Pavel Stoev

Fauna Europaea – all European animal species on the web

Abstract Fauna Europaea is Europes main zoological taxonomic index, making the scientific names and distributions of all living, currently known, multicellular, European land and freshwater animals species integrally available in one authoritative database. Fauna Europaea covers about 260,000 taxon names, including 145,000 accepted (sub)species, assembled by a large network of (>400) leading specialists, using advanced electronic tools for data collations with data quality assured through sophisticated validation routines. Fauna Europaea started in 2000 as an EC funded FP5 project and provides a unique taxonomic reference for many user-groups such as scientists, governments, industries, nature conservation communities and educational programs. Fauna Europaea was formally accepted as an INSPIRE standard for Europe, as part of the European Taxonomic Backbone established in PESI. Fauna Europaea provides a public web portal at faunaeur.org with links to other key biodiversity services, is installed as a taxonomic backbone in wide range of biodiversity services and actively contributes to biodiversity informatics innovations in various initiatives and EC programs.

Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data

Abstract We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae), found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT) scans, and a movie of the living specimen to document important traits of its ex-situ behaviour. By employing micro-CT scanning in a new species for the first time, we create a high-resolution morphological and anatomical dataset that allows virtual reconstructions of the specimen and subsequent interactive manipulation to test the recently introduced ‘cybertype’ notion. In addition, the transcriptome was recorded with a total of 67,785 scaffolds, having an average length of 812 bp and N50 of 1,448 bp (see GigaDB). Subsequent annotation of 22,866 scaffolds was conducted by tracing homologs against current available databases, including Nr, SwissProt and COG. This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.

Beyond dead trees: integrating the scientific process in the Biodiversity Data Journal

Driven by changes to policies of governments and funding agencies, Open Access to content and data is quickly becoming the prevailing model in academic publishing. Open Access benefits scientists with greater dissemination and citation of their work, and provides society as a whole with access to the latest research. Open Access is, however, only one facet of scholarly communication. Core scientific statements or assertions are intertwined and hidden in the scholarly narratives, and the data underlying these statements are often obscured to the point that replication of results is impossible (Nature Editorial 2012). This is in part a result of the way scientific papers are written as narratives, rather than sources of data. An often cited reason for the lack of published data is the absence of a reward mechanism for the individuals involved in creating and managing information (Smith 2009, Costello 2009, Vision 2010, McDade et al. 2011, Duke and Porter 2013). Preparing data for publication is a time consuming activity that few scholars will undertake without recognition from their peers. Data papers are a potential solution to this problem (Chavan and Penev 2011, Chavan and Penev 2013). They allow authors to publish data and receive reward through the traditional citation process. Coupling tools to rapidly and simply generate publications will incentivise this behaviour and create a culture of data curation and sharing within the biodiversity science community. If we are going to incentivise the mass publication of data, we also need mechanisms to ensure quality. Traditional peer review is one of the bottlenecks in standard publication practice (Hauser and Fehr 2007, Fox and Petchey 2010). A common criticism of peer review is the lack of transparency and accountability on the part of the reviewers. To cope with the additional volume of papers created by data publication and to move to a more transparent system, we need to rethink peer review. We need both new methods of reviewing and new tools to automate as much of the review process as possible. This requires a new publishing platform, not just a new journal. An abundance of small isolated datasets does not, however, allow us to address the fundamental problems within the biodiversity science community. These islands of data are only of value if connected and interlinked. The task of interlinking is performed by biodiversity data aggregators like the Global Biodiversity Information Facility (GBIF) and Encylopedia of Life (EOL) which form the backbone of data-driven biodiversity research. By automating the submission of data to these aggregators, we can increase their value to more than the sum of their parts, making small data big. A renewed appreciation of the value of small data will help to reduce the vast amount of research data that exists only on laptops and memory sticks - data that is often lost when people change roles or retire. Works of potentially very limited length can hold intrinsic value to the community, but are almost impossible to publish in traditional journals chasing impact factors. Examples include single species descriptions, local checklists and software descriptions, or ecological surveys and plot data. An infrastructure that allows datasets of any size to be important means we can publish them at any time. There is no need to wait for datasets to reach a critical mass suitable for publication in a traditional journal. Today, we are pleased to announce the official release of the first series of papers published in Biodiversity Data Journal (BDJ). After years of hard work in analyzing, planning and programming the Pensoft Writing Tool (PWT), we now have a publishing platform that addresses the key concerns raised above. This provides the first workflow to support the full life cycle of a manuscript - from writing through submission, community peer-review, publication and dissemination, all within a single online collaborative environment. Shortening distance between “data” and “narrative” publishing Most journals nowadays clearly separate data from narrative (text). Moreover, data publishing through data centres and repositories has almost become a separate sector within the scholarly publishing landscape. BDJ is not a conventional journal, nor is it a conventional “data journal”. It aims to integrate data and text in a single publication by converting several kinds of biodiversity data (e.g., species occurrences, checklists, or data tables) into the text for human-readable use, while simultaneously making data units from the same article harvestable and downloadable. The text itself is marked up and presented in a highly structured and machine readable form. BDJ aims to integrate small data into the text whenever possible. Supplementary data files that underpin graphs, hypotheses and results can also be uploaded on the journal’s website and published with the article. Nonetheless, this is usually not possible for large or complex data, for which we recommend deposition in an established open international repository (for details, see Penev et al. 2011): Large primary biodiversity data sets (e.g., institutional collections of species-occurrence records) should be published with the GBIF Integrated Publishing Toolkit (IPT); small data sets of this kind are imported into the article text through an Excel template, available in PWT. Genomic data should be deposited with INSDC (GenBank/EMBL/DDBJ), either directly or via a partnering repository, e.g. Barcode of Life Data Systems (BOLD). Transcriptomics data should be deposited in Gene Expression Omnibus (GEO) or ArrayExpress. Phylogenetic data should be deposited at TreeBASE, either directly or through the Dryad Data Repository. Biodiversity-related geoscience and environmental data should be deposited in PANGAEA. Morphological images other than those presented in the article should be deposited at Morphbank. Images of a specific kind should be deposited in appropriate repositories if these exist (e.g., Morphosource for MicroCT data). Videos should be uploaded to video sharing sites like YouTube, Vimeo or SciVee and linked back to the article text. Similarly, audio files should go to platforms like FreeSound or SoundCloud, and presentations to Slideshare. In addition, multimedia files can also be uploaded as supplementary files on the journal’s website. 3D and other interactive models can be embedded in the article’s HTML and PDF. Any other large data sets (e.g., ecological observations, environmental data, morphological and other data types) should be deposited in the Dryad Data Repository, either prior to or upon acceptance of the manuscript. Other specialised data repositories can be used if these offer unique identifiers and long-term preservation. All external data used in a BDJ paper must be cited in the reference list, and links to these data (as deposited in external repositories) must be included in a separate data resources section of the article. All datasets, images or multimedia are freely downloadable from the text under the Open Data Commons Attribution License or a Creative Commons CC-Zero waiver / Public Domain Dedication. The article text is available under a Creative Commons (CC-BY) 3.0 license. Primary biodiversity data within an article can be exported in Darwin Core Archive format, which makes them interoperable with biodiversity tools based on the Darwin Core standard. By facilitating open access to the data that underlie every publication, BDJ is setting a new standard in transparency and repeatability in biodiversity science. Perpetual and universal access to primary data stimulates scientific progress by helping authors build upon existing datasets. BDJ’s commitment to supporting automated data aggregation and interlinking is happening alongside multiple advances in biodiversity informatics infrastructure that herald the dawning of an era of collaborative, big-data biodiversity science (Page 2008, Patterson et al. 2010, Thessen and Patterson 2011, Parr et al. 2012).

The centipede genus Eupolybothrus Verhoeff, 1907 (Chilopoda: Lithobiomorpha: Lithobiidae) in North Africa, a cybertaxonomic revision, with a key to all species in the genus and the first use of DNA barcoding for the group.

Abstract The centipede genus Eupolybothrus Verhoeff, 1907 in North Africa is revised. A new cavernicolous species, Eupolybothrus kahfi Stoev & Akkari, sp. n., is described from a cave in Jebel Zaghouan, northeast Tunisia. Morphologically, it is most closely related to Eupolybothrus nudicornis (Gervais, 1837) from North Africa and Southwest Europe but can be readily distinguished by the long antennae and leg-pair 15, a conical dorso-median protuberance emerging from the posterior part of prefemur 15, and the shape of the male first genital sternite. Molecular sequence data from the cytochrome c oxidase I gene (mtDNA–5’ COI-barcoding fragment) exhibit 19.19% divergence between Eupolybothrus kahfi and Eupolybothrus nudicornis, an interspecific value comparable to those observed among four other species of Eupolybothrus which, combined with a low intraspecific divergence (0.3–1.14%), supports the morphological diagnosis of Eupolybothrus kahfi as a separate species. This is the first troglomorphic myriapod to be found in Tunisia, and the second troglomorph lithobiomorph centipede known from North Africa. Eupolybothrus nudicornis is redescribed based on abundant material from Tunisia and its post-embryonic development, distribution and habitat preferences recorded. Eupolybothrus cloudsley-thompsoni Turk, 1955, a nominal species based on Tunisian type material, is placed in synonymy with Eupolybothrus nudicornis. To comply with the latest technological developments in publishing of biological information, the paper implements new approaches in cybertaxonomy, such as fine granularity XML tagging validated against the NLM DTD TaxPub for PubMedCentral and dissemination in XML to various aggregators (GBIF, EOL, Wikipedia), vizualisation of all taxa mentioned in the text via the dynamically created Pensoft Taxon Profile (PTP) page, data publishing, georeferencing of all localities via Google Earth, and ZooBank, GenBank and MorphBank registration of datasets. An interactive key to all valid species of Eupolybothrus is made with DELTA software.

Interlinking journal and wiki publications through joint citation: Working examples from ZooKeys and Plazi on Species-ID

Abstract Scholarly publishing and citation practices have developed largely in the absence of versioned documents. The digital age requires new practices to combine the old and the new. We describe how the original published source and a versioned wiki page based on it can be reconciled and combined into a single citation reference. We illustrate the citation mechanism by way of practical examples focusing on journal and wiki publishing of taxon treatments. Specifically, we discuss mechanisms for permanent cross-linking between the static original publication and the dynamic, versioned wiki, as well as for automated export of journal content to the wiki, to reduce the workload on authors, for combining the journal and the wiki citation and for integrating it with the attribution of wiki contributors.

Revolving SEM images visualising 3D taxonomic characters: application to six species of the millipede genus Ommatoiulus Latzel, 1884, with description of seven new species and an interactive key to the Tunisian members of the genus (Diplopoda, Julida, Julidae)

Abstract A novel illustration technique based on scanning electron microscopy is used for the first time to enhance taxonomic descriptions. The male genitalia (gonopods) of six species of millipedes are used for construction of interactive imaging models. Each model is a compilation of a number of SEM images taken consecutively while rotating the SEM stage 360°, which allows the structure in question to be seen from all angles of view in one plane. Seven new species of the genus Ommatoiulus collected in Tunisia are described: Ommatoiulus chambiensis, Ommatoiulus crassinigripes, Ommatoiulus kefi, Ommatoiulus khroumiriensis, Ommatoiulus xerophilus, Ommatoiulus xenos, and Ommatoiulus zaghouani spp. n. Size differences between syntopic adult males of Ommatoiulus chambiensis and Ommatoiulus xerophilus spp. n. from Châambi Mountain are illustrated using scatter diagrams. A similar diagram is used to illustrate size differences in Ommatoiulus crassinigripes, Ommatoiulus khroumiriensis spp. n. and Ommatoiulus punicus (Brölemann, 1894). In addition to morphological differences, the latter three species display allopatric distribution and different habitat preferences. A dichotomous interactive key with a high visual impact and an intuitive user interface is presented to serve identification of the 12 Ommatoiulus species so far known from Tunisia. Updates on the North African Ommatoiulus fauna in general are presented.

A review of the millipede genus Sinocallipus Zhang, 1993 (Diplopoda, Callipodida, Sinocallipodidae), with notes on gonopods monotony vs. peripheral diversity in millipedes

Abstract The millipede genus Sinocallipus is reviewed, with four new cave-dwelling species, Sinocallipus catba, Sinocallipus deharvengi, Sinocallipus jaegeri and Sinocallipus steineri, being described from caves in Laos and Vietnam. With the new records the number of species in the genus reaches six and the genus range is extended to Central Vietnam and North and Central Laos. Both, Sinocallipus jaegeri from Khammouan Province in Laos and Sinocallipus simplipodicus Zhang, 1993 from Yunnan, China, show high level of reduction of eyes, which has not been recorded in other Callipodida. Peripheral characters such as the relative lengths of antennomeres, the number of ocelli, the number of pleurotergites or even the shape of paraprocts and the coloration seem to provide more information for the distinction of the species than do the relatively uniform gonopods. The differences in gonopods mainly concern the shape and length of cannula, the length and shape of coxal processes g and k, and the number of the acicular projections of the femoroid. An explanation is offered for the function of the trochanteral lobe of 9th leg-pair. It provides mechanical support for the cannula and seems to assist sperm charge and insemination during copulation. An identification key to the species in the genus is produced to accommodate the new species. The new species descriptions were automatically exported at the time of publication to a wiki (www.species-id.net) through a specially designed software tool, the Pensoft Wiki Convertor (PWC), implemented here for the first time together with a newly proposed citation mechanism for simultaneous journal/wiki publications.

A new cave‐dwelling millipede of the genus Bollmania Silvestri, 1896 from Yunnan, China, with remarks on the reduction of the second female leg‐pair (Diplopoda: Callipodida: Caspiopetalidae)

Bollmania beroni sp. n., described from a cave in Jianshui County, Yunnan, China is the first true troglo‐ and hygrophilic species in the genus. The new locality extends the range of Bollmania ca 2500 km towards SE, ca 1700 km SW of the only other Chinese record. Notes are given on B. orientalis (Silvestri, 1895), B. nodifrons Lohmander, 1933 and B. oblonga Golovatch, 1979, based on new material from Turkmenistan and Tajikistan, and on two unnamed, probably new species from Afghanistan. An updated key to the eight described species is presented. Original observations and illustrations of second female legs in various callipodid genera are presented, along with a literature review of this character, which has so far received little attention from taxonomists.

From text to structured data: Converting a word- processed floristic checklist into Darwin Core Archive format

Abstract The paper describes a pilot project to convert a conventional floristic checklist, written in a standard word processing program, into structured data in the Darwin Core Archive format. After peer-review and editorial acceptance, the final revised version of the checklist was converted into Darwin Core Archive by means of regular expressions and published thereafter in both human-readable form as traditional botanical publication and Darwin Core Archive data files. The data were published and indexed through the Global Biodiversity Information Facility (GBIF) Integrated Publishing Toolkit (IPT) and significant portions of the text of the paper were used to describe the metadata on IPT. After publication, the data will become available through the GBIF infrastructure and can be re-used on their own or collated with other data.

A common registration-to-publication automated pipeline for nomenclatural acts for higher plants (International Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank).

Abstract Collaborative effort among four lead indexes of taxon names and nomenclatural acts ( International Plant Name Index (IPNI), Index Fungorum, MycoBank and ZooBank) and the journals PhytoKeys, MycoKeys and ZooKeys to create an automated, pre-publication, registration workflow, based on a server-to-server, XML request/response model. The registration model for ZooBank uses the TaxPub schema, which is an extension to the Journal Tag Publishing Suite (JATS) of the National Library of Medicine (NLM). The indexing or registration model of IPNI and Index Fungorum will use the Taxonomic Concept Transfer Schema (TCS) as a basic standard for the workflow. Other journals and publishers who intend to implement automated, pre-publication, registration of taxon names and nomenclatural acts can also use the open sample XML formats and links to schemas and relevant information published in the paper.