Author: Pensoft Editorial Team

Zookeys, the first zoological journal to introduce automatic registration in ZooBank

The latest issue of ZooKeys – no. 346 – has been automatically registered in ZooBank on its day of publication last Friday. This marks the successful deployment of an automated registration-to-publication pipeline for taxonomic names for animals. The innovative workflow was jointly funded by the EU FP7 funded project pro-iBiosphere and a U.S. National Science Foundation project to develop the Global Names Architecture (DBI-1062441).

The process of post-publication recording and indexing of species names has a long tradition, in some cases dating as far back as the middle of 19th century. But now in the 21st century with the advance of modern technologies and the opportunity to publish taxonomic novelties online, the process of post-publication recording brought into focus the concept of automated pre-publication registration.

Why is this important? The proportion of ‘turbo-taxonomic’ papers describing hundreds of new species increases. Registration of hundreds of new species is an issue, however it is even more important that the final publication data of the pre-registered names are reported back to ZooBank on the day of publication.

Launched as an open access peer reviewed journal in 2008, to coincide and adopt from inception the International Code of Zoological Nomenclature changes for electronic publications, ZooKeys was the first journal to provide a mandatory in-house registration in ZooBank. Since 2008, it has contributed about one third of all names currently registered in ZooBank. With the adoption of the automated ZooBank registration, ZooKeyscontinues its mission to set novel trends in biodiversity publishing.

Implementation of automated workflows and invention of XML-based tools will facilitate the process of publication and dissemination of biodiversity information. It will pave the way for unification and streamlining the registration process, even more to building the next-generation e-infrastructure for a common global taxon names registry. Within the pro-iBiosphere project and in cooperation with Plazi that have created the TaxPub XML schema, an automated registration workflow for plants has already been established between the International Plant Names Index (IPNI) and the PhytoKeys journal, to be applied soon also for fungi between Index Fungorum and the journal MycoKeys.

Contact:

Dr. Richard Pyle
Bishop Museum, Honolulu
deepreef@bishopmuseum.org

An improved and expanded nomenclature for genetic sequences is introduced that corresponds with a ranking of the reliability of the taxonomic identification of the source specimens. This nomenclature is an advancement of the “Genetypes” naming system, which some have been reluctant to adopt because of the use of the “type” suffix in the terminology. The study was published in the open access journal Zookeys.

The use of genetic sequences has been increasing with each passing year but unfortunately, the separation between voucher specimens and genetic sequences is similarly growing. With increasing frequency, the link between the genetic sequences being used in analyses and the organisms from which they came is not being reported. The taxonomic determination remains solely the responsibility of the submitter of the sequences. Erroneous identifications are difficult to discover, and the perpetuation of the error in subsequent uses of the sequence data is nearly impossible to stop.

In the new nomenclature, genetic sequences are labeled “genseq,” followed by a reliability ranking (e.g., 1 if the sequence is from a primary type), followed by the name of the genes from which the sequences were derived (e.g., genseq-1 16S, COI). The numbered suffix provides an indication of the likely reliability of taxonomic identification of the voucher. Included in this ranking system, in descending order of taxonomic reliability, are the following: sequences from primary types – “genseq-1,” secondary types – “genseq-2,” collection-vouchered topotypes – “genseq-3,” collection-vouchered non-types – “genseq-4,” and non-types that lack specimen vouchers but have photo vouchers – “genseq-5.”

To demonstrate use of the new nomenclature, the authors of the study review recently published news species descriptions in the ichthyological literature that include DNA data and apply the GenSeq nomenclature to sequences referenced in those publications.

“Use of the new nomenclature and ranking system will improve integration of molecular phylogenetics and biological taxonomy and enhance the ability of researchers to assess the reliability of sequence data.”explains one of the authors Dr. Prosanta Chakrabarty, Museum of Natural Science, Louisiana State University. “We further encourage authors to update sequence information on databases such as GenBank whenever nomenclatural changes are made.”

Original Source:

Chakrabarty P, Warren M, Page LM, Baldwin CC (2013) GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources. ZooKeys 346: 29–41. doi: 10.3897/zookeys.346.5753

The supposedly widespread and variable Australasian liverwort species Radula buccinifera is nothing of the kind. The species was described in 1844, and reported for New Zealand in 1855. It has gone on to be the most commonly collected species in both countries, yet it doesn’t even occur in New Zealand, according to results of research led by Dr Matt Renner at Royal Botanic Gardens & Domain Trust.

Molecular and morphological evidence show that what was thought to be one species of leafy liverwort from Australia and New Zealand is in fact eight different species, and five of these are new to science. The study was published in the open access journal PhytoKeys.

The species is an Australian endemic restricted to the wetter parts of the south-east of the country. Records from the tropics are referable to other species, two of which are found only there. Another two species are endemic to Australia, and a third is shared between Australia and New Zealand. The species may have been confused because many appear similar, and are variable so overlap in form.

Better understanding of species diversity has implications for studies of biogeography, in that this ‘widespread species’ is actually a complex of geographically restricted species. Liverworts also contain many bioactive compounds, which exhibit a range of activity including anti-microbial and anti-retroviral properties, and the greater the recognized species diversity the greater the pool of potentially useful molecules.

“There may be no direct application of this research unless you are identifying liverworts, but direct application is only one kind of benefit, and solid taxonomic studies have many, the least of which is that we learn what is out there in the world around us.” comments the lead author Dr. Matt Renner.

Original Source:

Renner MAM, Devos N, Patiño J, Brown EA, Orme A, Elgey M, Wilson TC, Gray LJ, von Konrat MJ (2013) Integrative taxonomy resolves the cryptic and pseudo-cryptic Radula bucciniferacomplex (Porellales, Jungermanniopsida), including two reinstated and five new species. PhytoKeys 27: 1–113. doi: 10.3897/phytokeys.27.5523

A specimen preserved in a jar of alcohol in The Natural History Museum, London has remained the only record of the Mortlock Islands flying fox, one of the least known bat species on the planet, for over 140 years. That is until now. A team of bat biologists led by Dr. Don Buden from the College of Micronesia has collected new information about this “forgotten” species, and studied it in the wild for the first time. The study is reported today in the open access journal ZooKeys.

The original London specimen was collected in 1870 from the remote Mortlock Islands, a series of low-lying atolls and part of the Federated States of Micronesia in the west-central Pacific Ocean. British biologist Oldfield Thomas used this specimen to name the species Pteropus phaeocephalus in 1882. However, information uncovered by Dr. Buden proves that a German naturalist, voyaging on a Russian Expedition, got there first.

“We found a report written by F.H. Kittlitz in 1836 describing his expedition to the Pacific Islands in the late 1820s. In that report he describes the flying-foxes of the Mortlocks and names them Pteropus pelagicus. This means the species was named long before Thomas’s description in 1882.” said Buden.

According to internationally established rules for naming animals, the earliest available scientific name of a species must be officially adopted, so the Mortlock Islands flying fox is now correctly known as Pteropus pelagicus. Not only does Kittlitz correctly deserve credit for the discovery of the species, 50 years earlier than previously thought, but he can also be now credited for the “new” name. Furthermore, Buden and colleagues demonstrated that flying foxes from the nearby islands of Chuuk Lagoon, long regarded as a separate species (Pteropus insularis), are also best regarded as a subspecies of Pteropus pelagicus, showing that the species has a wider geographic distribution than previously realized.

New fieldwork in the Mortlock Islands revealed more than name changes. The ZooKeys article describes the first study of the behavior, diet, and conservation status of this flying fox, finding that the Mortlock Islands support a small population of 900 to 1200 bats scattered across a land surface of only 12 km² (4.6 square miles). Legal rules have brought better protection to the species, which was once heavily hunted. But the future of the species is still uncertain in its island home. Rising sea levels, generated by climate change, threaten the flying foxes’ habitat and food resources through flooding, erosion, and contamination of freshwater supplies.

“This remarkable study shows how much we have to learn about Pacific Islands mammals. “said Prof. Tim Flannery of Macquarie University in Sydney, who was not involved in the research. “Where there was darkness, Dr. Buden and colleagues have shed light.”

Co-authors of the ZooKeys study included Dr. Kristofer Helgen of the Smithsonian Institution in Washington, D.C., and Gary Wiles of the Department of Fish and Wildlife, Washington State.

 

Original source:

Buden DW, Helgen KM, Wiles GJ (2013) Taxonomy, distribution, and natural history of flying foxes (Chiroptera, Pteropodidae) in the Mortlock Islands and Chuuk State, Caroline Islands. ZooKeys 345: 97. doi:10.3897/zookeys.345.5840

The representatives of the Limacodidae moth family are widely known as slug moths due to the resemblance of their stunningly colored caterpillars to slug species. Within this popular family the Parasa undulata group is perhaps one of the most intriguing, due to the beautiful green wing pattern typical for those species. In a recent revision, published in the open access journal Zookeys, scientists describe two new species from the group and provide a first record of a conifer-feeding caterpillar.

The two new species, Parasa viridiflamma and Parasa minwangi described from China and Taiwan both have the distinguishable green pattern typical for the group. They have a wingspan of averagely around 2 – 2.5 cm and can be seen mainly in mid-elevations of mountains. The resemblance of the wing pattern of P. viridiflamma to mystical green flames has also inspired its name, derived from the Latin words viridis (green) and flamma (flame).

The revision of this group in Taiwan and China, compiled by Shipher Wu, National Taiwan University and Weichun Chang, Council of Agriculture, Taiwan, contains another intriguing discovery. The scientists provide the first record of a caterpillar from the group feeding exclusively on pine trees, Picea morrisonicola, in Taiwan.

“This case represents the first record of conifer-feeding behavior in this family as well as the first specialist herbivore in the genus. Meanwhile, the background match between Picea leaves and larval colouration is shared with other Picea-feeding insects. This phenomenon is worth further investigation in the aspect of convergent evolution of crypsis, or camouflaging, associated with a particular plant.” explains Shipher Wu, one of the authors.

Original Source:

Wu S, Chang W (2013) Review of the Parasa undulata (Cai, 1983) species group with the first conifer-feeding larva for Limacodidae and descriptions of two new species from China and Taiwan (Lepidoptera, Limacodidae). ZooKeys 345: 29. doi:10.3897/zookeys.345.6179

The open access model has created a range of new opportunities for the dissemination and popularization of scientific research, but many society- or institution-based academic journals continue on a subscription basis. Two of the success stories at Pensoft come from society journals which decided to go open access – the first one to join the Pensoft family Journal of Hymenoptera Research and the latest addition in our open access family Subterranean Biology.

In 2011, the International Society of Hymenopterists (ISH) decided to move their publication, the Journal of Hymenoptera Research (JHR), from a conventional, subscription-based model to open access with Pensoft Journal Systems (PJS 2.0). Subterranean Biology has decided to take full advantage from the complex open access model offered by Pensoft in spring, 2013.

At Pensoft, fully electronic and largely automated workflows are the norm. Content is published simultaneously in several formats (PDF, HTML and XML) that are complemented by options for print on demand of reprints or whole issues. From now on, the content in the journal will be fully linked and exported to taxonomic databases such as the Encyclopedia of Life, Species-ID and PubMed Central. The articles will also benefit from professional archiving in the world’s leading scholarly archives.

One of the main advantages experienced by society journals is a flexible schedule allowing an unlimited number of published articles per year, as opposed to the earlier restriction of a set number of issues per year. The Journal of Hymenoptera Research for example has reported 60 % growth, with 398 published pages in 3 issues in the first quarter of 2013 in comparison with 242 pages in 2 issues in 2012. Subterranean Biology also has almost completed its second issue and started a third, to top up previous restriction of two issues per year.

Open access facilitates public outreach of research through press releases associated with published articles. Since May 2011, Pensoft has been supporting authors in “translating” the technical texts into press releases with accessible language and illustrative media, which then result in postings on science news distributors, mass and scientific media and through the social networks (Twitter, Facebook, Google+, etc.). The service means a wider outreach and popularity for the research performed by the authors as well as for hymenoptera research more broadly.

The most visited article in the Journal of Hymenoptera Research about a new species of miniature fairy fly Tinkerbella nana, which has over 5,800 views on the website and over 2,700 views on EurekAlert. The research also enjoyed wide coverage in world media including National Geographic, the Daily Mail, Die Welt and many more. The most visited paper in Subterranean Biology has also benefitted the advantage of a press release. The new translucent snail species enjoys more than 15,100 views, and has made a great impression in the media and across the social networks.

Taxonomic descriptions, introduced by Linnaeus in 1735, are designed to allow scientists to tell one species from another. Now there is a new futuristic method for describing new species that goes far beyond the tradition. The new approach combines several techniques, including next generation molecular methods, barcoding, and novel computing and imaging technologies, that will test the model for big data collection, storage and management in biology. The study has just been published in the Biodiversity Data Journal.

While 13,494 new animal species were discovered by taxonomists in 2012, animal diversity on the planet continues to decline with unprecedented speed. Concerned with the rapid disappearance rates scientists have been forced towards a so called ”turbo taxonomy” approach, where rapid species description is needed to manage conservation.

While acknowledging the necessity of fast descriptions, the authors of the new study present the other ‘extreme’ for taxonomic description: “a new species of the future”. An international team of scientists from Bulgaria, Croatia, China, UK, Denmark, France, Italy, Greece and Germany illustrated a holistic approach to the description of the new cave dwelling centipede species Eupolybothrus cavernicolus, recently discovered in a remote karst region of Croatia. The project was a collaboration between GigaScience, China National GeneBank, BGI-Shenzhen and Pensoft Publishers.

Eupolybothrus cavernicolus has become the first eukaryotic species for which, in addition to the traditional morphological description, scientists have provided a transcriptomic profile, DNA barcoding data, detailed anatomical X-ray microtomography (micro-CT), and a movie of the living specimen to document important traits of its behaviour. By employing micro-CT scanning in a new species, for the first time a high-resolution morphological and anatomical dataset is created – the ”cybertype” giving everyone virtual access to the specimen.

“Communicating the results of next generation sequencing effectively requires the next generation of data publishing.” says Prof. Lyubomir Penev, Managing director of Pensoft Publishers. “It is not sufficient just to collect ”big” data. The real challenge comes at the point when data should be managed, stored, handled, peer-reviewed, published and distributed in a way that allows for re-use in the coming big data world.”, concluded Prof. Penev.

“Next generation sequencing is moving beyond piecing together a species genetic blueprint to areas such as biodiversity research, with mass collections of species in “metabarcoding” surveys bringing genomics, monitoring of ecosystems and species-discovery closer together. This example attempts to integrate data from these different sources, and through curation in BGI and GigaScience‘s GigaDB database to make it interoperable and much more usable.” says Dr Scott Edmunds from BGI and Executive Editor of GigaScience.

Original Sources:

Stoev P, Komerički A, Akkari N, Shanlin Liu, Xin Zhou, Weigand AM, Hostens J, Hunter CI, Edmunds SC, Porco D, Zapparoli M, Georgiev T, Mietchen D, Roberts D, Faulwetter S, Smith V, Penev L (2013) Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data. Biodiversity Data Journal 1: e1013. DOI: 10.3897/BDJ.1.e1013

Edmunds SC, Hunter CI, Smith V, Stoev P, Penev L (2013) Biodiversity research in the “big data” era: GigaScience and Pensoft work together to publish the most data-rich species description. GigaScience 2:14 doi:10.1186/2047-217X-2-14

 

Additional information:

Pensoft and the Natural History Museum London have received financial support by the EU FP7 projects ViBRANT and pro-iBiosphere. The China National GeneBank (CNGB) and GigaScience teams have received support from the BGI. The DNA barcodes were obtained through the International Barcode of Life Project supported by grants from NSERC and from the government of Canada through Genome Canada and the Ontario Genomics Institute.

 

Contacts:

Scott Edmunds
Executive Editor, GigaScience
Email: scott@gigasciencejournal.com

Vincent Smith
Editor-in-Chief, Biodiversity Data Journal
Email: vince@vsmith.info

 

Relationship between the bee Braunsapis puangensis and the invasive creeping daisy could be beneficial to crops and biodiversity in Fiji

Can invasive species be beneficial for the region? A recent study, published in the open access Journal of Hymenoptera Research, aimed to obtain empirical data on the activity and distribution of the bee species Braunsapis puangensis in the Suva area of Fiji and examine its association with the invasive creeping daisy Sphagneticola trilobata. The paper suggests that the invasive creeping daisy could in fact have a positive influence on a wild bee pollinator species, thus benefitting crops and biodiversity on the islands.

A recent survey by Mr. Abhineshwar Prasad of The University of the South Pacific, reported over 100 species of arthropods associated with road side patches of S. trilobata, including Hymenoptera such as parasitoid wasps, honey bees and solitary bees. One species of solitary bee, Braunsapis puangensis was locally abundant on patches of S. trilobata in the Laucala Bay area of Suva. This bee species is probably of Indian origin and was most likely carried to Fiji by anthropogenic means.

“There is growing concern regarding the global decline of honey bee populations and the implications of this demise for the pollination of crops. In the future we may rely on other insect species to perform crop pollination services, including naturally-occurring native or introduced species of bees.” comments one of the authors of the paper, Dr. Simon Hodge from Lincoln University in New Zealand. “Pollination success of generalist plants tends to be positively related to pollinator diversity, so any habitat modifications that increase the number of pollinating species present at a site would tend to be of some inherent value.”

The situations described above give the impression that the presence of some exotic flowering plants may be of benefit by encouraging higher numbers of pollinating species to occur at a site. Outside of agro-ecological systems, many studies have indicated that even flowering plants considered as invasive may have positive effects on insects, especially on nectar and pollen feeding species.

“Our study suggests it is important to realize that although  S. trilobata is considered an invasive ‘nuisance weed’ in one context, it may be of value to crop growers, and commercial honey producers, by attracting and augmenting local populations of pollinating insects.”, explains Dr. Hodge.

 ###

Summary:

Prasad AV, Hodge S (2013) Factors influencing the foraging activity of the allodapine bee Braunsapis puangensison creeping daisy (Sphagneticola trilobata) in Fiji. Journal of Hymenoptera Research 35: 56. doi: 10.3897/JHR.35.6006

Long considered to be one of the most species-rich ant genera, latest research has stripped the ant genus Paratrechina down to a single species- Paratrechina longicornis. This particular ant is one of the most widely distributed, found in nearly every tropical and subtropical location on the planet due to accidental human transport, and is considered one of the world’s worst invasive ant species. A recent review of the genus in the open access Journal of Hymenoptera Research announces the discovery of a second species P. zanjensis, which presents a step forward into determining the native range of P. longicornis.

Native to Africa, and so far found only in miombo woodlands, the new species P. zanjensis is potentially specialized to this habitat. Miombo is the Swahili word for the Brachystegia genus of trees which are an important tree species within miombo woodlands. The specific name of this new species – zanjensis – is derived from the ancient Arabic name for the stretch of East African coast that encompasses parts of modern day Kenya, Mozambique, and Tanzania, where the species is found.

“Given the economic and ecological impacts of Paratrechina longicornis, discovering a close relative may provide us with insights into the biology of one of the world’s worst invasive ant species. For instance, now that we know another species exist within the genus, comparative studies can begin to perhaps understand the attributes that make P. longicornis such a good biological invader.” says Dr. John S. LaPolla of Towson University, USA.

Unlike its new relative, the long known P. longicornis, exhibits remarkable adaptability and is spread virtually worldwide through human activity and movement. The species is found almost in every urban center in the tropics as well as in greenhouses and other manmade structures in cool temperature climates. The remarkable ability of this ant to survive even in extremely human changed environment also makes it a well-known pest in tropical climates, commonly called crazy ant due to its erratic movements.

Due to this wide distribution and easy adaptation of P. longicornis the determination of its native range has proved a challenge to biologists. The current revision suggests that the species originates in Asia, as previously considered, however further investigation is needed to confirm this thesis.

“Given the available distribution information on P. longicornis, we conclude that P. longicornis remains most likely native to southeastern Asia, and that the discovery of a new species native to Africa makes Paratrechina yet another example of an ant genus that possesses an Afro-Asian distribution.”, explains Dr. John S. LaPolla.

Original Source:

LaPolla JS, Hawkes PG, Fisher JN (2013) Taxonomic review of the ant genus Paratrechina, with a description of a new species from Africa. Journal of Hymenoptera Research 35: 71. doi: 10.3897/JHR.35.5628

Open Access Week 2013 is here, and Pensoft would like to continue to take the opportunity to highlight different aspects of the central role that Open Access plays in our activities.

A great deal has  been written and said for and against open access, but one of the biggest arguments in support of open access publishing is contained in the so called 4R – reuse, revise, remix, redistribution of scientific results, data, images and text. Pensoft, as an open access publisher, shares its positive experience of image reuse on Wikimedia to promote the movement during Open Access Week 2013.

When words become diluted in a long and extensive argument, statistics still speak out clearly. About 4000 media items derived from Pensoft publications have been uploaded to Wikimedia Commons. Together, these media files have been used more than 33 000 times across various wiki supported pages, in more than 50 languages.  Wikimedia pages using these items get more than 3 000 000 views monthly from across the globe.

The most reused image is the one of the brown lacewing Micromus variegatus used more than 6 500 times across several languages. The leader is closely followed by the beetle Pterostichus punctatissimus, with around 1400 uses and a moth from the Anoba sp. Trigonoides species complex, with just 200 less.

Multimedia from articles that grasped the imagination of the public, such as the famous carnivore – the Olinguito, are used on over 40 Wikipedias. Similarly the spider version of Bigfoot – Trogloraptor marchingtoni, has been used over 14 languages. In both cases the multimedia files have been featured on the main pages, across several languages.

Science is publicly funded and as such it is only logical to reach back to the public. Open access guarantees easy access and reuse of scientific publications for the benefit of the scientific community, citizen scientists and the general public.

In 2008, Pensoft launched its first open-access journals named ZooKeys and BioRisk. In 2010, PhytoKeys, an open access journal in plant systematics, phylogeny and biogeography was also launched and shortly after, in December 2010, five society journals moved to Pensoft’s open access journal publishing platform.  The latest addition to the Pensoft family is the Biodiversity Data Journal, offering several flagship innovations to taxonomic and data publishing, and exclusively offering a Platinum mode of open access.