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On the day when botanists decided to go for electronic publishing at the IBC2011 Melbourne, we have received a confirmation message from the National Library of Medicine of the USA, that PhytoKeys is accepted for archiving in PubMedCentral. In practice this means that all content of PhytoKeys will be archived as PDF and  XML files. In addition, all figures will be archived as separate files as well. The full text will be nicely readable on the PMC website and indexed through the huge machine of NLM, NCBI, etc.

MycoKeys – a new journal in systematic and biology of fungi (including lichens) was launched by Pensoft Publishers. The Editor-in-Chief of the new journal is Dr Thorsten Lumbsch from The Field Museum, Chicago assisted by an authoritative Editorial Team.  All content is published open access and is free to read, download, print, and distribute.

MycoKeys builds upon the success of its sister journals ZooKeys and PhytoKeys. It is more than a journal. It is a linked environment built upon its own content management software. MycoKeys offers numerous innovative ways to publish and disseminate information on the taxonomy and ecology of fungi (including lichens). The journal will provide mandatory registration of all new taxa in MycoBank. All new species will be supplied by the publisher to the Encyclopedia of Life (EOL), Globalnames, the Plazi Treatment Repository and the Wiki Species-ID on the day of publication of the article. The content of the article itself will be marked-up at the level of taxonomic descriptions, taxon names, citations and references, identification keys, georeferenced localities, and other taxon information.

MycoKeys  provides automated cross-linking through the Pensoft Taxon Profile of all taxa names mentioned on its pages with major indexing and aggregation platforms, such as the Global Biodiversity Information Facility (GBIF), Encyclopedia ofLife (EOL), the International Plant Name Index (IPNI), MycoBank, Index Fungorum, LIAS,  the National Center for Biodiversity Information (NCBI),  GenBank and Barcode of Life, the Biodiversity Heritage Library (BHL), PubMed, PubMedCentral,  Mendeley and many others.

MycoKeys  will provide a strong support and infrastructure for open data publishing, either as supplementary data and/or multimedia files or through internationally recognized indexers (GBIF) and data repositories, such as GenBank,  Barcode of Life, Dryad,  TreeBASE, Pangaea and others.

MycoKeys  will increase public awareness of science results in all aspects of mycology through its own established system of press releases and news announcements associated to published articles, to mass media, science and general blogs, social networks  and others.

"This in exciting time for systematic mycology, with rapid advances being made through molecular phylogenetic approaches, and the concomitant development of online information repositories. Increasingly effective ways of making the results of such work rapidly and widely available are required. MycoKeys is especially attractive as it provides a means of promptly disseminating substantial works with large numbers of coloured photographs at no cost to the authors. It does this with an innovative publishing approach, with fair open access policies, and most significantly a linked association with the world’s leading biodiversity platforms and databases. " said Professor David L. Hawksworth CBE, an Honorary President of the International Mycological Association.

"Undoubtedly, there is a growing need of an authoritative, cutting-edge technology journal in mycology to respond to the challenges of cybertaxonomy era and especially of the forthcoming semantic Web of linked data. The phenomenal success of ZooKeys in zoological systematics, and the excellent start of PhytoKeys in botany, on which experience MycoKeys builds upon, convinced a team of editors from leading mycological institutions to put efforts in establishing of a just new-generation mycology journal" adds Dr Thorsten Lumbsch, Editor-in-Chief of MycoKeys.

MycoKeys is published in four different formats: (1) high-resolution, full-color print version (2) PDF identical to the printed version; (3) HTML to provide links to external resources and semantic enhancements to published texts for interactive reading; (4) XML version compatible to PubMedCentral archiving and providing a machine-readable copy to facilitate future data mining. Neither restriction nor charges are imposed on the use of color illustrations.

MycoKeys will be presented at the International Botanical Congress (IBC2011, Booth No 21) in Melbourne (24-30 July 2011) and at all forthcoming international mycological congresses and conferences.  Mycologists and  lichenologists are welcome to submit manuscripts and discuss innovative publishing projects.

The Eucalantica genus belongs to the relatively primitive micro-moth group, Yponomeutidae. Six new species have been described by Mr. Jae-Cheon Sohn from the University of Maryland, College Park, USA and Mr. Kenji Nishida from Universidad de Costa Rica, San José, Costa Rica and published in the open access taxonomy journal Zookeys.
 
“Yponomeutid moths are important group in tracing the evolution of plant association in Lepidoptera. In spite of this importance, the family has been neglected by systematists and its biodiversity and phylogeny remain poorly understood” comments Mr. Sohn, Ph. D. candidate. Previous descriptive works have concentrated on the Holarctic and Australian faunas, the species diversity of yponomeutids from the Neotropics remains significantly underestimated as Eucalantica being a good example.

Eucalantica has been known by only a single Nearctic species. A review of the genus found six new species: E. costaricae, E. ehecatlella, E. icarusella, E. powelli, and E. pumila, all five from Costa Rica; E. vaquero from southern USA and Mexico. “Our discoveries suggest that a high diversity of Eucalantica occurs in the tropical highlands of Central America and the genus is more diverse and widely distributed than previously thought” adds Mr. Nishida.

The study demonstrates how poor is our knowledge on the real diversity of life on Earth. According to some estimates, only less than 20% of extant species are described. Thousands of species become extinct every year before they are named. Intensified taxonomic inventories and large-scale conservation measures may improve the situation towards more complete documentation and preservation of the wonderful world of biodiversity.

Original source: Sohn J-C, Nishida K (2011) A taxonomic review of Eucalantica Busck (Lepidoptera: Yponomeutidae) with descriptions of six new species. ZooKeys 118: 75–96. doi: 10.3897/zookeys.118.956

One of the smallest ever cave-dwelling ground beetles (Carabidae), has recently been discovered in two caves in the Rhodopi Mountains, Bulgaria, and described under the name Paralovricia beroni. The beetle is completely blind and is only 1.8-2.2 mm long. The study was published in the open access journal ZooKeys.

“When we saw this beetle for first time, it became immediately clear that it belongs to a genus and species unknown to science. Moreover, its systematic position within the family of Carabidae remained unclear for several years. After a careful study of its closest relatives Lovricia and Neolovricia, discovered in caves of the Dinaric Alps of Croatia, we came to the conclusion that all three genera  belong to a new subtribe which we describe now under the name Lovriciina”, commented Borislav Gueorguiev from the National Natural History Museum in Sofia, Bulgaria.

The species of this group are extremely rare and are known only from a few specimens. Lovricia jalzici was described in 1979 which is presently known only from a single female specimen found at the cave Gospodska pećina in Croatia;  Lovricia aenigmatica is known from one male and one female found at an unnamed pit near the peak Sveti Jure on the Biokovo Mountains and from another female from Lovrićija Jama II (Sveti Jure, Biokovo);  lastly, Neolovricia ozimei  was described also very recently (2009), and is known from one female found in the cave Špilja u Radinovcima in the Biokovo Mountains, Croatia.

The new discovery sheds light on the paleogeographic history of the Balkans. The currently known distribution of this group of beetles with common origin is widely disjointed between the Dinarides (West Balkans) to the Rhodopes (Еast Balkans).

“To explain this” – adds the lead author Pier Мauro Ciachino, from Torino, Italy –  “we must go back at least to the Late Oligocene (29-24 million years) where a continuum of land connected the Dinarides and Rhodopes mountains, allowing colonization by this phyletic lineage. Conversely, a paleogeographic event that could be placed at the origins of the separation of Paralovricia (in the Rhodopes) from a common ancestor – which then enabled a further differentiation of Lovricia and Neolovricia in the Dinarides – may be identified in the Early Miocene (20.5-19 Ma) when a strip of lowlands, covered with freshwater lakes and marshes seems to have divided the Dinarides from the Rhodopes.”

Original article:  Giachino P, Gueorguiev B, Vailati D (2011) A new remarkable subterranean beetle of the Rhodopes: Paralovricia n. gen. beroni n. sp. belonging to Lovriciina new subtribe (Coleoptera: Carabidae: Trechinae: Bembidiini). ZooKeys 117: 59-72. doi: 10.3897/zookeys.117.1612

A team of researchers from the Czech University of Life Sciences discovered four new species of jewel beetles (Buprestidae) from South-eastern Asia. This family of beetles is named for their particularly beautiful body and fascinating, shiny colours.

All new species belong to the genus Philanthaxia. Before the publication of this study, 61 species had been known from this genus. Currently, it comprises of 65 species, with a primarily Southeast-Asian distribution, except for two species extending to the Australasian region”, said Oto Nakládal, a co-author of the study.

The new species P. pseudoaenea occurs in Thailand, while P. jakli, P. chalcogenioides and P. lombokana are distributed on some Indonesian islands (Sumatra, Borneo, Lombok). The biology of all these species is unknown, just as the host plants, because all specimens were obtained from the locals.

The specialists also described sexual dimorphism of Philanthaxia iris. This species had originally been described on the basis of a single female from Java, and male specimens had not been known so far. Due to the specimen from a local collector, also from Java, it was possible to describe a male.

Inventories of biodiversity “hot-spots”, such as Southeast Asia, is extremely important because of the increasing extinction rates due to rapid changes of natural habitats. Several species become extinct before even known to science. “Mankind is not even able to evaluate the real losses associated with species extinction, because every individual species is, as a rule, a result of millions of years of evolution and adaptation and has therefore its unique role in the ecosystems” Nakládal added.

Original source: [Bílý S, Nakládal O (2011) Four new species of the genus Philanthaxia Deyrolle, 1864 from Southeast Asia and comments on P. iris Obenberger, 1938 (Coleoptera, Buprestidae, Thomassetiini). ZooKeys 116: 37–47. doi: 10.3897/zookeys.116.1403]

A team of researchers investigated a desert tortoise from the Southwest USA and northwestern Mexico. What was thought to be a simple problem in species identification turned out to be a very complex matter. Their investigations required forensic genetics and several other methods. In the end, they found it necessary to describe a new species. More than that, the discovery has very important implications for conservation and the development of the deserts of southern California.

The new species, Morafka’s Desert Tortoise (Gopherus morafkai) from Tiburon Island, Sonora, Mexico. Photo courtesy of Taylor Edwards, 2010.

Since the original description of Agassiz’s Land Tortoise, scientifically called Gopherus agassizii, facts have been nothing less than Dazed and Confused. One hundred and fifty years ago in 1861, James Graham Cooper described a new species of tortoise from the deserts of California. From the get-go, factual confusion has been more common than not. The publication date has consistently been inappropriately attributed to 1863, and even the original common name, Agassiz Land Tortoise, was inexplicably changed to the Desert Tortoise, a moniker that is commonly used today. But there’s more than just a new name.

For 150 years, Agassiz’s Land Tortoise has been masking the existence of at least two species whose distributions are restricted to either side of the Colorado River. Prof. Bob Murphy of the Royal Ontario Museum, Toronto, Canada and the Kunming Institute of Zoology, Chinese Academy of Sciences, and colleagues from the US Geological Survey, Arizona Research Laboratories, California Academy of Sciences, and Lincoln University have now started to unravel a Gordian knot. As if coming straight out of an episode of the TV series CSI, they went into the laboratory and obtained DNA data from the original 150-year-old type specimen, as well as from a more recently described species inhabiting the tip of the Baja California peninsula. The effort in forensic genetics documented that the named species was from California, and not Arizona as sometimes claimed. The enigmatic species from Baja California was previously thought to be a transplant from Tiburon Island, Sonora, Mexico, but turns out to be from California, or at least its founding mother was from there. All of this meant that the population in Arizona and adjacent Mexico was an unnamed, new species, one whose identity had been hidden for more than a century.

The new rock-dwelling species, Gopherus morafkai, is named for the late Prof. David J. Morafka, a pioneer in tortoise research. The results of the research are published in the open access journal ZooKeys.

More than a species description.
The recognition of Morafka’s Desert Tortoise means that Agassiz’s Desert Tortoise has lost a whopping 70 percent of its range! Arizona and adjacent Mexico can no longer serve as a genetic reservoir for the Western species. And given that the Western species was already listed as being threatened because of drastic decline in the number of individuals—a consequence of disease, urban expansion and habitat destruction—the description of the new species may turn up the heat on politicians and developers with respect to the massive construction of solar energy sites in prime Desert Tortoise habitat in the Mojave Desert. Perhaps this flagship centurion of the Southwest should be upgraded to Endangered status? Because Morafka’s Desert Tortoise has lost 30% of its range, perhaps protection for this species should be fast-tracked? Only time will tell.

The complete story remains untold. The knot remains untied. It is possible that Morafka’s Desert Tortoise may consist of two species. And so, back to the field and lab goes the team, inspired by knowing that Dave Morafka would be very pleased with the progress.

Pensoft Publishers announced their data publishing policies and guidelines for biodiversity data in response to the increasing demands from institutions and scientists to open scientific data to anyone who would be interested to use them.

“An opinion survey amongst the authors, readers and editors of the Pensoft journal ZooKeys carried out in April convinced us that the majority of respondents (84 %) are willing to publish their data, so that to make them available to anyone to use, share or integrate with other data” said Dr Lyubomir Penev, managing director of Pensoft Publishers. Among the most important incentives to publish data, the scientists mentioned  that  “open data increases transparency and the overall quality of science, the potential for collaborative research as well as an opportunity to increase academic credit in the form of citations. Therefore, providing a service to ensure a permanent publication record for published data is of key importance for the success of the project”, adds Dr Penev.

The core of the data publishing project is the concept of “Data Paper” developed in a cooperation with the Global Biodiversity Information Facility (GBIF). Data Papers are peer-reviewed scholarly publications that describe the published datasets and provide an opportunity for data authors to receive academic credit for their efforts. Data Paper manuscripts contain all the important elements of the descriptions of the data (metadata) and are submitted to publishers by a "push-a-button" mechanism. Once submitted, the manuscripts undergo peer-review and editorial process. The Global Unique Identifier (GUID) of the published dataset is cross-linked to the Digital Object Identifier (DOI) of the data paper, to allow further possibilities for data usage and data citation metrics.

Currently, Pensoft offers the opportunity to publish Data Papers describing (i) species occurrence data and checklists, (ii) Barcode-of-Life genome data and (iii) biodiversity-related software tools, such as interactive keys or others.

Pensoft reached an agreement for cooperation in data hosting and developing of data publishing workflows with the GBIF, the Dryad Data Repository and the Consortium for Barcode of Life.

“Data publishing becomes increasingly important and already affects the policies of the world’s leading science funding frameworks and organizations. Opening and integrating biodiversity data will be the future basis to increase efficiency of monitoring the processes of global change, conservation of nature and saving life on our planet” concluded Dr Vincent Smith, coordinator of the European Union FP7 project ViBRANT, in the framework of which a part of the work has been carried out.

Here is a related GBIF press release.
Ecology Metadata as Peer-Reviewed Data Papers article on sciencemag.org.

New findings of researchers from Tel-Aviv University (Gil Wizen and Avital Gasith) show that predator-prey interactions between ground beetles belonging to the genus Epomis and amphibians are much more complex than expected. The study was published in the open access journal ZooKeys.

“Amphibians are typical insect predators and their diet may include adult beetles, ground beetles in particular. The recently filmed successful attacks of the beetles on toads and frogs brought new insights on the amphibian-insect interactions, and documented the uncommon phenomenon of invertebrates preying on vertebrate animals,” said the senior author Gil Wizen.

Previous research has shown that Epomis larvae feed exclusively on amphibians and that this food source is essential for completion of their life cycle, while the diet of the adult beetles consists of terrestrial invertebrates as well as dead vertebrates. Wizen and Gasith’s current study shows that adult Epomis beetles can prey upon live amphibians, in addition to their regular diet.

According to the study, the genus Epomis is represented in Israel by two species: E. dejeani and E. circumscriptus. In the central coastal plain these species have similar distribution but do not occur in the same sites. The researchers recorded Epomis sharing shelter with amphibians during the day, but preying on them during the night. In the laboratory, predation behaviour of the adult beetles on five amphibian species was observed: the Green Toad (Bufo viridis), the Savignyi’s Frog (Hyla savignyi), the Levant Green Frog (Rana bedriagae), the Banded Newt (Triturus vittatus), and the Fire Salamander (Salamandra salamandra infraimmaculata). These observations showed that the diet of the two Epomis species overlaps only partially, with only one of the species (E. dejeani) preying on the Banded Newt.
 
The results of this study serve as additional evidence that Epomis beetles, both larvae and adults, are specialized predators of amphibians. Moreover, these beetles prey upon several amphibian species.

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.