真菌生命之树项目（Assembling the Fungal Tree of Life）和美国真菌系统学研究现状

<正>美国的现代真菌系统学研究始于上世纪九十年代初期,以一系列分子系统学文章的发表为标志,其中代表性的工作有Vilgalys&Gonzalez(1990),White et al.(1990),Bruns et al.(1992),     

The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome

A recurrent topic in phylogenomics is the combination of various sequence alignments to reconstruct a tree that describes the evolutionary relationships within a group of species. However, such approach has been criticized for not being able to properly represent the topological diversity found among gene trees. To evaluate the representativeness of species trees based on concatenated alignments, we reconstruct several fungal species trees and compare them with the complete collection of phylogenies of genes encoded in the Saccharomyces cerevisiae genome. We found that, despite high levels of among-gene topological variation, the species trees do represent widely supported phylogenetic relationships. Most topological discrepancies between gene and species trees are concentrated in certain conflicting nodes. We propose to map such information on the species tree so that it accounts for the levels of congruence across the genome. We identified the lack of sufficient accuracy of current alignment and phylogenetic methods as an important source for the topological diversity encountered among gene trees. Finally, we discuss the implications of the high levels of topological variation for phylogeny-based orthology prediction strategies.     

Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

We have used three independent phylogenomic approaches (concatenated alignments, single-, and multi-gene supertrees) to reconstruct the fungal tree of life (FTOL) using publicly available fungal genomes. This is the first time multi-gene families have been used in fungal supertree reconstruction and permits us to use up to 66% of the 1,001,217 genes in our fungal database. Our analyses show that different phylogenomic datasets derived from varying clustering criteria and alignment orientation do not have a major effect on phylogenomic supertree reconstruction. Overall the resultant phylogenomic trees are relatively congruent with one another and successfully recover the major fungal phyla, subphyla and classes. We find that where incongruences do occur, the inferences are usually poorly supported. Within the Ascomycota phylum, our phylogenies reconstruct monophyletic Saccharomycotina and Pezizomycotina subphyla clades and infer a sister group relationship between these to the exclusion of the Taphrinomycotina. Within the Pezizomycotina subphylum, all three phylogenies infer a sister group relationship between the Leotiomycetes and Sordariomycetes classes. However, there is conflict regarding the relationships with the Dothideomycetes and Eurotiomycetes classes. Within the Basidiomycota phylum, supertrees derived from single- and multi-gene families infer a sister group relationship between the Pucciniomycotina and Agaricomycotina subphyla while the concatenated phylogeny infers a poorly supported relationship between the Agaricomycotina and Ustilagomycotina. The reconstruction of a robust FTOL is important for future fungal comparative analyses. We illustrate this point by performing a preliminary investigation into the phyletic distribution of yeast prion-like proteins in the fungal kingdom.     

BBID: the biological biochemical image database

The Biological Biochemical Image Database is a WWW accessible relational database of archived images from research articles that describe regulatory pathways of higher eukaryotes. Pathway information is annotated and can be queried in the study of complex gene expression. In this way, complex regulatory pathways can be tested empirically in an efficient manner in the context of large-scale gene-expression systems.     

SNPdbe: constructing an nsSNP functional impacts database

Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution;SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introduce SNPdbe-SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. Database entries represent nsSNPs in dbSNP and 1000 Genomes collection, as well as variants from UniProt and PMD. SAASs come from >2600 organisms; 'human' being the most prevalent. The impact of each SAAS on protein function is predicted using the SNAP and SIFT algorithms and augmented with experimentally derived function/structure information and disease associations from PMD, OMIM and UniProt. SNPdbe is consistently updated and easily augmented with new sources of information. The database is available as an MySQL dump and via a web front end that allows searches with any combination of organism names, sequences and mutation IDs. AVAILABILITY: http://www.rostlab.org/services/snpdbe.     

Mapping the Tree of Life: Progress and Prospects

Summary: The intent of this article is to provide a critical assessment of our current understanding of life''s phylogenetic diversity. Phylogenetic comparison of gene sequences is a natural way to identify microorganisms and can also be used to infer the course of evolution. Three decades of molecular phylogenetic studies with various molecular markers have provided the outlines of a universal tree of life (ToL), the three-domain pattern of archaea, bacteria, and eucarya. The sequence-based perspective on microbial identification additionally opened the way to the identification of environmental microbes without the requirement for culture, particularly through analysis of rRNA gene sequences. Environmental rRNA sequences, which now far outnumber those from cultivars, expand our knowledge of the extent of microbial diversity and contribute increasingly heavily to the emerging ToL. Although the three-domain structure of the ToL is established, the deep phylogenetic structure of each of the domains remains murky and sometimes controversial. Obstacles to accurate inference of deep phylogenetic relationships are both systematic, in molecular phylogenetic calculations, and practical, due to a paucity of sequence representation for many groups of organisms.     

Depicting the Tree of Life: the Philosophical and Historical Roots of Evolutionary Tree Diagrams

It is a popularly held view that Darwin was the first author to draw a phylogenetic tree diagram. However, as is the case with most popular beliefs, this one also does not hold true. Firstly, Darwin never called his diagram of common descent a tree. Secondly, even before Darwin, tree diagrams were used by a variety of philosophical, religious, and secular scholars to depict phenomena such as “logical relationships,” “affiliations,” “genealogical descent,” “affinity,” and “historical relatedness” between the elements portrayed on the tree. Moreover, historically, tree diagrams themselves can be grouped into a larger class of diagrams that were drawn to depict natural and/or divine order in the world. In this paper, we trace the historical roots and cultural meanings of these tree diagrams. It will be demonstrated that tree diagrams as we know them are the outgrowth of ancient philosophical attempts to find the “true order” of the world, and to map the world “as it is” (ontologically), according to its true essence. This philosophical idea would begin a fascinating journey throughout Western European history. It lies at the foundation of the famous “scala naturae,” as well as religious and secular genealogical thinking, especially in regard to divine, familial (kinship), and linguistic pedigrees that were often depicted by tree images. These scala naturae would fuse with genealogical, pedigree thinking, and the trees that were the result of this blend would, from the nineteenth century onward, also include the element of time. The recognition of time would eventually lead to the recognition of evolution as a fact of nature, and subsequently, tree iconographies would come to represent exclusively the evolutionary descent of species.     

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。     

AraCyc: a biochemical pathway database for Arabidopsis

AraCyc is a database containing biochemical pathways of Arabidopsis, developed at The Arabidopsis Information Resource (http://www.arabidopsis.org). The aim of AraCyc is to represent Arabidopsis metabolism as completely as possible with a user-friendly Web-based interface. It presently features more than 170 pathways that include information on compounds, intermediates, cofactors, reactions, genes, proteins, and protein subcellular locations. The database uses Pathway Tools software, which allows the users to visualize a bird's eye view of all pathways in the database down to the individual chemical structures of the compounds. The database was built using Pathway Tools' Pathologic module with MetaCyc, a collection of pathways from more than 150 species, as a reference database. This initial build was manually refined and annotated. More than 20 plant-specific pathways, including carotenoid, brassinosteroid, and gibberellin biosyntheses have been added from the literature. A list of more than 40 plant pathways will be added in the coming months. The quality of the initial, automatic build of the database was compared with the manually improved version, and with EcoCyc, an Escherichia coli database using the same software system that has been manually annotated for many years. In addition, a Perl interface, PerlCyc, was developed that allows programmers to access Pathway Tools databases from the popular Perl language. AraCyc is available at the tools section of The Arabidopsis Information Resource Web site (http://www.arabidopsis.org/tools/aracyc).     

Rooting the Animal Tree of Life

Identifying our most distant animal relatives has emerged as one of the most challenging problems in phylogenetics. This debate has major implications for our understanding of the origin of multicellular animals and of the earliest events in animal evolution, including the origin of the nervous system. Some analyses identify sponges as our most distant animal relatives (Porifera-sister hypothesis), and others identify comb jellies (Ctenophora-sister hypothesis). These analyses vary in many respects, making it difficult to interpret previous tests of these hypotheses. To gain insight into why different studies yield different results, an important next step in the ongoing debate, we systematically test these hypotheses by synthesizing 15 previous phylogenomic studies and performing new standardized analyses under consistent conditions with additional models. We find that Ctenophora-sister is recovered across the full range of examined conditions, and Porifera-sister is recovered in some analyses under narrow conditions when most outgroups are excluded and site-heterogeneous CAT models are used. We additionally find that the number of categories in site-heterogeneous models is sufficient to explain the Porifera-sister results. Furthermore, our cross-validation analyses show CAT models that recover Porifera-sister have hundreds of additional categories and fail to fit significantly better than site-heterogenuous models with far fewer categories. Systematic and standardized testing of diverse phylogenetic models suggests that we should be skeptical of Porifera-sister results both because they are recovered under such narrow conditions and because the models in these conditions fit the data no better than other models that recover Ctenophora-sister.     

Speciation across the Tree of Life

Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.     

Ageing of the human corneal stroma: structural and biochemical changes

High and low angle X-ray diffraction patterns from the corneal stroma give information about the mean intermolecular spacing of the collagen molecules and the mean interfibrillar spacing of the collagen fibrils, respectively. X-ray data were collected, using a high intensity synchrotron source, from human corneas and sclera at approximately physiological hydration. The spacings were measured as a function of tissue age. Between birth and 90 years there is an increase in the cross-sectional area associated with each molecule in corneal collagen from approx. 3.04 nm² to 3.46 nm², and an increase in scleral collagen from approx. 2.65 nm² to 3.19 nm². These changes may be due to an increase in the extent of non-enzymatic cross-linking between collagen molecules over the age range. We have investigated this possibility by measuring collagen glycation using the thiobarbituric acid assay and the subsequent advanced glycation end-products (AGEs) using fluorescence emission. The results obtained have shown an age-related increase in glycation and AGEs in both tissues. We have also demonstrated a decrease in the interfibrillar spacing of corneal collagen with increasing age which may be related to changes in the proteoglycan composition of the interfibrillar matrix.     

Fungal relationships and structural identity of their ectomycorrhizae

Aproximately 5,000–6,000 fungal species form ectomyorrhizae (ECM), the symbiotic organs with roots of predominantly trees. The contributing fungi are not evenly distributed over the system of fungi. Within Basidiomycota exclusively Hymenomycetes and within Ascomycota exclusively Ascomycetes contribute to the symbiosis. Hymenomycetes play a big part, Ascomycetes a minor role; Zygomycetes only form exceptionally ECM. Responsible for ascomycetous ECM are mostly Pezizales with their hypogeous derivatives, whereas Boletales, Gomphales, Thelephorales, Amanitaceae, Cantharellaceae, Cortinariaceae, Russulaceae, and Tricholomataceae are the most important ectomycorrhizal relationships within Hymenomycetes. ECM, as transmitting organs between soil and roots, are transporting carbohydrates for growth of mycelium and fruitbodies from roots and have to satisfy the tree’s demand for water and nutrients. The latter task particularly influences the structure of ECM as nutrients are patchily distributed in the soil and saprotrophic as well as ectomycorrhizal fungi can act as strong competitors for nutrients. In focusing these requirements, ECM developed variously structured hyphal sheaths around the roots, the so-called mantles, and differently organized mycelium that emanates from the mantle, the so-called extramatrical mycelium. The mantles can be plectenchymatous consisting of loosely woven, differently arranged hyphae or they are densely packed, forming a pseudoparenchyma similar to the epidermis of leaves. The extramatrical mycelium grows either as simple scattered hyphae from the mantle into the soil or it can be united to undifferentiated rhizomorphs with a small reach or to highly organized root-like organs with vessel-like hyphae for efficient water and nutrient transport from distances of decimeters. Cystidia, sterile and variously shaped hyphal ends, possibly appropriate for preventing animal attack, in addition, can cover mantles and rhizomorphs. Although only a limited number of species could be considered, some general conclusions are possible.The genus Tuber forms needle-shaped cystidia and lacks rhizomorphs and clamps. Gomphales ECM are identified by rhizomorphs with ampullate inflations at septa of some hyphae and by oleoacanthocystidia or/and oleoacanthohyphae. Thelephoraceae reveal a great diversity of mantle structures and of extramatrical mycelium, with some additional optional characters, i.e., dark brown color, cystidia, blue granules, amyloid hyphae, or amyloid septa. Bankeraceae are mostly characterized by plectenchymatous mantles with star-like pattern and chlamydospores. Russulaceae possess smooth and hydrophilic ECM. Russula forms plectenchymatous mantles with knob-bearing cystidia, so-called russuloid cystidia, or pseudoparenchymatous mantles without cystidia. Lactarius lacks cystidia and shows laticifers within plectenchymatous or within pseudoparenchymatous mantles. The Boletales families Boletaceae, Gyroporaceae, Melanogastraceae, Paxillaceae, Rhizopogonaceae, Sclerodermataceae, and Suillaceae have the most advanced rhizomorph type, the so-called boletoid rhizomorphs, and reveal generally plectenchymatous mantles, frequently with ring-like patterns. Gomphidiaceae and Albatrellaceae provide cystidia, plectenchymatous mantles, and amyloidy; Gomphidiaceae are generally growing in ECM of Suillaceae and Rhizopogonaceae. Cortinariaceae reveal plectenchymatous mantles and undifferentiated or differentiated rhizomorphs or lack rhizomorphs at all. Cortinarius and Dermocybe are distinct by irregularly shaped, bent to tortuous ECM with many rhizomorphs, some growing over the mycorrhizal tip into the soil. Inocybe lacks rhizomorphs and its emanating hyphae are furnished by many secondary septa and prominent clamps with a hole. Rozites lacks rhizomorphs, too, and reveals a distinctly amyloid gelatinous mantle matrix. Descolea and Descomyces are covered by bolbitioid cystidia. Lastly, the genus Tricholoma forms plectenchymatous mantles and a high diversity of rhizomorphs. Some of the ectomycorrhizal features are used to hypothesize relationships at different taxonomic levels. These conclusions are compared with recently developed molecular hypotheses. Correspondence between the two types of hypotheses are evident, while some conflicts wait for a settlement.