TOLKIN – Tree of Life Knowledge and Information Network: Filling a Gap for Collaborative Research in Biological Systematics

The development of biological informatics infrastructure capable of supporting growing data management and analysis environments is an increasing need within the systematics biology community. Although significant progress has been made in recent years on developing new algorithms and tools for analyzing and visualizing large phylogenetic data and trees, implementation of these resources is often carried out by bioinformatics experts, using one-off scripts. Therefore, a gap exists in providing data management support for a large set of non-technical users. The TOLKIN project (Tree of Life Knowledge and Information Network) addresses this need by supporting capabilities to manage, integrate, and provide public access to molecular, morphological, and biocollections data and research outcomes through a collaborative, web application. This data management framework allows aggregation and import of sequences, underlying documentation about their source, including vouchers, tissues, and DNA extraction. It combines features of LIMS and workflow environments by supporting management at the level of individual observations, sequences, and specimens, as well as assembly and versioning of data sets used in phylogenetic inference. As a web application, the system provides multi-user support that obviates current practices of sharing data sets as files or spreadsheets via email

The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age

The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies anatomy ontology with the goal of capturing anatomical data in a systematic and computable manner. An ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies anatomy ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebrafish terms specified as subtypes of teleost terms. We found that the details of ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies anatomy ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways.This work was supported by the National Science Foundation (NSF DBI 0641025), National Institutes of Health (HG002659), and the National Evolutionary Synthesis Center (NSF EF-0423641)

Opportunities and challenges for digital morphology

Advances in digital data acquisition, analysis, and storage have revolutionized the work in many biological disciplines such as genomics, molecular phylogenetics, and structural biology, but have not yet found satisfactory acceptance in morphology. Improvements in non-invasive imaging and three-dimensional visualization techniques, however, permit high-throughput analyses also of whole biological specimens, including museum material. These developments pave the way towards a digital era in morphology. Using sea urchins (Echinodermata: Echinoidea), we provide examples illustrating the power of these techniques. However, remote visualization, the creation of a specialized database, and the implementation of standardized, world-wide accepted data deposition practices prior to publication are essential to cope with the foreseeable exponential increase in digital morphological data

Web-Integrated Taxonomy and Systematics of the Parasitic Wasp Family Signiphoridae (Hymenoptera, Chalcidoidea)

This work focuses on the taxonomy and systematics of parasitic wasps of the family Signiphoridae (Hymenoptera: Chalcidoidea), a relatively small family of chalcidoid wasps, with 79 described valid species in 4 genera: Signiphora Ashmead, Clytina Erdös, Chartocerus Motschulsky and Thysanus Walker. A phylogenetic analysis of the internal relationships in Signiphoridae, a discussion of its supra-specific classification based on DNA sequences of the 18S rDNA, 28S rDNA and COI genes, and taxonomic studies on the genera Clytina, Thysanus and Chartocerus are presented. In the phylogenetic analyses, all genera except Clytina were recovered as monophyletic. The classification into subfamilies was not supported. Out of the four currently recognized species groups in Signiphora, only the Signiphora flavopalliata species group was supported. The taxonomic work was conducted using advanced digital imaging, content management systems, having in sight the online delivery of taxonomic information. The evolution of changes in the taxonomic workflow and dissemination of results are reviewed and discussed in light of current bioinformatics. The species of Thysanus and Clytina are revised and redescribed, including documentation of type material. Four new species of Thysanus and one of Clytina are described. The taxonomy of Chartocerus is reviewed, including redescriptions of 25 out of 33 currently valid species, most based on type or topotypical material

Bioinformatics for comparative cell biology

For hundreds of years biologists have studied the naturally occurring diversity in plant and animal species. The invention of the electron microscope in the rst half of the 1900's reveled that cells also can be incredible complex (and often stunningly beautiful). However, despite the fact that the eld of cell biology has existed for over 100 years we still lack a formal understanding of how cells evolve: It is unclear what the extents are in cell and organelle morphology, if and how diversity might be constrained, and how organelles change morphologically over time.(...

Lehevaablaste perekonna Empria (Hymenoptera, Tenthredinidae) taksonoomia ja fülogenees

Väitekirja elektrooniline versioon ei sisalda publikatsioone.Elurikkust on teaduslikult kirjeldatud üle 250 aasta, kuid suurem osa (hinnanguliselt 80–90%) sellest on teadusele ikka veel tundmata. Suurema osa palja silmaga nähtavast kirjeldatud ja kirjeldamata elurikkusest moodustavad putukad. Neid on teada ligi miljon liiki, kuid avastamata võib olla lausa kümme korda rohkem. Üks liigirikkamaid putukaseltse on kiletiivalised (nt. herilased, mesilased ja sipelgad), kuhu kuulub ka doktoritöös uuritud põhja poolkeral levinud 60 liigiline perekond Empria. Tegemist on lehevaablastega, kes vastsestaadiumis on kõik taimtoidulised ja meenutavad liblikaröövikuid. Täiskasvanud empriad on väiksed (4–9 mm) mustad putukad. Iseloomulikuks tunnuseks on tagakehal paiknevad valged laigud, mille põhjal on perekonda teistest lehevaablastest kerge eristada. Liikide määramine on paraku aga võimalik pea ainult mikroskoobi abiga ja seejuures tuleb tavaliselt isastel genitaalkapslist eraldada peenisvalvid ja emastel munetid. Aga kui see on tehtud, siis on liikide määramine üldjuhul lihtne igaühele, kuna tavaliselt erinevad eri liikidel peenisvalvid ja munetid väga selgesti. Võib öelda, et on lihtsalt vaja galeriid kõikide liikide peenisvalvidest ja munetitest ning seejärel üles leida otsitav. Doktoritöö raames koostati ida poolkera empria liikide (50) jaoks määramistabel koos fotodega peenisvalvidest ja munetitest (lääne poolkera liikide kohta oli vastav info juba olemas). Nende seas on 13 uut liiki teadusele, millest 9 ootab veel nimetamist. Lisaks kasutati 46 liigi (nii ida kui lääne poolkeralt) DNA andmeid põlvnemissuhete väljaselgitamiseks. Edasiste uurimuste ülesandeks oleks kirjeldada seni teadusele tundmatud liigid ja välja selgitada kõikide liikide toidutaimed (rohkem kui pooltel teadmata). Lähemat uurimist vääriks empria ka liigitekke aspektist, kuna perekonnas paistab olevat enam-vähem pidev skaala nii rohkem kui vähem eristunud liikidest ja mõnede liigirühmade või -paaride puhul polegi liigipiirid päris selged. Aga miks meil üldse neid empria liike vaja tunda? Otsest majanduslikku tähtsust neil pole (Põhja-Ameerikas võivad paar liiki siiski olla maasika kahjurid). Teaduse seisukohalt on aga tegemist ühe pusletükiga teadmiste üldises mosaiikpildis, mille kokkupanemine aitab meil üha paremini mõista ümbritsevat maailma.Although scientists have been describing biodiversity for more than 250 years, most of the species (probably 80–90%) remain unknown. Insects form the largest proportion of known and unknown macroscopic biodiversity. Nearly million insect species have been described, but the number of undescribed species could be ten times greater. Among the insects, order Hymenoptera (e.g. ants, bees, and wasps) is one of the largest, which also includes the sawfly genus Empria (60 species). Sawflies are plant feeding and caterpillar-like in the immature stage. Adults of Empria are small (4–9 mm) black insects. Characteristic of the genus are pale paired patches on abdominal terga, which makes it easy to distinguish from other sawflies. Species identification, however, is possible only using a microscope and usually penis valves need to be dissected from genital capsules of males and ovipositors from females. If this is done, the species identification is generally quite easy for anyone with a microscope, because the differences between penis valves and ovipositors of different species are usually obvious. It could be said that you simply need a gallery of penis valves and ovipositors to determine a species. The doctoral thesis includes a key to adults of Empria from eastern hemisphere (50 species) with photos of penis valves and ovipositors (corresponding information was already available for species of western hemisphere). There are 13 species new to science, 9 of which are still without a name. In addition, DNA sequence data from 46 species (including both hemispheres) was used to reconstruct the phylogeny of the genus. Future studies should describe the remaining unknown species and elucidate the host plants of all the species (unknown in more than half of the species). Closer look at Empria could also contribute to speciation studies, as there appear to be more or less continuous variation from highly distinct species to species pairs or groups with fuzzy species boundaries. Why is it necessary to know Empria species at all? The genus is not economically particularly important (couple of species in North America can be pests of strawberry), but from a scientific point of view the knowledge about it can be considered as a piece of a puzzle, assembling of which continuously improves our ability to make sense of the world

Bringing Together Species Observations: A Case Story of Sweden's Biodiversity Informatics Infrastructures

Biodiversity informatics produces global biodiversity knowledge through the collection and analysis of biodiversity data using informatics techniques. To do so, biodiversity informatics relies upon data accrual, standardization, transferability, openness, and "invisible" infrastructure. What biodiversity informatics mean to society, however, cannot be adequately understood without recognizing what organizes biodiversity data. Using insights from science and technology studies, we story the organizing "visions" behind the growth of biodiversity informatics infrastructures in Sweden-an early adopter of digital technologies and significant contributor to global biodiversity data-through interviews, scientific literature, governmental reports and popular publications. This case story discloses the organizational formation of Swedish biodiversity informatics infrastructures from the 1970s to the present day, illustrating how situated perspectives or "visions" shaped the philosophies, directions and infrastructures of its biodiversity informatics communities. Specifically, visions related to scientific progress and species loss, their institutionalization, and the need to negotiate external interests from governmental organizations led to unequal development across multiple infrastructures that contribute differently to biodiversity knowledge. We argue that such difference highlights that the social and organizational hurdles for combining biodiversity data are just as significant as the technological challenges and that the seemingly inconsequential organizational aspects of its infrastructure shape what biodiversity data can be brought together, modelled and visualised

Phenotyping in the era of genomics: MaTrics—a digital character matrix to document mammalian phenotypic traits

A new and uniquely structured matrix of mammalian phenotypes, MaTrics (Mammalian Traits for Comparative Genomics) in a digital form is presented. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics. MaTrics was developed within a project aimed to find genetic causes of phenotypic traits of mammals using Forward Genomics. This approach requires genomes and comprehensive and recorded information on homologous phenotypes that are coded as discrete categories in a matrix. MaTrics is an evolving online resource providing information on phenotypic traits in numeric code; traits are coded either as absent/present or with several states as multistate. The state record for each species is linked to at least one reference (e.g., literature, photographs, histological sections, CT scans, or museum specimens) and so MaTrics contributes to digitalization of museum collections. Currently, MaTrics covers 147 mammalian species and includes 231 characters related to structure, morphology, physiology, ecology, and ethology and available in a machine actionable NEXUS-format*. Filling MaTrics revealed substantial knowledge gaps, highlighting the need for phenotyping efforts. Studies based on selected data from MaTrics and using Forward Genomics identified associations between genes and certain phenotypes ranging from lifestyles (e.g., aquatic) to dietary specializations (e.g., herbivory, carnivory). These findings motivate the expansion of phenotyping in MaTrics by filling research gaps and by adding taxa and traits. Only databases like MaTrics will provide machine actionable information on phenotypic traits, an important limitation to genomics. MaTrics is available within the data repository Morph·D·Base (www.morphdbase.de)

National Seminar on Biodiversity Regime: Emerging challenges and opportunities 22 May 2008

National seminar on Biodiversity Regime: Emerging challenges and opportunities 22 May 200

Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy