Towards resolving the complete fern tree of life

In the past two decades, molecular systematic studies have revolutionized our understanding of the evolutionary history of ferns. The availability of large molecular data sets together with efficient computer algorithms, now enables us to reconstruct evolutionary histories with previously unseen completeness. Here, the most comprehensive fern phylogeny to date, representing over one-fifth of the extant global fern diversity, is inferred based on four plastid genes. Parsimony and maximum-likelihood analyses provided a mostly congruent results and in general supported the prevailing view on the higher-level fern systematics. At a deep phylogenetic level, the position of horsetails depended on the optimality criteria chosen, with horsetails positioned as the sister group either of Marattiopsida-Polypodiopsida clade or of the Polypodiopsida. The analyses demonstrate the power of using a 'supermatrix' approach to resolve large-scale phylogenies and reveal questionable taxonomies. These results provide a valuable background for future research on fern systematics, ecology, biogeography and other evolutionary studies.     

Towards a taxonomic revision of the genus Echinococcus

Echinococcus remains a significant public health problem worldwide and, in several regions, the aetiological agents of cystic hydatid disease/echinococcosis are extending their range. The taxonomy of Echinococcus has been a controversial issue for decades, but the outcome of recent molecular epidemiological studies has served to reinforce proposals made ten years ago to revise the taxonomy of Echinococcus. A formal nomenclature is essential for effective communication, and provides the stability that underpins epidemiological investigations. It will also serve to recognize the contribution of early taxonomists.     

Towards building the tree of life: a simulation study for all angiosperm genera

Comprehensive phylogenetic trees are essential tools to better understand evolutionary processes. For many groups of organisms or projects aiming to build the Tree of Life, comprehensive phylogenetic analysis implies sampling hundreds to thousands of taxa. For the tree of all life this task rises to a highly conservative 13 million. Here, we assessed the performances of methods to reconstruct large trees using Monte Carlo simulations with parameters inferred from four large angiosperm DNA matrices, containing between 141 and 567 taxa. For each data set, parameters of the HKY85+G model were estimated and used to simulate 20 new matrices for sequence lengths from 100 to 10,000 base pairs. Maximum parsimony and neighbor joining were used to analyze each simulated matrix. In our simulations, accuracy was measured by counting the number of nodes in the model tree that were correctly inferred. The accuracy of the two methods increased very quickly with the addition of characters before reaching a plateau around 1000 nucleotides for any sizes of trees simulated. An increase in the number of taxa from 141 to 567 did not significantly decrease the accuracy of the methods used, despite the increase in the complexity of tree space. Moreover, the distribution of branch lengths rather than the rate of evolution was found to be the most important factor for accurately inferring these large trees. Finally, a tree containing 13,000 taxa was created to represent a hypothetical tree of all angiosperm genera and the efficiency of phylogenetic reconstructions was tested with simulated matrices containing an increasing number of nucleotides up to a maximum of 30,000. Even with such a large tree, our simulations suggested that simple heuristic searches were able to infer up to 80% of the nodes correctly.     

植物生命之树重建的现状、问题和对策建议

生命之树的概念源自1859年达尔文的《物种起源》, 但利用分子数据重建植物生命之树的研究则在20世纪90年代才开始兴起。近年来, 随着测序技术、分析方法和计算能力的快速发展, 植物生命之树重建研究取得了显著成果。本文首先概述了当前以及未来很长一段时间内植物生命之树重建工作的重点, 包括植物属级和种级水平的系统发育研究、植物系统发育基因组学研究、分子和形态数据联合分析、包括灭绝与现存植物类群的生命之树重建, 以及超大植物生命之树重建等5个方面; 然后简要概括国内植物生命之树重建研究的现状, 指出了我国在植物生命之树重建领域发展中所存在的问题, 并从“类群研究体系、学科评价体系、国家顶层设计, 以及拓展国际合作”等方面对学科未来的发展提出了一些对策建议。     

Using comparative genomics to uncover new kinds of protein‐based metabolic organelles in bacteria

Bacterial microcompartment (MCP) organelles are cytosolic, polyhedral structures consisting of a thin protein shell and a series of encapsulated, sequentially acting enzymes. To date, different microcompartments carrying out three distinct types of metabolic processes have been characterized experimentally in various bacteria. In the present work, we use comparative genomics to explore the existence of yet uncharacterized microcompartments encapsulating a broader set of metabolic pathways. A clustering approach was used to group together enzymes that show a strong tendency to be encoded in chromosomal proximity to each other while also being near genes for microcompartment shell proteins. The results uncover new types of putative microcompartments, including one that appears to encapsulate B₁₂‐independent, glycyl radical‐based degradation of 1,2‐propanediol, and another potentially involved in amino alcohol metabolism in mycobacteria. Preliminary experiments show that an unusual shell protein encoded within the glycyl radical‐based microcompartment binds an iron‐sulfur cluster, hinting at complex mechanisms in this uncharacterized system. In addition, an examination of the computed microcompartment clusters suggests the existence of specific functional variations within certain types of MCPs, including the alpha carboxysome and the glycyl radical‐based microcompartment. The findings lead to a deeper understanding of bacterial microcompartments and the pathways they sequester.     

Analysis of phenetic trees based on metabolic capabilites across the three domains of life

Here, we used data of complete genomes to study comparatively the metabolism of different species. We built phenetic trees based on the enzymatic functions present in different parts of metabolism. Seven broad metabolic classes, comprising a total of 69 metabolic pathways, were comparatively analyzed for 27 fully sequenced organisms of the domains Eukarya, Bacteria and Archaea. Phylogenetic profiles based on the presence/absence of enzymatic functions for each metabolic class were determined and distance matrices for all the organisms were then derived from the profiles. Unrooted phenetic trees based upon the matrices revealed the distribution of the organisms according to their metabolic capabilities, reflecting the ecological pressures and adaptations that those species underwent during their evolution. We found that organisms that are closely related in phylogenetic terms could be distantly related metabolically and that the opposite is also true. For example, obligate bacterial pathogens were usually grouped together in our metabolic trees, demonstrating that obligate pathogens share common metabolic features regardless of their diverse phylogenetic origins. The branching order of proteobacteria often did not match their classical phylogenetic classification and Gram-positive bacteria showed diverse metabolic affinities. Archaea were found to be metabolically as distant from free-living bacteria as from eukaryotes, and sometimes were placed close to the metabolically highly specialized group of obligate bacterial pathogens. Metabolic trees represent an integrative approach for the comparison of the evolution of the metabolism and its correlation with the evolution of the genome, helping to find new relationships in the tree of life.     

四种不同生活型树种细根寿命及影响因素

以4种不同生活型树种(常绿阔叶和针叶树种、落叶阔叶和针叶树种)为研究对象,通过微根管法现地观测细根的生长动态,比较不同生活型树种细根寿命在种内和种间的差异,探讨影响细根寿命的主要因子,研究结果对理解和预测森林生态系统碳及养分循环过程具有重要的理论意义。结果表明:(1)细根形态特征(分枝结构和直径)显著影响种内细根寿命,分枝等级越低、直径越小,细根的寿命越短;(2)4个树种的细根寿命表现出明显的土层效应和季节效应,即随土壤深度增加,细根的累积存活率逐渐增加,寿命延长;而不同季节出生的细根其寿命长短模式在树种间不一致,春季或夏季出生的细根寿命要长于秋冬季;(3)常绿树种(柳杉、石栎)的细根寿命要长于落叶树种(池杉、麻栎),同时,针叶树种(池杉、柳杉)的细根寿命要长于阔叶树种(麻栎、石栎)。在同一树种内,细根寿命受细根直径、根系分枝结构、土壤环境因子(土层)等因素显著影响,但在不同树种间,细根寿命可能更依赖于树木生长速率、碳分配模式等树木整体的功能性状差异。     

景观类型——面向当代风景园林学的一种分类法

当代风景园林项目中所蕴含的设计哲学和形式来源缺乏一种系统的分类与讨论。通过提出11种类型,构建一种当代分类法。这些类型包括：场所精神、反传统主义、奇观、赛博格、数字景观、不确定性、管理主义、行动主义、弹性、景观都市主义和宏大规划。分类不企图将风景园林师的所有工作归入明确类型,而是强调其可识别性特质,不仅对特定项目,对整个风景园林学科也具有重要作用。每一种类型既可作为潜在语言工具,为当代设计构建更广泛的讨论基础,又可作为明确主题,帮助设计师更自觉地探索设计的原创性。望以此激发对景观类型的讨论。     

Biodiversity in the New Zealand divaricating tree daisies: Olearia sect. nov. (Compositae)

The trees and shrubs in Olearia sect. Divaricaster, sect. nov., are found in North, South, and Stewart Islands of New Zealand. They are distinguished by their small, opposite leaves borne on brachyblasts (short shoots), long shoots which abort apically, solitary or fascicled capitula, flowers with purple style arms, and a very distinctive insect fauna. The ten species and three subspecies, including the new O. fimbriata, O. gardneri and O. virgata subsp. centralis are revised and a key and distribution maps provided. The section includes four threatened species: O. hectorii, O. polita and the two new species. Species density is mapped in grid cells 1° latitude by 1° longitude. Areas west of the geological Median Tectonic Zone (Nelson, Westland and Fiordland) show relatively low diversity. The highest diversity, six species in one grid cell, is recorded in north-west Otago, around Mt Aspiring and the Humboldt Mountains. This region is also geologically significant as several allochthonous terranes are juxtaposed there. In the central South Island O. laxiflora, O. fimbriata and O. odorata have concentric distributions around what were Tertiary basins and inland seas. Members of the section favour fertile, lowland sites on alluvium and have suffered reduction in population size over the last century due to agricultural development. Several species, such as O. hectorii, the 'swamp gum', occur in sites which are periodically flooded. Olearia solandri is a coastal species, often growing as a mangrove associate, but occasionally found inland. The anomalous inland populations are discussed and their location attributed to geological uplift.     

Latitude,tree species diversity and the metabolic theory of ecology

The latitudinal diversity gradient (LDG) has been known for over a century, but its origin remains poorly understood. Because both latitude and species richness are broadly related to temperature, environmental temperature has been proposed as a driver of the LDG. Recently, Wang et al. (2009, Proceedings of the National Academy of Sciences USA, 106 ,13388–13392) used datasets compiled from tree distributions in eastern Asia and North America to compare the species richness?temperature relationship between the two regions at several spatial scales and framed their analyses in the context of the metabolic theory of ecology. Here, we show that their datasets lack comparability between eastern Asia and North America and that some aspects of their analyses probably biased their results, casting doubt on some of their conclusions.     

Differential responses of antioxidant enzymes in pioneer and late-successional tropical tree species grown under sun and shade conditions

To investigate the ability of pioneer and late-successional species to adapt to a strong light environment in a reforestation area, we examined the activities of antioxidant enzymes in relation to photosystem II, chlorophyll a fluorescence and photosynthetic pigment concentration for eight tropical tree species grown under 100% (sun) and 10% (shade) sunlight irradiation. The pioneer (early-succession) species (PS) were Cecropia pachystachya, Croton urucurana, Croton floribundus and Schinus terebinthifolius. The non-pioneer (late succession) species (LS) were Hymenaea courbaril L. var. stilbocarpa, Esenbeckia leiocarpa, Cariniana legalis and Tabebuia roseo-alba. We observed a greater decline in the ratio of variable to maximum chlorophyll a fluorescence (F_v/F_m) under full sunlight irradiation in the late-successional species than in the pioneer species. The LS species most sensitive to high irradiance were C. legalis and H. courbaril. In LS species, chlorophyll a, chlorophyll b and total chlorophyll concentrations were higher in the shade-grown plants than in plants that developed under full sunlight, but in the PS species C. floribundus and C. pachystachya, we did not observe significant changes in chlorophyll content when grown in the two contrasting environments. The carotenoids/total chlorophyll ratio increased significantly when plants developed under high-sunlight irradiation, but this response was not observed in the PS species S.terebinthifolius and C. pachystachya. The improved performance of the pioneer species in high sunlight was accompanied by an increase in superoxide dismutase (SOD, EC 1.15.1.1) activity, though no light-dependent increase in the activity of ascorbate peroxidase (APX, EC 1.11.1.11) was observed. The activity of catalase (CAT, EC 1.11.1.6) was reduced by high irradiation in both pioneer and late-successional species. Our results show that pioneer species perform better under high-sunlight irradiation than late-successional species, as indicated by increased SOD activity and a higher F_v/F_m ratio. C. legalis was the LS species most susceptible to photoinhibition under full sunlight conditions. These results suggest that pioneer plants have more potential tolerance to photo-oxidative damage than late-successional species associated with the higher SOD activity found in pioneer species. Reduced photoinhibition in pioneer species probably results from their higher photosynthetic capacities, as has been observed in a previous survey carried out by our group.     

Towards inference of a biochemical ontology from a metabolic database

In order to predict the metabolic fate of an arbitrary compound based solely on structure, it is useful to be able to identify substructural 'functional groups' that are biochemically reactive. These functional groups are the substructural elements that can be removed and replaced to transform one compound into another. This problem of identifying functional groups is related to the problem of classifying compounds. The research presented here discusses the state of the art in biochemical databases and how these sources may be applied to the problem of classifying compounds based solely on structure. We describe a biochemical informatics system for processing molecular data and describe how 100 255 compositional (hasA) relationships are inferred between 835 abstractions and 9500 metabolites from the KEGG Ligand database. Specifically, we focus on the identification of amino acids and consider ways in which the inference of biochemical ontologies for metabolites will be improved in the future.     

中国新记录属——异型盘菌属（英文）

异型盘菌属Allophylaria首次在我国发现,包括1个新种和1个中国新记录种,均来自云南。新种小孢异型盘菌A.minispora的鉴别特征为子囊盘类白色,具柄;子囊顶孔在碘液中呈蓝色,32?45×3.8?5μm;子囊孢子梭形,无油滴,4.3?5.8×1.5?2.5μm;习居于草本植物茎上。原产于澳大利亚的果荚生异型盘菌A.atherospermatis首次在中国报道。提供了上述种的宏观和微观特征的详细描述及图示。     

Systematics of a widespread Southeast Asian frog,Rana chalconota (Amphibia: Anura: Ranidae)

The abundant Sundaland forest frog, Rana chalconota, has long been considered a single widespread species, although some authors have recommended its division into regional subspecies. The discovery of co‐occurring pairs of morphologically distinct populations in three widely separated parts of the range led to a morphological and molecular analysis of populations from all parts of the known range. The results suggest that R. chalconota consists of at least seven species from Thailand through Borneo and Java. Existing names are applied to three of these species, R. chalconota (Schlegel), R. raniceps (Peters) and R. labialis Boulenger. We describe four others as new species and suggest the existence of one or two additional, unnamed species. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 123–147.     

中国盾盘菌属分类研究(英文)

对我国盾盘菌属馆藏标本和近年来采集的材料进行分类学研究表明,中国已知该属31种。描述了3个新种,命名为柯氏盾盘菌、长孢盾盘菌和假小孢盾盘菌,对新种与其相近种的区别进行了讨论;根据前人的形态描述,对S. erinaceus,S.olivascens和S. lusatiae在中国的分布提出了质疑;根据对相关馆藏标本的观察,指出S. barlae、S. superba和S. vitreola在我国的报道系基于错误鉴定,它们应从中国物种名录中排除。文中提供了该属中国已知种的分种检索表。     

Global analysis reveals that cryptic diversity is linked with habitat but not mode of life

The ubiquity of genetically distinct, cryptic species is limiting any attempt to estimate local or global biodiversity as well as impeding efforts to conserve species or control pests and diseases. Environmental factors or biological traits promoting rapid diversification into morphologically similar species remain unclear. Here, using a meta‐analysis of 1230 studies using DNA sequences to search for cryptic diversity in metazoan taxa, we test two hypotheses regarding the frequency of cryptic taxa based on mode of life and habitat. First, after correcting for study effort and accounting for higher taxonomic affinities and biogeographical region of origins, our results do not support the hypothesis that cryptic taxa are more frequent among parasitic than free‐living taxa. Second, in contrast, the results support the hypothesis that cryptic taxa are more common in certain habitats than others: for a given study effort, more cryptic taxa are found in freshwater than in terrestrial or marine taxa. These findings suggest that the greater heterogeneity and fragmentation of freshwater habitats may promote higher rates of genetic differentiation among its inhabitants, a general pattern with serious implications for freshwater conservation biology.