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An innovative workflow reveals new research potential of the Barcode of Life Data Systems (BOLD). A recently published article in the Biodiversity Data Journal (BDJ) used specimen records downloaded from BOLD in tabular format and imported these into a human-readable text developed in manuscript within the Pensoft Writting Tool (PWT). Data were used to study the species distributions of ten Nearctic species of braconid wasps from the Microgastrinae subfamily.

BOLD is originally designed to support the generation and application of DNA barcode data. However, the repository also holds unexplored treasures of additional data that provide unique potential for many other research uses.

Currently almost 4 million sequences (over 3.4 million of them DNA barcodes) are stored in BOLD, including coverage for more than 143K animal species, 53K plant species, and 16K fungi and other species, and this impressive storage of information is continuing to grow every day.

A team of researchers, led by Dr Jose Fernandez-Triana from the University of Guelph, Canada, have now explored how the unique amount of data stored on the BOLD platform can be utilised for new research purposes. Choosing tiny parasitic wasps for their case study they selected a sample of 630 specimens and 10 North American species. Data stored on BOLD were then used to uncover a significant number of new records of locality, provinces, territories and states.

The research was then secured a fast publication via BDJ, a community peer-reviewed, open-access, comprehensive online platform, designed to accelerate publishing, dissemination and sharing of biodiversity-related data of any kind.

“Import of structured data into human-readable text is important but it does not represent the whole story. More importantly, the data can be downloaded straight from the article text by anyone for further re-use, or be automatically exported to data aggregators, such as the Global Biodiversity Information Facility (GBIF). In this way, data platforms could get more peer-reviewed content from scholarly publications and scientists will be properly credited for their efforts” said Prof. Lyubomir Penev, founder of Pensoft Publishers.

Original Source:

Fernandez-Triana J, Penev L, Ratnasingham S, Smith M, Sones J, Telfer A, deWaard J, Hebert P (2014) Streamlining the use of BOLD specimen data to record species distributions: a case study with ten Nearctic species of Microgastrinae (Hymenoptera: Braconidae). Biodiversity Data Journal 2: e4153. doi: 10.3897/BDJ.2.e4153

Additional information:

The workflow is part of the Data Publishing Toolkit elaborated within the EU FP7 funded project EU BON (Grant agreement No 308454).

A newly described tarantula species from Western Brazilian Amazonia was named Bumba lennoni in honor of John Lennon, a founder member of the legendary band the Beatles. The new species is part of the tarantula family Theraphosidae which comprises the largest spider species in the world. The study was published in the open access journal ZooKeys.

The name of the new species came across when the authors of the study Fernando Pérez-Miles, from the University of the Republic, Uruguay, and Alexandre Bonaldo and Laura Miglio, both from the Museu Paraense Emilio Goeldi, Brazil, found out that they are all great fans of the Beatles music.

The genus, Bumba, which is proposed as replacement of the old one Maraca, already taken and used for Orthoptera, also has a story behind the choice of name. The new name is taken from Brazilian theatrical folk tradition of the popular festival called Boi-bumbá (hit my bull), which takes place annually in North and Northeastern Brazil.

The new species, as other tarantulas, has defensive urticating hairs on the abdomen which produce irritation upon contact with the skin or sensible tissues.

The specimens used in the study were captured manually or in traps during the night in Caxiuaná, Pará, Brasil, which suggest they could be mainly nocturnal animals.

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Original Source:

Perez-Miles F, Bragio Bonaldo A, Miglio L (2014) Bumba, a replacement name for Maraca Pérez-Miles, 2005 and Bumba lennoni, a new tarantula species from western Amazonia (Araneae, Theraphosidae, Theraphosinae). ZooKeys 448: 1-8. doi: 10.3897/zookeys.448.7920

Scientists from the Department of Life Science, National Taiwan Normal University and the Biodiversity Research Center, Academia Sinica described a new endemic land snail species. The new species Aegista diversifamilia was long confused for the widely distributed A. subchinensis. The study was published in the open access journal ZooKeys.

Aegista subchinensis was first described in 1884 and was thought to be widely distributed in Taiwan. In 2003, one of the co-authors Dr. Yen-Chang Lee noticed that there was morphological divergence between the western and eastern populations of A. subchinensis separated by the Central Mountain Range, a major biogeographic barrier in Taiwan. Dr. Lee suggested that there might be cryptic species within the one identified as A. subchinensis at the time.

To prove Dr. Lee’s suggestion, Ph.D. candidate of Department of Life Science, National Taiwan Normal University, Chih-Wei Huang and his collaborators applied three molecular markers combined with morphological analysis to estimate the divergence and relationship among the closely related snails.

“When we examined the phylogeny from each gene,” Huang says, “it suggested that the eastern A. subchinensis was more closely related to A. vermis, a similar land snail species inhabited in Ishigaki Island, than the western A. subchinensis.”

They confirmed that what was thought to be A. subchinensis from eastern Taiwan was in fact a new species, which they named as A. diversifamilia. The name means the diverse forms of human families.

“When we were preparing the manuscript,” Dr. Lee explains, “it was a period when Taiwan and many other countries and states were struggling for the recognition of same-sex marriage rights. It reminded us that Pulmonata land snails are hermaphrodite animals, which means they have both male and female reproductive organs in single individual. They represent the diversity of sex orientation in the animal kingdom. We decided that maybe this is a good occasion to name the snail to remember the struggle for the recognition of same-sex marriage rights.”

The new species is larger in shell size and flatter in shell shape than A. subchinensis. The two species are also geographically separated by the Lanyang River, which makes this the first report suggesting that the Lanyang River is a biogeographic barrier for lowland terrestrial animals.

Original source:

Huang C-W, Lee Y-C, Lin S-M, Wu W-L (2014) Taxonomic revision of Aegista subchinensis (Möllendorff, 1884) (Stylommatophora, Bradybaenidae) and a description of a new species of Aegista from eastern Taiwan based on multilocus phylogeny and comparative morphology. ZooKeys 445: 31–55. doi: 10.3897/zookeys.445.7778

Additional Information:

Funding: Center for Information Technology Innovation and Biodiversity Research Center, Academia Sinica.

A new study led by a Canadian marine zoologist reviews the world list of specialist driftwood talitrids, which so far comprises a total of 7 representatives, including two newly described species. These tiny animals with peculiar habits all live in and feed on decomposing marine driftwood. Dispersed across distant oceanic islands they use floating driftwood to hitch a ride to their destination. The study was published in the open access journal Zoosystematics and Evolution.

Tourists are familiar with talitrids as sandhoppers, found in burrows on sand beaches, or shorehoppers, which are non-burrowers associated with wrack thrown up by the high tide. But they probably do not suspect the existence of an additional ecological group of marine talitrids, which are obligately associated, both for food and shelter, with driftwood.

These tiny animals just like tourists have travelled a long way to reach their destination. They travel on floating driftwood logs, which serve them both as a means of transportation and as a food source.

“Specialist driftwood talitrids are rare and difficult to study group because of their small size and cryptozoic habitat. Only seven species are presently known in the world list, but this is almost certainly because of inadequate searching in the right places.”comments the author of the study Dr. Dave Wildish, “Fisheries and Oceans Canada”.

Driftwood is common at higher latitudes in the driftline of both northern and southern hemispheres, although all seven species recorded so far are from the northern hemisphere.

A characteristic feature of specialist driftwood talitrids is their small size (less than 15mm body length, technically termed “dwarfism”). One species which as an adult is less 8mm in body length is one of the smallest talitrids known.

Dwarfism in specialist driftwood talitrids is achieved by a form of “neoteny”. This means that adults retain juvenile features but become sexually mature at an early stage in development. Neotenous development in driftwood talitrids involves: fewer moults per life cycle, sexualisation beginning at an earlier moult number, and the size increment at each moult remaining the same.

This adaptation is key to specialist driftwood talitrids because it allows the hitchhiker to live within the floating driftwood and thereby the possibility of a much longer ride to a new home. Passive dispersal on other media, such as wrack, can be short-lived due to break up of the floating wrack. Passive dispersal to distant places is made possible by the driftwood talitrid hitching a ride on the floating driftwood log; a process which could take these little travellers a considerable amount of time.

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 Original Source:

Wildish D (2014) New genus and two new species of driftwood hoppers (Crustacea, Amphipoda, Talitridae) from northeast Atlantic and Mediterranean coastal regions. Zoosystematics and Evolution 90(2): 133-146. doi: 10.3897/zse.90.8410

Additional Information:

Wildish, D.J. 1972.Post embryonic growth and age in some littoral Orchestia (Amphipoda, Talitridae). Crustaceana Supplement 3: 267-274.

Wildish, D. J. 2012. Long distance dispersal and evolution of talitrids (Crustacea: Amphipoda: Talitridae) in the northeast Atlantic islands. Journal of Natural History 46: 2329-2348.

Wildish, D. J., Pavesi, L and Ketmaier, V. 2012. Talitrid amphipods (Crustacea: Amphipoda: Talitridae) and the driftwood ecological niche: a morphological and molecular study. Journal of Natural History 46: 2677-2700.

Pavesi, L, Wildish, D.J, Gasson,P, Lowe, M and Ketmaier, V. 2014. Further morphological and molecular studies of driftwood hoppers (Crustacea: Amphipoda: Talitridae) from Mediterranean/Northeast Atlantic coastlines. Journal of Natural History. In press.

Since the launch Biodiversity Data Journal (BDJ) and the associated Pensoft Writing Tool (PWT) Pensoft has continued to strive towards improvement and excellence, aiming to introduce novelties and further develop these products. We are pleased to share three important innovations introduced by us in the last months.

First, PWT now features an import API (Application Programming Interface), which allows import of complex manuscripts (e.g., authors details, occurrence records, species descriptions, in-text citations, references, images, etc.) straight from external databases, for examplescratchpads.eu and others. This novel and globally uniquefeature could seem a challenge for an “ordinary” biodiversity scientist to use, however with the help of a data manager authors will be pleasantly surprised by the amount of time and effort the tool can save.

The Gulf Sand gecko is a remarkable desert reptile in that it is the only lizard found habitually on sabkha substrate across large parts of the eastern Arabian Peninsula. These arid salt flats constitute one of the harshest habitats on earth, due to their extraordinary salinity.

The Gulf gecko, Pseudoceramodactylus khobarensis, belongs to a genus with a single species, and it is well adapted to this substrate featuring spiny scales beneath the fingers, long extremities and swollen nostrils.

Data on its distribution range showed a conspicuous gap between eastern United Arab Emirates and coastal Oman, across a distance of more than 450km. Yet previous research had shown that genetic variability was relatively low for this gecko species.

During a recent fieldtrip in Oman, an international team of herpetologists, led by Dr. Salvador Carranza of the Institute of Evolutionary Biology in Barcelona, visited this area, almost devoid of vegetation аs well as access roads and tracks, and was able to spot for the first time specimens of this exceptional gecko in inland Oman. These localities, situated almost 250 km, east and west, from previously recorded occurrences fill in the distributional gap for this species and help to better understand the genetic and morphological variability patterns observed. The study was published in the open access journal Biodiversity Data Journal.

The researchers have analyzed genetic data for several specimens of the species and their results indicate that there is connectivity between populations inhabiting different parts of the Arabian Peninsula.

“We were really surprised to find this species so far away from the coast, where the only records for Oman were known. But the habitat was indeed ideal for them: vast salt flats stretching between elongate sand dunes” said Dr. Margarita Metallinou, first author of the study. “We realized that the lack of records was simply due to the extremely difficult accessibility to this area”. This artifact, common in biodiversity studies in little known parts of the world, can severely distort our understanding of species diversity.

In the case of the Gulf gecko, the findings of this work confirm that this species probably inhabits larger inland areas than we currently know of.

Original Source:

Metallinou M, Vasconcelos R, Šmíd J, Sindaco R, Carranza S (2014) Filling in the gap: two new records and an updated distribution map for the Gulf Sand gecko Pseudoceramodactylus khobarensis Haas, 1957. Biodiversity Data Journal 2: e4011. doi: 10.3897/BDJ.2.e4011

Research on zoantharians, a group of animals related to corals and anemones, by researchers James Reimer of the University of the Ryukyus in Okinawa, Japan, Angelo Poliseno of Universita Politecnica delle Marche in Italy, and Bert Hoeksema from Naturalis Biodiversity Center, Netherlands, has demonstrated how little we know about marine diversity in the so-called “center of marine biodiversity” located in the central Indo-Pacific Ocean. The study was published in the open access journal ZooKeys.

The researchers utilized previously collected specimens from Indonesia, the Philippines, Malaysia, and Papua New Guinea, combined with field images from Dr. Hoeksema to examine species of Zoantharia, marine cnidarians commonly found in shallow subtropical and tropical oceans throughout the world. The study was published in the open access journal ZooKeys.

“The central Indo-Pacific is commonly called the “Coral Triangle” due to its high hard coral diversity, in fact the highest in the world” said Reimer, “but in fact for many groups of marine animals we really have little concrete information on diversity, or numbers of species, in this region.”

Previous research included brief reports on a few species of Zoantharia, but until now no formal attempts had been made to list species from this region. Surprisingly, of the 24 potential species identified by the researchers, at least 9 are undescribed.

Much of the work was performed by Dr. Reimer in the Netherlands in 2012, when he visited the Naturalis Museum and Dr. Hoeksema to examine their Zoantharia collection. “What struck me as particularly amazing was the fact that Naturalis housed over 600 Zoantharia specimens collected over the years, and in many cases, even specimens from 1930 had not yet been formally examined,” stated Reimer. “This research demonstrates the real importance of museum collections, as well as the lack of expert researchers for many taxonomic groups.”

“Unfortunately, for many regions of the world, we are only just beginning to examine diversity, despite some of these areas being among the most threatened,” added Reimer. It is hoped future specimen collections will allow further analyses and formal descriptions of these previously unreported species.

Original Source:

Reimer J, Poliseno A, Hoeksema B (2014) Shallow-water zoantharians (Cnidaria, Hexacorallia) from the Central Indo-Pacific. ZooKeys 444: 1-57. doi: 10.3897/zookeys.444.7537

Typical cave-dwelling organisms, unpigmented and eyeless, were discovered in a karst area located in northeastern Brazil. The organisms were assigned to a new genus and species of freshwater flatworm and may constitute an oceanic relict. They represent the first obligate cave-dwelling flatworm in South America. The study was published in the open access journal ZooKeys.

Freshwater flatworms occur on a wide range of habitats, namely streams, lagoons, ponds, among others. Some species also occur in subterranean freshwater environments.

Brazil has more than 11,000 caves, but their species diversity is largely unknown. Field work by Rodrigo Ferreira, from University of Lavras, Brazil, in a karst area located in northeastern Brazil, has found the first obligate cave-dwelling flatworm in South America. Flatworm researchers from University of Vale do Rio dos Sinos (UNISINOS), Brazil, Ana Leal-Zanchet and Stella Souza, described it as a new genus and species.

The new species, which was named Hausera hauseri, is a typical cave-dwelling organism, unpigmented and eyeless. The genus and species names were proposed in honour to a Hungarian biologist, the late Prof. Dr. Josef Hauser, who immigrated to Brazil and studied freshwater flatworms over many years.

The sampling area of the new species is unique in comparison with other karst areas in Brazil. Most Brazilian limestone formations are located in inner portions of the country, which must have prevented marine groups from colonizing these caves in the past. In contrast, this karst area is located near the sea, and its limestone outcrops are at low altitude, which has allowed different invertebrates to colonize the caves during sea level rises in the past. Thus, the new species may constitute an oceanic relict as is the case of other cave-dwelling invertebrates found in this karst area in northeastern Brazil.

Original source:

Leal-Zanchet et al. (2014) A new genus and species for the first recorded cave-dwelling Cavernicola (Platyhelminthes) from South America. Zookeys 442: 1-15. doi:10.3897/zookeys.442.8199

Fauna Europaea started in 2000 as an EC-FP5 four-year project, delivering its first release in 2004. After 14 years of steady progress and successful participations in several EC projects, as a part of the EC-FP7 European Biodiversity Observation Network project (EU BON), to increase the general awareness of the work done by the contributors and to extend the general dissemination of the Fauna Europaea results, the Biodiversity Data Journal has applied its novel e-Publishing tools to prepare data papers for all 56 major taxonomic groups.

Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level, and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 species name. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education.

‘Contributions on Fauna Europaea’ is the second series launched by the Biodiversity Data Journal after the Checklist of British and Irish Hymenoptera and the first one that embraces thematic data-papers structured in a common pattern extracted from a large database. This novel publication model will assemble in a single-issue 56 data-papers on different taxonomic groups covered by the Fauna Europaea project in the period 2000-2014 and a range of accompanying papers highlighting various aspects of this project (gap-analysis, design, taxonomic assessments, etc.).

This is the first collection of data-papers of this scale. It will formalise and effectively publish the results of nearly 500 contributors building the largest European animal (taxonomic) database. The new publication model provides a reliable mechanism for citation and bibliographic indexing of large and uniformly structured databases.

“The publication of Fauna Europaea data papers brings a number of benefits for science, for example it stimulates experts to hand-over descriptive details on their groups, triggers new ways of community networking and participation, motivates experts to update their data, supports a better documentation of their achievements, including issues like ‘micro-publications’, and increase an ownership feeling with the associated effort” said Dr Yde de Jong, coordinator of the Fauna Europaea and Pan-European Species directories Infrastructure (PESI) projects.

The launch of this large collection of data papers coincides with one more cutting-edge innovation of the Biodiversity Data Journal, the publication of an API, a first of its kind, to import complex and data-rich manuscripts, which include text, data, images, in-text citations, references, in fact anything that a manuscript may contain.

“I am happy that these exciting innovations coincided with the first birthday of the Biodiversity Data Journal. Just a year ago we launched this new concept with the motto: Making your data count! These novel approaches and tools are an excellent example how our concept evolved!” comments Prof. Lyubomir Penev, Managing Director of Pensoft Publishers.

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Original Sources:

de Jong Y, Verbeek M, Michelsen V, Bjørn P, Los W, Steeman F, Bailly N, Basire C, Chylarecki P, Stloukal E, Hagedorn G, Wetzel F, Glöckler F, Kroupa A, Korb G, Hoffmann A, Häuser C, Kohlbecker A, Müller A, Güntsch A, Stoev P, Penev L (2014) Fauna Europaea – all European animal species on the web.Biodiversity Data Journal 2: e4034. doi: 10.3897/BDJ.2.e4034

Gibson D, Bray R, Hunt D, Georgiev B, Scholz T, Harris P, Bakke T, Pojmanska T, Niewiadomska K, Kostadinova A, Tkach V, Bain O, Durette-Desset M, Gibbons L, Moravec F, Petter A, Dimitrova Z, Buchmann K, Valtonen E, de Jong Y (2014) Fauna Europaea: Helminths (Animal Parasitic). Biodiversity Data Journal 2: e1060. doi: 10.3897/BDJ.2.e1060

Additional information:

The Fauna Europaea project (EVR1-1999-20001) has been funded by the European Commission for a period of four years (1 March 2000 – 1 March 2004) within the Fifth Framework Programme (5FP). Fauna Europaea has assembled a database of the scientific names and distribution of all living multicellular European land and fresh-water animals. The publication of the data papers was supported by the Seventh Framework Programme (FP7) projects Virtual Biodiversity Research and Access Network for Taxonomy (ViBRANT) and European Biodiversity Observation Network project (EU BON).

Pensoft Publishers specialize in academic and professional book and journal publishing, mostly in the field of biodiversity science and natural history. The Biodiversity Data Journal(BDJ) and the associated Pensoft Writing Tool (PWT), were launched by Pensoft as the first workflow ever to put together article authoring, community peer-review, publishing and dissemination within a single online collaborative platform.

The classical treatise “Flora of Northumberland and Durham” by Nathaniel John Winch is re-published through the innovativeAdvanced Books platform as an example of combining modern information technology together with historical scholarship to create a new sort of resource and data re-use. This publication will be supporting ongoing research on the botany of the region, which can be seen as a model for other regions in Europe.

The on-line semantically enriched re-publication marries the meticulous detail of old books with the interconnectedness of the internet bringing advantages of the digitization and markup efforts such as data extraction and collation, distribution and re-use of content, archiving of different data elements in relevant repositories and so on.

“Historic biodiversity literature is not just of cultural interest, it can be used to chart biogeographic change and help us understand the impacts of environmental change on biodiversity. Even if we are trying to predict future scenarios for biodiversity, understanding the changes of the past will help understand the changes we should expect in the future” said Dr Quentin Groom from the Meise Botanical Garden, Belgium, who initiated the project and marked up the original text.

The North-east of England has seen many changes since the publication of Winch’s Flora. In the 19th Century the area was a powerhouse of the industrial revolution. It was an important coal mining area and significant for the production of iron and steel. It was also a centre for industries such as shipbuilding and engineering. In contrast the uplands in the west of the region were some of the most isolated areas in England, covered in blanket bog and rarely visited.

Since that time heavy industry and mining have declined, but the population has continued to grow. Agriculture and forestry have become mechanized changing the countryside perhaps beyond the recognition of Winch. Many of the plants and localities he mentions have disappeared and a large number of new species have been introduced. The local botanists are still very active in the region. With GPS systems and modern maps they are mapping theregion’s flora in ever more detail.

The extensive efforts of Quentin Groom from the Botanic Garden Meise and editor of this re-publication combined with the cutting-edge technologies for semantic enhancements used by Pensoft’s Advanced Books platform, have resulted in additional details including links to the original citations and coordinates of the mentioned localities. In some cases the habitat that Winch described for a locality differs dramatically from what can be found in the same location nowadays.

The flora, for example, frequently mentions Prestwick Carr, an area of lowland bog, once full of rare species. Sadly it was largely drained just thirty years after the publication of the flora. Yet in recent years the Northumberland Wildlife Trust has been working to restore the bog to its former glory. “When reading Winch’s flora, it is easy to see what has been lost, but more importantly what remains to be conserved”, comments Groom.

The re-publication of Winch’s flora is just one step towards fully understanding all the impacts on wild plants of all the environmental changes that have occurred since the 19th century. Nevertheless, digitization of this flora not only tells us about plants but also about the history of science. Between the lines of this flora one can see a rudimentary understanding of ecology and the beginnings of research on phytogeography.

Consider that in 1831 Charles Darwin set sail on the Beagle, collecting and cataloguing biodiversity around the world, much as Winch had done in North-east England over the preceding 30 years. Field botany at the time was not just a hobby, but a serious pursuit that led to many new discoveries.

Understanding the causes of biodiversity change is only possible if you have data over a long period. The North-east England has an enviable botanical history dating back to William Turner (1508-1568), the so-called, Father of English Botany, who came from Morpeth in Northumberland. Yet he was only the first in a long list of North-eastern botanists, including John Wallis (1714-1793), Nathaniel John Winch (1769-1838), John Gilbert Baker (1834-1920), George Ralph Tate (1805-1871), Gordon Graham and George Swan (1917). Their publications and the works of many others have contributed to a large corpus of literature on the region’s flora.

The re-publication is supported by the FP7 funded EU project European Biodiversity Observation Network (EU BON).

Original Source:

Winch N (2014) Flora of Northumberland and Durham. Advanced Books: e4002. doi:10.3897/ab.e4002

Additional Information:

The Advanced Books platform is launched by Pensoft to publish new books or re-publish such previously available in paper or PDF only, in an advanced and semantically enhanced HTML and XML formats, to accelerate open access, data publication, mining, sharing and reuse. Advanced Books builds on the novel approaches developed by Pensoft’s journals.

This re-publication of the “Flora of Northumberland and Durham” originally published in 1831 by Nathaniel John Winch is supported by the FP7 funded EU project European Biodiversity Observation Network (EU BON) (Grant agreement No 308454