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We are pleased to announce that after almost two years of testing ZooKeys was accepted for archival and display in PubMedCentral, the wold’s leading archive for biomedical literature, based at the National Library of Medicine (NLM) of the USA. Here is a link to ZooKeys’ articles on PMC.

Thus, ZooKeys becomes the first journal in biodiversity science to use a domain-specific extension (TaxPub) of the general NLM mark up schema that permits automatic extraction and retrieval of specific information on biological taxa, such as taxon treatments and their features from an article’s text.

We hope that the experience accumulated by ZooKeys will be used by other taxonomic journals to make biodiversity information openly accessible and easy to use – a process that has been inspired by Donat Agosti and the Plazi team.

A team of researchers from the University of the Free State in South Africa (René Fourie and Charles Haddad) and the Royal Museum for Central Africa in Belgium (Rudy Jocqué) discovered very poorly known purse-web spiders of the genus Calommata in Africa. Four of the species described are new to science. The study was published in the open access journal ZooKeys.

What is really unique about purse-web spiders is that, in contrast to trapdoor spiders, they do not construct a structure to close the burrow. Instead, they build a purse-shaped web of dense silk that covers a chamber in which the spider waits for wandering prey to step on the web, before impaling it from beneath with its exceptionally long fangs.

Little is known on the biology of these small spiders as they are extremely difficult to locate in nature. The burrows of the African species have never been photographed, and the first ever photograph of a live African Calommata male, captured in a pitfall trap, was taken only last year by Ian Engelbrecht.  The spider shown on the photo (Calommata transvaalica male) is only 6.3 mm in length.

“While Calommata spiders have been collected elsewhere in Africa throughout the last century, albeit on rare occasions, our study was prompted by the recent rediscovery of these spiders in South Africa, nearly eight decades since the last specimen was collected here in 1923. Currently six African species are recognised, with an additional six species from East Asia and Israel.“  the author Charles Haddad said. 

The new discovery is expected to shed light on the evolutionary history of these spiders, known from two distant geographical regions, and to draw attention to the urgent need for their conservation. These spiders are mostly  threatened by habitat loss and urbanization.

Spanish researchers from the University of Leon (Nicolás Pérez Hidalgo and M. Pilar Mier Durante) have discovered the plant lice Schizaphis piricola (Matsumura) in Madrid, Spain from a photography displayed on a social network platform: “Biodiversidad Virtual” (Ángel Umaran). The results have been published recently in the open access journal ZooKeys and are available for free download.

“This discovery is yet another example of how social networks play an important role in our knowledge of biodiversity and the detection and/or monitoring of invasive or endangered species”, said the lead author Nicolás Pérez Hidalgo.

Schizaphis piricola is the 103rd adventive plant lice species recorded in Europe and is probably introduced in other part of the continent as well. The aphid lives on pears and alternates with aquatic plants during the summer. The direct action of feeding by the aphids, and the indirect damage caused by the honeydew they excrete on the leaves, can affect the normal growth of pear trees.

Over the last few weeks, ZooKeys has published papers whose taxon treatments have been uploaded in wiki format to Species ID. Now the conversion to wiki has been automated and was described  in a recently published forum paper complemented by a sample paper, as well as by examples from previously published  PhytoKeys papers.

The proposed citation format gives proper credit both to the authors of the original description and to those who later contributed to the wiki version, within a combined reference displayed on the top of each wiki taxon page (see examples below). In addition, the URL addresses of the wiki pages of the (re-)described taxa are published in the journal paper, directly below the ZooBank LSIDs, thereby providing a permanent cross-linking between the journal description and its versioned wiki page.

To demonstrate the range of original sources to which this approach might be applicable, taxon treatments previously published in PLoS ONE, Zootaxa and other journals have been uploaded to the wiki from the Plazi Treatment Repository, including such extracted from the historical literature (e.g.,  from Grandidier’s "Histoire Physique, Naturelle et Politique de Madagascar", published in 1891).

We hope that the reconciliation of "static" and "dynamic" versions of a published treatment on a dedicated wiki page through a single citation record will increase the citation rates, discovery and exposition of original descriptions. The proposed workflow and citaion mechanism will also revive historical treatments on wiki for further updates and revisions.
 
There are some topics that need further to be explored, such as handling multiple treatmens per a taxon, or developing a future reputation system on this wiki that will eventually differentiate spelling corrections and similar "small" edits from contributions that actually added original data and updated or otherwise improved existing ones.
 
Source: ZooKeys (Stoev and Enghoff 2011)
http://species-id.net/wiki/Sinocallipus
http://species-id.net/wiki/Sinocallipus_catba
http://species-id.net/wiki/Sinocallipus_deharvengi
http://species-id.net/wiki/Sinocallipus_jaegeri
http://species-id.net/wiki/Sinocallipus_simplipodicus
http://species-id.net/wiki/Sinocallipus_steineri
http://species-id.net/wiki/Sinocallipus_thai

Source: ZooKeys (Bantaowong et al. 2011)
http://species-id.net/wiki/Amynthas_phatubensis
http://species-id.net/wiki/Amynthas_tontong
http://species-id.net/wiki/Amynthas_borealis
http://species-id.net/wiki/Amynthas_srinan

Source: PhytoKeys (Kress et al. 2010)
http://species-id.net/wiki/Larsenianthus
http://species-id.net/wiki/Larsenianthus_wardianus
http://species-id.net/wiki/Larsenianthus_careyanus
http://species-id.net/wiki/Larsenianthus_assamensis
http://species-id.net/wiki/Larsenianthus_arunachalensis

Source: PhytoKeys (Knapp 2010)
http://species-id.net/wiki/Solanum_kulliwaita
http://species-id.net/wiki/Solanum_dillonii
http://species-id.net/wiki/Solanum_oxapampense
http://species-id.net/wiki/Solanum_verecundum

Source: Plazi Treatment Repository
http://species-id.net/wiki/Nixonia_masneri
http://species-id.net/wiki/Anochetus_boltoni
http://species-id.net/wiki/Formica_herculeana
http://species-id.net/wiki/Camponotus_imitator
http://species-id.net/wiki/Chromis_abyssus
http://species-id.net/wiki/Phrynoponera_pulchella

A dedicated team of specialists in beetle systematics from around the globe have collaborated in a comprehensive, nearly 1000-pages monograph, of what is known about the higher classification and nomenclature of beetles, producing a complete catalogue of the nearly 5000 known extant and fossil high-level classification names for the first time. The data are presented in a classification framework and the publication dates are given for the majority of the more than 2500 references cited, in order to assess both availability and priority of the names.  A synoptic classification of world Coleoptera to the level of subtribes is provided as well.

The monograph is published in open access and is free to anyone to download, read, distribute and use and is also available in hardcover from the publisher.

One of the goals of these works is to provide a foundation of valid, accepted names, which will alleviate the unnecessary proposal of new taxa, facilitate decisions on priority, promote long-term stability of the classification, and pave the way for the ongoing transition of classical taxonomy into taxonomy of the digital age, or cybertaxonomy.

Although some nomenclatural problems will still need to be addressed in the future, this monograph, the largest of its kind in the zoological literature, will hopefully go a long way towards achieving the long-term stability of beetle nomenclature that is necessary for a coherent handling of names by largest international bioinformatics platforms such as Global Names Architecture (GNA), Global Biodiversity Information Facility (GBIF), Catalogue of Life and others.

Bouchard P, Bousquet Y, Davies AE, Alonso-Zarazaga MA, Lawrence JF, Lyal CHC, Newton AF, Reid CAM, Schmitt M, Ślipiński SA, Smith ABT (2011) Family-group names in Coleoptera (Insecta). ZooKeys 88: 1-972, doi: 10.3897/zookeys.88.807.

On March 11th, Pensoft published issue No. 8 of Subterranean Biology. The publication of this journal is the continuation of the previous Mémoires de Biospéologie (volume 63), formely directed by Christian Juberthie, France. The publication of the Mémoires de Biospéologie was the continuation of yet another journal: Notes Biospéologiques (Edited by R. Jeannel at the Muséum d’Histoire Naturelle then by the CNRS) and the Annales de Spéléologie (Edited by the CNRS) and particularly a special series Ann. Spéléol., Supplt. published by the Laboratoire Souterrain du CNRS.

Subterranean Biology is the fifth journal that moves to Pensoft publishes on behalf a scientific society, Société Internationale de Biospéologie (SIBIOS) / International Society for Subterranean Biology (ISSB) and will benefit from the innovative methods in publication and dissemination of scientific information, implemented through ZooKeys, PhytoKeys, and others of Pensoft’s own journals.

Subterranean Biology considers for publication original scientific papers dealing with any aspect of subterranean ecosystems and their components focusing on biology, ecology, evolution, conservation and all aspects of subterranenan life.

The journal created its own Twitter, Facebook, and Mendeley  profiles in addition to the RSS and email alerts provided on Pensoft’s website. Despite the contradicting opinions on the role of social networks, all these profiles greatly help to keep the reader informed on all published papers and news coming from the journal’s website.

In case the reader is or intends to become a member of any of these social networks, it would be really helpful to  suggest the journal to be followed by friends and colleagues, to increase the range of users unforeseen before just by few clicks! This could happen by clicking the button "Follow" in Twitter. In Facebook, one could share the journal’s page with friends through the "Share" link at bottom left side of the page; thereafter one can then choose to share it via a post on their profiles, which may appear in their friends’ News Feeds, or with specific friends via a message. In the academic network Mendeley, there is a "Share this group" box at bottom right side of the journal’s page.

ZooKeys authors Sam Heads, of the Illinois Natural History Survey, University of Illinois and Léa Leuzinger of the University of Fribourg, Switzerland, have discovered a 100 million-year-old fossil from a group of large, carnivorous, cricket-like insects that still exist today in southern Asia, northern Indochina and Africa.

“Schizodactylidae, or splay-footed crickets, are an unusual group of large, fearsome-looking predatory insects related to the true crickets, katydids and grasshoppers, in the order Orthoptera” said University of Illinois entomologist and lead author Sam Heads.

The find is from a fossil bed in Brazil. Although the specimen is different from modern splay-footed crickets, its general features are almost the same, revealing that the genus has been in evolutionary stasis for 100 million years.

The article, published in ZooKeys, vol. 77 (see also the wiki page of the species Schizodactylus groeningae) corrects the classification of another such fossil and shows that the genus has experienced almost no morphological change since the Early Cretaceous Period, a time when dinosaurs still lived, just before the breakup of the supercontinent Gondwana.

Evolutionary stasis is a common phenomenon at higher levels of the Linnaean system of biological classification (class, order and family). A body plan evolved in a kind of species, and found to work very well, is then adopted in slightly different forms by species after species. The truly extraordinary thing about the new fossil is that it is so much like its modern counterpart that it can be assigned to an existing genus – the lowest level of classification above a species – rather than to some higher taxonomic group, as is usually the case.

The news of this discovery provoked quite a reaction among scientific bloggers and newsgroups, being covered by the Economist; LiveScience; AstroBiology; NBC; Yahoo; Softpedia; Science Daily; Science Centric; PhysOrg: University of Fribourg; der Standard and others.

It was also covered on the Discovery Channel news show Daily Planet, and a clip is available to watch here (fast forward to 6 mins 50 secs).

ZooKeys published a large taxonomic revision (Talamas et al. 2011) where all occurrence data and the taxon checklist have been published both in text and also as supplementary files in Darwin Core Archive format. Such an approach permits occurrence data to be downloaded, indexed, published through the GBIF data portal and others, used and re-used. The present monograph may serve as a sample to follow. It also may help in fostering the links between the data creators and scholarly publishers.

Darwin Core Archive (DwC-A) is an international biodiversity informatics data standard and the preferred format for publishing data through the Global Biodiversity Information Facility (GBIF) network. Each Darwin Core Archive consists of at least three files: (1) one or more data files keeping all records of the particular dataset in a tabular format such as a comma-separated or tab-separated list; (2) the archive descriptor (meta.xml) file describing the individual data file columns used and mapping them to DwC terms; and (3) a metadata file describing the entire dataset which GBIF recommends to be EML (Ecological Metadata Language) 2.1.1 based. The format is defined in the Darwin Core text guidelines. Darwin Core is no longer strictly bound to occurrence data, and together with Dublin Core (on which its ideas are based), it is used by GBIF and others to encode data about organism names, taxonomies and species information.

The Darwin Core Archive dataset of the present paper was simultaneously published in and is also available through the GBIF’s  Integrated Publishing Toolkit (IPT) –
http://gbrds.gbif.org/browse/agent?uuid=12a6bf1f-f66e-408c-8c6c-771af210e6a8 .

ZooKeys and PhytoKeys would like to encourage taxonomists to review this revision and consider publishing your own data in conjunction with your manuscript.  The journals provide a ready-made solution for supporting this.

On February 8th,  Pensoft published the first gold Open Access and NLM Taxpub-based issue of the Journal of Hymenoptera Research. It is one of the first journals that Pensoft publishes for a scientific society  – The International Society of Hymenopterists – besides its own in-house journals (www.pensoft.net/journals), such as Zookeys. The implications are going beyond changing from a traditional pdf to a semantically enhanced version allowing immediate distribution of its content to a set of external aggregators such as Encylopedia of Life,  Plazi, Wikispecies or the Global Biodiversity Information Facility (GBIF), and so on.

The Journal of Hymenoptera Research will be published in four different formats: (a) Print format, (b) PDF format, identical to the print version, (c) Semantically enhanced HTML to provide interactive readings and links to external resources, and (d) XML version to be archived in PubMedCentral and other archives, to facilitate future use and reuse of the content. One may learn more on the advanced technologies of publication and dissemination from the journal’s Press Release. 

The Journal of Hymenoptera Research created its own Twitter, Facebook , and Mendeley  profiles in addition to the RSS and email alerts. Despite the contradicting opinions on the role of social networks, all these profiles greatly help to keep you informed on all published papers and news coming from the journal’s website.

If you are or intend to become a member of any of these social networks, it would be really helpful if you suggest the journal to be followed by your friends and colleagues, to increase the range of users unforeseen before, just by few clicks! This could happen by clicking the button "Follow" in Twitter. In Facebook, you could share the journal’s page with friends through the "Share" link at bottom left side of the page. You can then choose to share it via a post on their profiles, which may appear in their friends’ News Feeds, or with specific friends via a message. In the academic network Mendeley , there is a "Share this group" box at bottom right side of the journal’s page.

ZooKeys published a paper (Hendrich L, Balke M (2011) A simultaneous journal / wiki publication and dissemination of a new species description: Neobidessodes darwiniensis sp. n. from northern Australia (Coleoptera, Dytiscidae, Bidessini). ZooKeys 79: 11–20. doi: 10.3897/zookeys.79.803) showing simultaneous description of a new species and creation of a wiki page for the taxon on www.species-id.net. The link to the wiki page (www.species-id.net/wiki/Neobidessodes_darwiniensis) is published in the original description under the ZooBank’s LSID, so that readers may always link to the wiki page to see if there is a new information on the taxon there. Vice versa, readers of the wiki page will have always the possibility to link to the original journal description that will stay unchanged as in any other conventional journal article.

While the original authors should always be credited through citing the journal article, further contributors to the wiki page (either the authors themselves or other interested students of that taxon) may edit/add content and be credited consequently as well. Conseguent changes could be tracked by using the wiki "page history" option.

We consider that such an approach could help in resolving the lively discussed contradiction between the "fixed" character of conventional academic publications and the dynamic nature of scientific research and of Internet as media.

Species-id.net is a wiki-based environment that aims at creating species pages (descriptions, data on ecology, biology, distribution, keys, etc.) in addition to Wikispecies (catalogue) and Wikimedia Commons (image repository), as well as to any other biodiversity platform  that may wish to link to it. Species-id is expected to be used/edited mostly by biologists with professional interests in a particular taxon.