DNA barcoding has become one of hotspots of biodiversity research in the last five years. It is a method of rapid and accurate species identification and recognition using a short, standardized DNA region. DNA barcoding is now well established for animals, using a portion of the mitochondrial cytochrome coxidase subunit 1 (COI or cox1) as the standard universal barcode. However, in plants, progress has been hampered by slow substitution rates in mitochondrial DNA. A number of different chloroplast regions have been proposed. There has been considerable debate, but little consensus regarding region choice for DNA barcoding land plants. Direct comparative assessment of different barcoding regions is now a priority to enable a standard barcoding solution to be agreed in plants. The proposed chloroplast barcoding regions mainly include five coding (rpoB, rpoC1, matK, rbcL, UPA) and three non-coding (trnH-psbA, atpF-atpH, psbK-psbI) regions. In addition, nrITS is also suggested as a potential plant barcode. Limited by the universality and resolvability of single barcoding region, five combinations of these regions are proposed. In this review, the advance of these barcoding regions, both their universality of primers and resolving power are reviewed. The advantages, standards, workflow and existent dispute of DNA barcoding are summarized.

There is a dynamic interplay between ecology and evolution within community ecology. Phylogenetic community ecology describes the intraspecific and interspecific relationships within a community, aiming to reveal the processes driving community assembly at multiple scales. Previous research has highlighted the role of phylogenetic and historical biogeographical data in explaining current patterns of global biodiversity. The success of using DNA barcoding in the construction of tropical forest community phylogenies highlights the usefulness and challenges of long-term research on community ecology and phylogenetics based on forest dynamic plots. In this paper, we illustrate the feasibility of a synthesis between community ecology and evolutionary biology in order to resolve particular ecological issues on community phylogenetic structure, community niche structure, biogeography, and trait evolution. We summarize progress on the development of a plant DNA barcoding system, and introduce the usage of a combination of DNA markers (rbcL+matK+trnH-psbA) for fast species discrimination and community phylogenetic reconstruction. We also explore the utilization of well-resolved phylogenies to understand community ecology. We discuss the limitations of core plant DNA barcodes (rbcL+matK) when identifying congeners, and propose an improved sequencing strategy suitable for studies at the community level. We expect that plant DNA barcodes will prove very useful for the study of species diversity, mechanisms of biodiversity maintenance, phylogenetic beta diversity and functional trait evolution.

As one of the five major global environmental problems, invasive species have posed serious threats to native ecosystems, public health, and regional economies. Although much progress has been made in the field of biological invasions research in China over the last decade, there are still large knowledge gaps. This paper reviews progress in the field of biological invasions research since 2000 as it relates to China, covering the diversity, colonization and immigration patterns of invasive species, mechanisms and ecological effects of biological invasions, and management and control of invasive species. In China, 529 invasive alien species have been identified, which originated primarily from South and North America, and the major taxa included terrestrial plants, terrestrial invertebrates, and microorganisms. We found a higher prevalence of invasive species in the eastern and southern provinces, compared to the western and northern provinces in China. This pattern is likely due to the differences in the level of economic development and environmental suitability between the two regions. Moreover, with further economic development, China may face more serious biological invasions in the future. These invasions of alien species are largely the combined results of the interactions between the intrinsic traits of these species along with resource opportunities and disturbances by human beings. Many mechanisms are responsible for successful invasions of alien species, but phenotypic plasticity, adaptive evolution, enemy release, interspecific mutualism or commensalism, and new allelochemicals may be primary causative factors. Biological invasions in China have caused serious impacts on native ecosystems, including biodiversity and ecosystem services, alteration of biogeochemical cycles, threats to agricultural and forestry production, traffic and shipping, environmental safety, and public facilities. China has also made progress in the detection and monitoring of invasive species, risk analysis, biological control, radical elimination, and ecological restoration of degraded ecosystems. We suggest several issues that need to be addressed in invasive species research in the future, including territory-wide inventories, evolutionary ecology and genomics, direct and indirect ecosystem-level consequences, interactions between major components of global change and biological invasions, and management and control technologies.

Exploring the mechanisms underlying community species richness is a key issue in ecology and conservation biology, and many hypotheses based on small-scale, local processes have traditionally been used as explanations. The species pool hypothesis developed by Zobel et al. suggests that the variation in community species richness is not only associated with contemporary environmental factors and ecological processes (e.g. competition and predation), but also limited by the regional species pool. The regional species pool is the set of species in a certain region that are capable of coexisting in a target community, which is shaped by historical (e.g. glaciation and geological age) and regional processes (e.g. speciation, immigration, dispersion, and extinction). The species pool hypothesis suggests that the larger the area of a habitat type and the greater its geological age, the greater the opportunity for speciation and hence the larger the number of available species adapted to that particular habitat, which will in turn lead to higher community diversity. The species pool is generally studied at two spatial scales: the regional and the actual scales. While the regional species pool is primarily determined by biogeographic processes, the actual species pool (species present in the target community) is determined by both ecological processes (e.g. competition) and the regional pool. In this review, we introduce and discuss the concepts relating to, and evidence for the species pool hypothesis, together with methods for estimating the species pool.

Sinocalycanthus chinensis is the only representative in the genus Sinocalycanthus and an endangered species restricted in small areas of Lin′an City and Tiantai County, Zhejiang Province. Currently only two natural populations remain: the larger one is found in Lin′an City, consisting of seven subpopulations with nearly 1731 990 individuals in total; the smaller one is located at Tiantai County where 2000 individuals exist. The genetic diversity of the two natural populations and one recently introduced population at Tianmushan Natural Reserve, Lin′an City, Zhejiang Province, was assessed using allozyme markers. A population of Chimonanthus zhejiangensis from Hangzhou Botanical Gardens, Hangzhou City, Zhejiang Province, was included in this study for the purpose of comparison. The genetic diversity of S. chinensis turned out to be extremely low. Only five of 23 loci from 14 enzymes assayed were polymorphic. The polymorphism was largely due to alternative fixation of alleles on Mdh-4, Pgd-3 and Sod-1, and two mutations (Gpi-1 and Gpi-2) on one individual out of 553 in total. At species level the mean number of alleles per locus ( A ) was 1.2, the percentage of polymorphic loci ( P ) was 21.7%, and the observed heterozygosity ( H_o ) was 0.010. At population level the estimates were A =1.0～1.1, P =0～13.0%, and H_o =0～0.014. In contrast, the estimates for C. zhejiangensis were much higher ( A=1.5, P=39.1%, H_o =0.071) though there were only 16 individuals tested. Since no genetic variation was detected in the introduced population of S. chinensis at Tianmushan Natural Reserve, the introduction of the plant should not be considered as a success of ex situ conservation of the endangered species. Moreover, the range of subpopulations within Longtangshan National Natural Reserve is diminishing due to the growth of evergreen forests. So far no measures have been taken to stop this subpopulation from shrinking because of lack of knowledge of ecology and biology of the plant. This study exemplifies that we are unable to conduct in situ conservation and to practise ex situ conservation properly if we have no knowledge of the biology of the species we intend to conserve.

The majority of flowering plants and crops rely in whole or part on animals for pollination. The mutualism between plants and pollinators has attracted ecologists and evolutionists to use this type of interspecific interaction as a model system to study species adaptation and diversification since Charles Darwin. Recent debate on the nature of pollination systems call for studies of this interaction at different levels, ranging from single species to entire communities in a given area. At the species level, detailed studies suggest that floral traits are under selection from mutualists and antagonists as well as the physical environment. In contrast, studies at community-level are rare, but recent analyses indicate considerable spatial and temporal variation in both generalized and specialized pollination systems. This special issue of Biodiversity Science focuses on plant-pollinator interaction, presenting current research status in this area from China. Papers include floral traits and pollinator behaviors addressed by phenotypic manipulation, estimates of pollen removal and receipt, anatomy of flowers, histochemistry analysis and spatial and temporal comparison. The taxa being investigated include wild orchid and cultivated legume, endemic, endangered and invasive species with diverse sexual systems. These thirteen experimental studies and three reviews show the development of pollination biology in China and expose how to facilitate our understanding of the critical ecological proc-esses underlying interspecific interaction in both natural and agricultural ecosystems.

Figs (Ficus, Moraceae) constitute one of the greatest genera of flowering plants with ca. 750 species worldwide. Figs and fig wasps form an obligate specific mutualism, which is treated as the model system to study comparative biology of mutualism and co-evolution. This extraordinary system has received increasing attention because of its specificity and the development of the molecular technologies, although the phylogenetic reconstruction of both partners began in the 1990’s. In this paper, we summarized the research on phylogenetic relationships and fig-fig wasp co-evolution. We also analyzed interrelated researches in China and the future developing trends in research on this mutualism.

The impacts of invasive alien species on the genetic diversity and evolutionary responses of native species are poorly understood. Accumulating evidence shows that invasive plant species can lead to genetic erosion of natives directly through hybridization and gene infiltration, or even affect genetic diversity of natives through creation of new “genotypes”. Exotic species can also alter genetic diversity of natives indirectly through habitat fragmentation and modification, processes which influence gene flow within and among populations and result in inbreeding and genetic drift. On the other hand, some studies show that native species can respond evolutionarily to invasive plants, thereby reducing or eliminating invasive impacts. While interacting with invasive species, native species in both above- and below-ground ecosystems exhibit a series of evolutionary events such as adaptation, speciation or extinction. To more comprehensively evaluate the ecological impacts of biological invasions and the adaptive potential of natives, here we review the impacts of invasive plants on biological (genetic) diversity of native species, and the evolutionary responses of natives. We also discuss relationships between the genetic and evolutionary responses of natives and the success of invasive plants, and propose topics for further research.

Among several paterns of species diversity variations, perhaps the most widely recognized one is the increasethat occurs from the poles to the tropics. A number of explanations have been put forward for this generallatitudinal trend in species diversity. Among these, it seems that the ESA hypothesis is more reasoanable.Based on the explanations advanced before, the author has proposed his own idea, that is the factors, whichinflunce the distribution of species, can be divided into two categories, one is environmental, another is biological, and the environmental factor is primary, the biological one is secondary.

It is an important part of biodiversity research to discover the patterns of species diversity over space and time in different scales and to find the mechanisms that control thepattern forming. These are also considered to be the main goals of studies on species diversity , which lay special emphasis on how the number of species changes and how great the species diverse with different biological attributes. This paper discusses at first the spatial patterns of species diversity , especially the modes of“species-area”from different aspects. The factors like latitudinal changes and habitat heterogeneity are considered to see how they affect the pattern forming of species diversity. Secondly , the paper′s discussion is concentrated on the patterns of species diversity over time. In the long- term evolution of all organisms , the process of total species- diversity increase would be interrupted by a series of mass extinctions that occur periodically. The recent progresses show that the patterns of species diversity between any two mass extinctions would be determined by the initial status immediately after the former mass extinction. On short- time scales , e.g. ecological succession in a community , circannual rhythms and seasonality , some special patterns have been found in species- diversity changes. In addition , the results of some researches demonstrated that more species tended to live on a host if they had coevolved for a longer time.

Conservation genetics is a new field of research focusing on the studies and practices of biodiversity conservation based on the principles and techniques of population genetics. During the past decades, genetic studies have made increasingly great contributions to biodiversity conservation in theory and practice. In this paper, we briefly introduce the concept and history of conservation genetics, and highlight progress in plant conservation genetics. Four major aspects of conservation genetics in plants are addressed, including plant phylogenetic reconstruction and identification of conservation units, the relationship between genetic diversity and species fitness, population genetic structure and conservation strategies, as well as the identification and utilization of plant genetic resources. In addition, the great importance of genetic studies in plant conservation is discussed.

Spatial patterns of biodiversity are results of contemporary climate, disturbance, and geological history. In this paper, we review the historical hypothesis which explains historical importance in shaping biodiversity patterns, focusing on the recent development in its studies on mechanisms, parameter selection, and relative importance of historical factors versus contemporary climate. Based on literature research, we conclude that, (1) the historical events significantly affect the present patterns of biodiversity, and that these effects are masked by the strong collinearity between historical processes and contemporary climate; (2) historical processes are more significant in influencing distributional patterns of species with small ranges (or endemic species) than those of wide-spread species; (3) measurement of historical processes is a challenge in testing historical hypothesis, as the surrogates currently used are strongly collinear with contemporary climates. Phylogenetic analysis may be help assess the importance of historical hypothesis in controlling spatial patterns of biodiversity.

Since Darwin and the earliest theory of population genetics, it has been well known that breeding system plays an important role in genetic diversity and evolution of organisms. After elucidation of the rationale for the use of protein electrophoresis in assesment of breeding system of plants, experimental results obtained by Chinese and foreign scientists has been cited. Although many characters of plants such as life form, mode of reproduction etc. do influence genetic structure of populations, the most significant matter is the relationship between breeding system and population genetic differentiation. Since that we can make a deduction from breeding system to population genetic structure, and further to sample strategies which are critically important to monitoring genetic diversity of in situ conservation and ex situ conservation.

Although there have been extensive studies on the genetics of endangered plant species , it is still highly debatable about the role of population genetics in rare plant conservation. The genetic diversity of endangered species may be lost due to genetic drift and inbreeding , but this loss is more likely to be a symptom of endangerment rather than its cause. There is no clear-cut relationship between the level of genetic diversity and species viability. Changes in the genetic structure of plant populations may exert negative influence on population persistence if this change involves loss of self2incompatibility alleles or genetic assimilation through hybridization with a reproductively compatible relative.

Effective conservation of traditional crop varieties is the basis of the long-term utilization of agricultural biodiversity, and will be one of the essential factors for the sustainable development of agriculture. Due to the intensive production practices in modern agriculture, a great number of traditional crop varieties have been rapidly replaced by the improved high-yielding varieties, which has caused severe “genetic erosion” in the genepool of crop species, and significantly reduced genetic diversity of crop varieties. It is therefore essential to preserve the shrinking crop biodiversity before it is completely lost. On-farm conservation is an important and dynamic in situ conservation method that conserves crop varieties in agricultural ecosystems. On-farm conservation can be defined as the continued cultivation and management of a diverse set of crop populations by farmers in the agro-ecosystems where a crophas evolved, and it allows the evolution of conserved crop varieties to be continued in their original habitats. However, in spite of the increasing interests in this method and a relatively large number of research and case studies reported in this field, there has been no significant achievement for on-farm conservation and many questions remain unanswered: Is on-farm conservation practical and achievable? Can on-farm conservation actually be conducted in modern agriculture? Is on-farm conservation a trade-off with agricultural development? What are the scientific issues for on-farm conservation? What incentives can their be for farmers to conserve genetic diversity in their farming ecosystems? All these questions need to be addressed scientifically with satisfaction when conducting effective on-farm conservation. It is therefore necessary to have a better understanding of on-farm conservation, to study mechanisms and scientific basis of on-farm conservation, and to be innovative to open a new dimension for on-farm conservation action. The biodiverse deployment of rice varieties, mixed planting of modern hybrid rice with traditional rice varieties in Yunnan Province, not only provided an excellent method of controlling rice disease and increasing rice productivity, but also demonstrated a powerful model for conserving traditional rice varieties in an effective and sustainable way. This model of mixed planting of a diverse set of crop varieties links farmer's long term benefit, socioeconomic concerns, and the actual conditions of locally based agro ecosystems appropriately with conservation activities. This model of using biodiversity to preserve biodiversity of crop varieties is a long term approach that will be sustainable and beneficial to farmers whose general living standard will be raised. It might provide possible solution for on-farm conservation of traditional rice varieties in a feasible and sustainable way., and probably has potential for other crop species, too.

Due to differences in the significance of populations, limits in funds for species conservation and conflict between conservation and economic development, deciding what and where to conserve is an essential step in managing important species, especially endangered species and wild relatives of crops and domesticated animals. There are three approaches to identifying populations for priority conservation of important species, including genetic variation-based, genetic distinctiveness-based and genetic contribution based. The genetic variation based approach chooses populations with high genetic variation, especially allelic diversity, for priority conservation. This approach does not consider genetic distinctiveness. Some distinctive alleles in populations with low genetic variation may not receive effective conservation based on this approach. In contrast, the distinctiveness-based approach, such as those based on evolutionarily significant units, chooses distinct populations for priority conservation. The genetic contribution based approach, a synthesis considering genetic variation and distinctiveness, is the most appropriate approach in determining which populations need priority conservation. We propose that this work should be considered urgent in China for some endangered or rare species.

Natural hybridization mediated by pollen flow has been considered as an important factor to drive speciation in Rhododendron, one of the largest genera within alpine plants. The diversity of Rhododendron species is centered in southwestern China, yet the potential role of interspecific pollination in natural hybridization has not been empirically examined in this area. Here we investigated the flowering period and floral visitors, and conducted a series of pollination experiments to examine breeding systems and hybrid compatibility within four Rhododendron which are frequently sympatric in Yunnan Province. Rhododendron delavayi and R. decorum are clearly distinct by their morphological traits, but the putative hybrids R. agastum and R. irroratum are morphologically between the other two species. We observed that R. delavayi flowered from the beginning of March to the end of May, R. agastum and R. irroratum flowered from the beginning of March to the beginning of April, and after their flowering periods ended, R. decorum began to flower until the end of May. The anthesis of single flowers of the four Rhododendron species was almost one week. The floral visitors belong to the Hymenoptera and Diptera Orders, and Apis cerana cerana visited all of the four Rhododendron species. We found that R. delavayi, R. agastum and R. decorum are self-incompatible, but not R. irroratum. No breeding barrier between any of the four species was detected by artificial pollination, and the hybrid seeds were fertile. The hybrids between four species showed equivalent fitness to their par-ents. We suggest that the role of potential interspecific pollination is essential to hybrid speciation and evolu-tion of Rhododendron species.

This paper discussed the scientific concept of species and the biological nature of species as a natural group. It is high diversity of species that makes it impossible to produce general , applicable and theoretically significant species concepts for all the organisms existing or once existed on the earth. Species communities of composition diversity should have characters which correspond with different biological aspects of individual species , i. e. species diversity should acturally be the biological diversity of species. There are many different methods to measure the degree of species diversity , but the total number of species should be the most explicit and direct one. A lot of studies in the last decade tried to value how many species exist in the world. The origin of species diversity is through speciation , and its loss through species extinction. The model and mechanism of speciation and extinction and the possible causes were briefly discussed. The author strongly argues that there exists a close relationship between biogeographic analysis and species diversity researches. Pattern identification and component analysis on fauna and flora should be an important part of species diversity researches on a relatively large scale.

Conservation genetics deals with the genetic factors that affect extinction risk and genetic management regimes required to minimize these risks. In this review, we introduce the advance from the genetic diversity study and the influence of genetic diversity on ecosystem. Until now, most of conservation genetic studies still adopt selective neutral genetic markers, which generate a large amount of valuable information for conservation theory and practice. Two important implications of conservation genetics are introduced: (1) the identification of individuals, genetic unit or species, which is very important for conservation strategy making and efficiency improving; and (2) cryptic bottleneck caused by reproduction and dispersal limitation, which is often neglected in conservation practice. Generally, neutral genetic markers may not provide enough information for the genetic basis of species adaptation. In recent years, along with the development of genomics, more and more studies begin to investigate the genetic basis of adaptation by using adaptive genetic markers. Limited by lack of the functional gene information, most of these studies adopt the genome scanning approach. The development of landscape genetics promotes the understanding of the neglected relationship between genetic diversity and the landscape heterogeneity. In addition to the genetic diversity study itself, some studies found that plant genetic diversity may influence the ecosystem structure and function. This illustrates that genetic diversity in both endangered species and common species can play an important role to ecosystem integrity and sustainability. Finally, we briefly discuss how to integrate the genetic diversity into conservation practice more effectively. And, we also indicate the gap between Chinese and international advanced studies at the area of conservation genetics.

Most plants regenerate by seed bank. Animal activities affect seed fate from their departure from the parent plants to the establishment of seedlings. Animals play dual roles in plant regeneration , including consuming seeds and dispersing seeds to suitable sites for seedling recruitment . These two roles are trade-off . Studying the relationship between plant regeneration and animals will help to understand population dynamics , coevolution between animals and plants , community succession , the role of animals in ecosystem function and biodiversity. In recent studies , oaks and pines have been extensively studied species. It is well known that rodents and birds are the chief predators and dispersers for large seeds.

A fascinating issue for ecologists is to develop a general theory exploring the mechanisms of formation and stabilization of biodiversity. Although diverse hypotheses have been proposed to account for the geographic distribution of biodiversity, many of them are not applicable to all species or under a variety of conditions. The metabolic rate hypothesis is a recently-developed hypothesis that can quantify relationships between the dynamic processes of individual and population evolution and patterns of biodiversity, and between species richness and environmental factors. This theory is based on the energetic-equivalence rule and fractal-like distribution network models, and can not only explain the origin of biodiversity but also the maintenance of biodiversity. Herein, we analyze and compare this new hypothesis to other related hypotheses of metabolism-biodiversity theory. We suggest that this hypothesis is more likely to become a unified theory explaining the formation of biological diversity than others we assessed. We also discuss important issues relevant to further advancing the area of metabolism-biodiversity theory.

The term “Tree of Life” was first used by Charles Darwin in 1859 as a metaphor for describing phylogenetic relationships among organisms. Over the past three decades, the recognized tree of life has improved considerably in overall size and reliability due to an increase in diversity of character resources, a dramatic growth in useable data, and the development of tree-reconstruction methods. As a bridge connecting phylogeny, evolution and related disciplines, such as molecular biology, ecology, genomics, bioinformatics and computer science, the tree of life is increasingly widely used. In this paper, we review the history and progress of tree of life studies and focus on its application in the following fields: (1) the reconstruction of phylogenetic trees at different taxonomic hierarchies to understand phylogenetic relationships among taxa; (2) investigation of the origins of taxa and biogeographic patterns based on dating estimation and biogeographic reconstruction; (3) examination of species’ diversification and its causes by integrating dated trees, ecological factors, environmental variation and key innovations; (4) the study of the origin and patterns of biodiversity, predating biodiversity dynamics, and development of conservation strategies. Finally, we evaluate the difficulties from matrix alignment, gene tree incongruence and “rogue taxa” distraction in tree reconstruction due to massive increases of useable data and in the context consider “supertree” building in the future.

The tribe Triticeae Dumort. in the grass family (Poaceae) contains three of the world most important cere-al crops, namely, wheat (Triticum aestivum L. ), barley (Hordeum vulgare L. ), and rye (Secale cereale L. ), as well as many economically valuable forage grasses. Because the tribe Triticeae comprises a greatnumber of species, covers a remarkably wide disribution area in the world, and inhabits various ecologicalenvironments, tremendous morphological and genetic variations are found between and within species inthis tribe. As a vast reservoir of genetic resources, species in the Triticeae have a great potential for the im-provement of wheat, barley, and rye varieties in the plant breeding programmes through transferring use-ful genes from wild to cultivated species. However, the present knowledge and investigation of biodiversityin the Triticeae is considerably insufficient, which largely affects the appropriate utilization of the geneticresources in the tribe. Nowadays, the change of the global environments makes some species of Triticeae inan endangered state. Therefore , it is very important and urgent to strengthen the further investigation ofthe genetic diversity in the Triticeae and to have effective strategy to the conservation of this vast geneticreservoir.

The future of human being may rely on biodiversity, and thus depends on how to investigate, conserve, and rationally use biodiversity. Species is the basic unit of biodiversity, and therefore rational delimitation of species is one of the crucial issues for biodiversity pursuits. However, no species concept published until now is both scientific and operative. A tentative species concept is proposed here just for discussion.

One of the diverse species concepts defined before may only perceive one aspect of the mature species like “the blind men feel the elephant” while the mature species at the final speciation stage should have integrated all species concepts. Most “species” in the nature are on the way to the final speciation stage. However, before reaching the final speciation stage, these species undertake further cycles of speciation. Species from the repeated splits of the incomplete divergences show incomplete reproductive isolations, frequent interspecific gene flow and reticulate evolutions. In addition, the earliest divergent gene differs between different pairs of species. Therefore, the divergence orders for different species concepts vary greatly between organisms. Such random divergences lead to the extreme difficulty to define a common and accurate species concept for all “species” on the speciation way. It is better to delimitate species, publish new species and conduct taxonomic revisions based on conditions and approaches of as many species concepts as possible. In addition, incomplete reproductive isolations, limited interspecific gene flow and some ‘abnormal’ individuals not ascribed to any species due to interspecific hybridizations and within-population mutations should be widely acknowledged during species delimitations. Such circumscribed species may be more objective and scientific than previously delimitated based only on one single species concept.

Biological invasions have caused tremendous ecological and socio-economic damages worldwide. Therefore, it is important to develop methods for their effective management. Biological invasion is a process of adaptive evolution in which hybridization and introgression play an important role in promoting invasive species by changing their invasiveness. Therefore, understanding how the genetic mechanisms of hybridization and introgression influence biological invasion will facilitate effective control of invasive species. The escape of transgenes with special functions into populations of wild relatives through hybridization and introgression may change the invasiveness and weediness of the wild relatives, causing undesired environmental problems. This paper introduces the role of hybridization and introgression in adaptive evolution and speciation, and discusses how an alien species can change its adaptability, competitive ability, and invasiveness in new habitats through introgressive hybridization. Hybridization and introgression can cause polyploid and homoploid evolution of plant species, thereby influencing the fitness of new species and promoting the formation of an invasive species in new habitats. At the same time, with the rapid development of transgenic technologies, transgenic crops are being extensively released into the environment for commercial production. Biological invasion is a complicated evolutionary and ecological process, and future research should investigate the roles of hybridization and introgression in biological invasions in the context of the myriad factors that influence the process.

The 750 species of Ficus (Moraceae) constitute the most distinctive and widespread genus of tropical plants. There are species-specific mutualisms between fig trees and their pollinating insects ( Agaonidae ) and perplexing relationships within the ecosystem. Valuable research results in the areas of the systematics of Ficus and fig wasps, the origin and maintenance of dioecy, biodiversity, co-evolution and ethology are provided by the approaches of systematics, biogeography, ecology, and conservation biology. China′s ancient biogeographic realm, its unique geographic traits and the diversity of its fig flora (71 dioecious species) make it an ideal location to study these questions. Up to now, we have determined less than 20 species of pollinators ( Agaonidae ) of the 98 fig/pollinator mutualisms in China, and our knowledge of these fig trees and related animals is still very limited. In utilizing the resourceful advantages of Chinese biota and geography, well-organized programs will advance smoothly and stimulate further research into fig trees and associated animals.

In recent years , it has been emphasized that the principles and methods of molecular phylogenetics should have potential and practical value in biodiversity conservation , especially in species conservation. It is a critical issue and the first step as well to identify those units which have evolutionary significance from different populations of a species concerned in species conservation. Phylogenetic relationships among those populations could shed valuable light on this issue. In addition , the data from molecular phylogenetic study are also helpful for us to understand the status and process of populations.

Among the candidate DNA barcoding loci suggested for land plants, only rbcL and trnH-psbA are available for barcoding bryophytes. However, both loci have limitations in discriminating among species. The present study evaluated the feasibility of using the cpDNA rps4 locus as an additional marker to complement other candidate barcodes for bryophytes. We analyzed 3,365 rps4 sequences retrieved from GenBank using pair-wise distance and phylogenetic methods. Our results demonstrated the universality of rps4 in bryophytes; the locus covers 96% of moss families and 88% of liverwort families. The rps4 locus resolved 73.0% of the species we tested. The discriminatory ability of rps4 is better than that of rbcL-a in each of the six bryophyte genera (i.e. Plagiochila, Tortula, Plagiomnium, Pyrrhobryum, Pogonatum, Grimmia) most commonly represented in the database. Moreover, large numbers of rps4 sequences from individuals of known bryophyte identities have been compiled in GenBank, thereby providing a reference for species identification. Therefore, we propose rps4 as an additional barcode, especially when rbcL and trnH-psbA do not perform well in certain bryophyte taxa.

Microbes with rich species and genetic diversity are widely distributed throughout various habitats in the world. China possesses a variety of climate zones, geographic environments, and complex ecosystems, which play a large role shaping the complex biodiversity of this country. Microbial diversity has been widely studied and well documented by Chinese scientists. For example, a total of ca. 14,700 eukaryotic microbe species have been recorded, including ca. 14,060 fungi, ca. 300 oomycetes, and ca. 340 slime molds. Within the Fungi, there have been 473 medicinal fungal species and 966 edible fungal taxa recorded. However, recent studies have documented much high species diversity of prokaryotic microbes using molecular techniques, which have greatly promoted the study level of microbial diversity in China. This review paper summarizes recent research progress of microbial (i.e., archaea, bacteria, fungi, oomycetes, and slime molds) diversity in China based on traditional and molecular techniques.

Three species of wild rice , i.e. ,Oryza rufipogon , Oryza of ficinalis and Oryza meyeriana , were found in China , and had been listed as the national second-grade protected plants ( gradually endangered species) of China. It was investigated that Chinese wild rice have been in imminent danger due to rapid loss of their natural community. Oryza rufipogon is in most imminent danger , while Oryza officinalis and Oryza meyeriana are less imminent . The main cause is economic activities which led to the loss of habitat , continuous deterioration of habitat quality , sustained reduction of habitat and invasion of exotic species. At present , some measures have been taken to protect Chinese wild rice , such as in situ conservation (on-site maintenance) and ex situ conservation (off-site maintenance) . Ex situ conservation includes seed-preserved genebank ,whole plant-preserved field genebank and callus-conserved cryopreservation. Chinese wild rice species possess many excellent characteristics , such as extreme cold-tolerance , high resistance to diseases and pests , good quality and high content of protein , senescence-tolerance of functional leaves , strong regenerating capability , good quality of lush growth , good growing dominance , which have been widely used in conventional rice breeding and hybrid rice breeding , and huge social and economic benefits have been achieved. Rapid progress has been made in biotechnology of Chinese wild rice , especially in anther culture , protoplast culture , somatic cell hybridization and gene transfer. It can be expected that Chinese wild rice resources will play more and more important role in rice breeding.

In this review , we discuss two applications of mtDNA analysis in zoological conservation biology. One is to describe and manage genetic diversity , an issue more relevant to long2term planning for conservation. Another is its use as a tool for the short-term demographic management of populations. We emphasize its use in recognizing Evolutionary Significant Units ( ESUs) and Management Units (MUs) . ESUs are recognized to partition genetic diversity and assess conservation value and can be identified as populations having significant phylogenetic divergence of mtDNA from other populations , with corroborating divergence of allele frequencies at nuclear loci. MUs are defined as demographically independent breeding units and are identified as populations having distinctive allele frequencies , regardless of phylogenetic structure and the level of genetic divergence. ESUs and MUs are both important units in conservation biology. The use of mtDNA should be in concert with analysis of nuclear loci in order to obtain reliable data for conservation.

Angiosperm phylogenetics investigates the evolutionary history and relationships of angiosperms based on the construction of phylogenetic trees. Since the 1990s, nucleotide or amino acid sequences have been widely used for this and angiosperm phylogenetic analysis has advanced from using single or a combination of a few organellar genes to whole plastid genome sequences, resulting in the widely accepted modern molecular systematics of angiosperms. The current framework of the angiosperm phylogeny includes highly supported basal angiosperm relationships, five major clades (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales), orders grouped within these clades, and core groups in the monocots or eudicots. However, organellar genes have some limitations; these involve uniparental inheritance in most instances and a relatively low percentage of phylogenetic informative sites. Thus, they are unable to resolve some relationships even when whole plastid genome sequences are used. Therefore, the utility of biparentally inherited nuclear genes with more information about evolutionary history, has gradually received more attention. Nevertheless, there are still some plant groups that are difficult to place in the angiosperm phylogeny, such as those involving the relative positions of the five major groups as well as those of several orders of eudicots. In this review, we discuss the applications, advantages and disadvantages of marker genes, the deep relationships that have been resolved in angiosperm phylogeny, groups with uncertain positions, and the challenges that remain in resolving an accurate phylogeny for angiosperms.

The widespread adoption of improved high-yield rice varieties , which in a large scale replaced traditional and local rice varieties , has resulted in a great genetic erosion of the cultivated rice genepool. This process has narrowed genetic background of the cultivated rice. As a result , modern rice varieties become vulnerable and can not stand the attack of new disease and insect pests , and the unfavorable changes of environments. Meanwhile , the long2term use of chemical pesticides and herbicides significantly deteriorated agricultural ecosystem. In order to change this vicious cycle of the rice ecosystem , it is very important and necessary to explore and utilize the genetic biodiversity in the rice genepool to broaden the genetic background of the cultivated rice. The rice genepool encompasses varieties of Asia rice and African rice , weedy rice , wild species of rice in the genus Oryz a , and species in the related genera of the tribe Oryzeae. These are the essential germplasm resources for the further improvement of cultivated rices. However , due to the change of agricultural patterns , rapid development of social economy , industrialization and urbanization , biodiversity of the rice genepool , including wild species of rice , is under threat . Many populations of wild Oryz a species have been extinct from their original sites or are diminishing. Therefore , it is absolutely necessary and essential to strategically safeguard and conserve biodiversity of the rice genepool and to effectively utilize the elite rice germplasm resources in rice breeding programs. This is the only way to guarantee the long2term and sustainable production of rice varieties.

Endemism, the restriction of a taxon’s distribution to a specified geographical area, is central to the study of biogeography. Understanding endemism not only concerns a number of evolutionary and biogeographical issues, but also plays an important role in maintaining biodiversity and in the selection of priority areas for conservation. In recent years, various measures and analytical methods have been used to investigate patterns of endemism for various taxa from different regions. The emergence of these new measurements has benefited from the construction of phylogenetic trees and the implementation of data from spatial statistics. Some of these measures, such as phylogenetic diversity, phylogenetic endemism, and biogeographically weighted evolutionary distinctiveness deserve much more attention. Here, we review progress in the methodology used to measure the distribution patterns of endemism. These metrics have generally developed from a single time or space perspective to space-time united patterns. Specifically, the metrics include species richness, phylogenetic diversity and evolutionary distinctiveness, plus all there in combination as well as the weight of species range size. Moreover, we propose that studies on the distribution patterns of Chinese endemic taxa should pay attention to species diversity, phylogenetic diversity, species β-diversity, and phylogenetic β-diversity. In particular, model simulation analysis should be emphasized and implemented during investigations. These studies will provide fundamental knowledge for comprehensive recognition of scale-induced differences and for the detection of mechanisms underlying the distribution patterns of endemic taxa, and therefore provide theoretical support for biodiversity conservation.

This is a mini-review on the historical changes in the concept of species. Biologists use different methods or criteria to discriminate species, leading to the formation of different species concepts, e.g. biological species, morphospecies, ecological species, evolutionary species, phylogenetic/cladistic species, or their combinations. These concepts respectively reveal a specific profile of the species’ attributes, as well as reflecting the objective existence of these creatures as different species, but not being satisfied with everyone. For eukaryotes, reproductive isolation (incapable of reproducing fertile offspring) should be the key for two populations to differentiate into two different species, no matter how much they differ morphologically. The mechanisms underlying such isolation might be geographical, behavioral, or otherwise. Reproductive isolation is certainly accompanied by some morphological or genetic changes that are often used as criteria by taxonomists or molecular evolutionary biologists to distinguish species, although these attributes may not be associated with reproductive isolation itself. Extinct species known only from fossils are impossible to be classified taxonomically according to reproductive isolation. The exact definition of the term “species” is still controversial, as a species concept based on reproductive isolation is usually not applicable, but a usable species definition (e.g. morphospecies) is regarded to be artificial.