Author: Pensoft Editorial Team

The open-access journal PhytoKeys – known for applying cutting edge technologies in publishing and dissemination to accelerate biodiversity research – is pioneering an electronic-only publishing workflow in a series of papers published over the course of the first week of January 2012 (see related press release).

As of the 1st of January 2012, extensive new changes took effect to the way plant scientists name new plants, algae, and fungi. Traditionally, the publication of new plant names, which is governed by the International Code of Botanical Nomenclature (ICBN), has never allowed publication of new names in anything other than print on paper. "Without such codes governing naming, there would be chaos, potentially impacting all branches of life sciences as the name of a species – be it a pathogen or a crop – represents a fundamental part of communicating knowledge about the natural world." said Dr. Sandra Knapp from the Natural History Museum London, Deputy Editor-in-Chief of PhytoKeys and author of the first electronic-only description of a new species, Solanum umtuma (a relative of tomatoes and many other important plant species), published on 1st of January 2012.

Lead authors, ex-pat New Zealander Dr. Matt von Konrat, based at the Field Museum in Chicago, and Dr. Peter De Lange, a plant scientist of the Department of Conservation, described – also in PhytoKeys – a new liverwort species from New Zealand under the revolutionary new rules that allow electronic publication.

"The electronic publishing of new names will not only facilitate the work of taxonomists and publishers", said Dr. W. John Kress from the Smithsonian Institution, Editor-in-Chief of the open access journal PhytoKeys, "but this innovation will accelerate the whole process of scientific discovery and description of new plants. 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"! "This is particularly pertinent to biodiversity hotspots, such as New Zealand", added both von Konrat and de Lange.

"Scientific papers published in PhytoKeys are freely downloadable for anyone to read and use, which is particularly significant in smaller countries like New Zealand, where many individual researchers and smaller institutions would not otherwise have access to many scientific serials", commented Prof. Lyubomir Penev, Founder and Managing Editor of PhytoKeys.

The newly described species is from a group of plants commonly referred to as liverworts. "This group of generally small-sized plants forms an incredibly conspicuous and significant component in New Zealand ecosystems. Based on our present knowledge, New Zealand may have almost 10% of the world’s species of liverworts – a little-known but widespread group of plants – which are related to those that first colonized land millions of years ago. That is an astonishing figure", said Dr. von Konrat.

New Zealand has a high proportion of endemic plant species that are not found anywhere else in the world. Some of these are like the Tuatara’s of the plant world, and are very significant towards our understanding of early land plant evolution. On the other hand, "the new species underscores how this enigmatic group of plants has been largely overlooked compared to seed plants and our fauna, especially on many of our offshore islands which harbour significant biodiversity" commented Dr. Peter de Lange.’

Liverworts are being increasingly recognized by everyday New Zealand people and world-wide as beautiful and important contributions to global biodiversity, as important environmental indicators and as potential indicators of global warming. Indeed, in 2011, two liverworts – the highly threatened Frullania wairua (itself known only from a seriously threatened tree, Bartlett’s Rata) and Lejeunea hawaikiana – received a top 10 listing in the annual New Zealand Plant Conservation Network "vote for your favourite plant" competition.

The new liverwort species, named Frullania knightbridgei, is particularly noteworthy because it involved national and international participants from universities, museums, and government departments", said von Konrat, "and was named after a prominent New Zealand conservationist, Phil Knightbridge, who earlier this year passed away." "The continued collaborative efforts between agencies such as the Department of Conservation and international research institutes such as The Field Museum and our partners, which currently have the resources to undertake expensive DNA analysis, will help uncover more of the as yet hidden biodiversity of this group of plants. The new species was first discovered in Rakiura/Stewart Island, an area of high rainfall, which is particularly significant as this group of plants, together with mosses, are able to soak up water like a sponge and critical in preventing deleterious effects of high rainfall," said von Konrat.

Original sources:
von Konrat M, de Lange P, Matt Greif M, Strozier L, Hentschel J, Heinrichs J (2012) Frullania knightbridgei, a new liverwort (Frullaniaceae, Marchantiophyta) species from the deep south of Aotearoa-New Zealand based on an integrated evidence-based approach. PhytoKeys 8: 13-36. doi: 10.3897/PhytoKeys.8.2496
Vorontsova MS, Knapp S (2012) A new species of Solanum (Solanaceae) from South Africa related to the cultivated eggplant. PhytoKeys 8: 1-11. doi: 10.3897/PhytoKeys.8.2462

The changes to the publication requirements of new names for algae, fungi and plants accepted at the XVIII International Botanical Congress in Melbourne in July 2011 initiated several important challenges to scientists, publishers and information specialists. To address practical questions arising from the Congress decisions, the open access journal PhytoKeys will publish a series of seven exemplar papers, one each day for the first week of 2012, starting from the 1st of January. The completed journal issue will be printed as an additional, though not mandatory, form of archiving on the 7th of January 2012.

"Electronic-only publishing in botany means that publishers do not need to produce printed versions of their journals to verify that a new name has been effectively published", said Dr Sandra Knapp from the Natural History Museum London, deputy editor of PhytoKeys and one of the authors of the first electronic-only description of a new African species of Solanum (the genus name for tomatoes and many other important plant species), published on the 1st of January 2012. "This important change, however, needs to be supported by strong, responsible practices by both publishers and authors, one of the most important being the proper archiving of the published paper" added Dr Knapp, "It is important to reiterate that these new rules do not mean new names can be published anywhere online; authors and publishers must work together."

"Beyond the mandatory deposition in trusted international electronic archives, such as the open access archive of the National Library of Medicine of the United States, the best possible guarantee for a proper preservation of the published information is open access. This allows an unlimited number of copies to be freely downloaded and stored in different institutional and private archives throughout the world, as well as being available to researchers, particularly in developing countries, who otherwise would not have access to many scientific serials", commented Dr Matt von Konrat from the Field Museum of Chicago, author of a new species of liverwort (closest living descendants of the earliest plants to grow on land) from New Zealand, to be published electronically on the 2nd of January 2012.

From the 1st of January 2012 PhytoKeys will publish taxonomic papers on the day they are approved by the editors. The electronic versions of the paper will be archived in PubMedCentral. In addition, each species description will be exported on the day of publication to the Encyclopedia of Life, to the Wiki environment Species-id. All biological data will be shared or linked with many international databasing initiatives. The bibliographic information in each paper will be harvested automatically by the Citebank database of the Biodiversity Heritage Library, the main German aggregator for biological information Vifabio.de and many others. Although not required by the Code, each new flowering plant species description will bear a unique identifier from the International Plant Names Index (IPNI), housed at Royal Botanical Gardens Kew in the UK.

Will PhytoKeys continue to produce a printed version? "Definitely, yes!", replied Prof. Lyubomir Penev, managing editor of the journal and founder of Pensoft Publishers, who launched PhytoKeys in 2009. "We shall not only maintain printing a full-color printed version of the journal, but will continue sending complimentary copies to leading botanical libraries to ensure 100 % secure archiving".

"PhytoKeys was the first journal to announce the new changes to the Code of Nomenclature for algae, fungi and plants in a paper published during the main sessions of the Melbourne Congress, bringing the news to a wide audience. Now we are proud to pioneer the practical implementation of these new rules, paving the way for other taxonomic journals to follow", concluded Dr W. John Kress from the Smithsonian Institution in Washington D.C., Editor-in-Chief of PhytoKeys.

Original source:
Vorontsova MS, Knapp S (2012) A new species of Solanum (Solanaceae) from South Africa related to the cultivated eggplant. PhytoKeys 8: 1-11. doi: 10.3897/PhytoKeys.8.2462

Additional Information:
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.5.185

A mysterious line where two millipede species meet has been mapped in northwest Tasmania, Australia. Both species are common in their respective ranges, but the two millipedes cross very little into each other’s territory. The ‘mixing zone’ where they meet is about 230 km long and less than 100 m wide where carefully studied.

The mapping was done over a two-year period by Dr Bob Mesibov, who is a millipede specialist and a research associate at the Queen Victoria Museum and Art Gallery in Launceston, Tasmania. His results have been published in the open access journal ZooKeys.

‘I have no idea why the line is so sharp’, said Dr Mesibov. ‘The boundary runs up and down hills, crosses rivers and different bedrocks and soils, and ignores vegetation type and climate differences. Its position and its sharpness seem to be the result of an unexplained biological arrangement between the two millipede species.’

Biogeographers use the term ‘parapatry‘ for the case where two species ranges meet but do not overlap, or overlap very little. Dr Mesibov said that parapatry has been reported before in other species of millipedes and in other terrestrial invertebrate animals, in Tasmania and elsewhere in the world. However, parapatric boundaries often parallel a geographical feature, such as a ridgeline, or a steep rainfall gradient.

‘There does not seem to be an ecological or a geographic explanation for this particular boundary, or for any part of it. It is also longer than any other parapatric boundary I know about. At 230 km, it is 50% longer than the boundary between England and Scotland, and the ‘border control’ is a lot better than what we humans can do.’

The two millipede species, Tasmaniosoma compitale and T. hickmanorum, are in the same genus and thought to be closely related. They were first scientifically described in 2010, by the same author and again in ZooKeys. The parapatric boundary was mapped as a background study for later investigations of speciation in this group of millipedes, and of the mechanism of parapatry.

SOURCE:
Mesibov R (2011) A remarkable case of mosaic parapatry in millipedes. In: Mesibov R, Short M (Eds) Proceedings of the 15th International Congress of Myriapodology, 18-22 July 2011, Brisbane, Australia. ZooKeys 156: 71–84. doi: 10.3897/zookeys.156.1893

PREVIOUS NEWS COVERAGE:
http://www.abc.net.au/news/2011-08-02/020811-millipedes/2821498 [Australian TV news story, and accompanying online text]

RELATED BACKGROUND:
Mesibov, R (2010) The millipede genus Tasmaniosoma Verhoeff, 1936 (Diplopoda: Polydesmida: Dalodesmidae) from Tasmania, Australia, with descriptions of 18 new species. ZooKeys 41: 31-80. doi: 10.3897/zookeys.41.420

MILLIPEDE WEBSITE LINKS:
Tasmanian Multipedes (a student/naturalist guide to the centipedes, millipedes and velvet worms of Tasmania)
http://www.polydesmida.info/tasmanianmultipedes

External Anatomy of Polydesmida (a student/naturalist guide to how Polydesmida millipedes are built; this is the group to which the two parapatric millipede species belong)
http://www.polydesmida.info/polydesmida/

Millipedes of Australia (a taxonomist’s resource – no images or identification keys)
http://www.polydesmida.info/millipedesofaustralia/

Field work by researcher Fred Kraus from Bishop Museum, Honolulu has found the world’s smallest frogs in southeastern New Guinea. This also makes them the world’s smallest tetrapods (non-fish vertebrates). The frogs belong to the genus Paedophryne, all of whose species are extremely small, with adults of the two new species – named Paedophryne dekot and Paedophryne verrucosa – only 8-9 mm in length. The study was published in the open access journal ZooKeys.

Previous research had led to the discovery of Paedophryne by Kraus in 2002 from nearby areas in New Guinea, but the genus was not formally described until last year (Kraus 2010, also in Zookeys). The two species described earlier were larger, attaining sizes of 10-11 mm, but the genus still represents the most miniaturized group of tetrapods in the world.

“Miniaturization occurs in many frog genera around the world,” said the author, “but New Guinea seems particularly well represented, with species in seven genera exhibiting the phenomenon.  Although most frog genera have only a few diminutive representatives mixed among larger relatives, Paedophryne is unique in that all species are minute.”  The four known species all inhabit small ranges in the mountains of southeastern New Guinea or adjacent, offshore islands.  Their closest relatives remain unclear.

The members of this genus have reduced digit sizes that would not allow them to climb well; all inhabit leaf litter, and their reduced digits may be a corollary of a reduced body size required for inhabiting leaf litter and moss.  Habitation in leaf litter and moss is common in miniaturized frogs and may reflect their exploitation of novel food sources in that habitat. The frogs’ small body sizes have also reduced the egg complements that females carry to only two, although it is not yet known whether both eggs are laid simultaneously or at staged intervals.

Original source:
Kraus F (2011) At the lower size limit for tetrapods, two new species of the miniaturized frog genus Paedophryne (Anura, Microhylidae). ZooKeys 154: 71–88. doi: 10.3897/zookeys.154.1963

References:
Kraus, F. (2010) New genus of diminutive microhylid frogs from Papua New Guinea. ZooKeys 48 (2010) : 39-59. doi: 10.3897/zookeys.48.446

The National Museum of Natural History, Smithsonian Institution in Washington, DC, has obtained and released DNA barcodes for 2,808 frozen tissue samples of birds. Of the 1,403 species represented by these samples, 1,147 species have not been barcoded previously. The data are deposited in GenBank and the Barcode of Life Data Systems and are described in a form of ‘project description’ of the data release in the open access journal ZooKeys.

“This data release increases the number of bird species with standard barcodes by 91%. It is even more important, however, that the data release and the formal description of the dataset have been announced in a scholarly publication, a ‘data paper’. It allows data creators to be credited for their work, and also communicates to other scientists that such a dataset has been released and is available freely for re-use in future studies”, said the lead author Dr David Schindel from the Consortium for Barcode of Life. "It also sets out the data creators’ near-term plans for the scholarly use of the data and asks others to respect their intent for a six-month period." The paper invites others to use the data for any number of purposes immediately, and to provide feedback on any inconsistencies they find. Schindel said: "We plan to publish a more full description and analysis of the dataset in the coming months, but we saw no reason to deny access to the community and to miss an opportunity for crowd-sourced data curation."

The paper has been published as part of a policy of rapid data release for genome information known as the ‘Fort Lauderdale Principles’ launched for large genomics projects by the Wellcome Trust in 2003. These principles describe a system of shared responsibility, that would be needed in order to create incentives to construct, publish and then use large public genome datasets such as that of the Human Genome Project.

The dataset represents samples from 27 countries (Argentina, Australia, Botswana, Brazil, Gabon, Greece, Guyana, Iceland, Johnston Atoll, Mariana Islands, Mexico, Mongolia, Myanmar, Pakistan, Panama, Papua New Guinea, Philippines, Puerto Rico, Russia, South Korea, St. Vincent, Swaziland, Sweden, United Kingdom, United States, Uruguay, and the former Soviet Union).

Original source:
Schindel D, Stoeckle M, Milensky C, Trizna M, Schmidt B, Gebhard C, Graves G (2011) Project Description: DNA Barcodes of Bird Species in the National Museum of Natural History, Smithsonian Institution, USA. ZooKeys 152: 87-91. doi: 10.3897/zookeys.152.2473

New findings by Virginie Stevens (CNRS), Jean Clobert (CNRS), Michel Baguette (Muséum National d’Histoire Naturelle) and colleagues show that interactions between dispersal and life-histories are complex, but general patterns emerge. The study was published as open access paper in the journal Ecology Letters.

As dispersal plays a key role in gene flow among populations, its evolutionary dynamics under environmental changes is particularly important. The inter-dependency of dispersal with other life history traits may constrain dispersal evolution, and lead to the indirect selection of other traits as a by-product of this inter-dependency.

Identifying the dispersal’s relationships to other life-history traits will help to better understand the evolutionary dynamics of dispersal, and the consequences for species persistence and ecosystem functioning under global changes. Dispersal may be linked to other life-history traits as their respective evolutionary dynamics may be inter-dependent, or, because they are mechanistically related to each other.

The authors identified traits that are predicted to co-vary with dispersal, and investigated the correlations that may constrain dispersal using published information on butterflies. The quantitative analysis revealed that (1) dispersal directly correlated with demographic traits, mostly fecundity, whereas phylogenetic relationships among species had a negligible influence on this pattern, (2) gene flow and individual movements are correlated with ecological specialisation and body size, respectively and (3) routine behaviours only affected short-distance dispersal. Together, these results provide important insights into evolutionary dynamics under global environmental changes, and are directly applicable to biodiversity conservation.

Specialist species with narrow tolerance to temperature are also those butterflies that have weak dispersal ability. For such species, the combination of habitat fragmentation and climate warming is thus a kind of ‘double penalty’. Those species should thus be the priority targets in conservation actions. Besides, these results show that the size of a butterfly is not a reliable proxy of most of the components of its ability to disperse across inhospitable parts of landscapes, and is particularly poor at describing species’ ability to maintain spatial gene flow.

Original source:
Ecology Letters, (2011) doi: 10.1111/j.1461-0248.2011.01709.x
http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2011.01709.x/abstract

Larkspurs, monkshoods, and aconites are plants, widely cultivated for their beauty and medicinal properties. They all belong to the Delphinieae, a natural group of 650-700 species ranging from Eurasia into North America, with a few species on tropical African mountains.

A broadly sampled molecular phylogeny for this group has revealed that three Mediterranean species constitute an ancient separate evolutionary line that is the sister group to all remaining Delphinieae. The British physician John Hill already recognized these species’ distinctness in 1756, and Jabbour and Renner here resurrect the genus name he had proposed for them.

Of the three species in Hill’s genus Staphisagria, one is an important medicinal plant found all around the Mediterranean basin, the other two are endemic to Corsica, Majorca, Sardinia, and the Archipelago of Hyères in the South of France. In an article in the open access journal Phytokeys, Jabbour and Renner from the Institute of Systematic Botany at the University of Munich illustrate and discuss the newly recognized genus, explaining how its three species share traits that fit neither in Delphinium nor in Aconitum, fitting with their long independent evolutionary history.

Original source:
Jabbour F, Renner SS (2011) Resurrection of the genus Staphisagria J. Hill, sister to all the other Delphinieae (Ranunculaceae). PhytoKeys 7: 21–26. doi: 10.3897/phytokeys.7.2010

The open access zoological journal ZooKeys published by Pensoft reported a substantial growth in 2011, in comparison to 2010, says an analysis dedicated to journal’s jubilee 150th issue, By the end of November 2011, the journal published more than 10,000 pages and 420 articles (to compare with 4,962 pages and 180 articles in 2010). Since its launch in July 2008, ZooKeys published more than 19,000 pages and 780 articles of valuable information on new discoveries in the fascinating world of animals (from mammals and birds to insects and corals). The growth rate will reach 120% by the end of the year.

In a field like taxonomy which constantly generates data, dissemination is one of the most crucial aspects. An open access journal has the benefit of easy distribution of information, leading to increasing relevance of the data, as it is being recognized by a larger audience.

ZooKeys is the first journal in the fields of biodiversity and taxonomy to implement a detailed schema for mark-up of its content, which allows automated extraction and dissemination of information from within the text of an article. The mark-up technology, through so called “semantic enhancements”, allows the user to add enormous additional information from external Web-based sources, which is updated in real time on query, during the reading process.

“ZooKeys is an amazing and true success story” said the journal’s Editor-in-Chief, Dr Terry Erwin from the Smithsonian Institution, Washington. “The key of the ZooKeys success is simple and  can be expressed easily: open access and perpetual innovations!”

The unique editorial workflow of ZooKeys was created and implemented in a close collaboration with the non-profit Swiss organization Plazi, and the National Library of Medicine in the USA. The Journal supplies information to the world’s largest biodiversity platforms, such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life, KeyCentral, as well as to wiki-based platforms such as Wikispecies, Wikimedia Commons, Species-ID, and many others.

“ZooKeys is not just a journal. It is an interactive environment that transforms the process of conventional publishing and sets up new standards in scholarly communication in biodiversity sciences. We are happy that our services help to describe so many still undiscovered species on Earth and to contribute to their identification and protection!” added the journal’s managing editor Dr Lyubomir Penev from the Bulgarian Academy of Sciences, Sofia.

Original source:
Erwin T, Stoev P, Georgiev T, Penev L (2011) ZooKeys 150: Three and a half years of innovative publishing and growth. In: Smith V, Penev L (Eds) e-Infrastructures for data publishing in biodiversity science. ZooKeys 150: 5–14. doi: 10.3897/zookeys.150.2431

Electronic infrastructures open new horizons for collaboration and acceleration of the research on world’s biodiversity. International collaborative platforms, such as scratchpads.eu,  yield  opportunities, unknown before, to scientists to put together historical and newly collected data coming from different sources and working groups, says a special issue of the open access journal ZooKeys presenting the results of the EU-funded project ViBRANT.

ViBRANT stands for “Virtual Biodiversity Research and Access Network for Taxonomy” and is a European Union e-infrastructure project running December 2010 to 2013 that will support the development of virtual research communities involved in biodiversity science. ViBRANT combines  the efforts of scientists from 17 European institutions to provide a more integrated and effective framework for those managing biodiversity data on the Web.

 
“ViBRANT is not only about e-infrastructures” commented the project coordinator Dr Vincent Smith from the Natural History Museum, London. “ViBRANT’s core mission is to mobilize the treasures of biological data accumulated over centuries of scientific discoveries and to open them for collaboration to all who are keen to describe, record and safe the life on our Planet!”

ViBRANT’s mission is clearly reflected by the collection of research and review articles published by the project partners but also by scientists from USA and Australia.  The value of this book is re-inforced by the exemplar papers that demonstrate how innovations in e-infrastructures are implemented in real time and on real data.

The book focuses on opening and publishing of biodiversity data, a process that is largely promoted and supported  by institutions, international organisations and governments because it allows the multiplication and intensification of efforts invested by the previous and contemporary generations of scientists.

The 150th jubilee issue of ZooKeys.

For more details, please contact:

Dr. Vincent S. Smith, Cybertaxonomist
The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
Web: http://vsmith.info/, http://scratchpads.eu/, http://phthiraptera.info/
E-mail: vince@vsmith.info, Tel: +44 (0) 207 942 5127

Dr D.McL. Roberts
Dept. Zoology, The Natural History Museum,
Cromwell Road, London SW7 5BD, Great Britain
Tel: +44 (0)20 7942 5086
Email: dmr@nomencurator.org
Web page: http://scratchpads.eu
http://www.nhm.ac.uk/research-curation/projects/euk-extreme/

Open access to information about biodiversity is of crucial importance to society, directly affecting areas such as conservation and climate change research and education. “Non-Commercial” restrictions on the reuse of this information are a major barrier to addressing these problems, says a review paper published in the open access journal ZooKeys.

Halting the loss of biodiversity demands that information on organisms, ecosystems, their properties, and their interactions, is easily found and readily available. This requires sharing. Creative Commons (CC) provides a set of licenses to facilitate this. However, Non-Commercial (NC) restrictions are commonly added to Creative Commons licences, intended to prevent commercial exploitation. The article shows that the ambiguity between “non-for-profit” and “non-commercial” prohibits many legitimate re-uses of NC licensed materials, and imposes significant risks that affect for-profit and not-for-profit organizations alike.

“The concept of ‘commercial advantage‘, the heart of the NC licenses, is very broad and ill defined” says lead author Dr Gregor Hagedorn from the Julius Kühn-Institute in Berlin, Germany. “It potentially excludes all public relation activities that increase the recognition of an organisation and may thus confer commercial advantages later on. Furthermore, the non-open NC licenses are usually incompatible with open Creative Commons licenses, severely restricting the use of NC licensed materials.”

The review arose from discussions within an EU funded infrastructure project (ViBRANT) that several authors of the article participate in, on how best to license materials produced within the project. To ensure the widest possible use of biodiversity information, the authors of the ZooKeys publication argue that publicly funded projects should use open CC licenses such as CC BY or CC BY-SA. These are used by most Open Access publishers, the Wikimedia Foundation projects, and many other open content initiatives.

Original source:
Hagedorn G, Mietchen D, Morris RA, Agosti D, Penev L, Berendsohn WG, Hobern D (2011) Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information. In: Smith V, Penev L (Eds) e-Infrastructures for data publishing in biodiversity science. ZooKeys 150: 127–149. doi: 10.3897/zookeys.150.2189

Part of the work was carried out within the European Union’s Virtual Biodiversity Research and Access Network initiative (ViBRANT).