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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

The subtropical evergreen and deciduous broad-leaved mixed forest (SEDBMF) is one of the most important forest vegetation types in subtropical mountainous regions. It can provide an important foundation to maintain regional ecological security and conserve biodiversity. To further explore maintenance mechanisms of species diversity in SEDBMF, a 6-ha forest dynamics plot was established in Hubei Qizimei Mountains National Nature Reserve, western Hubei Province in 2015. All living woody stems with diameter at breast height (DBH) ≥ 1 cm were tagged, identified, measured, and mapped according to the methods of CTFS (Center for Tropical Forest Science). Community composition, diameter class structure, and characteristics of the spatial structure of dominant species were analyzed. Results showed that there were in total 50,316 stems and 36,596 independent individuals, belonging to 245 species 124 genera 57 families. Seven species that are national protected plants and 76 rare species (density ≤ 1 stem/ha) occurred in this plot. Among those stems, 61.2% of total species and 52.6% of the total stems were deciduous tree species. The structure of DBH size-classes of all stems showed a reverse “J” shape. The average stem DBH was 4.38 cm and there were only 175 stems with DBH ≥ 30 cm in this plot. The top four dominant species in the plot were Carpinus fargesiana, Cyclobalanopsis multinervis, Daphniphyllum macropodum, and Liquidambar acalycina. They nearly distributed all around the plot but large size trees (DBH ≥ 10 cm) showed relatively different spatial distributions. Based on community composition and stem size structure, the Qizimei Mountains forest dynamics plot belongs to the middle stage of secondary forests after anthropogenic disturbance. Consequently, monitoring long-term forest dynamics in this plot will promote a deeper understanding of community assemblage rules and maintenance mechanisms of species diversity during the natural recovery process in SEDBMF.

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.

Mammals are key indicators for biodiversity conservation and management due to their high diversity, wide distribution range, and sensitivity to habitat changes. Recently launched by the Chinese Academy of Sciences, the Mammal Diversity Monitoring Network of Sino BON (Sino BON-Mammal) is a key member of the Biodiversity Monitoring Networks of Sino BON for the monitoring and inventory of terrestrial mammal resources in China. Firstly, this paper reviews several major advances in terrestrial mammal diversity observations in both China and other parts of the world. We then provide an overview of Sino BON-Mammal, including the major scientific goals, monitoring framework, methods, and data products. In addition, we also summarize some working advances of the Mammal Diversity Observation Network of Sino BON since 2011. This overview will be helpful for the development of national observation programs of mammal diversity in China.

Genetic diversity and species diversity are the two basic levels of biodiversity; recent studies have indicated the parallel effects of environment properties on these two levels of biodiversity. Here we introduce the species-genetic diversity correlation model regarding the parallel effects of environment properties on genetic diversity and species diversity. Based on the four basic processes in community ecology and population genetics (i.e. mutation and speciation, selection, drift, dispersal), we further discuss the theoretical foundations of the parallel effects of environment properties on these two levels of biodiversity. The studies conducted on these effects have shown significant importance in ecology and conservation biology, especially in the age of global change; however, few studies consider these two levels of biodiversity together but most consider only one in the biodiversity research so far. Therefore, we review the recent progress and outline the future directions in the study of the parallel effects of environmental properties on genetic diversity and species diversity. We hope this will benefit and promote the related studies in China.

Hybridization and polyploidization are common phenomena in plants and play important roles in speciation and diversification of extant species. Previous studies using ecological, physiological and molecular investigations have provided a framework for understanding the underlying mechanisms of plant hybridization and polyploidization. In this review, we examine the roles of epigenetic variation in species evolution from an evolutionary perspective. We summarize recent advances in Arabidopsis thaliana, Oryza sativa and species of Brassica to elucidate the correlations between phenotypic novelty and epigenetic variation. Based on currently available observations, we propose that future studies should emphasize the roles of epigenetic variation at both the natural population and species levels, and that statistical methods need to be improved to identify causative epigenetic variations at the genome-wide level.

Plants from aquatic to terrestrial ecosystems have undergone a very complex evolution, and their evolutionary pathways of large numbers of genes may be different from one another, so that traditional phylogenetic trees cannot show true evolutionary relationships. The phylogenetic network graph is a good solution to show the complex relationships of reticulate evolution, including vertical evolution and horizontal evolution. In this paper, we selected Chlamydomonas reinhardtii and four terrestrial plants, and screened 1,668 one-to-one orthologous genes to reconstruct the phylogenetic relationship of terrestrial plants based on phylogenomics. Results showed that phylogenetic trees were different based on different analysis strategies. The 1,668 genes were analyzed separately and 15 different topologies were found. The phylogenetic network of the orthologous genes obtained from the five species was analyzed, and the results showed that in a very robust phylogenetic network map, only five species have nine different split branches, suggesting a very complex evolutionary relationship network. Futhermore, the difference in split branches between algae and bryophytes or lycophytes is very small, which may be one of the reasons influencing the phylogenetic tree conflict, and implies that early terrestrial plants underwent a complex radiate evolution.

Species distribution, catalogues, phylogeny, and life history traits are the data basis of biodiversity studies, playing critical roles in understanding species origins, evolution, and conservation biodiversity. Recently, a large number of scientific data-sharing platforms have been created, greatly contributing to the development of biodiversity informatics. However, it is difficult for most researchers to deal with big data with high complexity and heterogeneity. Determining how to select and utilize these data accurately and effectively becomes a huge challenge for ecologists and conservation biologists. To better deal with existing problems related to scattered distributed data, we classify biodiversity data resources into four groups (species distribution, catalogues, phylogeny and life history traits), and select representative databases (e.g. Global Biodiversity Information Facility, The Plant List, Open Tree of Life, and The Plant Trait Database (TRY) for demonstration. For each database, data type, and sampling design, geographic coverage and data availability are reported, and selected publications using these datasets are briefly introduced. Meanwhile, we describe recent achievements on the construction of China’s biodiversity digital platforms in each section. Overall, we hope that this paper provides a starting point for researchers to be familiar with these databases and use them correctly, and could have the potential to stimulate the development of related fields in research and conservation of biodiversity under the efforts of researchers and the public.

Gaoligong Mountains, known for its richest biodiversity, locates in the Indo-Burma Biodiversity Hotspot. However, our knowledge of the fauna in the alpine habitat of Mt. Gaoligong is still lacking due to complex terrain and poor accessibility. From October 2014 to June 2016, infrared cameras were established to monitor the biodiversity of mammals and birds in the alpine habitat of Mt. Gaoligong, Lushui County, Yunnan. In this survey, we selected three sample plots, North (Jinman), Central (Tingming Lake), and South (Pianma Pass), and in each sample plot, 20 cameras were established for 10,400 camera trapping days and 1,342 effective images were obtained. We identified 18 species of mammals and 44 species of birds belonging to 9 orders and 28 families, including 11 species listed as State Key Protected Wild Animals. The most abundant species was Tarsiger chrysaeus, along with Ithaginis cruentus, Zoothera mollissima, Ochotona forresti, and Ailurus fulgens. Luscinia pectoralis was recorded for the first time in Mt. Gaoligong. A one year survey at the Jinman sample plot revealed that faunal diversity in the alpine habitat had strongly seasonality, i.e. the months from May to October had much higher abundance than the other months. This was a consequence of the high immigration rate to alpine habitats during this period due to altitudinal movement and autumn migration. This survey is the first time to use infrared cameras for alpine faunal surveys at Mt Gaoligong, and the generated data provided a scientific basis for the protection and management of this nature reserve.

Natural hybridization plays a pivotal role in the formation of new species during the evolution of organisms. There are two principal types of hybrid speciation: polyploidization and homoploid hybrid speciation. The former has been regarded as an important force driving plant speciation, whereas the latter has proved to be a main mode of speciation based on an increasing number of cases, which have reported successful crosses between the species at the same ploidy level. However, only a few cases of homoploid hybrid speciation have been documented when strict criteria are applied. Therefore, molecular evidence involving more genomic loci and morphological investigations from different kinds of hybrid zones, as well as assessments of existing speciation models and new computer stimulations, are required for further understanding the genetic basis of the initial and entire process of speciation. Through the historical reconstruction of gene flow between diverging lineages, additional organismal models for hybrid speciation need to be developed to reveal the effects of natural selection on the formation of reproductive isolation, and to discern the ecologically adaptive changes and the formation rules of novel diversity in the process of hybrid speciation. Here I briefly review the history of studies examining natural hybridization and speciation to introduce concept changes, research methods, and the latest advances of natural hybridization and speciation, to identify the unsolved core and basic scientific questions and to provide feasible suggestions for future studies and the protection of biodiversity involved in natural hybridization.

In order to balance development, nature reserves, and community, it is necessary to understand community characteristics and willingness. Between September and November of 2014, we surveyed infrastructure, demographic factors, economic activity, development willingness, and the demands of all 151 concerned resident sites of the Shiwandashan National Nature Reserve in Guangxi. Methods included semi-structured interviews, key people interviews complemented with a literature review, seasonal calendars, market surveys, participatory forest surveys, and community demand interviews. In 2015, we carried out focused complementary investigations on the communities located in the nature reserve. Results on the characteristics of the communities of the Shiwandashan reserve included minority culture, forest-based land utilization, high dependence on natural resources, less infrastructure development, low market accessibility, and minimal financial resources for development. There were diverse perspectives on community development, but almost all focused on subsistence needs. The demands of the communities for the nature reserve mainly included infrastructure development and forest resources use. Holistically, topics including considering the community status, threats faced by the nature reserve, development strategy of the nature reserve, species and vegetation distributions, prioritized working areas, focused communities, and urgent activities were discussed and then, suggestions were given based on the research. Specific measures included developing forest restoration and ecological compensation in priority areas, to meet the demands of the communities located in the nature reserve and realize ecological immigration if possible and establishing some projects on infrastructure construction, community culture development, and building the local brand. Meanwhile, it is necessary to establish co-management institutions, provide training to community residents and nature reserve staff and to strengthen publicity and education. This study provides some suggestions on methods and contents of community work during its primary phase and future directions were also discussed including at the micro-level (establishing an indicator system to estimate village or family status) and at the macro-level (achieving good effects of community development by legal and standard construction and allied stakeholders) which is also significant for other aspects of nature reserve management.

The study of the relationship between biodiversity and ecosystem functioning (BEF) is a hot topic in the field of terrestrial ecosystem ecology, and is of great significance for the efficient use and management of ecosystems. Furthermore, it plays an important role in the restoration of degraded ecosystems and biodiversity conservation. Alpine grassland is the main ecosystem type found in the Qinghai-Tibet Plateau. In recent years, progress has been made on species diversity and ecosystem functioning and their mutual relationship in alpine grasslands. This paper analyzes existing problems in the research of grassland biodiversity and ecosystem functioning in terms of the study of underlying ecological processes and the impacts on ecosystem multi-functionality under global change. The effects of different grassland types, grassland degradation, grazing disturbance, simulated climate change, mowing, fertilization, enclosure, and replanting on the relationship between biodiversity and ecosystem functioning in alpine grasslands are also thoroughly reviewed in this paper. Moreover, deficiencies and future research directions of alpine grassland BEF are identified: carrying on the BEF research of alpine grasslands based on the functional diversity of species, comprehensively considering the effects of abiotic factors such as resource supply levels, disturbance intensity and scale, and environmental fluctuation on the relationship between species diversity and ecosystem function, and paying attention to the effect of scale and element coupling on BEF research of alpine grasslands under global climate change. Finally, based on research progress and conclusions of BEF in alpine grasslands, we put forward suggestions to improve the utilization rate of alpine grassland resources and biodiversity conservation, including strengthening grazing management, protecting biodiversity, improving governance of degraded grasslands, maintaining biodiversity function, strengthening innovation and protection concepts and enhancing ecosystem functioning that has been seriously weakened by climate change and human disturbance.

To understand the extinction risk of lycophytes and ferns in China, we conducted an evaluation of the two groups according to IUCN Red List Categories and Criteria (version 3.1) at the national level. During a period of 16 months, a group of three researchers evaluated each taxon by means of reading literature, checking herbarium specimens, and consulting colleagues working on lycophytes and ferns in China. A total of 30 colleagues share their knowledge, mainly regarding living status and distribution, on Chinese lycophytes and ferns. Here we present a preliminary red list of Chinese lycophytes and ferns which includes 2,244 taxa of the following categories: 43 Critically Endangered (CR, among which six have probably been already extinct) , 68 Endangered (EN), 71 Vulnerable (VU), 66 Near Threatened (NT), 1,124 Least Concern (LC), and 872 Data Deficient (DD). The taxa which have been taken into account include species, subspecies, and varieties only, with forms and hybrids excluded. Of the 182 threatened species (VU, EN, and CR), 79 are endemic (or nearly) to China. Conservation priorities are suggested for the 79 threatened and endemic species, especially the 24 critically endangered species which include Adiantum meishanianum, A. nelumboides, Angiopteris chingii, Asplenium cornutissimum, Bolbitis hainanensis, Huperzia quasipolytrichoides var. rectifolia, Isoëtes orientalis, I. taiwanensis, I. yunguiensis, Paesia taiwanensis, Parathelypteris subimmersa, Polystichum basipinnatum, P. cavernicola, P. minutissimum, P. oblanceolatum, P. speluncicola, Pronephrium longipetiolatum, Pseudocyclosorus caudipinnus, Pteridrys lofouensis, Pteris angustipinna, Selliguea cruciformis, Tectaria ebenina, T. hekouensis, and Woodsia okamotoi. This red list is of a preliminary nature as a rather high proportion of taxa belong to DD (up to 872, ca. 39 % of total taxa in China). To gain a complete and precise red list, further evaluation work, especially taxonomic revisions based on field observations, is needed for the lycophytes and ferns in China. These include Angiopteris, Asplenium, Athyrium, Deparia, Dryopteris, Huperzia, Polystichum, Pteris, Selaginella, Polypodiaceae, and Thelypteridaceae which are still relatively poorly understood in terms of taxonomy and conservation.

Assessing and determining patterns and hotspots of biodiversity are the foundation of biodiversity conservation planning. Situated in the hinterland of the Qinghai-Tibetan Plateau, and being the source of the Yangtze, Yellow and Lancang rivers, the Sanjiangyuan region is considered to be one of the most abundant and concentrated areas of plateau species worldwide. We conducted bird censuses in the Maixiu Area of Sanjiangyuan National Nature Reserve in March, May and August of 2014. We examined the spatial patterns and identified bird community hotspots, and the conservation gaps of current zoning. Our results showed that: (1) there were 89 bird species in the Maixiu Area belonging to 10 orders, 29 families and 57 genera, among which 12 species belonged to the List of Key Protected Wild Animals of China and 11 species were listed in appendices I and II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES); (2) there were differences in bird community composition among habitat types and along an elevational gradient, and bird diversity in low altitude, forest habitats was higher than that found in high altitude, meadow habitats; (3) bird diversity decreased from forest to glaciers and snowberg, and from northeast to northwest and southeast; hotspots of endangered birds were concentrated in southwestern alpine meadows, which differed from the hotspots of the overall bird community; and (4) the core zone of the reserve matched the hotspots of overall birds well, but failed to match the hotspots of endangered birds, which might be not conducive to their protection. Our results may help to make more effective decisions for biodiversity conservation in this region.

Nature reserves are a cornerstone of global conservation. Although the network of global protected areas has expanded substantially over the last few decades, many protected areas are not effective and the use of protected areas as a conservation tool has been criticized due to its inefficiency. Understanding which institutional conditions of protected areas are effective is therefore a key research priority. Shennongjia National Nature Reserve offers a fascinating case to investigate the effectiveness of protected areas in China. This reserve is exceptionally important for conservation as it harbors the remaining subtropical mixed broadleaved evergreen and deciduous forests in the northern hemisphere, numerous endemic and endangered species, and viable populations of the snub-nosed monkey (Rhinopithecus roxellana hubeiensis). From an institutional perspective, Shennongjia Nature Reserve experienced a heavily exploited deforestation period and forest cover rebounded since the establishment of the reserve and the implementation of the Natural Forest Conservation Program (NFCP) and the Sloping Land Conversion Program (SLCP). We assessed the effectiveness of the Shennongjia Nature Reserve in conserving forests and habitat of the snub-nosed monkey based on landuse datasets of 1980, 1990, 2010 and 2015, respectively; combining DEM, distribution and behavioral characteristics of the snub-nosed monkey, and constructing the criterion of the survival function of the snub-nosed monkey and metapopulation capacity. Results showed that the forest area increased by 34.27% and forest coverage increased 16.42%, of which 82.77% of the newly gained forest recovered from shrubs and sparse forests since the establishment of the reserve. The area of the most suitable habitat for the snub-nosed monkey increased 17.70%, and metapopulation capacity of the habitat increased 515.17%. Furthermore, since the implementation of NFCP and SLCP, the forest area and forest coverage increased 23.24% and 12.77%, respectively, the most suitable habitat area for the snub-nosed monkey increased 14.29%, and the metapopulation capacity increased 367.20%. Our results indicate that the Shennongjia Nature Reserve is efficient for forest conservation and snub-nosed monkey habitat provision.

Dajinshan Island is part of Jinshan Three-Islands Marine Natural Reserve. Soil on the island has not been polluted by human activities and it is therefore an ideal place to study island ecosystem diversity. To understand the composition and ecological distribution of soil fauna communities in different natural forest vegetation types on Dajinshan Island, the soil fauna communities in three natural forests including bamboo forest, arboreal forest, and shrubbery were investigated during autumn 2015. Each forest included both north slope and south slope regions. A total of 12,769 individuals of soil fauna belonging to 28 groups were collected. The dominant groups were Acari and Collembola, accounting for 70.15% and 19.27%, respectively. The common groups were Protura, Hemiptera, Hymenoptera and Enchytraediae, and they accounted for 7.06% of the total in terms of individual numbers. The dominant groups were Acari (74.26%, 65.32%) and Collembola (16.52%, 22.49%) in both north slope and south slope regions, but differed in common groups and rare groups. The soil fauna communities were different in the three natural forests. In both north and south slope region, the density of soil fauna followed the order of: shrubbery > arboreal forest > bamboo forest, but the number of groups of soil fauna followed the order of: shrubbery > bamboo forest > arboreal forest. Different ecological indexes of soil fauna communities in the three natural forests were different. Shannon-Wiener index, Pielou index, and Simpson index followed the following order: shrubbery > arboreal forest > bamboo forest in both north and south slope regions. The Shannon-Wiener index was significantly different in the three natural forests. The higher soil fauna diversity in shrubbery was probably induced by the favorable microenvironment.

We used the forest fragmentation model to assess forest fragmentation in China based on a 50-m forest cover map in 2010. Six different fragmentation types including interior forest, perforated forest, edge forest, patch forest, transitional forest and undetermined were obtained. We reported the forest fragmentation status in different administration scales (by country, province, and county) based on Chinese administration boundary map of 2010, At the national scale, the patch forest accounted for the largest proportion (49.05%), while the interior forest was the smallest (3.40%). At the regional scale, Northeast China had the lowest forest fragmentation, while Southwest China had moderate forest fragmentation. The highest forest fragmentation areas were mainly distributed in the North China Plain, Central China, Shandong Peninsula and the Huang-Huai-Hai Plain. At the provincial scale, the highest forest fragmentation was located in Shanghai and Tianjin, and the lowest forest fragmentation was located in Yunnan Province and Heilongjiang Province. At the county scale, the lowest forest fragmentation was located in counties in Shaanxi Province. Overall, our results have clearly shown that forest fragmentation occurs extensively and varies substantially over China in 2010. Our study will provide data support for the forestry administrative sector to conduct better forest management and to optimize forestry production and forest spatial patterns, which can improve forest ecosystem services and biodiversity conservation.

Litter fall is a significant component of forest ecosystems and has important ecological functions in material cycling and nutrient balance of forest ecosystems. In this study, we studied litter fall production, composition, spatial and temporal dynamics in a 15-ha northern tropical karst seasonal rainforest dynamics plot in Nonggang National Nature Reserve, Guangxi. We set up 90 litter fall traps, and collected litter fall weekly since May 2012. All litter fall in each trap was dried, classified and weighed. We used litter fall data from January 2013 to December 2014. The total annual litter production in 2013 and 2014 was 4,858.0 kg/ha and 4,928.8 kg/ha, respectively. Litter fall of leaves accounted for 85% while other components made up a small amount. Fruit litter fall was significantly higher in 2013. There were two litter fall peaks in each year, one in spring (March and April) and the other occurring in autumn to early winter (between August and November). The peak of fruit litter fall peak occurred in August. There were no significant inter-annual fluctuations in other litter fall components. The prevailing ecological factors of litter fall production were significantly different between 2013 and 2014. Litter fall production was significantly influenced by aspect and mean DBH (diameter at breast height). Composition and spatio-temporal dynamics of litter fall reflected material cycles affected by multiple biotic and abiotic factors. Our results provide basic information to reveal the unique characteristics of material circulation and energy flows in the geological background and geomorphology of karst.

Reproductive isolation is essential for sympatric populations of closely related species to maintain species integrity and to prevent genetic introgression caused by hybridization. Primulina is the largest genus of Gesneriaceae in China, with a high degree of species diversity and endemism. Most species of the genus are karst habitat specialists (i.e. calciphiles), and many closely related species show a sympatric distribution in karst landscapes. To better understand the mechanism of sympatry in Primulina, post-pollination reproductive isolation, including pollen competition, fruit set, seed mass, seed germination, and pollen viability, was investigated in two closely related species, P. eburnea and P. mabaensis. Results indicated that the total post-pollination isolation strength for P. eburnea and P. mabaensis was 0.09 and 0.13, respectively, which were not strong enough to prevent hybridization completely. The strength of reproductive isolation from pollen competition and seed germination of P. eburnea and P. mabaensis was negative, suggesting facilitation for gene flow between species; while the strength of the fruit set, seed mass, and pollen viability showed a weak role in preventing interspecies hybridization. However, the two species are able to maintain their integrity well, as rare hybrid individuals are found in nature, suggesting that the existence of pre-pollination isolation mechanisms may play a more important role in maintaining species boundaries in these two species.