Blog

Molecular data have shown that three Australian Cucurbitaceae species initially collected in 1856 but never accepted as separate species are distinct from each other and that one of them is the closest relative of the honeymelon, Cucumis melo. The names for these species are sorted out in a study published in the open access journal PhytoKeys.

Research published in the Proceedings of the National Academy of Sciences, USA (DOI: 10.1073/pnas.1005338107) last year had shown that northern Australia harbours the sister species of the honeymelon, Cucumis melo, which previously had been hypothesized to occur in Africa.  It turned out that the Australian honeymelon relative had in fact been collected and named Cucumis picrocarpus by one of the fathers of Australian botany, Ferdinand von Mueller, in 1856, but then been erroneously synonymized. The same thing happened with another of Mueller’s discoveries, this one being a species of loofah (the genus Luffa), which had was been erroneously synonymized and was then forgotten until 2011. Matters were complicated by some of Mueller’s 1856 collections arriving in the herbarium of the Royal Botanical Gardens Kew in disarray, so that two species were mounted on one and the same herbarium sheet. This naturally led to a confused idea of the morphology of the supposed species.

The researchers sorted out what is what on the Kew herbarium sheet, which then received an additional new barcode number assigned by the Kew herbarium to reflect that it carries two plant species, not just one. A high-resolution color photo of this historically interesting herbarium sheet is contained in the paper.

The study provides an example of the continuing need to link herbarium science with molecular results to sort out the names and wild relatives of economically important groups, such as melons and loofahs.

Original Source: Telford IRH, Schaefer H, Greuter W, Renner SS (2011) A new Australian species of Luffa (Cucurbitaceae) and typification of two Australian Cucumis names, all based on specimens collected by Ferdinand Mueller in 1856. PhytoKeys 5: 21–29. doi: 10.3897/phytokeys.5.1395

The Nomenclature Section of the 18th International Botanical Congress in Melbourne, in July 2011, proposed and approved sweeping changes to the way scientists name new plants, algae, and fungi. To demonstrate the efficiency of electronic publishing, the first open access plant taxonomy journal PhytoKeys published a correspondence note by a team of botanists from various USA institutions (Smithsonian Institution, The Missouri Botanical Garden, The Chicago Botanical Garden, and The Field Museum of Chicago), led by Dr James Miller from the New York Botanical Garden. The correspondence was written, submitted, edited, proofread, and published by PhytoKeys during the congress in just four days.

The changes in the International Code of Botanical Nomenclature begin on the cover of the document: the title was broadened to make explicit that the Code applies not only to plants, but also to algae and fungi. The new title is the International Code of Nomenclature for algae, fungi, and plants (ICN). In addition, for the first time in history the Code will allow for the electronic publication of names of new taxa.  In an effort to make the publication of new names more accurate and efficient, the requirement for a Latin validating diagnosis or description was changed to allow either English or Latin for these essential components of the publication of a new name.  Both of these latter changes will take effect on 1 January 2012.

The nomenclatural rules for fungi will see several important changes, the most important of which is probably the adoption of the principle of “one fungus, one name.” Paleobotanists will also see changes with the elimination of the concept of “morphotaxa” from the Code, that is the different names for one and the same species described after different parts of a fossil, should now be united under one name.

“The electronic publishing of new names will not only facilitate the taxonomists and the publishers”, said Dr W. John Kress from the Smithsonian Institution, Editor-in-Chief of PhytoKeys, “but this innovation will make the whole process of scientific discovery and description of new plants and fungi much more efficient, rapid and freely available for anyone to read and use. As natural habitats are degraded at an ever faster rate, it is crucial that botanists speed-up their work on finding and describing new species of plants before they are threatened with extinction”!

“Although the journal PhytoKeys has taken a leading role in electronic publishing of new plants while at the same time establishing an archival agreement with PubMedCentral of the National Library of Medicine of the US, we shall continue to deposit a full-color printed version of the journal in the six leading botanical libraries of the world, situated in the USA, UK, Russia, and China. Such a practice will certainly comfort those who worry about the perpetuity of electronic publications over time and will guarantee safe preservation of the published and printed information” adds Dr Lyubomir Penev, Managing Editor of PhytoKeys.

Original Source: Miller JS, Funk VA, Wagner WL, Barrie F, Hoch PC, Herendeen P (2011) Outcomes of the 2011 Botanical Nomenclature Section at the XVIII International Botanical Congress. PhytoKeys 5: 1-3. doi: 10.3897/phytokeys.5.1850

The press release on the special issue on the flora of Marquesas lslands (PhytoKeys 4) enjoyed more than 1200 visits by science journalists and media on the day we posted it! The potential number of end readers should be at a magnitude more.

Here is a Google link to see how it was reflected by media during the first day.

Our small press office is always keen to work with you on news announcements regarding your research findings published in PhytoKeys. It is important for all: for the authors, for the journal, and most importantly, for increasing public awareness of our science!

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.