Tag: taxonomy

From Sherborn to ZooBank: Moving to the interconnected digital nomenclature of the future

From the outside, it can seem that taxonomy has a commitment issue with scientific names. They shift for reasons that seem obscure and unnecessarily wonkish to people who simply want to use names to refer to a consistent, knowable taxon such as species, genus or family. However, the relationship between nomenclature and taxonomy, as two quite separate but mutually dependent systems, is a sophisticated way of balancing what we know and what is open to further interpretation.

Nomenclature is a bureaucracy that follows rules and is tied to published records and type specimens. It provides a rigid framework or skeleton for knowledge. Taxonomy, on the other hand, is a data-driven science, influenced by interpretation and resulting in concepts that are open to further test and change. To actually get the answers right, taxonomy needs to be responsive and fluid as a system of knowledge. The link between nomenclature and the published record is also the junction with the data that fuels taxonomic interpretation.

Biodiversity informatics aims to solve this issue, and its founding father is Charles Davies Sherborn. His magnum opus, Index Animalium, provided the bibliographic foundation for current zoological nomenclature. In the 43 years he spent working on this extraordinary resource, he anchored our understanding of animal diversity through the published scientific record. No work has equaled it, and it is still in current and critical use.

This special volume of the open-access journal ZooKeys celebrates Sherborn, his contributions, context and the future for the discipline of biodiversity informatics. The papers in this volume fall into three general areas of history, current practice and frontiers.

The first section presents facets of Sherborn as a man, scientist and bibliographer, and describes the historical context for taxonomic indexing from the 19th century to today. The second section discusses existing tools and innovations for bringing legacy biodiversity information into the modern age. The final section tackles the future of biological nomenclature, including digital access, innovative publishing models and the changing tools and sociology needed for communicating taxonomy.

In the late 1880s Charles Davies Sherborn recognised the need for a full index of names to the original sources that gave them legitimacy, their first publications. He set about making a complete index for names of animals, which are the largest group of described organisms (1.4 million of the current 1.8 million described species are animals). Because this work began while the very basics of nomenclatural rules were being thrashed out, the work itself affected how those rules were codified.

Sherborn’s monumental work, Index Animalium, comprises more than 9,000 pages in 11 volumes and about 440,000 names. This was on the scale of other hugely ambitious tasks at the time that changed the course of communication such as the Oxford English Dictionary. The error rates are astonishingly low, and it became, and it remains to date the most complete reference source for animal nomenclature. Taxonomic studies rely on Sherborn’s work today. While the future for information access is one of the most exciting frontiers for our increasingly interconnected, accelerated society, biodiversity information will continue to be grounded in this seminal work. The future for biodiversity informatics is built on Sherborn’s work, and is expanding to be digital, diversified and accessible.

The publisher of this volume, the journal ZooKeys, is itself a pioneer in developing a more stable and accessible scientific nomenclature. Together with PhytoKeys, ZooKeys is piloting an innovative workflow with a pre-publication automated pipeline for registration of nomenclatural acts. This initiative comes from the EU FP7 project pro-iBiosphere, and in close collaboration with ZooBank (the official online registry for scientific names of animals), Zoological Record, IPNI, MycoBank and Index Fungorum, and the Global Names project. The volume was inspired by a symposium held in Sherborn’s honour at the Natural History Museum (NHM), London, on the 150th year of his birth in 2011, organised by the International Commission on Zoological Nomenclature (ICZN), in collaboration with the Society for the History of Natural History (SHNH).

Sherborn was a man with a vision for the future and respect for the accomplishments of the past. He would have celebrated the new tools for the ambitious goal of linking all biological information through names that are readable for both machines and humans. He would have understood the tremendous power of interconnected names for biodiversity science overall. And he would have knuckled down and got to work to make it happen.

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Original source:

Michel E (2016) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. In: Michel E (Ed.) Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond. ZooKeys 550: 1-11. doi: 10.3897/zookeys.550.7460

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Anchoring Biodiversity Information – Sherborn Special Issue is available to read and order from here.

Seventy-four cuckoos in the nest: A new key to all North European cuckoo wasp species

Captivating with their bright, vivid and brilliantly metallic bodies, the cuckoo wasps are also fascinating with their curious lifestyle, which has given them this common name. However, in terms of their taxonomic grouping, they have been quite problematic due to similarities between species and a wide range of variations within them.

To shed light on the issue, an international research team, led by MSc Juho Paukkunen, Finnish Museum of Natural History, Helsinki, provides descriptions and illustrations of all 74 species found in the Nordic and Baltic countries, including one new, in their recent publication in the open-access journal ZooKeys.

Beautiful in appearance, the cuckoo wasps penetrate the nests of unrelated solitary wasps and solitary bees to lay their eggs, similar to how a cuckoo bird does in songbird nests. With their armoured bodies and the ability to curl up into a tight ball the cuckoo wasps are well-defended against the owners of the nests and their stings and jaws. At the larval stage, they take advantage of their hosts by either parasitising them or stealing their food, eventually killing the host’s offspring.

Within the Nordic representatives of the family there are an exceptionally large number of red-listed and endangered species. This is one of the reasons why the authors intend to trigger more interest among their fellow entomologists about these curious wasps. They have compiled all relevant information concerning their distribution, abundance, habitats, flight season and host species. The authors have tried to keep their identification key as comprehensive and concise as possible, by singling out the essential information on diagnostic characters.

In the present study, the researchers describe a new species, called Chrysis borealis, which can be translated as ‘Northern’ cuckoo wasp. Although the male and female individuals are very similar, there is a significant variation in the colouration within the species. It is especially noticeable between the specimens collected from the northern localities and those from the southern ones. For instance, while the middle section of the body in southern specimens is either bright blue or violet with a greenish shimmer, in northern individuals it is nearly black, turning to greenish or golden green at the periphery.

The varying shades within a certain species are quite common among the cuckoo wasps. While it is often that distinctive colouration among other wasps and insects indicates their separate origin and therefore, taxonomic placement, within the emerald family it can be a mere case of habitat location with the northern populations typically darker.

Such tendencies often lead to doubts such as the one the authors have faced regarding their new species. It has been suggested that the Northern cuckoo wasp is in fact yet another variation of the very similar C. impressa, which is generally slightly brighter in colour, but at the same time distributed in warmer localities. However, using DNA sequence information and morphometric analysis, the team shows that there are enough consistent differences to separate them as distinct species, although they are defined as evolutionarily young siblings.

With their research the authors intend to provide a basis for further and more detailed studies on the distribution, biology and morphology of the North European representatives of these intriguing wasps.

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Original source:

Paukkunen J, Berg A, Soon V, Odegaard F, Rosa P (2015) An illustrated key to the cuckoo wasps (Hymenoptera, Chrysididae) of the Nordic and Baltic countries, with description of a new species. ZooKeys 548: 1-116. doi: 10.3897/zookeys.548.6164

Tramp ant caught globetrotting under false name

A century-old mystery surrounding the origin of an invasive ant species was recently solved by an international team of scientists. Since 1893, when it was first discovered as an invasive species in the Canary Islands, entomologists have been debating where this mystery species came from. While some insisted on the Mediterranean, some proposed Arabia and others argued for Africa. The correct answer? Asia.

The authors of the study, published in the open-access journal ZooKeys, solved the taxonomic puzzle by fitting together disparate pieces of evidence. “I was having a terrible time trying to distinguish this one Asian species from the mysterious ant that was coming in on shipments from the Caribbean, Europe and Africa,” says Dr. Eli Sarnat, University of Illinois, about his research at the Smithsonian on tramp ants that were intercepted at US ports.

Tramp ants, many of which are pest species, are spread across the globe by stowing away in the cargo of ships and planes, thus posing rising environmental, food security and public health concerns.

The same day Sarnat was working on the mysterious ant in the Smithsonian, he received an email from Dr. Evan Economo, Okinawa Institute of Science and Technology (OIST). Economo and Dr. Georg Fischer, also affiliated with OIST, had included Madagascar samples of the species in a genetic analysis, and the results unexpectedly placed it within a group of Asian species. The closest genetic match to the enigmatic ant turned out to be the very same Asian species that Sarnat had found in the Smithsonian collection.

The last piece of the riddle was discovered thanks to the painstaking work of Dr. Benoit Guénard. Guénard, a professor at the University of Hong Kong, had spent years mapping the global distributions of every ant species known to science. When he compared the ranges of the mysterious ant with the common Asian species, the two fit together like a jigsaw puzzle.

Evidence gathered from classic taxonomy, modern genetic analysis, and exhaustively researched distribution maps all pointed to the same conclusion.

“What had long been considered two different species — one found across a wide swath of Asia and the other a tramp species spread by humans across Europe, Africa, the Americas and Australia — are actually one single supertramp species,” Economo explained. “It is striking that we had these two continental super-common invaders with almost entirely complementary ranges right under our noses, yet until now no one noticed they were actually the same species,”

Original source:

Sarnat EM, Fischer G, Guénard B, Economo EP (2015) Introduced Pheidole of the world: taxonomy, biology and distribution. ZooKeys 543: 1-109.doi: 10.3897/zookeys.543.6050

Additional information:

This work was supported by USDA APHIS Identification Technology Program (13-8130-1439-CA), subsidy funding to OIST, and NSF (DEB-1145989). This work was supported by USDA APHIS Identification Technology Program (13-8130-1439-CA), subsidy funding to OIST, and NSF (DEB-1145989).

Lava attraction: 74 new beetle species found hiding in plain sight on a Hawaiian volcano

Confined to the limits of Haleakala volcano, Maui Island, Hawaii, the beetle fauna there turns out to be not only extremely diverse, but very abundant as well. When Prof. James Liebherr of the Cornell University Insect Collection thoroughly sampled beetle populations on the volcano, he identified 116 species of round-waisted predatory beetles, including 74 new to science. The taxonomic revision, complete with descriptions of the new species, is now published in the open-access journal ZooKeys.

The present discoveries and observations are certainly surprising due to their scale, even though it has been long known that the Hawaiian Islands support disproportionately high levels of biodiversity. For this group of native round-waisted beetles, called Mecyclothorax in the zoological naming system, there are 239 species across the Hawaiian Islands, all of them descended from a single colonizing species.

The 116 species known from Haleakala make that volcano the center of biodiversity for this group within Hawaii. These beetles’ evolution during the 1.2-million-year lifespan of Haleakala volcano means they have speciated faster than most organisms on Earth, including the Hawaiian Drosophila and the cichlid fishes of eastern Africa.

No less striking is the fact that the 74 newly described beetle species previously evaded discovery within the limits of Haleakala’s 1,440 km2 of surface area. Reasons for this include the restricted distributions of many of the beetle species, and the previous lack of comprehensive field sampling. During his research, Prof. Liebherr examined all quarters of the mountain to eventually find many places of 1′ latitude × 1′ longitude where more than 20Mecyclothorax species lived closely together within a limited area of forest.

Most of these diverse microhabitats were discovered in windward rainforests. Moreover, different forest areas, geographically isolated from each other by volcanic lava flows, steep valleys, or extensive mudflows, supported different sets of species. “Haleakala volcano is a large pie with different sets of beetle species living in the different slices,” comments Prof. Liebherr. “Actually the different pie slices are just like the original Hawaiian land divisions called ahu pua’a, showing that the Hawaiian people had a keen sense for how their island home was organized.”

Additionally, the round-waisted beetle species seem to thrive across a wide range of altitudes, with their populations covering the major part of the mountain’s height. Historical as well as modern records have identified representatives of these insects from 450-metre elevation up to the volcano’s summit at 3000 m. However, given land conversion and the influx of alien invasive plants, habitats below about 1000 m have been seriously disrupted, and these elevations support few native beetles.

Looking to the future, Liebherr points out that “the substantial level of sympatry, associated with occupation of diverse microhabitats by these beetles, provides ample information useful for monitoring biodiversity of the natural areas of Haleakala.”

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Original source:

Liebherr JK (2015) The Mecyclothorax beetles (Coleoptera, Carabidae, Moriomorphini) of Haleakala-, Maui: Keystone of a hyperdiverse Hawaiian radiation. ZooKeys 544: 1-407. doi: 10.3897/zookeys.544.6074

Rare Amazonian butterfly named after British national treasure Sir David Attenborough

A beautiful new Black-eyed Satyr species has become the first butterfly named in honour of the popular naturalist and TV presenter Sir David Attenborough. Although not the first animal to be named after the British national treasure, the butterfly is so rare that it is known only from lowland tropical forests of the upper Amazon basin in Venezuela, Colombia, and Brazil. The study, conducted by an international team of researchers, led by Andrew F. E. Neild, Natural History Museum, London, and Shinichi Nakahara, McGuire Center for Lepidoptera and Biodiversity and Entomology & Nematology Department, University of Florida, is published in the open-access journal ZooKeys.

The presently described Attenborough’s Black-eyed Satyr, scientifically called Euptychia attenboroughi, has such a restricted distribution that all of its known sites lie within 500 kilometres from each other in the north-west of the upper Amazon basin.

Best known for scripting and presenting the BBC Natural History’s ‘Life’ series, Sir David Attenborough is also a multiple winner of the BAFTA award and a president of Butterfly Conservation.

“Other animals and plants have previously been dedicated to Sir David, but it makes us happy and proud to be the first to dedicate a butterfly species in his name,” says Andrew Neild. “Although we are a large team from several countries from across four continents and speaking different languages, we have all been deeply influenced and inspired by Sir David’s fascinating and informative documentaries.”

The butterfly’s atypical wings in comparison to its relatives, have been the reason the scientists took to plenty of diagnostic characters to define its taxonomic placement. The peculiar patterns and morphology initially led the researchers to think the species could be even a new genus.

“It was a surprise for us that DNA data supported inclusion of this new species in the existing genus Euptychia, since this species lacked a distinctive structural character which was considered to be shared by all members of the genus” explains Shinichi Nakahara.

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Original Source:

Neild AFE, Nakahara S, Zacca T, Fratello S, Lamas G, Le Crom J-F, Dolibaina DR, Dias FMS, Casagrande MM, Mielke OHH, Espeland M (2015) Two new species of Euptychia Hübner, 1818 from the upper Amazon basin (Lepidoptera, Nymphalidae, Satyrinae). ZooKeys 541: 87-108. doi: 10.3897/zookeys.541.6297

Get to know them faster: Alternative time-efficient way to describe new moth species

Having collected thousands of moth and butterfly species from across Costa Rica, famous ecologist Daniel Janzen, University of Pennsylvania, and his team were yet to find out many of their names. When they sought help from Dr. Gunnar Brehm, the taxonomist realised he needed too much time to describe species in the framework of an extensive revision of the genus, especially as there are still only a few biologists skilled to do this.

In the end, he found a way to revise the Neotropical looper moth genus Hagnagorafast and efficiently through avoiding wordy descriptions, but focusing on diagnostic characters, illustrated external characters, genitalia structures and DNA barcoding instead. His study is available in the open-access journal ZooKeys.

Having been put together back in the 19th century, most of the species within the Neotropical moth genus Hagnagora had been described by 1913. In modern days, it seemed necessary for the taxon to be revised. As a result, Dr. Gunnar Brehm herein publishes a “concise revision” comprising twenty species. It includes two species that have been revived from synonymy, two subspecies reinstated to a species level, four species excluded from the genus and the description of three new to science. In honour of the people who had funded the research, the new species have been named after them.

Following the revision, the research concludes not only the DNA molecules divergence between the separate species, but some subtle differences such as size, form of the wing blotches or the shape of the male genitalia.

Curious characteristic behaviour traits have also been noted within the genus. The representatives of the discussed genus fold their wings vertically while resting just like most butterflies and unlike the majority of related geometrid moths. Similarly, three of the revised species were noticed to be active during the day when they would often perch on moist substances like rotting plants, mud or dung, from whose fluids they would find vital nutrients.

The author stresses on the fact that taxonomists can hardly keep up with the pace inventories are being compiled, nor with the accelerating destruction of tropical rainforests. “Taxonomists therefore need to accelerate their workflows and try to make their papers useful not only to other taxonomists but for ecologists who need their support”, Dr. Gunnar Brehm says.

“What used to be one species ten years ago, known as Hagnagora anicata, is now regarded as a complex of six species, and more might be discovered in South American rain forests”, Brehm says. “Integrating information of molecules and morphology, as concisely as possible, appears to be one promising way to cope with the problem of slow taxonomy”, he explains in conclusion.

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Original source:

Brehm G (2015) Three new species of Hagnagora Druce, 1885 (Lepidoptera, Geometridae, Larentiinae) from Ecuador and Costa Rica and a concise revision of the genus. ZooKeys 537: 131-156. doi: 10.3897/zookeys.537.6090

The owls beyond the Andes: Divergence between distant populations suggests new species

They might be looking quite identical, while perched above humanised farmlands and grasslands across several continents, but each of the populations of two owl species, living in the opposite hemispheres, might actually turn out to be yet another kind. This suggestion has been made by Dr. Nelson Colihueque and his team from Universidad de Los Lagos, Chile, based on new genetic divergence analyses of the Common Barn and the Short-eared Owl populations from southern Chile and comparing them with those from other geographic areas. The study is published in the open-access journal ZooKeys.

Although much has been known about the two widespread owl species, the knowledge about them has so far been restricted mainly to aspects such as their diet, conservation status and habitats. On the other hand, their genetic divergence in comparison with populations in distant areas has received little attention. Moreover, their taxonomical status is still based on traditional identification rather than modern methods such as the herein utilised mitochondrial COI sequencing.

Thus, the Chilean research team concluded a significant genetic divergence among the populations of both species from a few distinctive groups. In the case of the Common Barn Owl they compared the new analysis of its South American representatives with already available such data about populations from North America, Northern Europe and Australasia. For the Short-eared Owl, they compared Chilean and Argentinean birds with North American and North Asian.

One of the reasons behind such an evolutionary divergence might be the geographic isolation, experienced by the peripheral South American populations of both owl species. It is a consequence of the Andean Mountains acting as a natural barrier.

“In the case of the Common Barn Owl, the existence of geographic barriers to gene flow among populations on different continents is to be expected, and this in combination with its non-migratory or short-distance migratory behaviour, should contribute to promote the genetic divergence,” further explain the authors.

In conclusion, the researchers call for additional studies to clarify the taxonomic identification of these owl populations.

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Original source:

Colihueque N, Gantz A, Rau JR, Parraguez M (2015) Genetic divergence analysis of the Common Barn Owl Tyto alba (Scopoli, 1769) and the Short-eared Owl Asio flammeus (Pontoppidan, 1763) from southern Chile using COI sequence. ZooKeys 534: 135-146. doi: 10.3897/zookeys.534.5953

The first long-haired ones: New wasp group proposed for 5 new species from India

Long accustomed to parasitising spider eggs, a large worldwide genus of wasps has as few as 24 known representatives in India. However, Dr. Veenakumari, ICAR-National Bureau of Agricultural Insect Resources, and her team have recently discovered five new species of these interesting wasps from different parts of the country. Because of their uniqueness and their strong resemblance to each other, as well to aid taxonomic studies they have been considered as constituting a group of their own. The discoveries and the suggestion of ‘the first long-haired ones’ species group are available in the open-access journal Deutsche Entomologische Zeitschrift.

Among the unique features that bring together the new five species, discovered by Drs. Veenakumari Kamalanathan, Prashanth Mohanraj and F. R. Khan, are the long hair-like structures along the margins of both of their wings. This is also the reason behind the authors’ choice of naming the proposed group adikeshavus, meaning ‘first one to have long hairs’ in Sanskrit.

Within this parasitic superfamily of wasps each group has been long accustomed to a specific host. The tribe to which the new five wasp species belong, for instance, is characterised by its exclusive preference for spider eggs. Parallel evolution accounts for the tiny wings of these wasps which allows them to slip through the silk strands of the egg sacs which are deposited in leaf litter by the spiders. Furthermore, all these species have a uniform length of 1 to 2 mm as a result of their getting used to parasitising relatively medium-sized spider eggs.

With over a thousand species supposed to exist in this genus the scientists suggest that their clustering into groups is a necessity to facilitate future studies.

The authors conclude that it is highly likely that this group of wasps will yield a much larger number of species of parasitoids attacking spider eggs in India.

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Original source:

Kamalanathan V, Mohanraj P, Khan FR (2015) ‘The adikeshavus-group’: A new species group of Idris Förster (Hymenoptera, Platygastridae) from India, with descriptions of five new species. Deutsche Entomologische Zeitschrift 62(2): 247-260. doi: 10.3897/dez.62.6219

Streamlining the Import of Specimen or Occurrence Records Into Taxonomic Manuscripts

Repositories and data indexing platforms, such as GBIF, BOLD systems, or iDigBio hold documented specimen or occurrence records along with their record ID’s. In order to streamline the authoring process, save taxonomists’ time, and provide a workflow for peer-review and quality checks of raw occurrence data, the ARPHA team has introduced an innovative feature that makes it possible to easily import specimen occurrence records into a taxonomic manuscript (see Fig. 1).

For the remainder of this post we will refer to specimen data as occurrence records, since an occurrence can be both an observation in the wild, or a museum specimen.

Fig. 1: Workflow for directly importing occurrence records into a taxonomic manuscript.

Until now, when users of the ARPHA writing tool wanted to include occurrence records as materials in a manuscript, they would have had to format the occurrences as an Excel sheet that is uploaded to the Biodiversity Data Journal, or enter the data manually. While the “upload from Excel” approach significantly simplifies the process of importing materials, it still requires a transposition step – the data which is stored in a database needs to be reformatted to the specific Excel format. With the introduction of the new import feature, occurrence data that is stored at GBIF, BOLD systems, or iDigBio, can be directly inserted into the manuscript by simply entering a relevant record identifier.

The functionality shows up when one creates a new “Taxon treatment” in a taxonomic manuscript prepared in the ARPHA Writing Tool. The import functions as follows:

the author locates an occurrence record or records in one of the supported data portals;
the author notes the ID(s) of the records that ought to be imported into the manuscript (see Fig. 2, 3, and 4 for examples);
the author enters the ID(s) of the occurrence records in a form that is to be seen in the materials section of the species treatment, selects a particular database from a list, and then simply clicks ‘Add’ to import the occurrence directly into the manuscript.

In the case of BOLD Systems, the author may also select a given Barcode Identification Number (BIN; for a treatment of BIN’s read below), which then pulls all occurrences in the corresponding BIN (see Fig. 5).

Fig. 2: (Left) An occurrence record in iDigBio. The UUID is highlighted; Fig. 3: (Right) An occurrence record in GBIF. The GBIF ID and the Occurrence ID is highlighted. (Click on images to enlarge)

Fig. 4: (Left) An occurrence record in BOLD Systems. The record ID is highlighted.; Fig. 5: (Right) All occurrence records corresponding to a OTU. The BIN is highlighted. (Click on images to enlarge)

We will illustrate this workflow by creating a fictitious treatment of the red moss, Sphagnum capillifolium, in a test manuscript. Let’s assume we have started a taxonomic manuscript in ARPHA and know that the occurrence records belonging to S. capillifolium can be found in iDigBio. What we need to do is to locate the ID of the occurrence record in the iDigBio webpage. In the case of iDigBio, the ARPHA system supports import via a Universally Unique Identifier (UUID). We have already created a treatment for S. capillifolium and clicked on the pencil to edit materials (Fig. 6). When we scroll all the way down in the pop-up window, we see the form which is displayed in the middle of Fig. 1.

Fig. 6: Edit materials.

From here, the following actions are possible:

insert (an) occurrence record(s) from iDigBio by specifying their UUID’s (universally unique identifier) (Fig.2);
insert (an) occurrence record(s) from GBIF by entering their GBIF ID’s (Fig.3);
insert (an) occurrence record(s) from GBIF by entering their occurrence ID’s (note that unfortunately not all GBIF records have an occurrence ID, which is to be understood as some sort of universal identifier) (Fig. 3);
insert (an) occurrence record(s) from BOLD by entering their record ID’s (Fig. 4);
insert a set of occurrence records from BOLD belonging to a BIN (barcode index number) (Fig. 5).

In this example, select the fifth option (iDigBio) and type or paste the UUID b9ff7774-4a5d-47af-a2ea-bdf3ecc78885 and click Add. This will pull the occurrence record for S. capillifolium from iDigBio and insert it as a material in the current paper (Fig. 6). The same workflow applies also to the aforementioned GBIF and BOLD portals.

Fig. 7: Materials after they have been imported.

This workflow can be used for a number of purposes but one of its most exciting future applications is the rapid re-description of Linnaean species, or new morphological descriptions of species together with DNA barcode sequences (a barcode is a taxon-specific highly conserved gene that provides enough inter-species variation for statistical classification to take place) using the Barcode Identification Numbers (BIN’s) underlying an Operational Taxonomic Units (OTU). If a taxonomist is convinced that a species hypothesis corresponding to OTU defined algorithmically at BOLD systems clearly presents a new species, then he/she can import all specimen records associated with that OTU via inserting that OTU’s BIN ID in the respective fields.

Having imported the specimen occurrence records, the author needs to define one specimen as holotype of the news species, other as paratypes, and so on. The author can also edit the records in the ARPHA tool, delete some, or add new ones, etc.

Not having to retype or copy/paste species occurrence records, the authors save a lot of efforts. Moreover, they automatically import them in a structured Darwin Core format, which can easily be downloaded from the article text into structured data by anyone who needs the data for reuse.

Another important aspect of the workflow is that it will serve as a platform for peer-review, publication and curation of raw data, that is of unpublished individual data records coming from collections or observations stored at GBIF, BOLD and iDigBio. Taxonomists are used to publish only records of specimens they or their co-authors have personally studied. In a sense, the workflow will serve as a “cleaning filter” for portions of data that are passed through the publishing process. Thereafter, the published records can be used to curate raw data at collections, e.g. put correct identifications, assign newly described species names to specimens belonging to the respective BIN and so on.

Additional Information:

The work has been partially supported by the EC-FP7 EU BON project (ENV 308454, Building the European Biodiversity Observation Network) and the ITN Horizon 2020 project BIG4 (Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow’s researchers and entrepreneurs), under Marie Sklodovska-Curie grant agreement No. 542241.

Novel cybercatalog of flower-loving flies suggests the digital future of taxonomy

Charting Earth’s biodiversity is the goal of taxonomy and to do so the scientists need to create an extensive citation network based on several hundred million pages of scientific literature. By providing a novel taxonomic ‘cybercatalog’ of southern African flower-loving (apiocerid) flies, Drs. Torsten Dikow and Donat Agosti demonstrate how the network of taxonomic knowledge can be made available through links provided to online data providers. Their work is available in the open-access Biodiversity Data Journal.

The present research showcases that the information cannot only be made available to the reader who follows the links, but also to machines that use the growing number of digital, online resources that are linked through persistent identifiers.

Primary data providers for taxonomic information such as species names (ZooBank), specimen images (Morphbank), species descriptions (Plazi), and digitized literature (BHL, Biodiversity Heritage Library; BioStor; and BLR, Biodiversity Literature Repository) play an important role in making data on species available in electronic form. Aggregators such as the Global Biodiversity Information Facility (GBIF) and the Encyclopedia of Life (EoL) gather this information automatically to distribute it even further to audiences beyond the reach of the life sciences.

In contrast to previous species catalogs, in cybercatalogs access to information is provided through links to open-access, online data repositories such as the ones listed above. Taxonomists and other users can now access this literature, species descriptions, and specimen records immediately without a search in a natural history library or collection. The cybercatalog takes advantage of a new publishing platform within the Biodiversity Data Journal that makes it easy to upload species information and links to data about these species through a CheckList template. Furthermore, the Biodiversity Data Journal now allows future updates and re-publications of the cybercatalog with the new unique persistent identifier (DOI, Digital Object Identifier) whenever a new species is described or other taxonomic changes take place.

The authors argue that cybercatalogs are indeed the future of taxonomic catalogs since the online data in them are easily accessible to anyone.

“It is a taxonomist’s dream to have online access to all previously published information on a species and through this step the discipline of taxonomy can (re-)position itself as a central resource within the life sciences and beyond to the public and society at large,” add the authors. “Online access will also help to narrow the gap between the South and the North as a fantastic example of unhindered access to our knowledge of the global biological diversity, which is increasingly under pressure from human populations.”

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For the realization of this project Plazi and Pensoft were partially supported by the EC-FP7 EU BON project (ENV 30845) (Building the European Biodiversity Observation Network).

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Original source:

Dikow T, Agosti D (2015) Utilizing online resources for taxonomy: a cybercatalog of Afrotropical apiocerid flies (Insecta: Diptera: Apioceridae). Biodiversity Data Journal 3: e5707. doi: 10.3897/BDJ.3.e5707