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.
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.
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.
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.
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.
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.
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.
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.
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.
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 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.
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.
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.
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.
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.
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.
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.
Sponsors
Biodiversity Committee, CAS
Botanical Society of China
Institute of Botany, CAS
Institute of Zoology, CAS
Institute of Microbiology, CAS
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