STBase: One Million Species Trees for Comparative Biology

Comprehensively sampled phylogenetic trees provide the most compelling foundations for strong inferences in comparative evolutionary biology. Mismatches are common, however, between the taxa for which comparative data are available and the taxa sampled by published phylogenetic analyses. Moreover, many published phylogenies are gene trees, which cannot always be adapted immediately for species level comparisons because of discordance, gene duplication, and other confounding biological processes. A new database, STBase, lets comparative biologists quickly retrieve species level phylogenetic hypotheses in response to a query list of species names. The database consists of 1 million single- and multi-locus data sets, each with a confidence set of 1000 putative species trees, computed from GenBank sequence data for 413,000 eukaryotic taxa. Two bodies of theoretical work are leveraged to aid in the assembly of multi-locus concatenated data sets for species tree construction. First, multiply labeled gene trees are pruned to conflict-free singly-labeled species-level trees that can be combined between loci. Second, impacts of missing data in multi-locus data sets are ameliorated by assembling only decisive data sets. Data sets overlapping with the user’s query are ranked using a scheme that depends on user-provided weights for tree quality and for taxonomic overlap of the tree with the query. Retrieval times are independent of the size of the database, typically a few seconds. Tree quality is assessed by a real-time evaluation of bootstrap support on just the overlapping subtree. Associated sequence alignments, tree files and metadata can be downloaded for subsequent analysis. STBase provides a tool for comparative biologists interested in exploiting the most relevant sequence data available for the taxa of interest. It may also serve as a prototype for future species tree oriented databases and as a resource for assembly of larger species phylogenies from precomputed trees.     

A gross anatomy ontology for hymenoptera

Hymenoptera is an extraordinarily diverse lineage, both in terms of species numbers and morphotypes, that includes sawflies, bees, wasps, and ants. These organisms serve critical roles as herbivores, predators, parasitoids, and pollinators, with several species functioning as models for agricultural, behavioral, and genomic research. The collective anatomical knowledge of these insects, however, has been described or referred to by labels derived from numerous, partially overlapping lexicons. The resulting corpus of information--millions of statements about hymenopteran phenotypes--remains inaccessible due to language discrepancies. The Hymenoptera Anatomy Ontology (HAO) was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy. The HAO was built using newly developed interfaces within mx, a Web-based, open source software package, that enables collaborators to simultaneously contribute to an ontology. Over twenty people contributed to the development of this ontology by adding terms, genus differentia, references, images, relationships, and annotations. The database interface returns an Open Biomedical Ontology (OBO) formatted version of the ontology and includes mechanisms for extracting candidate data and for publishing a searchable ontology to the Web. The application tools are subject-agnostic and may be used by others initiating and developing ontologies. The present core HAO data constitute 2,111 concepts, 6,977 terms (labels for concepts), 3,152 relations, 4,361 sensus (links between terms, concepts, and references) and over 6,000 text and graphical annotations. The HAO is rooted with the Common Anatomy Reference Ontology (CARO), in order to facilitate interoperability with and future alignment to other anatomy ontologies, and is available through the OBO Foundry ontology repository and BioPortal. The HAO provides a foundation through which connections between genomic, evolutionary developmental biology, phylogenetic, taxonomic, and morphological research can be actualized. Inherent mechanisms for feedback and content delivery demonstrate the effectiveness of remote, collaborative ontology development and facilitate future refinement of the HAO.     

基于IBM DB2的中国寄生性膜翅目昆虫资源数据库构建

以IBM DB2数据库作为开发平台,根据寄生性膜翅目昆虫数据的特点组建了分类地位表、寄主表、形态特征图和生物学特性表,将寄生性膜翅目的中文名、拉丁名、定名人、寄主、形态特征、图形、生物学特性等信息分别存储于这4个表中,构建出中国寄生性膜翅目昆虫资源数据库。用Visual Basic 6.0编制了友好的人机对话界面,即信息的录入和修改界面、信息查询界面和用户管理界面,使数据库的应用与维护更加便捷。     

Overview of FEED, the feeding experiments end-user database

The Feeding Experiments End-user Database (FEED) is a research tool developed by the Mammalian Feeding Working Group at the National Evolutionary Synthesis Center that permits synthetic, evolutionary analyses of the physiology of mammalian feeding. The tasks of the Working Group are to compile physiologic data sets into a uniform digital format stored at a central source, develop a standardized terminology for describing and organizing the data, and carry out a set of novel analyses using FEED. FEED contains raw physiologic data linked to extensive metadata. It serves as an archive for a large number of existing data sets and a repository for future data sets. The metadata are stored as text and images that describe experimental protocols, research subjects, and anatomical information. The metadata incorporate controlled vocabularies to allow consistent use of the terms used to describe and organize the physiologic data. The planned analyses address long-standing questions concerning the phylogenetic distribution of phenotypes involving muscle anatomy and feeding physiology among mammals, the presence and nature of motor pattern conservation in the mammalian feeding muscles, and the extent to which suckling constrains the evolution of feeding behavior in adult mammals. We expect FEED to be a growing digital archive that will facilitate new research into understanding the evolution of feeding anatomy.     

Phylogenetic definitions and taxonomic philosophy

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names.     

If I only had a brain: exploring mouse brain images in the Allen Brain Atlas

The combination of a powerful well-designed user interface with detailed high-quality data sets can create new possibilities for data exploration and analysis. The Allen Brain Atlas (http://www.brain-map.org) provides a collection of tools for examining a set of images that detail gene expression in the mouse brain. Powerful web-based viewers for individual images and parallel examination of related images interact with an external application for three-dimensional views. The underlying dataset, generated via high-throughput analysis of expression patterns of more than 21,000 genes in adult mouse brains, provides three-dimensional views of gene expression patterns displayed in the context of an anatomical ontology. Facilities for filtering views, saving views of interest, annotating images and sharing views via email support the ongoing process of analysis and provide a model for the future of integrated tools for analysing large image data sets.     

Flies and congruence

Competing phylogenetic hypotheses have become the rule in modern systematics. While the problem of incongruence between character sets has become extremely acute due to the generation of molecular data, it is by no means specific to molecular and morphological comparisons. The role of the modern systematist is to interpret incongruence between character sets and to come to some conclusion regarding a phylogenetic hypothesis of the organisms in question. Two aspects of congruence analysis are examined using the Drosophilidae as an example. The first includes the quantification of congruence and the types of phylogenetic inference that can be made from such analyses. The second aspect concerns an examination of character evolution in order to identify characters and taxa that might be contributing to incongruence in phylogenetic analysis. © 1994 Wiley-Liss, Inc.     

Third meeting of the International Society for Phylogenetic Nomenclature: a report

The Third Meeting of the International Society for Phylogenetic Nomenclature (ISPN) convened at Dalhousie University in Halifax, Canada, from 20 to 22 July 2008. In addition to contributed talks, the conference included a progress report on the PhyloCode 'Companion Volume', a discussion of how to complete this book in a timely fashion, a demonstration of the online registration data base (RegNum), plenary talks, and Council and business meetings. Topics discussed at the meeting include problems created by rank-based nomenclature in various eukaryotic taxa, dealing with hybrids in rank-based and phylogenetic nomenclature, phyloinformatics, the choice of names to use when the taxonomic content associated with available names varies, teaching phylogenetic nomenclature, and the application of phylogenetic nomenclature to specific taxa.     

On experiences of i2b2 (Informatics for integrating biology and the bedside) database with Japanese clinical patients' data

Informatics for Integrating Biology and the Bedside (i2b2) is a database system to facilitate sharing and reuse of clinical patients' data collected in individual hospitals. The i2b2 provides an ontology based object-oriented database system with highly simple and flexible database schema which enables us to integrate clinical patients' data from different laboratories and different hospitals. 392 patients' data including carcinoma and non-carcinoma specimens from cancer patients are transported from the Integrated Clinical Omics Database (iCOD) to the i2b2 database for a feasibility study to check applicability of i2b2 ontology and database schema on Japanese clinical patients' data. No modification is required for the i2b2 data model to deal with Japanese characters. Some modification of ontology is required to integrate biomedical information extracted from the cancer patients' data. We believe that the i2b2 system will be practical infrastructure to integrate Japanese clinical databases if appropriate disease ontology for Japanese patients is provided.     

Bacterial diversity in suspected prosthetic joint infections: an exploratory study using 16S rRNA gene analysis

Formation of biofilm is a prominent feature of prosthetic joint infections (PJIs) and constitutes a challenge to current sampling procedures and culture practices. Molecular techniques have a potential for improving diagnosis of biofilm-adapted, slow-growing and non-culturable bacteria. In this exploratory study we investigated the bacterial diversity in specimens from 22 patients clinically suspected of having PJIs. Bacteriological cultures were performed according to standard practice. A total of 55 specimens from 25 procedures ('specimen sets') were submitted to broad range 16S rRNA gene PCR, cloning, sequencing and phylogenetic analysis. More than 40 bacterial taxa within six phyla were identified in 14 specimen sets originating from 11 patients. Direct observation of biofilm was made in selected specimens by fluorescence in situ hydridization. 16S rRNA gene analysis and bacteriological cultures were concordant for 15/25 specimen sets (60%; five positive, 10 negative); additional taxa were detected in four sets by gene analysis, and discrepant results were obtained for six sets, five of which were negative on culture. Polymicrobial communities were revealed in 9/14 sets by gene analysis and 1/10 sets by culture (P?相似文献   

Classification of Kobresia fragilis C. B. Clarke (Cyperaceae) and related taxa

The classification of Kobresia fragilis C. B. Clarke and related taxa were studied based on gross morphology and nutlet epidermal micromorphology. About 13 names have been involved in the species group. They could not be clearly defined using the morphological characters employed by previous authors. Thus, more than 200 sheets of 89 specimens of related taxa were studied thoroughly, and the taxonomic significance of morpbological characters was re-evaluated. In order to further understand the classification of K. fragilis and its allies, micromorphology of nutlet epidermis of these taxa was observed under scanning electron microscope. Based on the results, K. curvata C. B. Clarke and K. fragilis were recognized. Other names were treated as synonymies of K. fragilis. K. clarkeana (Kükenthal) Kükenthal, K. clarkeana var. megalantha Kükenthal and K. curticeps (C. B. Clarke) Kükenthal var. gyirongensis Y. C. Yang were reduced to new synonymies of K. fragilis. K. curvata was distinct from K. fragilis on both morphological and micromorphological basis. One specimen of K. fragilis collected from Luqu, Gansu, China, represents anew distribution record of this species in Gansu.     

Digital Herbarium of Moscow State University: The Largest Russian Biodiversity Database

In 2015–2016, 785887 specimens were scanned at the Herbarium of Moscow State University (MW), which comprised 77.7% of the total collection. The metadata of the digital herbarium include the identifier (ID) of each specimen, its species name, and geographical reference (area code). As the largest in Russia database with respect to biodiversity, the Herbarium includes 712925 images of specimens of vascular plants and 72962 specimens of bryophytes. The digital herbarium is interrelated with the Catalogue of Life international database and has enriched it with 160 new species. Images of 781882 specimens have been put online as JPG files (the resolution is 300 dpi) on the web portal of the National Depository Bank of Live Systems (https://plant.depo.msu.ru/). The portal is open for all Russian biological collections.     

Divergence time estimation using fossils as terminal taxa and the origins of Lissamphibia

Were molecular data available for extinct taxa, questions regarding the origins of many groups could be settled in short order. As this is not the case, various strategies have been proposed to combine paleontological and neontological data sets. The use of fossil dates as node age calibrations for divergence time estimation from molecular phylogenies is commonplace. In addition, simulations suggest that the addition of morphological data from extinct taxa may improve phylogenetic estimation when combined with molecular data for extant species, and some studies have merged morphological and molecular data to estimate combined evidence phylogenies containing both extinct and extant taxa. However, few, if any, studies have attempted to estimate divergence times using phylogenies containing both fossil and living taxa sampled for both molecular and morphological data. Here, I infer both the phylogeny and the time of origin for Lissamphibia and a number of stem tetrapods using Bayesian methods based on a data set containing morphological data for extinct taxa, molecular data for extant taxa, and molecular and morphological data for a subset of extant taxa. The results suggest that Lissamphibia is monophyletic, nested within Lepospondyli, and originated in the late Carboniferous at the earliest. This research illustrates potential pitfalls for the use of fossils as post hoc age constraints on internal nodes and highlights the importance of explicit phylogenetic analysis of extinct taxa. These results suggest that the application of fossils as minima or maxima on molecular phylogenies should be supplemented or supplanted by combined evidence analyses whenever possible.     

Congruence between molecular phylogeny and cuticular design in Echiniscoidea (Tardigrada,Heterotardigrada)

Although morphological characters distinguishing echiniscid genera and species are well understood, the phylogenetic relationships of these taxa are not well established. We thus investigated the phylogeny of Echiniscidae, assessed the monophyly of Echiniscus, and explored the value of cuticular ornamentation as a phylogenetic character within Echiniscus. To do this, DNA was extracted from single individuals for multiple Echiniscus species, and 18S and 28S rRNA gene fragments were sequenced. Each specimen was photographed, and published in an open database prior to DNA extraction, to make morphological evidence available for future inquiries. An updated phylogeny of the class Heterotardigrada is provided, and conflict between the obtained molecular trees and the distribution of dorsal plates among echiniscid genera is highlighted. The monophyly of Echiniscus was corroborated by the data, with the recent genus Diploechiniscus inferred as its sister group, and Testechiniscus as the sister group of this assemblage. Three groups that closely correspond to specific types of cuticular design in Echiniscus have been found with a parsimony network constructed with 18S rRNA data. © 2013 The Linnean Society of London     

A total evidence assessment of the phylogeny of North American euctenizine trapdoor spiders (Araneae, Mygalomorphae, Cyrtaucheniidae) using Bayesian inference

North American trapdoor spiders of the subfamily Euctenizinae (Cyrtaucheniidae) are among the most diverse mygalomorph spiders (trapdoor spiders, tarantulas, and their relatives) on the continent in terms of species numbers and ecological habits. We present a generic level phylogenetic study of the subfamily based on a total evidence approach. Our dataset comprises approximately 3.7 kb of molecular characters (18S and 28S rRNA gene sequences) and 71 morphological characters scored for 32 taxa. When analyzed independently, these data sets, particularly the morphology, depict very different views of mygalomorph and euctenizine relationships, albeit with weak support. However, when these data are combined we recover a tree topology that is supported by high posterior probability for most nodes. The combined data recover a phylogenetic pattern for euctenizines different than previously published and indicate the presence of a narrowly endemic new genus from central California. While euctenizine monophyly is unequivocal, the monophyly of a number of other mygalomorph groups is questionable (e.g., Cyrtaucheniidae, Mecicobothriodina, Rastelloidina). This non-monophyly is noteworthy, as our analysis represents the first employing a total evidence approach for mygalomorphs, a group known to be morphologically conservative.     

Molecular and morphological evidence of Alvinellidae relationships (Terebelliformia, Polychaeta, Annelida)

In this study we assessed the phylogenetic relationships of the hydrothermal vent polychaete group Alvinellidae, based on parsimony analyses of combined morphological and molecular data. Morphological data were obtained from newly examined specimens and literature information of 16 terminal taxa belonging to Alvinellidae, Ampharetidae, Pectinariidae, Terebellidae, Trichobranchidae, and the outgroups Oweniidae and Sabellidae. Molecular data were based on 28S rRNA from 13 of the 16 morphological terminals (10 previously published sequences plus three new ones). The combined analysis indicated the clades ((Alvinellidae, Trichobranchidae) Pectinariidae) and (Ampharetidae, Terebellidae). Alvinellidae, Ampharetidae and Terebellidae, as currently delineated, are monophyletic. The positions of Trichobranchidae and Pectinariidae contradicted traditional views, and they also had low Bremer support and merit further studies. Well-supported clades included Alvinellidae and Terebellinae. Previous statements that Alvinellidae are either nested within Ampharetidae or the sister to this taxon were not supported. The traditional but here contradicted view that Terebellidae and Trichobranchidae are closely related may be based on plesiomorphic similarities between these two taxa.     

Avian skulls represent a diverse ornithuromorph fauna from the Lower Cretaceous Xiagou Formation,Gansu Province,China

We describe six specimens consisting of cranial remains and associated partial presacral axial series belonging to ornithuromorph birds from the Changma locality of the Lower Cretacous Xiagou Formation of northwestern Gansu Province, China. Comparison among specimens is limited by the paucity of overlapping elements, their differing exposed views, and, in some specimens, poor preservation. Despite this, three separate taxa are represented, evidenced by differences in their dentary dentitions: one specimen is edentulous, another has sharp, closely spaced, relatively high-crowned and peg-like teeth, and a third preserves blunt, relatively low-crowned teeth placed in a communal groove, a morphology previously reported among adult birds only in Hesperornithiformes. We propose that the high-crowned specimen may be referred to Gansus yumenensis based on shared similarities with the closely related Iteravis huchzermeyeri, including a very similar dentition and an edentulous premaxilla with elongate, unfused frontal processes and no palatal processes. The two other specimens are considered new taxa, for which we erect the names Meemannavis ductrix gen. et sp. nov. and Brevidentavis zhangi gen. et sp. nov. These new specimens confirm that the Changma locality is dominated by ornithuromorph birds and contribute to a better understanding of this important avifauna. The observed variation in dental morphology hints at trophic diversity like that observed in ornithuromorphs from the penecontemporaneous Jehol Group of northeastern China.     

A glossary of scientific terms used in the Russian-language literature on parasitic and blood-sucking arthropods

The glossary includes the major terms and concepts most often used in the Russian literature on parasitology and medico-veterinary entomology. Each term is explained, and some are supplemented with more common English equivalents. The glossary covers only the common terms and does not include those referring to very specific topics and concepts; the names of arthropod taxa and morphological terms are also not included. The list of terms is by no means a comprehensive glossary and is not supposed to be a normative edition.