Vladimir Blagoderov

Episodic radiations in the fly tree of life

Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms, yet recent research has suggested that fly relationships have been obscured by multiple episodes of rapid diversification. We provide a phylogenomic estimate of fly relationships based on molecules and morphology from 149 of 157 families, including 30 kb from 14 nuclear loci and complete mitochondrial genomes combined with 371 morphological characters. Multiple analyses show support for traditional groups (Brachycera, Cyclorrhapha, and Schizophora) and corroborate contentious findings, such as the anomalous Deuterophlebiidae as the sister group to all remaining Diptera. Our findings reveal that the closest relatives of the Drosophilidae are highly modified parasites (including the wingless Braulidae) of bees and other insects. Furthermore, we use micro-RNAs to resolve a node with implications for the evolution of embryonic development in Diptera. We demonstrate that flies experienced three episodes of rapid radiation—lower Diptera (220 Ma), lower Brachycera (180 Ma), and Schizophora (65 Ma)—and a number of life history transitions to hematophagy, phytophagy, and parasitism in the history of fly evolution over 260 million y.

Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples

Abstract The concept of semantic tagging and its potential for semantic enhancements to taxonomic papers is outlined and illustrated by four exemplar papers published in the present issue of ZooKeys. The four papers were created in different ways: (i) written in Microsoft Word and submitted as non-tagged manuscript (doi: 10.3897/zookeys.50.504); (ii) generated from Scratchpads and submitted as XML-tagged manuscripts (doi: 10.3897/zookeys.50.505 and doi: 10.3897/zookeys.50.506); (iii) generated from an author’s database (doi: 10.3897/zookeys.50.485) and submitted as XML-tagged manuscript. XML tagging and semantic enhancements were implemented during the editorial process of ZooKeys using the Pensoft Mark Up Tool (PMT), specially designed for this purpose. The XML schema used was TaxPub, an extension to the Document Type Definitions (DTD) of the US National Library of Medicine Journal Archiving and Interchange Tag Suite (NLM). The following innovative methods of tagging, layout, publishing and disseminating the content were tested and implemented within the ZooKeys editorial workflow: (1) highly automated, fine-grained XML tagging based on TaxPub; (2) final XML output of the paper validated against the NLM DTD for archiving in PubMedCentral; (3) bibliographic metadata embedded in the PDF through XMP (Extensible Metadata Platform); (4) PDF uploaded after publication to the Biodiversity Heritage Library (BHL); (5) taxon treatments supplied through XML to Plazi; (6) semantically enhanced HTML version of the paper encompassing numerous internal and external links and linkouts, such as: (i) vizualisation of main tag elements within the text (e.g., taxon names, taxon treatments, localities, etc.); (ii) internal cross-linking between paper sections, citations, references, tables, and figures; (iii) mapping of localities listed in the whole paper or within separate taxon treatments; (v) taxon names autotagged, dynamically mapped and linked through the Pensoft Taxon Profile (PTP) to large international database services and indexers such as Global Biodiversity Information Facility (GBIF), National Center for Biotechnology Information (NCBI), Barcode of Life (BOLD), Encyclopedia of Life (EOL), ZooBank, Wikipedia, Wikispecies, Wikimedia, and others; (vi) GenBank accession numbers autotagged and linked to NCBI; (vii) external links of taxon names to references in PubMed, Google Scholar, Biodiversity Heritage Library and other sources. With the launching of the working example, ZooKeys becomes the first taxonomic journal to provide a complete XML-based editorial, publication and dissemination workflow implemented as a routine and cost-efficient practice. It is anticipated that XML-based workflow will also soon be implemented in botany through PhytoKeys, a forthcoming partner journal of ZooKeys. The semantic markup and enhancements are expected to greatly extend and accelerate the way taxonomic information is published, disseminated and used.

How Time Flies for Flies: Diverse Diptera from the Triassic of Virginia and Early Radiation of the Order

Abstract The most diverse and best-preserved early fauna of flies (order Diptera) is described from the Late Carnian (Late Triassic, ca. 220 Ma) of Virginia, USA. Complete flies are preserved as aluminosilicate films on very fine-grained shales from the Cow Branch Formation, which is part of the Newark Supergroup of Early Mesozoic rift basins from eastern North America. The dipteran fauna consists of eight families (one new), 11 genera (five new), and 16 species (11 new), and includes the following taxa (Blagoderov and Grimaldi are the authors of all new names): Architipula youngi Krzemiński, Metarchilimonia krzeminskorum n.gen., n.sp., and M. solita n.sp. (Limoniidae); Triassopsychoda olseni n.gen., n.sp. (Psychodidae); Culicomorpha indet.; Yalea argentata (Krzemiński), Y. rectimedia n.sp., Alinka cara Krzemiński (Procramptonomyiidae); Veriplecia rugosa n.sp., Virginiptera certa n.gen., n.sp., V. similis n.sp., V. lativentra n.sp. (Paraxymyiidae); Brachyrhyphus distortus n.gen. n.sp. (Protorhyphidae); ?Crosaphis virginiensis n.sp. (Crosaphididae); and Prosechamyia trimedia n.gen., n.sp., P. dimedia n.sp. (Prosechamyiidae, new family). Particularly significant is a culicomorphan with a long proboscis, which is the earliest fossil record of a structure specialized apparently for blood feeding. Also, Prosechamyia appears to be a stem group to the very diverse infraorder Brachycera, the earliest definitive members of which appear in the Early Jurassic. Phylogenetic relationships of major clades of living and extinct nematocerous Diptera are analyzed, indicating that infraordinal-level diversification was complete by the Late Triassic. Flies did not reach modern levels of ecological abundance until the mid-Jurassic, apparently due to diversification within most infraorders by that time.

The phylogenetic relationships among infraorders and superfamilies of Diptera based on morphological evidence

Members of the megadiverse insect order Diptera (flies) have successfully colonized all continents and nearly all habitats. There are more than 154 000 described fly species, representing 10–12% of animal species. Elucidating the phylogenetic relationships of such a large component of global biodiversity is challenging, but significant advances have been made in the last few decades. Since Hennig first discussed the monophyly of major groupings, Diptera has attracted much study, but most researchers have used non‐numerical qualitative methods to assess morphological data. More recently, quantitative phylogenetic methods have been used on both morphological and molecular data. All previous quantitative morphological studies addressed narrower phylogenetic problems, often below the suborder or infraorder level. Here we present the first numerical analysis of phylogenetic relationships of the entire order using a comprehensive morphological character matrix. We scored 371 external and internal morphological characters from larvae, pupae and adults for 42 species, representing all infraorders selected from 42 families. Almost all characters were obtained from previous studies but required revision for this ordinal‐level study, with homology assessed beyond their original formulation and across all infraorders. We found significant support for many major clades (including the Diptera, Culicomorpha, Bibionomorpha, Brachycera, Eremoneura, Cyclorrhapha, Schizophora, Calyptratae and Oestroidea) and we summarize the character evidence for these groups. We found low levels of support for relationships between the infraorders of lower Diptera, lower Brachycera and major lineages of lower Cyclorrhapha, and this is consistent with findings from molecular studies. These poorly supported areas of the tree may be due to periods of rapid radiation that left few synapomorphies in surviving lineages.

No specimen left behind: industrial scale digitization of natural history collections

Abstract Traditional approaches for digitizing natural history collections, which include both imaging and metadata capture, are both labour- and time-intensive. Mass-digitization can only be completed if the resource-intensive steps, such as specimen selection and databasing of associated information, are minimized. Digitization of larger collections should employ an “industrial” approach, using the principles of automation and crowd sourcing, with minimal initial metadata collection including a mandatory persistent identifier. A new workflow for the mass-digitization of natural history museum collections based on these principles, and using SatScan® tray scanning system, is described.

Fossil Sciaroidea (Diptera) in Cretaceous Ambers, Exclusive of Cecidomyiidae, Sciaridae, and Keroplatidae

Abstract The Recent world fauna of Sciaroidea, or fungus gnats, comprises approximately 4000 described species in eight families: Bolitophilidae, Cecidomyiidae, Diadocidiidae, Ditomyiidae, Keroplatidae, Lygistorrhinidae, Mycetophilidae, and Sciaridae. Larvae live primarily in decaying vegetation, feeding on fungal mycelia, and they can be among the most abundant insects of temperate forests. Stem-group families appeared in the Jurassic, with large Tertiary deposits being composed almost entirely of living genera, so the Cretaceous is essential for understanding the origins and diversification of Recent families. Sixty-six specimens were studied from six major deposits of Cretaceous amber, spanning 40 million years from the Early to Late Cretaceous: Lebanon (ca. 125 Ma), northern Spain (120 Ma), northern Myanmar (Burma) (ca. 105 Ma), northern Siberia (two sites, 105 and 87 Ma), New Jersey (90 Ma), and western Canada (80 Ma). New taxa are the following: Docidiadia burmitica (n.gen., n.sp.) (Diadocidiidae); Thereotricha sibirica, (?)T. agapa (n.gen., n.spp.) (Sciaroidea incertae sedis); Archaeognoriste primitiva, Lebanognoriste prima, Plesiognoriste carpenteri, P. zherikhini, Protognoriste amplicauda, P. goeleti, P. nascifoa, Leptognoriste davisi, L. microstoma (n.gen., n.spp.) (Lygistorrhinidae). In Mycetophilidae sensu stricto: Alavamanota burmitina, n.sp. (Manotinae), Neuratelia maimecha, n.sp., Allocotocera burmitica, n.sp., Pseudomanota perplexa, n.gen., n.sp. (Sciophilinae Sciophilini); Apolephthisa bulunensis, n.sp., Synapha longistyla, n.sp., Dziedzickia nashi, n.sp., Saigusaia pikei, n.sp., Syntemna fissurata, n.sp., Gregikia pallida, n.gen., n.sp., Gaalomyia carolinae, n.gen., n.sp. (Sciophilinae Gnoristini); Nedocosia exsanguis, N. sibirica, N. canadensis, N. novacaesarea, n.gen., n.spp.; Ectrepesthoneura succinimontana, E. swolenskyi, n.spp.; Izleiina mirifica, I. spinitibialis, n.gen., n.spp.; Zeliina orientalis, Z. occidentalis, n.gen., n.spp.; Temaleia birmitica, n.gen., n.sp., Lecadonileia parvistyla, n.gen., n.sp.; Disparoleia cristata, n.gen., n.sp.; Hemolia matilei, H. glabra, n.gen., n.spp.; and Protragoneura platycera, n.sp. (Sciophilinae Leiini). Relationships of the fossil genera are phylogenetically assessed with living genera. The Burmese amber fauna contains an inordinate abundance and diversity of sciaroids, perhaps because of a wetter paleoclimate in that region.

Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science.

Abstract The Scratchpad Virtual Research Environment (http://scratchpads.eu/) is a flexible system for people to create their own research networks supporting natural history science. Here we describe Version 2 of the system characterised by the move to Drupal 7 as the Scratchpad core development framework and timed to coincide with the fifth year of the project’s operation in late January 2012. The development of Scratchpad 2 reflects a combination of technical enhancements that make the project more sustainable, combined with new features intended to make the system more functional and easier to use. A roadmap outlining strategic plans for development of the Scratchpad project over the next two years concludes this article.

Bringing collections out of the dark

Natural history collections are an incomparable treasure and source of knowledge. Collected over centuries of field exploration, these repositories contain a sample of the world’s biodiversity, and represent a monumental societal investment in research and applied environmental science (Network Integrated Biocollections Alliance 2010). Knowledge derived from the 1.5–3 billion specimens (Arino 2010, Duckworth et al. 1993) within these collections has made vital contributions to the study of taxonomy, systematics, invasive species, biological conservation, land management, pollination and biotic responses to climate change (Chapman 2005). Despite these activities, natural history collections are significantly underutilised due to the difficulty of obtaining and analysing data within and across collections. Digitisation and mobilisation of specimen and associated data removes this impediment, but presents major technical and organisational challenges. The largest of these is how to capture specimen data fast enough to achieve digitisation of entire collections while maintaining sufficient data quality. Until recently, episodic and incremental funding has had limited success with natural history digitisation, largely addressing local projects within single institutions or across niche research communities. New funding, coupled with more collaborative approaches to digitisation, and technical advances with scanning and imaging systems have begun to change this. The collection of eighteen articles published here examines some of these developments, providing a snapshot of current digitisation efforts and progress across these themes. The first of these papers by Reed Beaman and Nico Cellinese (2012) looks at the transformative potential of natural history specimen digitisation, both in terms of driving new developments in technical infrastructure, as well as in new applications for the digitised products of this work. Fundamental to the increase in efficiency of these programmes is the modularisation of the digitisation process. Collections digitisation is broadly defined to include transcription into electronic format of various types of data associated with specimens, the capture of digital images of specimens, and the georeferencing of specimen collecting localities. These steps are examined by Gill Nelson and colleagues (2012), who are quite literally based at the ‘hub’ of National Science Foundation efforts to advance the digitisation of North American biological collections in the United States. Based on studies of major digitisation efforts across the U.S., Nelson et al. break down the clusters of digitisation activities into workflows that can be adopted by other digitisation efforts. A fundamental step in any digitisation programme is the aggregation or federation of digital output so it can be collectively searched and discovered. The European Union funded Open-UP project is one such effort within Europe, and is described by Anton Guntsch and Walter Berendsohn (2012) in their paper on the mobilisation of natural history multimedia resources through the EUROPEANA data portal. The challenges surrounding the coordination of digitisation efforts are also looked at through a series of projects trying to address these problems, nationally or via thematic networks. In some cases these are best practice networks such as the U.S. Virtual Herbarium described by Mary Barkworth and Zack Murrell (2012). In other cases these projects provide a service infrastructure such as the Finnish Digitarium (Tegelberg et al. 2012). Even operating within the confines of a single large institution can be a challenge: different stakeholders have different priorities that can be difficult to accommodate within the budgets of single institutions. Marc Gofferje and Jon Peter van den Oever (2012) describe a range of solutions to address these issues at NCB Naturalis. Part of the solution lies in improving the efficiency of an institutions digitisation process, as illustrated at the New York Botanic Gardens (Tulig et al. 2012) and the Royal Botanic Gardens Edinburgh (Haston et al. 2012). Attempts to automate digitisation are confounded by the fact that different types of organisms require very different types of preservation. Plants and fungi are typically prepared as dried, flattened specimens attached to archival quality paper, with printed label data mounted on the sheet. This pre-adapts herbaria to rapid digitisation. In contrast insects, which are the most numerous organisms in collections, are typically mounted by pinning individuals on entomological pins, which are accompanied by tiny (often folded) labels beneath each specimen. The particular demands of mass digitising entomological specimens are the subject of five papers, which have methodologically converged on the scanning whole collection drawers. GigaPan, described by Matthew Bertone and colleagues (2012) was arguably the first of these approaches, enabling the low cost capture of gigapixel panoramas of insect museum drawers containing many hundreds of specimens. More recently SatScan, developed in association with the Natural History Museum London (Blagoderov et al. 2012), and in use at the Australian National Insect Collection (Mantle et al. 2012) has enabled these panoramas to be obtained with minimal distortion. SatScan is accompanied by software used to select and annotate images of individual specimens. The drawer scanning approach has been incorporated as part of the U.S. InvertNet digitisation programme (Dietrich et al. 2012), and has resulted in a new, low cost instrument called DScan (Schmidt et al. 2012). A contrasting approach to accessing digital images is described by Quentin Wheeler and colleagues (2012), who are exploring the use of telemicroscopy to enable remote researchers to access and manipulate specimens beyond their physical reach. Although not strictly mass digitisation, the potential effect of this network of remote access microscopes is similar, enabling researchers to examine insect material located at major institutions over a network connection. Even with this automation, a significant labour force is still critical for many digitisation projects. Paul Flemons and Penny Berents (2012) explore the use of volunteers to increase the rate of digitising insect collections. This has enabled the Australian Museum to capture label data and images for 16,000 specimens in just 5 months. Label data transcription is a major problem in many digitisation projects. Andrew Hill and colleagues (2012) describe their software to crowdsource label transcription through a workforce of citizen scientists. Embedding quality control techniques and design elements to keep contributors motivated, Notes On Nature provides a toolkit for transcription of ledgers and labels of natural history specimens. Andrea Thomer and colleagues (2012), extend this transcription work into new territory using Wiki-style templates to crowdsource data extraction from century-old field notebooks. This enables interoperability of the underlying data without losing the narrative context from which these observations are drawn. The series closes with a paper by Randall Schuh (2012), who looks at methods to integrate specimen databases into the practice of revisionary systematics, closing the loop between digitising, extracting and reusing data in taxonomic research. In bringing together this special issue on digitisation we have sought to represent a wide selection of projects and techniques. These papers provide a snapshot of activity in what is a fast moving field that is seeing ever-increasing degrees of collaboration across disciplines and between collection-based institutions. Many of these projects deal with the unique challenges associated with major collections that have built up over several centuries, with different communities of practice and different user groups. Despite these differences, the standards for collection acquisition, preservation and documentation are broadly consistent, meaning that there is sufficient common ground to bring together the enormous amounts of data that are being exposed through these activities. We expect that in the next decade these data will become the new frontier for natural history collection management and research.

Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys

Abstract We describe a method to publish nomenclatural acts described in taxonomic websites (Scratchpads) that are formally registered through publication in a printed journal (ZooKeys). This method is fully compliant with the zoological nomenclatural code. Our approach supports manuscript creation (via a Scratchpad), electronic act registration (via ZooBank), online and print publication (in the journal ZooKeys) and simultaneous dissemination (ZooKeys and Scratchpads) for nomenclatorial acts including new species descriptions. The workflow supports the generation of manuscripts directly from a database and is illustrated by two sample papers published in the present issue.

Alpha e-taxonomy: responses from the systematics community to the biodiversity crisis

SummaryThe crisis facing the conservation of biodiversity is reflected in a parallel crisis in alpha taxonomy. On one hand, there is an acute need from government and non-government organisations for large-scale and relatively stable species inventories on which to build major biodiversity information systems. On the other, molecular information will have an increasingly important impact on the evidential basis for delimiting species and is likely to result in greater scientific debate and controversy on their circumscription. This paper argues that alpha-taxonomy built on the Internet (alpha e-taxonomy) can provide a key component of the solution. Two main themes are considered: (1) the potential of e-taxonomic revisions for engaging both the specialist taxonomic community and a wider public in gathering taxonomic knowledge and deepening understanding of it, and (2) why alpha-species will continue to play an essential role in the conventional definition of species and what kinds of methodological development this implies for descriptive species taxonomy. The challenges and requirements for sustaining e-taxonomic revisions in the long-term are discussed, with particular reference to models being developed by five initiatives with botanical exemplar websites: CATE (Creating a Taxonomic E-Science), Solanaceae Source, GrassBase and EDIT (European Distributed Institute of Taxonomy) exemplar groups and scratchpads. These projects give a clear indication of the crucially important role of the national and regional taxonomic organisations and their networks in providing both leadership and a fruitful and beneficial human and technical environment for taxonomists, both amateur and professional, to contribute their expertise towards a collective global enterprise.