoring and managing the outstanding world heritage in the Northern Hemisphere.

The important roles of soil fauna diversity and associated indicative functions of environment changes have received increasing attention from both academic circles and government decision makers. This paper summarizes the current situation of soil fauna monitoring in developed countries and related work in China. We introduce the objectives and structure of the thematic monitoring network of soil fauna diversity (TMNSFD), and highlighted some aspects that need attention. The TMNSFD proposed to establish permanent monitoring plots within forest plots established by Chinese Forest Biodiversity Monitoring Network for monitoring soil fauna including earthworms, mites, springtails, nematodes and protists. During the years 2016-2020, TMNSFD may choose typical forest ecosystems as priority ecosystems for soil fauna monitoring, which cover temperate forest ecosystems (including broadleaved Korean pine mixed forests in Changbaishan, Jilin Province and warm temperate deciduous broadleaved forests in Donglingshan, Beijing), subtropical forest ecosystems (including typical subtropical evergreen broadleaved forests in Gutianshan, Zhejiang Province, lower subtropical evergreen broadleaved forests in Dinghushan, Guangdong Province, and north subtropical evergreen broad-leaved forests in Dujiangyan, Sichuan Province), tropical forest ecosystems (tropical rainforests in Xishuangbanna, Yunnan Province and Jianfengling, Hainan Province), as well as mountainous dark coniferous forests in Liziping, Sichuan Province. By 2030, TMNSFD soil fauna monitoring plots may cover various ecosystems including forests, grasslands, wetlands, deserts, farmland, urban areas and other typical ecosystems in different regions of China. TMNSFD emphasizes the value of applied molecular biology technology, unified monitoring methods, and manipulation experiments to simulate the effects of global change on soil fauna during the processes of monitoring. We propose monitoring soil fauna diversity once every 5 years in established monitoring plots. The objective of TMNSFD is to provide reliable and integrated data of soil fauna diversity via the establishment of standard monitoring methods and a data-sharing network at the national level, which could support the development of ecological civilization in China.

Studying the dynamic characteristics, species coexistence and biodiversity conservation mechanisms of subtropical forest ecosystems is important in the study of the quantitative characteristics and spatial gap distribution patterns. Based on census data from the 20 ha dynamics plot of the subtropical evergreen broad-leaved forest in Dinghushan in 2015, we analyzed the geometric characteristics and spatial distribution pattern of gaps in the plot by combining aerial image processing technology of unmanned aerial vehicles and GIS. Results show that the gap fraction is 13.72%, the gap density is 35.75 no./ha, and the average gap area is 38.37 m². Results also show that: (1) The number of gaps in the area is negatively exponentially distributed with the increase of gap area, that is, the gap is small and the marginal effect is not significant. (2) The average area of ??forest gaps in over-mature forest stands is larger than that in mature forests, while the mature forest is more likely to have more small gaps and fewer large gaps. (3) In different habitats, the distribution of gaps in each habitat shows the same pattern as that found in the whole plot. However, the difference in the valley is significant when compared with other habitats, and gap area and gap density in the valley are larger than other habitats. The ridge gap is also distinctive, and its gap density is lower than other habitats. (4) Gap area is significantly correlated with topographic factors. It was significantly negatively correlated with altitude and convexity, and had a significantly positive correlation with aspect and gradient. Based on these comparative analyses, a monitoring system of forest canopy changes and patterns can be established using drones, to dynamically monitor forest gaps and the undergrowth community.

In recent years, there have been more and more appeals for sharing of biodiversity data. ‘Biodiversity data paper’ has been proposed as a reward mechanism for sharing data by individual scientists. Some data journals dedicated to publishing data papers have been founded. In this paper, we analyze the number of articles, coverage of biological groups, article views, and citations of two representative data journals (Biodiversity Data Journal and Scientific Data). Results show that the number of articles in both data journals has been steadily increasing. Biodiversity data papers cover a wide range of biological groups in Animalia, Plantae and Fungi. The article views and citations also show encouraging performance. These results indicate that data papers are being accepted by more and more researchers. Analysis of author regions of biodiversity data papers indicates a disequilibrium in the data sharing culture among different geographical regions. We suggest Chinese researchers and journals in related fields pay more attention to biodiversity data papers and trends of data sharing policies, as well as improving data sharing practices.

Ecological niche modeling (ENM) is widely used in the study of biological invasions and conservation biology. Maxent is the most popular algorithm and is being increasingly used to estimate species’ realized and potential distributions. Most modelers use the default Maxent setting to fit niche models, which originated from an earlier study containing 266 species, with the purpose of seeking their realized distributions. However, recent studies have shown that Maxent uses a complex machine learning method. It is sensitive to sampling bias and tends to overfit training data, and is only transferrable at low thresholds. Default settings based on Maxent outputs are sometimes not reliable, making it difficult to interpret. Using Halyomorpha halys and classical modeling approaches (i.e., niche models that were calibrated in native East Asia and transferred to North America), we tested the complexity and performance of the Maxent model under different settings of regulation multipliers and feature combinations, and chose a fine-tuned setting with the lowest complexity. We then compared the response curves and model interpolative and extrapolative validations between models calibrated using default and fine-tuned settings. Our purpose was to explore the effects of the model’s complexity on niche model performance in order to improve the development and application of Maxent in China. We argue that selection of environmental variables is crucial for model calibration, which should include ecological relevance and spatial correlation. Reducing sampling bias and delimitating a proper geographic background, together with the comparison of response curves and complexity of Maxent models built under different settings, is very important for fitting a good niche model. In the case of H. halys, the default and fine-tuned settings are different, however the response curve is much smoother in the fine-tuned model, and the omission error is lower in introduced areas when compared to default model, suggesting that the fine-tuned model reflects the response of H. halys to environmental factors more reasonably and precisely predicts the potential distribution.

The Red List of Ecosystems is a growing toolbox for assessing risks to biodiversity at the ecosystem level, which is complementary to the Red List of Threatened Species and important for the protection of key species’ habitats. The IUCN Red List of Ecosystems Criteria was adopted as an official global standard for assessing the risks to ecosystems by the IUCN Council. With the revision and extension of the IUCN Red List of Ecosystems Criteria, this framework is gradually improved, which plays an important role in biodiversity conservation and ecosystem management. However, it faces challenges in ecosystem mapping, the concepts of ecosystem collapse and practical application. This paper reviews the development of the Red List of Ecosystems and introduces the five criterions in the IUCN Red List of Ecosystems protocol (declining in distribution, restricted distribution, abiotic degradation, biotic degradation and quantitative estimates of risk of ecosystem collapse) and how it is used. While focusing on the challenges in the assessment with the IUCN Red List of Ecosystems Criteria, we also discuss the potential solutions to these problems based on remote sensing and ecological models. We points out that the explicit definition of ecosystem collapse and the classification system of ecosystems is essential for applying the IUCN Red List of Ecosystems Criteria; the scale effects have great impacts on the results of assessment; assessment at hierarchical scales may be a potential method to provide spatial information for the IUCN Red List of Ecosystems; incorporating remote sensing and ecological models into this framework is an important way to study the IUCN Red List of Ecosystems Criteria in the near future.

In recent years, the Chinese Biodiversity Monitoring and Research Network (Sino BON) has developed rapidly, which provides an unprecedented platform for long-term biodiversity monitoring and research. The near-surface remote sensing (NsRS) platform, an important component of the Sino BON-Synthesis (Synthesis Center of Sino BON) and equipped with LiDAR (Light Detection and Ranging) as the core technique, has developed a mature technology system integrating hardware and software, which can provide digital products such as topographic modeling under forest, stand height, stand surface structure, gap or internal boundaries, canopy closure dynamics, vegetation community division, fine spatial structure within the community, individual tree height and diameter at breast height, canopy morphology, circumference and cover, species identification, sub-meter three-dimensional landscape map and so on. Therefore it can be used to acquire multiple spatiotemporal scales of biodiversity observations and offer scientists and managers specialized and effective technical support for biodiversity evaluation and conservation. In this paper, we provide a comprehensive review on the history and recent development of remote sensing technology in biodiversity studies. Then, we summarize the important indices of biodiversity that can be extracted from remote sensing data based on the direct and indirect methods for remote sensing monitoring of biodiversity and suggest spatial and temporal scales that should be referenced against the selection of different types of remote sensing data. Next we describe in detail the application of the state-of-the-art NsRS platform at home and abroad and figure out that the near-surface remote sensing platform represented by unmanned aerial vehicle (UAV), characterized by flexibility, high efficiency, low cost and high resolution, will be an important means for biodiversity monitoring in the near future. Because it can act as an indispensable intermediate bridge between satellite platform, manned aviation platform and ground survey platform when conducting the biodiversity information scaling. Finally, based on currently available techniques and equipment of the NsRS platform, we conclude that further improvement of the platform construction will greatly help us to obtain three-dimensional quantitative habitat information. And it will be a long-term, significant step for the biodiversity observation network in China to have transformed into an intelligent decision and service platform with trans-scale hierarchy dynamic monitoring ability and multi-source information integration technology.

The Himalayas are a biodiversity hotspot. In this study, the taxonomic diversity of climbing plants in the Himalayan region and its connection with neighbouring regions were analyzed, the distribution patterns of climbers in the Himalayas and the Indo-Gangetic Plain were compared, and mechanisms were discussed. Results showed that: (1) The Himalayan region harbored a total of 1,083 climbing species in 309 genera and 72 families. Approximately 66.9% (725 species) of these species were woody or semi-woody climbers (lianas) and the remaining 33.1% (358 species) were herbaceous (vines). Twining climbers accounted for 51.3% of the climbing plants in this region. (2) The climbing plant flora in the Himalayas was significantly affected by neighboring floras. About 74.1% (802 species) of the climbers in the Himalayas were also found in Southeast Asia, 548 species (50.6%) were found in South Asia, and 530 species (48.9%) were found in Southwest China. Only 125 climbers (11.5%) were endemic to this region and no endemic genus was recorded. (3) Species diversity of climbing plants and their proportion in the flora gradually decreased from east to west in the Himalayas. Twining climbers and lianas became more dominant in the western regions. At the genus level, species diversity of most climber-rich genera decreased westward across the Himalayas and species diversity of only a few genera (e.g. Vicia and Cuscuta) showed an increase from east to west. (4) The distribution patterns of climbing plants in the Himalayas and the Indo-Gangetic Plain were consistent. However, species diversity was higher in the Himalayas and its decreasing trend westward was more significant. At the genus level, the average decreasing rate of climber-containing genera from east to west is 8.4 genera per 100 km in the Himalayas and 6.3 genera per 100 km in the Indo-Gangetic Plain. A total of 272 climber-containing genera in the Himalayas were shared with the Indo-Gangetic Plain, and 196 genera were not found in the west regions (Central Asia and Iranian plateau). In the 196 genera, 61 genera (31.1%) were distributed more to the west in the Himalayas than in the Indo-Gangetic Plain, while only 8 genera (4.1%) were distributed more to the west in the Indo-Gangetic Plain than in the Himalayas. In conclusion, species diversity and distributional characteristics of climbers in the Himalayas were attributed in part to the geographical location of this region, the altitudinal and longitudinal gradients of climate and habitats, and the diversification of adjacent floras. The similarities of the distribution patterns of climbing plants in the Himalayas and the Indo-Gangetic Plain may be primarily due to similar east-west water gradients.

The regional tree of life, reconstructing the tree of life to include the regional species pool, has been a research focus in biological science over the past decade. Informed by phylogenetic relationships among coexisting species, a regional tree of life can connect evolutionary and ecological factors during the evolution of a biota and thus has become an efficient tool to trace its temporal and spatial diversification. In this paper, we summarize the application of a regional tree of life in floristic studies in the following three fields: (1) To reveal temporal patterns of a flora by estimating divergence time and evolutionary rates based on the tree of life; (2) To reveal spatial patterns of the biodiversity in a flora and to guide the regionalization of floristic zones by integrating phylogenetic and spatial data; and (3) By integrating biogeographic and environmental data and investigating how taxa respond to paleogeographic events and thus climate change to reveal the underlying ecological, geographical and historic factors of the formation of the floristic biodiversity pattern. In addition, we highlight the relationship between the regional and global tree of life and indicate the potential to identify biased divergence times with incomplete taxa sampling using a regional tree of life. Finally, we suggest that future studies should integrate current mega data at different scales in hotspots to elucidate biodiversity patterns in a worldwide framework.

Traditional attempts of floristic studies typically focus on the analyses of taxonomic composition and areal-types of flora, often ignoring the rich context that evolutionary history can provide. In this study, based on the recent study examining the delineation of floristic regions in Yunnan, by combining data on the distributions and phylogenetic relationships of 1,983 genera of native seed plants, we explore how taxonomic composition, phylogenetic relatedness, and phylogenetic structure vary across the different geographic regions in this area. As predicted, phylogenetic diversity was well correlated with taxonomic diversity among the geographic regions. Using null model analyses, we found evidence of nonrandom phylogenetic structure across the region. Also, phylogenetic relatedness was well correlated with taxonomic composition between geographic regions in Yunnan. Cluster analyses of the similarities of phylogenetic relatedness and taxonomic composition show that geographic regions with tropical floristic affinity form a single cluster separate from another cluster composed of geographic regions with temperate floristic affinity. Our results show that the integration of phylogenetic information can help us to better understand the characteristics and origin of flora.

Alpine areas are global biomes with extreme environments and distinct boundaries. Studies on the geography of alpine flora help us to understand the formation of flora in an extremely cold and segregated environment, as well as the floristic relations between mountains. We integrated alpine flora data from 14 main mountain ranges in China, measured floristic similarities using the Jaccard index, and explored the percentage composition of areal-types of seed plants and the effects of geographical distance and environmental variation on flora similarities using correlation analyses and Mantel tests. Results indicated that Chinese alpine zones harbor a flora characterized by high species richness, with 3,670 species (including 340 subspecies units) belonging to 489 genera and 65 families recorded in the alpine zone of 14 main mountain ranges. These genera are mainly constituted of areal-types of North Temperate distribution and their sub-types, Cosmopolitan, Old World Temperate, East Asia and Sino-Himalayan, while the Sino-Japanese type is absent. Those endemic to China revealed a distinct presence in alpine flora (5.2%). Based on the data from 14 alpine zones, geographical patterns of alpine floristic composition were characterized by a significant latitudinal decrease of tropic and East Asia areal-types, and an increase of northern temperate types. Along the longitudinal gradient, the percentages of Mediterranean types decreased while the northern temperate types increased, and East Asian elements peaked in the middle position. The alpine floras of 14 mountains were significantly correlated in terms of geographical element composition when measured at the genus level, revealing two groups of higher floristic correlations, mountains surrounding the Qinghai-Tibet Plateau and separated northern mountains, respectively. The alpine flora of Taiwan Island is more closely related with that of the northern mountains rather than that of the mountains found in Southwest China, which have more comparable latitudes. We found that geographic distance was the primary factor for deviation between alpine floras, while the physiognomy of alpine zones also influenced floristic composition, and the maximum temperature of warmest month (MTWM) was a critical climatic factor for geographical deviation of alpine flora composition in China, which suggests the potential stress effects of global warming on alpine flora.

Sprouting, a life history strategy found in woody plant communities, enables woody plants to persist in situ through disturbance events. The ‘persistence niche’ of sprouting has important influences on species coexistence, community assembly, and ecosystem stability. However, the mechanism of the ‘persistence niche’ in maintaining species diversity is not well understood. Based on data collected in a 5 ha plot in a mid-subtropical evergreen broad-leaved forest in the Gutianshan National Natural Reserve of Zhejiang Province, China, we analyzed the characteristics of sprouting and their relationships with species diversity. Our results revealed that the sprouting species had a great proportion of 63.95% in richness and a high proportion of 38.53% in abundance, especially a higher abundance proportion of 59.51% of potential sprouting at the community level. Sprouting occurred in most taxa, and there was high ability of sprouting in Fagaceae, Ericaceae, Hamamelidaceae, and Theaceae. There were significant negative correlations between abundance proportion of sprouting species and the biodiversity index of the community, despite no relationships between richness proportion of sprouting species and biodiversity index. Therefore, the sprouters could retain their position in forests and reduce biodiversity of the forest community. This trade-off of sprouting may result in the maintenance of community stability.

Amphibians and reptiles are important indicator species of ecosystem health, and they are sensitive to environmental changes and are often regarded as critical “early warning systems”. Many of their populations are undergoing rapid decline and therefore a long-term monitoring system is imperative to identify immediate threats to the animals. Monitoring program on Chinese amphibians began in the Zoige wetlands in 1997. Since 2000, a great number of monitoring studies of amphibians and reptiles have been carried out in mountains of Southwest China, Taiwan, and other regions with rich biodiversity. In 2011, the Ministry of Environmental Protection officially launched the “Amphibian Observation Initiative of China” program, which expanded regional programs to country-wide using both qualitative and quantitative methods to collect amphibian biodiversity data across long-term temporal scales. From an ecosystem viewpoint, long-term monitoring studies should include not only species distribution, richness, and population structure, but also population growth, key life-history traits, species interactions (e.g., predation, competition, and mutualism), community structure, and other dynamic factors. The program “Monitoring and Research of Amphibians and Reptiles in Key Areas of China” will cover 22 key areas with rich biodiversity and high habitat heterogeneity across China. As part of the Chinese Biodiversity Monitoring and Research Network (Sino BON), this program aims to combine intensive field surveys and ecological modeling techniques to evaluate population dynamics and community structures of amphibian and reptile species in the study areas.

Seed dispersal facilitates the recruitment of plants, which has profound influences upon the spatial distribution of forest plants and the maintenance of biodiversity. Recently, the role of primates in the process of seed dispersal has been increasingly studied. Primates play an important and special role in plant recruitment and vegetation regeneration in the form of feeding on fruits and dispersing seeds. The selection of different fruits is not only closely related to the quality of fruits and the feeding competition of sympatric animals, but also varies greatly with morphological, physiological, and behavioral features of different primates. According to the processes of fruit treatment, the patterns of seed dispersal by primates can be classified as endozoochory, epizoochory, and synzoochory. These patterns have different effects on the distance of seed dispersal, seed germination, and the establishment of seedlings. The most effective pattern is endozoochory, characterized by long-distance dispersal and high rates of seed germination and seedling establishment. Seed dispersal by many primate species helps to restore degraded habitats. Studies on the ecological processes of seed dispersal by primates and determined factors would be conducive to determine the role of primates in the forest ecological system, the contribution of primates to vegetation regeneration, and to provide theoretical evidence for forest ecosystem management and biodiversity conservation.

As the most direct and active ecological interface of the interaction between forest and its environment, the forest canopy, known as the earth’s “eighth continent”, contains the greatest forest biological diversity, and plays an important role in the formation and maintenance of biodiversity as well as the processes and functions of the ecosystem. However, the forest canopy is highly sensitive to global climate change and human disturbance. In the wake of increasing human activities and global climate change, the forest ecosystem, especially the forest canopy, is facing a serious threat. Therefore, protection of forest canopy biodiversity and sustainable utilization are increasingly important issues in modern ecology research under the scenarios of climate change, and have gained more and more attention in the fields of forest ecology, climatology, and environmental science. Accordingly, in 2015, the Chinese Forest Canopy Biodiversity Monitoring Network was created within the framework of Sino BON. This network includes biodiversity monitoring plots those were or will be equipped with forest canopy cranes. According to international standards, the network will unify monitoring parameters of forest canopy biodiversity using monitoring standards and norms, and conduct long-term monitoring of plant diversity (including epiphytic seed plants and epispore plants), fauna diversity, microbial diversity and their dynamic changes, through large scale zonal forest canopies. Combined with monitoring of the microclimate, we will build four dynamic databases (including a forest canopy microclimate database, canopy plant, canopy arthropod, and canopy microbial). The network is expected to discern the change patterns of forest canopy biodiversity of typical forest ecosystems in China, and to reveal how they influence the functioning of forest ecosystems and respond to global change.

Hybridization among diverging (interspecific or intraspecific) groups involves gene flow and genetic recombination. Increasingly, studies have shown that hybridization, a process of genetic exchanges, occurs widely in the divergence and unity of animals, plants, and microorganisms, and acts as an important mechanism for the formation and maintenance of biological diversity. The rapid development of high-throughput sequencing technology and the widespread application of genome-level techniques provides an unprecedented opportunity for us to further evaluate the universality and evolutionary significance of hybridization. However, selecting appropriate research techniques and strategies to detect the potential hybridization and evaluate its characteristics becomes a common question. In this review, we attempt to synthesize methods from phylogenetics and population genetics of the genomic era to provide biodiversity and evolutionary researchers a practical reference for testing hybridization.