生命条形码与生命之树

生命条形码和生命之树的研究与应用在近十年内备受关注,成为生命科学研究领域的两个热点。本文综述了生命条形码和生命之树的概念来源、研究现状、面临问题与解决方案,并对其发展前景进行了展望。生命之树概念的形成有着悠久的历史渊源,DNA条形码的提出和实施则只有十年的历史,两者均得益于测序技术和生物信息技术的蓬勃发展;但两者的目的不同,生命条形码技术旨在实现对物种的快速鉴定,而生命之树研究的主要目的则是重建生命世界的起源和进化历史以及各生物类群之间的亲缘关系,因此应根据两者不同的目标任务而采取相应的发展思路和顶层设计。本文针对目前生命条形码和生命之树研究领域遇到的瓶颈和问题进行了阐述,并提出了相应的解决方案。最后,作者建议我国学者抓住机遇．与多个领域的学者和工程技术人员广泛合作,推动DNA条形码鉴定技术和生命之树理论研究的快速发展。     

Conditions in Home and Transplant Soils Have Differential Effects on the Performance of Diploid and Allotetraploid Anthericum Species

Due to increased levels of heterozygosity, polyploids are expected to have a greater ability to adapt to different environments than their diploid ancestors. While this theoretical pattern has been suggested repeatedly, studies comparing adaptability to changing conditions in diploids and polyploids are rare. The aim of the study was to determine the importance of environmental conditions of origin as well as target conditions on performance of two Anthericum species, allotetraploid A. liliago and diploid A. ramosum and to explore whether the two species differ in the ability to adapt to these environmental conditions. Specifically, we performed a common garden experiment using soil from 6 localities within the species’ natural range, and we simulated the forest and open environments in which they might occur. We compared the performance of diploid A. ramosum and allotetraploid A. liliago originating from different locations in the different soils. The performance of the two species was not affected by simulated shading but differed strongly between the different target soils. Growth of the tetraploids was not affected by the origin of the plants. In contrast, diploids from the most nutrient poor soil performed best in the richest soil, indicating that diploids from deprived environments have an increased ability to acquire nutrients when available. They are thus able to profit from transfer to novel nutrient rich environments. Therefore, the results of the study did not support the general expectation that the polyploids should have a greater ability than the diploids to adapt to a wide range of conditions. In contrast, the results are in line with the observation that diploids occupy a wider range of environments than the allotetraploids in our system.     

Life history variation among female surfperches (Perciformes: Embiotocidae)

Synopsis Life history variation within the family Embiotocidae is extensive and involves differences in age of first reproduction, fecundity schedules, growth rates, longevity and size of young. Based on maximum reported body lengths, there are three distinct size groups among the family's 23 species. Small species do not exceed 215 mm TL, medium-size species attain 275 to 335 mm TL, and the large species attain 380 to 470 mm TL. The longevity oh surfperches varies from two to ten years, growth is indeterminate, and females of the medium-and large-size groups may delay first reproduction beyond age one. With one exception, all species show increasing length-specific fecundities. The life history characteristics of females differ among the three size groups. Relative to smaller species, the largest species have moderately high fecundity, delayed maturity and long life. Medium-size species have low fecundity, may delay maturity for 1 to 3 years and have intermediate life spans. Small species have generally higher, but variable, fecundity, do not delay maturity, and are short lived. Among the small North American species, the trend in fecundity varies inversely with environmental predictability. Fecundity is highest in the species which occupies highly seasonal freshwater environments. Coastal species produce moderately large broods and species which occupy stable deep water environments produce the smallest broods.     

Factors driving adaptive radiation in plants of oceanic islands: a case study from the Juan Fernández Archipelago

Adaptive radiation is a common evolutionary phenomenon in oceanic islands. From one successful immigrant population, dispersal into different island environments and directional selection can rapidly yield a series of morphologically distinct species, each adapted to its own particular environment. Not all island immigrants, however, follow this evolutionary pathway. Others successfully arrive and establish viable populations, but they remain in the same ecological zone and only slowly diverge over millions of years. This transformational speciation, or anagenesis, is also common in oceanic archipelagos. The critical question is why do some groups radiate adaptively and others not? The Juan Fernández Islands contain 105 endemic taxa of angiosperms, 49% of which have originated by adaptive radiation (cladogenesis) and 51% by anagenesis, hence providing an opportunity to examine characteristics of taxa that have undergone both types of speciation in the same general island environment. Life form, dispersal mode, and total number of species in progenitors (genera) of endemic angiosperms in the archipelago were investigated from literature sources and compared with modes of speciation (cladogenesis vs. anagenesis). It is suggested that immigrants tending to undergo adaptive radiation are herbaceous perennial herbs, with leaky self-incompatible breeding systems, good intra-island dispersal capabilities, and flexible structural and physiological systems. Perhaps more importantly, the progenitors of adaptively radiated groups in islands are those that have already been successful in adaptations to different environments in source areas, and which have also undergone eco-geographic speciation. Evolutionary success via adaptive radiation in oceanic islands, therefore, is less a novel feature of island lineages but rather a continuation of tendency for successful adaptive speciation in lineages of continental source regions.     

Biological affinity, phenotypic variation and palaeoecology of Tetradium Dana, 1846

Comparisons of morphologies and modes of life of the Ordovician fossil Tetradium Dana, 1846, with chaetetid sponges, tabulate corals, and Recent rhodophytes show that several defining Tetradium characteristics are incompatible with its chaetetid and tabulate classifications. All Tetradium characteristics fit a rhodophyte identification, however, as a calcified uniaxial corticated florideophyte. It is argued from functional morphology that the fundamental subsquare cross-section of the Tetradium tube is an adaptation for close packing, which implies that the basic growth form is compact and should have developed where conditions were optimal. More open forms are derived from it and probably occupied less-favourable environments.
Palaeoecological studies from the Ottawa Valley, Canada, show that the Tetradium growth form is correlated with environmental stress and became more open as salinity increased: i.e. the compact T. fibratum form lived in normal marine conditions, radiating bundles of T. cellulosum tubes in low to middle hypersalinity and single T. syringoporoides tubes in high hypersalinity. Different Tetradium growth forms from the study area are phenotypic variants of a single species, rather than different species and genera. Therefore, classifications that divide Tetradium into different species and genera based only on growth form have no biological basis. There is little evidence of interspecific interactions with Tetradium .     

Halotolerant and halophilic fungi

Extreme environments have for long been considered to be populated almost exclusively by prokaryotic organisms and therefore monopolized by bacteriologists. Solar salterns are natural hypersaline environments characterized by extreme concentrations of NaCl, often high concentrations of other ions, high uv irradiation and in some cases extremes in pH. In 2000 fungi were first reported to be active inhabitants of solar salterns. Since then many new species and species previously known only as food contaminants have been discovered in hypersaline environments around the globe. The eukaryotic microorganism most studied for its salt tolerance is Saccharomyces cerevisiae. However, S. cerevisiae is rather salt sensitive and not able to adapt to hypersaline conditions. In contrast, some species like Debaryomyces hansenii, Hortaea werneckii, and Wallemia ichthyophaga have been isolated globally from natural hypersaline environments. We believe that all three are more suitable model organisms to study halotolerance in eukaryotes than S. cerevisiae. Furthermore, they belong to different and distant taxonomic groups and have developed different strategies to cope with the same problems of ion toxicity and loss of water.     

A taxonomic revision of the North American species of Stigmella (Lepidoptera: Nepticulidae)

Abstract. A revision of the fifty-one species of the genus Stigmella from North America is presented. Thirty-one species are recorded only from the U.S.A., seventeen species and one subspecies from the U.S.A. and Canada and three species and one subspecies are known only from Canada. Five species are new: Stigmella inconspicuella (U.S.A., California); S.heteromelis (California); S.sclerostylota (Arkansas); S.longisacca (California) and S.plumosetaeella (Arizona). Life histories, mine characteristics and larval habits are given where known. These are collated from field study, material examined, breeding records and the literature. A list of host plants is also provided.
A neotype is designated for Nepticula prunifoliella Clemens, previously considered to be possibly dipterous.
Although most Stigmella species have different genital morphology, some pairs of species do not. In these pairs, however, external features and characteristics of the mine often differ – some pairs also differ in distribution or season. The taxonomic implications are discussed in the individual treatments – not all the problems, however, can be resolved without further rearing studies and collection. Species-groups have been designated on the basis of morphology. Some species are, however, structurally intermediate between species-groups and others may resemble Ectoedemia Busck in aspects of the male genitalia while their female genitalia, external features and venation are typical of Stigmella.     

Identification of Bacterial Strains Isolated from the Mediterranean Sea Exhibiting Different Abilities of Biofilm Formation

The Mediterranean Sea has rarely been investigated for the characterization of marine bacteria as compared to other marine environments such as the Atlantic or Pacific Ocean. Bacteria recovered from inert surfaces are poorly studied in these environments, when it has been shown that the community structure of attached bacteria can be dissimilar from that of planktonic bacteria present in the water column. The objectives of this study were to identify and characterize marine bacteria isolated from biofilms developed on inert surfaces immersed in the Mediterranean Sea and to evaluate their capacity to form a biofilm in vitro. Here, 13 marine bacterial strains have been isolated from different supports immersed in seawater in the Bay of Toulon (France). Phylogenetic analysis and different biological and physico-chemical properties have been investigated. Among the 13 strains recovered, 8 different genera and 12 different species were identified including 2 isolates of a novel bacterial species that we named Persicivirga mediterranea and whose genus had never been isolated from the Mediterranean Sea. Shewanella sp. and Pseudoalteromonas sp. were the most preponderant genera recovered in our conditions. The phenotypical characterization revealed that one isolate belonging to the Polaribacter genus differed from all the other ones by its hydrophobic properties and poor ability to form biofilms in vitro. Identifying and characterizing species isolated from seawater including from Mediterranean ecosystems could be helpful for example, to understand some aspects of bacterial biodiversity and to further study the mechanisms of biofilm (and biofouling) development in conditions approaching those of the marine environment.     

Spider diversity responds strongly to edge effects but weakly to vegetation structure in riparian forests of Southern Brazil

Riparian forests bordering open terrestrial environments may have three microhabitats differing in structure and conditions: a grassland/pasture-forest edge (GE), a forest interior (FI) and a river–forest edge. The influence of such edge effects and vegetation characteristics on spider diversity of riparian forests was evaluated in Southern Brazil. Four different rivers were sampled on the tree–shrub strata with a beating tray, twice per season for 2 years. There were six transects per river, two per microhabitat. We compared spider abundance, species richness and composition. Vegetation variables sampled were vertical structure and (horizontal) density, canopy height and cover. Overall 42,057 spiders were sampled, 28 spider families and 440 species. The FI had higher spider abundance than the edges. Average species richness differed among rivers. Microhabitats did not differ in average richness, although overall richness (from sample-based rarefaction) was higher for GE than FI. High abundances in FI may result from lowered stress due to abiotic conditions, while higher GE richness may result from a faunal superposition between forest species and those from the grassland/pasture. Only canopy cover returns a positive relationship with spider diversity (richness and adult abundance). This might result from more spider species preferring to build webs or hunt under low-light environments. Rivers had spider faunas differing in composition but among microhabitats species composition was the same. Vegetation structure has been hypothesized to affect spiders, but this impact might be best seen in specific subgroups or guilds within spiders, not in the whole assemblage.     

DISTURBANCE,LIFE HISTORY STRATEGIES,AND SEED FATES IN ALPINE HERBFIELD COMMUNITIES

Species responses to disturbance are governed primarily by their life history and physiological traits and by the characteristics of the disturbance. Species reproductive traits are especially important in determining the potential of species to establish and to persist following disturbance. Herein, I review available literature on relationships among disturbance, species life histories, and seed fates in tundra environments. Research conducted on these relationships in alpine herbfield vegetation on the Beartooth Plateau, Montana, over the past 9 yr by my colleagues and myself is synthesized. In tundra environments, species reproductive capacities are often similar to those in more temperate environments, but short, cool growing seasons constrain seed production and reduce seedling growth and survival. Highly variable growing season conditions result in large differences in seed production and seedling establishment among years. On disturbed sites, disturbance characteristics determine the seed and seedling environment and influence rates of establishment. In these windy environments, relationships among soil surface characteristics and seed morphological attributes determine both the horizontal and vertical movement of seeds on exposed soils. Once seeds are incorporated into the soil, soil physical and chemical properties determine temperature and nutrient regimes and have the greatest effects on seed germination and seedling growth and survival. Examining the seed fates of herbfield species with varying life histories illustrates that the identities of species that establish following disturbance are largely predictable from their reproductive traits. Disturbance characteristics determine the success of different reproductive strategies and significantly influence community structure.     

Local and Landscape Factors Driving the Structure of Tropical Anuran Communities: Do Ephemeral Ponds have a Nested Pattern?

The sets of species in animal and plant communities often comprise nested subsets of the species in broader communities. Although most mechanisms causing nested patterns are known and have been demonstrated for different environments and taxa, how amphibian communities are structured in ephemeral ponds in tropical disturbed landscapes remains unknown. We investigated if pond size, duration, presence of trees (local factors), and the proportion of forest cover surrounding ponds (landscape factor) affect anuran species richness and composition, and if pond assemblages showed a nested pattern. We sampled 11 ephemeral ponds in a pasture matrix near a large Atlantic Forest remnant in Brazil and measured local and landscape variables inside two buffer zones around each pond (100 and 500 m). We marked 1514 individuals from 23 anuran species, and found that richness in ponds ranged from 3–14 species. Both local and landscape factors explained frog species richness in the sampled ponds, and seemed to affect community composition. Frog communities occurred in a non‐nested pattern, contrary to our expectations: species found in poor subsets were not found in larger, more complex ponds. Local and landscape characteristics create a variety of environments in ephemeral ponds, even in impoverished ones; these characteristics restrict pond occupancy for some species, and result in a non‐nested pattern.     

Evolutionary and organismic constraints on the relationship between spacer length and environmental conditions in clonal plants

The rate of lateral spread of clonal plants is considered a plastic trait that responds directly to environmental conditions. However, this response is likely constrained by evolutionary history and other species attributes. Here we ask how the relationships between lateral spread and the distribution of herbaceous plant species in different environments are influenced by the type of spacer (epigeogenous versus hypogeogenous rhizome), its persistence (integrator versus splitter), and the height and phylogeny of the plant. Analysis of spacer length of 367 species from temperate to arctic Europe revealed that other plant characteristics modulate the relationship between spacer length and environmental conditions. While plants with epigeogenous rhizomes, which have usually shorter spacers than hypogeogenous rhizomes, were associated with illuminated habitats, plants with hypogeogenous rhizomes were associated with warm habitats. These relationships were also shown within the specific rhizome type, as within the group of species with epigeogenous rhizomes, those having short spacers were associated with more light. The trend toward long spacers in warm environment was detected within both epigeogenous and hypogeogenous rhizome bearing species. Splitters were found to be associated with wet, nutrient rich habitats irrespective of rhizome type. When plant height was accounted for by using the ratio of spacer length to plant height (L:H) instead of absolute spacer length, no relationship with environmental variables was found until phylogenetic relationships among the species were taken into account. This implies that overall variability in L:H ratio in the dataset masked trends common for different taxonomic groups. Future comparative studies relating particular clonal growth forms or individual traits to environmental conditions should consider the constraints arising from other growth characteristics and evolutionary history of the subject species.     

Symbiont-induced speciation

Speciation induced by parasitic or mutualistic symbionts has been suggested for taxa ranging from plants to insects to monkeys. Previous models for symbiont-induced speciation have been based upon hybrid inferiority and selection for reinforcement genes. Taken on their own, however, such models have severe theoretical limitations and little empirical support. Two conditions that may favour symbiont-induced speciation are presented here: (1) interaction norms in which the outcomes of host/symbiont interactions differ between environments and (2) differential coadaptation of host and symbiont populations between environments or along an environmental gradient. Symbiont-induced speciation can be considered as one form of 'mixed-process coevolution': reciprocal evolution in which adaptation of a population of one species to a population of a second species (or coadaptation of the populations) causes the population of the second species to become reproductively isolated from other populations.     

Specific leaf mass, fresh: dry weight ratio, sugar and protein contents in species of Lamiaceae from different light environments

Samples from eleven species of Lamiaceae were collected from different light environments in Venezuela for laboratory analysis. The studied species were: Plectranthus scutellarioides (Ps), Scutellaria purpurascens (Sp), Hyptis pectinata (Hp)), H. sinuata (Hs). Leonorus japonicus (Lj), Plecthranthus amboinicus (Pa) Ocimum hasilicum (Ocb), O. campechianum (Occ) Origanum majorana (Orm), Rosmarinus officinali, (Ro) and Salvia officinalis (So). Protein and soluble sugar contents per unit of area were measured, Specific Leaf Mass (SLM) and fresh:dry weight (FW/DW) ratios were calculated. The higher values for soluble sugars contents were present in sun species: Lj, Pa, Ocb, Occ, Orm, Ro and So; the lower values were obtained in low light species: Ps, Sp, Hp, Hs. The values of protein content do not show any clear trend or difference between sun and shade environments. The lowest values for the fresh weight: dry weight ratio are observed in sun species with the exception of Lj and Pa, while the highest value is observed in Pa, a succulent plant. The higher values of specific leaf mass (SLM) (Kg DMm(-2)) are observed in sun plants. The two way ANOVA revealed that there were significant differences among species and between sun and low light environments for sugar content and FW:DW ratio. while SLM was significant for environments but no significant for species, and not significant for protein for both species and environments. The soluble sugar content, FW:DW ratio and SLM values obtained in this work, show a clear separation between sun and shade plants. The sugar content and FW:DW ratio are distinctive within the species, and the light environment affected sugar content. FW:DW ratio and SLM. These species may he shade-tolerant and able to survive in sunny environments. Perhaps these species originated in shaded environments and have been adapting to sunny habitats.     

新疆北部森林生态系统地衣植物生活型分析

Life forms of lichen of forest ecosystem in Northern Xinjiang were researched in the Kanas National Natural Reservation Area.They have been grouped into 6 types:Epipetria,Soil-epipetria,Epiphytia arboricosa,Epiphytia moss,Epiphytis grass and Dry-radicantia,in which the species of Epiphytia arboricosa account for 36.89% of the total species in this area,the species of Epipetria for 22.33% and Epiphytia grass the least.The results show that life forms of lichem at the srea in Northem Xinjiang are relatively rich,which indicates the biodiversity characteristics of lichen.     

Land‐use legacies in a central Appalachian forest: differential response of trees and herbs to historic agricultural practices

Question: Are contemporary herb and tree patterns explained by historic land use practices? If so, are observed vegetation patterns associated with life‐history characteristics, soil properties, or other environmental variables? Location: Southeastern Ohio, USA. Methods: Using archival records, currently forested sites were identified with distinct land use histories: cultivated, pasture (but not plowed), and reference sites which appear to have never been cleared. Trees were recorded by size and species on twenty 20 m × 20 m plots; percent cover was estimated for each herb species in nested 10 m × 10 m plots. Environmental characteristics were noted, and soil samples analysed for nutrient availability and organic matter. Nonmetric multidimensional scaling ordination was performed separately on both tree and herb datasets to graphically characterize community composition among plots. Life‐history traits were investigated to explain observed compositional differences. Results: Vegetation patterns were explained by current environmental gradients, especially by land‐use history. Cultivated and pasture sites had similar tree composition, distinct from reference sites. Herb composition of pasture and reference sites was similar and distinct from cultivated sites, suggesting the ‘tenacity’ of some forest herbs on formerly cleared sites. Tilling removes rhizomatous species, and disfavors species with unassisted dispersal. These life‐history traits were underrepresented on cultivated sites, although ant‐dispersed species were not. Conclusions: Historic land‐use practices accounted for as much variation in species composition as environmental gradients. Furthermore, trees and herbs responded differently to past land‐use practices. Life‐history traits of individual species interact with the nature of disturbance to influence community composition.     

Spatial segregation of plant species caused by Retama sphaerocarpa influence in a Mediterranean pasture: a perspective from the soil seed bank

Retama sphaerocarpa is a leguminous shrub whose important role in the semi-arid regions of south-eastern Spain has already been assessed: shrub canopies reduce light intensity, and thus evapotranspiration; also their extensive radical system take water and nutrients from great volumes of soil, concentrating them in the understorey. Consequently, subcanopy vegetation benefits from these facilitation processes, increasing its productivity. However, these shrublands have been rarely studied at a broader scale, i.e. as a savannah-like system composed of a variable number of shrubs scattered in a herbaceous matrix. As the microenvironmental conditions associated to the understorey are rather different from those of the open spaces among shrubs, species composition of the herbaceous matrix is expected to change accordingly. Thus, R. sphaerocarpa would be an important and still unknown source of spatial heterogeneity to the system. Our main purpose was to evaluate, through the soil seed bank, the heterogeneity in the herbaceous community induced by this shrub species. Soil samples were collected around adult shrubs from three positions relative to the canopy: near the centre of the shrubs, at the edge of the understorey, and completely outside the canopy. Floristic composition was evaluated by germination under greenhouse conditions. The results show that each position has a different floristic composition, characterised by a group of different species. The herbaceous species associated with the external position have functional traits which enable them to resist water stress and herbivore pressure, such as hairs, CAM metabolism, early flowering, horizontal growth or tiny stature. The species associated with the central position lack those traits, and are more competitive in more mesic environments, rich in nitrogen. The lowest number of seedlings and species was found in the internal position, suggesting that in our study the facilitation process may have less importance for community dynamics due to less stressful environmental conditions.     

Digest: Insights into diatoms diversity patterns*

Biological diversity is not equally distributed across the Tree of Life, and the causes are not yet well defined. Nakov et al. investigate this by exploring the reasons behind diatoms’ uneven species richness across different environments. Simple traits are not enough to fully understand the variation in diatoms’ species richness. Therefore, investigating the role of habitat may improve our understanding of biodiversity patterns.     

Spiniferites cruciformis: a fresh water dinoflagellate cyst?

Palynological studies of cored lacustrine sediments from the late Quaternary of Lake Kastoria, northern Greece, revealed a Late Glacial interval with abundant dinoflagellate cysts. Cyst assemblages include two identifiable species, Spiniferites cruciformis and Gonyaulax apiculata. The presence of the fresh water species G. apiculata is consistent with the lacustrine setting of these deposits, but that of S. cruciformis is anomalous. Previously, this species has only been recorded in abundance from presumed brackish marine sediments from the Black Sea and Marmara Sea sediments where geochemical data clearly record brackish salinities. Therefore, it has been regarded as a low salinity cyst type with a wide range of morphological variation that some workers have suggested to reflect salinity fluctuations. Specimens from Greece display only part of the range of morphological variability previously described from these (brackish) marine settings. Encountered morphological variation includes ellipsoidal/pentameral and cruciform endocyst shapes with rare intermediate shapes, and highly variable septa development. Specimens characterized by extremely reduced ornamentation known from (brackish) marine environments have not been recorded. Our records of S. cruciformis indicate that: (1) it could thrive in fresh water conditions; and (2) that apparently most of the strong morphological variations of the cysts are an intrinsic phenomenon for this taxon, and may only partly be linked to salinity variations as suggested earlier. We suggest that S. cruciformis essentially is a fresh water taxon, and that its records in (brackish) marine environments, with the exception of specimens with strongly reduced ornamentation, may be due to transportation, to short-lived fresh water surface conditions in such environments, or to tolerance of the species to brackish conditions.     

Life under multiple extreme conditions: diversity and physiology of the halophilic alkalithermophiles

Around the world, there are numerous alkaline, hypersaline environments that are heated either geothermally or through intense solar radiation. It was once thought that such harsh environments were inhospitable and incapable of supporting a variety of life. However, numerous culture-dependent and -independent studies revealed the presence of an extensive diversity of aerobic and anaerobic bacteria and archaea that survive and grow under these multiple harsh conditions. This diversity includes the halophilic alkalithermophiles, a novel group of polyextremophiles that require for growth and proliferation the multiple extremes of high salinity, alkaline pH, and elevated temperature. Life under these conditions undoubtedly involves the development of unique physiological characteristics, phenotypic properties, and adaptive mechanisms that enable control of membrane permeability, control of intracellular osmotic balance, and stability of the cell wall, intracellular proteins, and other cellular constituents. This minireview highlights the ecology and growth characteristics of the extremely halophilic alkalithermophiles that have been isolated thus far. Biochemical, metabolic, and physiological properties of the extremely halophilic alkalithermophiles are described, and their roles in resistance to the combined stressors of high salinity, alkaline pH, and high temperature are discussed. The isolation of halophilic alkalithermophiles broadens the physicochemical boundaries for life and extends the boundaries for the combinations of the maximum salinity, pH, and temperature that can support microbial growth.