Rarely-seen event of ant brood parasitism by scuttle flies video-documented

While many species of scuttle flies are associated with ants, their specific interactions with their hosts are largely unknown. Brood parasitism (attacking the immature stages, rather than the adult ants), for example, is an extremely rarely observed and little-studied phenomenon. However, a research team from the USA and Brazil, led by Dr. Brian Brown, Natural History Museum of Los Angeles County, have recently video-documented two such occasions. The observations are published in the open access Biodiversity Data Journal.

One of the videos, taken in Brazil, shows female scuttle flies attacking ants evacuating their nest. Having had their colony exposed, worker ants try to carry the brood to the nearest shelter. The flies follow these workers on foot, and bump into them in attempt to make them drop the larvae. The scientists have provided a video of an ant which, when harassed, left a larva in a partially exposed position and fled. Immediately, the fly attacked the larva, laying an egg inside its body. The fact that the flies attack the relatively soft-bodied larvae explains the puzzling structure of the ovipositor (egg-layer) of this species (Ceratoconus setipennis), which appears much less hardened than the ovipositor of species attacking adult ants. As a result of the present observation, however, their association with ants is no longer a mystery.

The second footage, filmed in Costa Rica, shows an undescribed species of scuttle fly (genus Apocephalus) that fly above the ants. When they spot a worker carrying brood, it would plunge down to it, approach the ant from behind and land on the (in this case) pupa. Then, it flips over onto its back, keeping the pupa between itself and the ant, while it lays an egg into the pupa from an upside-down position.

“The video documentation of two very different types of brood parasitism of ant species by scuttle flies was recorded in two countries within just a few months of one another,” conclude the authors. “This hints at the many remarkable behaviors of phorid flies that may still await discovery by the patient observer. It appears brood parasitism may not be as rare as was once assumed, and that there may be a tremendous amount of information to uncover about these behaviors.”


Original source:

Brown B, Hash J, Hartop E, Porras W, Amorim D (2017) Baby Killers: Documentation and Evolution of Scuttle Fly (Diptera: Phoridae) Parasitism of Ant (Hymenoptera: Formicidae) Brood. Biodiversity Data Journal 5: e11277. https://doi.org/10.3897/BDJ.5.e11277

Robust rattan palm assessed as Endangered, new Species Conservation Profile shows

An African rattan palm species has recently been assessed as Endangered, according to the IUCN Red List criteria. Although looking pretty robust at height of up to 40 m, the palm is restricted to scattered patches of land across an area of 40 km². It grows in reserves and conservation areas in Ghana and a single forest patch in Côte d’Ivoire. Its Species Conservation Profile is published in the open access Biodiversity Data Journal by an international research team, led by Thomas Couvreur, Institut de Recherche pour le Développement (IRD), France, in collaboration with the University of Yaoundé, Cameroon, Royal Botanic Gardens, Kew, UK, and the Conservatoire et jardin botaniques, Geneva, Switzerland.

oo_106255The rattan palm is confined to moist evergreen forests with high rainfall, located at 100 to 200 meters above sea level. The species is poorly known, yet it is likely very rare judging from the limited amount of forest habitat remaining across its range. Furthermore, the known populations are isolated from each other by large distances, which makes them particularly vulnerable.

Even though there are gaps of knowledge concerning the rattan palm species, the research team conclude that it is most likely currently declining, due to habitat loss, fragmentation and over-harvesting. Often mistaken for a sister species, commonly used in trade, the stems of the endangered species are largely used in furniture production. When longitudinally split into ribbons, the canes are also used as ropes for thatching, for making baskets and sieves, and to make traps.

“As with most African rattan species, there is inadequate information on the international trade, but it is likely to be negligible,” explain the scientists.

“Conservation measures are urgently needed to protect the habitat of this species and to control the unsustainable harvest of the stems. A promising solution might be sustainable cultivation of rattans to avoid the exploitation of wild populations,” suggests Ariane Cosiaux (IRD), the lead author of the study currently based in Cameroon.

With their present paper, the authors make use of a specialised novel publication type feature, called Species Conservation Profile, created by Biodiversity Data Journal, to provide scholarly credit and citation for the IUCN Red List species page, as well as pinpoint the population trends and the reasons behind them.


Original source:

Cosiaux A, Gardiner L, Ouattara D, Stauffer F, Sonké B, Couvreur T (2017) An endangered West African rattan palm: Eremospatha dransfieldii. Biodiversity Data Journal 5: e11176. https://doi.org/10.3897/BDJ.5.e11176

Biodiversity project in Azores delivers detailed abundance data for 286 arthropod species

In 1999, a long-term biodiversity project started at the Azores Islands (Portugal, Atlantic Ocean), the Biodiversity of Arthropods from the Laurisilva of the Azores (BALA) project (1999-2004). Its aim was to obtain detailed distributional and abundance data for a large fraction of arthropod fauna, living in all remaining native forests at seven of the Azores Islands.

After the first successful sampling of 100 sites at 18 native forest fragments over those five years, a second survey was accomplished in 2010-2011, where two sites per fragment were re-sampled. Now, Dr Paulo A.V. Borges and colleagues publish the complete list of the 286 species identified, including many species described as new to science in the open access journal Biodiversity Data Journal. They have also added detailed information on their distribution and abundance.

The resulting database has inspired the publication of many studies in the last ten years, including macroecological studies evaluating the abundance, spatial variance and occupancy of arthropods, the effects of disturbance and biotic integrity of the native forests on arthropod assemblages and the performance of species richness estimators.

image-2Moreover, these data allowed the ranking of conservation priorities for the fauna of the Azores, and allowed the estimation of extinction debt (the species likely to be wiped out because of past events) in the Azores. The present study has also inspired the development of the Azorean Biodiversity Portal and the Azores Island Lab.

The study stresses the need to expand the approaches applied in these projects to other habitats in the Azores, and, more importantly, to other less thoroughly surveyed taxonomic groups (e.g. Diptera and Hymenoptera).

“These steps are fundamental for getting a more accurate assessment of the biodiversity in the Azores archipelago, and we hope that can inspire similar biodiversity surveys at other islands,” say the authors.


Original source:

Borges P, Gaspar C, Crespo L, Rigal F, Cardoso P, Pereira F, Rego C, Amorim I, Melo C, Aguiar C, André G, Mendonça E, Ribeiro S, Hortal J, Santos A, Barcelos L, Enghoff H, Mahnert V, Pita M, Ribes J, Baz A, Sousa A, Vieira V, Wunderlich J, Parmakelis A, Whittaker R, Quartau J, Serrano A, Triantis K (2016) New records and detailed distribution and abundance of selected arthropod species collected between 1999 and 2011 in Azorean native forests. Biodiversity Data Journal 4: e10948. https://doi.org/10.3897/BDJ.4.e10948

Efficiency of insect biodiversity monitoring via Malaise trap samples and DNA barcoding

The massive decline of over 75% insect biomass reported from Germany between 1989 and 2013 by expert citizen scientists proves the urgent need for new methods and standards for fast and wide-scale biodiversity assessments. If we cannot understand species composition, as well as their diversity patterns and reasons behind them, we will fail not only to predict changes, but also to take timely and adequate measures before species go extinct.

An international team of scientists belonging to the largest and connected DNA barcoding initiatives (iBOL, GBOL, BFB), evaluated the use of DNA barcode analysis applied to large samples collected with Malaise traps as a method to rapidly assess the arthropod fauna at two sites in Germany between May and September.

One Malaise trap (tent-like structure designed to catch flying insects by attracting them to its walls and then funneling them into a collecting bottle) was set in Germany’s largest terrestrial protected natural reserve Nationalpark Bayerischer Wald in Bavaria. Located in southeast Germany, from a habitat perspective, the park is basically a natural forest. The second trap was set up in western Germany adjacent to the Middle River Rhine Valley, located some 485 kilometers away from the first location. Here, the vegetation is eradicated annually due to St. Martin’s fires, which occur every November. Their findings are published in the open access Biodiversity Data Journal.

DNA barcoding enables the identification of a collected specimen by comparing its BIN (Barcode Index Number) against the BOLD database. In contrast to evaluation using traditional morphological approaches, this method takes significantly less experience, time and effort, so that science can easily save up on decades of professional work.

However, having analyzed DNA barcodes for 37,274 specimens equal to 5,301 different BINs (i.e., species hypotheses), the entomologists managed to assign unambiguous species names to 35% of the BINs, which pointed to the biggest problem with DNA barcoding for large-scale insect inventories today, namely insufficient coverage of DNA barcodes for Diptera (flies and gnats) and Hymenoptera (bees and wasps) and allied groups. As the coverage of the reference database for butterflies and beetles is good, the authors showcase how efficient the workflow for the semi-automated identification of large sample sizes to species and genus level could be.

In conclusion, the scientists note that DNA barcoding approaches applied to large-scale samplings collected with Malaise traps could help in providing crucial knowledge of the insect biodiversity and its dynamics. They also invite their fellow entomologists to take part and help filling the gaps in the reference library. The authors also welcome taxonomic experts to make use of the unidentified specimens they collected in the study, but also point out that taxonomic decisions based on BIN membership need to be made within a comparative context, “ideally including morphological data and also additional, independent genetic markers”. Otherwise, the grounds for the decision have to be clearly indicated.

The study is conducted as part of the collaborative Global Malaise Trap Program (GMTP), which involves more than 30 international partners. The aim is to provide an overview of arthropod diversity by coupling the large-scale deployment of Malaise traps with the use of specimen-based DNA barcoding to assess species diversity.

Sequence analyses were partially defrayed by funding from the government of Canada through Genome Canada and the Ontario Genomics Institute in support of the International Barcode of Life project. The German Barcode of Life project (GBOL) is generously supported by a grant from the German Federal Ministry of Education and Research (FKZ 01LI1101 and 01LI1501) and the Barcoding Fauna Bavarica project (BFB) was supported by a 10-year grant from the Bavarian Ministry of Education, Culture, Research and Art.



Original source:

Geiger M, Moriniere J, Hausmann A, Haszprunar G, Wägele W, Hebert P, Rulik B (2016) Testing the Global Malaise Trap Program – How well does the current barcode reference library identify flying insects in Germany? Biodiversity Data Journal 4: e10671. https://doi.org/10.3897/BDJ.4.e10671

Foreign beetle species recorded for the first time in Canada thanks to citizen science

With social networks abound, it is no wonder that there is an online space where almost anyone can upload a photo and report a sighting of an insect. Identified or not, such public records can turn out to be especially useful — as in the case of an Old World beetle species — which appears to have recently entered Canada, and was recently discovered with the help of the BugGuide online portal and its large citizen scientist community.

Having identified the non-native rove beetle species Ocypus nitens in Ontario, Canada, based on a single specimen, author Dr Adam Brunke, affiliated with the Canadian National Collection of Insects, Arachnids and Nematodes, Ottawa, sought additional data to confirm his discovery.

Eventually, he found them in the citizen-generated North American digital insect collection BugGuide, created and curated by an online community of naturalists, insect enthusiasts and entomologists. After he verified as many as 26 digital photographs to be records of the same species, he concluded that the rove beetle has expanded its distribution to two new locations — Ontario, its first in Canada, and the state of Vermont, USA. His study is published in the open access Biodiversity Data Journal.

The species O. nitens is a fairly large rove beetle measuring between 12 and 20 mm in length and visibly distinguished by the characteristic form of the head and relatively short forewings. Furthermore, the insect is quite easy to spot because it prefers living around humans, often being spotted in woodlots and backyards.

As a result of the hundreds of years of Transatlantic trade, many species have been transported accidentally among various produce to subsequently adapt and establish on the other side of the ocean. While the rove beetle species O. nitens was first reported from the Americas in 1944, it was not until the turn of the new millennium that it escaped the small area in New England, USA, which had so far been its only habitat on the continent. Then, its distributional range began to rapidly expand. It is unlikely that the presence of this rove beetle, especially in Ontario, has long remained undetected, because of thorough and multiple sampling initiatives undertaken by professionals and students in the past.

The effect of the newly recorded species on the native rove beetles is still unknown. On the other hand, there are observations that several related beetles have experienced a drop in their populations in comparison to the records from the beginning of the century.

“Citizen-generated distributional data continues to be a valuable ally in the detection of adventive insects and the study of their distributional dynamics,” concludes the author.


Original source:

Brunke A (2016) First detection of the adventive large rove beetle Ocypus nitens (Schrank) in Canada and an update of its Nearctic distribution using data generated by the public. Biodiversity Data Journal 4: e11012. https://doi.org/10.3897/BDJ.4.e11012

LifeWatchGreece launches a Special Paper Collection for Greek biodiversity research

Developed in the 1990s and early 2000s, LifeWatch is one of the large-scale European Research Infrastructures (ESFRI) created to support biodiversity science and its developments. Its ultimate goal is to model Earth’s biodiversity based on large-scale data, to build a vast network of partners, and to liaise with other high-quality and viable research infrastructures (RI).

Being one of the founding LifeWatch member states, Greece has not only implemented LifeWatchGreece, but it is all set and ready to “fulfill the vision of the Greek LifeWatch RI and establish it as the biodiversity Centre of Excellence for South-eastern Europe”, according to the authors of the latest Biodiversity Data Journal‘s Editorial: Dr Christos Arvanitidis, Dr Eva Chatzinikolaou, Dr Vasilis Gerovasileiou, Emmanouela Panteri, Dr Nicolas Bailly, all affiliated with the Hellenic Centre for Marine Research (HCMR) and part of the LifeWatchGreece Core Team, together with Nikos Minadakis, Foundation for Research and Technology Hellas (FORTH), Alex Hardisty, Cardiff University, and Dr Wouter Los, University of Amsterdam.

lwg-presentationMaking use of the technologically advanced open access Biodiversity Data Journal and its Collections feature, the LifeWatchGreece team is publishing a vast collection of peer-reviewed scientific outputs, including software descriptions, data papers, taxonomic checklists and research articles, along with the accompanying datasets and supporting material. Their intention is to demonstrate the availability and applicability of the developed e-Services and Virtual Laboratories (vLabs) to both the scientific community, as well as the broader domain of biodiversity management.

The LifeWatchGreece Special Collection is now available in Biodiversity Data Journal, with a series of articles highlighting key contributions to the large-scale European LifeWatch RI. The Software Description papers explain the LifeWatchGreece Portal, where all the e-Services and the vLabs provided by LifeWatchGreece RI are hosted; the Data Services based on semantic web technologies, which provide detailed and specialized search paths to facilitate data mining; the R vLab which can be used for a series of statistical analyses in ecology, based on an integrated and optimized online R environment; and the Micro-CT vLab, which allows the online exploration, dissemination and interactive manipulation of micro-tomography datasets.

The LifeWatchGreece Special Collection also includes a series of taxonomic checklists (preliminary, updated and/or annotated); a series of data papers presenting historical and original datasets; and a selection of research articles reporting on the outcomes, methodologies and citizen science initiatives developed by collaborating research projects, which have shared human, hardware and software resources with LifeWatchGreece RI.

LifeWatchGreece relies on a multidisciplinary approach, involving several subsidiary initiatives; collaborations with Greek, European and World scientific communities; specialised staff, responsible for continuous updates and developments; and, of course, innovative online tools and already established IT infrastructure.


Original source:

Arvanitidis C, Chatzinikolaou E, Gerovasileiou V, Panteri E, Bailly N, Minadakis N, Hardisty A, Los W (2016) LifeWatchGreece: Construction and operation of the National Research Infrastructure (ESFRI). Biodiversity Data Journal 4: e10791. https://doi.org/10.3897/BDJ.4.e10791

Additional information:

This work has been supported by the LifeWatchGreece infrastructure (MIS 384676), funded by the Greek Government under the General Secretariat of Research and Technology (GSRT), ESFRI Projects, National Strategic Reference Framework (NSRF).

Species conservation profile of a critically endangered endemic for the Azores spider

Subject to continuing population decline due to a number of factors, an exclusively cave-dwelling (troglobitic) spider endemic to the Azores is considered as Critically Endangered according to the IUCN Red List criteria.

To provide a fast output, potentially benefiting the arachnid’s survival, scientists from the IUCN – Spider and Scorpion Specialist Group and the Azorean Biodiversity Group (cE3c) at University of Azores, where the main objective is to perform research that addresses societal challenges in ecology, evolution and the environment, also known as the three E’s from the centre’s name abbreviation, teamed up with colleagues from University of Barcelona, Spain, and the Finnish Museum of Natural History.

Together, they make use of a specialised novel publication type feature, called Species Conservation Profile, created by the open access journal Biodiversity Data Journal, to provide scholarly credit and citation for the IUCN Red List species page, as well as pinpoint the population trends and the reasons behind them.

The studied spider species (scientifically called Turinyphia cavernicola) is a pale creature with long legs, large eyes and a total size of merely 2 mm in length. These spiders never leave their underground habitats, which are strictly humid lava tubes and volcanic pits. There they build sheet webs in small holes and crevices on the walls of the caves.

The volcanic pit Algar do Carvão (Terceira, Azores), the main location of the species Turyniphia cavernicola.Not only is the species restricted to a single island within the Azorean archipelago (Portugal), but it is only found in three caves. Furthermore, out of the three, only one of them is home to a sustainable large population. These caves are under severe threat due to pasture intensification, road construction and tourist activities.

Although there is not much information about the species distribution through the years, with the spider having been discovered as recently as in 2008, the authors make the assumption that originally there have been significantly greater populations. Not only have they studied thoroughly another fifteen caves located on the island without finding any individuals, but they have identified increasing anthropogenic impact on the habitat.

“The species original distribution was potentially very large compared with the current,” the scientists explain. “Relatively intensive searches in and around the current caves where the species occurs have failed to find additional subpopulations.”

“The trend of decline is based on the assumption that this species can occur in all these caves and that the absence is due to anthropogenic disturbance on caves during the last 50 years,” they note.



Original source:

Borges P, Crespo L, Cardoso P (2016) Species conservation profile of the cave spiderTurinyphia cavernicola (Araneae, Linyphiidae) from Terceira Island, Azores, Portugal.Biodiversity Data Journal 4: e10274. doi: 10.3897/BDJ.4.e10274

More assassins on the radar: As many as 24 new species of assassin bugs described

As many as 24 assassin bugs new to science were discovered and described by Dr. Guanyang Zhang and his colleagues. In their article, published in the open access Biodiversity Data Journal, they describe the new insects along with treating another 47 assassin bugs in the same genus. To do this, the scientists examined more than 10,000 specimens, coming from both museum collections and newly undertaken field trips.

Assassin bugs are insects that prey upon other small creatures, an intriguing behavior that gives the common name of their group. There are some 7000 described species of assassin bugs, but new species are still being discovered and described every year.

The new species described by scientists Drs Guanyang Zhang, University of California, Riverside, and Arizona State University, Elwood R. Hart, Iowa State University, and Christiane Weirauch, University of California, Riverside, belong to the assassin bug genus Zelus.

Linnaeus, the Swedish scientist, who established the universally used Linnean classification system, described the first species (Zelus longipes) of Zelus in 1767. Back then, he placed it in the genus Cimex, from where it was subsequently moved to Zelus. All of Zhang & Hart’s new species are from the Americas. Mexico, Panama, Peru, Colombia and Brazil are some of the top countries harboring new species.

To conduct the research, Zhang examined more than 10,000 specimens and nearly all of them have been databased. These specimen records are now freely and permanently available to everybody. Zhang’s work demonstrates the value of natural history collections. The specimens used in his work come from 26 museums in nine countries. The discovery of the new species would not have been possible without these museums actively collecting and maintaining their insect collections.

It took more than a century for some of the new species to be formally recognized and described. The first specimens of the species Zelus panamensis and Zelus xouthos, for example, had been collected in 1911 and 1915 from Panama and Guatemala. However, since then they had been waiting quietly in the collection of the Smithsonian National Museum of Natural History, USA. Now, over 100 years later, they are finally discovered and given scientific names.

Meanwhile, more recently collected specimens also turned out to be new species. Specimens of Zelus lewisi and Zelus rosulentus were collected in 1995 and 1996 from Costa Rica and Ecuador, about two decades ago, a timeframe considered relatively short for taxonomic research. These interesting patterns of time lapse between specimen collecting and scientific description suggest that it is equally important to examine both long deposited in museums specimens and those newly collected from the field.

The kind of research performed by Zhang and his colleagues is called revisionary taxonomy. In revisionary taxonomy a researcher examines a large number of specimens of a group of organisms of his or her interest. This can be either a monophyletic lineage or organisms from a particular region. The scientist’s goal is to discover and describe new species, but also examine and revise previously published species.

Besides describing new species, the present taxonomic monograph treats another 47 previously described species. Nearly all species now have images of both males and females and illustrations of male genitalia. Some of these insects are strikingly brightly colored and some mimic wasps.



Original source:

Zhang G, Hart E, Weirauch C (2016) A taxonomic monograph of the assassin bug genusZelusFabricius (Hemiptera: Reduviidae): 71 species based on 10,000 specimens. Biodiversity Data Journal 4: e8150.doi: 10.3897/BDJ.4.e8150

Remarkably diverse flora in Utah, USA, trains scientists for future missions on Mars

Future Martian explorers might not need to leave the Earth to prepare themselves for life on the Red Planet. The Mars Society have built an analogue research site in Utah, USA, which simulates the conditions on our neighbouring planet.

Practicing the methods needed to collect biological samples while wearing spacesuits, a team of Canadian scientists have studied the diverse local flora. Along with the lessons that one day will serve the first to conquer Mars, the researchers present an annotated checklist of the fungi, algae, cyanobacteria, lichens, and vascular plants from the station in their publication in the open-access journal Biodiversity Data Journal.

oo_56706Located in the desert approximately 9 km outside of Hanksville, Utah, and about 10 km away from the Burpee Dinosaur Quarry, a recently described bone bed from the Jurassic Morrison Formation, the Mars Desert Research Station (MDRS) was constructed in 2002. Since then, it has been continuously visited by a wide range of researchers, including astrobiologists, soil scientists, journalists, engineers, and geologists.

Astrobiology, the study of the evolution and distribution of life throughout the universe, including the Earth, is a field increasingly represented at the MDRS. There, astrobiologists can take advantage of the extreme environment surrounding the station and seek life as if they were on Mars. To simulate the extraterrestrial conditions, the crew members even wear specially designed spacesuits so that they can practice standard field work activities with restricted vision and movement.

In their present research, the authors have identified and recorded 38 vascular plant species from 14 families, 13 lichen species from seven families, 6 algae taxa including both chlorophytes and cyanobacteria, and one fungal genus from the station and surrounding area. Living in such extreme environments, organisms such as fungi, lichens, algae, and cyanobacteria are of particular interest to astrobiologists as model systems in the search for life on Mars.

However, the authors note that there is still field work to be executed at the site, especially during the spring and the summer so that the complete local diversity of the area can be captured.Martian flora 2

“While our present checklist is not an exhaustive inventory of the MDRS site,” they explain, “it can serve as a first-line reference for identifying vascular plants and lichens at the MDRS, and serves as a starting point for future floristic and ecological work at the station.”


Original source:

Sokoloff P, Hamilton P, Saarela J (2016) The “Martian” flora: new collections of vascular plants, lichens, fungi, algae, and cyanobacteria from the Mars Desert Research Station, Utah.Biodiversity Data Journal 4: e8176. doi: 10.3897/BDJ.4.e8176

How the names of organisms help to turn ‘small data’ into ‘Big Data’

Innovation in ‘Big Data’ helps address problems that were previously overwhelming. What we know about organisms is in hundreds of millions of pages published over 250 years. New software tools of the Global Names project find scientific names, index digital documents quickly, correcting names and updating them. These advances help “Making small data big” by linking together to content of many research efforts. The study was published in the open access journal Biodiversity Data Journal.

The ‘Big Data’ vision of science is transformed by computing resources to capture, manage, and interrogate the deluge of information coming from new technologies, infrastructural projects to digitise physical resources (such as our literature from the Biodiversity Heritage Library), or digital versions of specimens and records about specimens by museums.

Increased bandwidth has made dialogue among distributed data centres feasible and this is how new insights into biology are arising. In the case of biodiversity sciences, data centres range in size from the large GenBank for molecular records and the Global Biodiversity Information Facility for records of occurrences of species, to a long tail of tens of thousands of smaller datasets and web-sites which carry information compiled by individuals, research projects, funding agencies, local, state, national and international governmental agencies.

The large biological repositories do not yet approach the scale of astronomy and nuclear physics, but the very large number of sources in the long tail of useful resources do present biodiversity informaticians with a major challenge – how to discover, index, organize and interconnect the information contained in a very large number of locations.

In this regard, biology is fortunate that, from the middle of the 18th Century, the community has accepted the use of latin binomials such as Homo sapiens or Ba humbugi for species. All names are listed by taxonomists. Name recognition tools can call on large expert compilations of names (Catalogue of Life, Zoobank, Index Fungorum, Global Names Index) to find matches in sources of digital information. This allows for the rapid indexing of content.

Even when we do not know a name, we can ‘discover’ it because scientific names have certain distinctive characteristics (written in italics, most often two successive words in a latinised form, with the first one – capitalised). These properties allow names not yet present in compilations of names to be discovered in digital data sources.

The idea of a names-based cyberinfrastructure is to use the names to interconnect large and small distributed sites of expert knowledge distributed across the Internet. This is the concept of the described Global Names project which carried out the work described in this paper.

The effectiveness of such an infrastructure is compromised by the changes to names over time because of taxonomic and phylogenetic research. Names are often misspelled, or there might be errors in the way names are presented. Meanwhile, increasing numbers of species have no names, but are distinguished by their molecular characteristics.

In order to assess the challenge that these problems may present to the realization of a names-based cyberinfrastructure, we compared names from GenBank and DRYAD (a digital data repository) with names from Catalogue of Life to assess how well matched they are.

As a result, we found out that fewer than 15% of the names in pair-wise comparisons of these data sources could be matched. However, with a names parser to break the scientific names into all of their component parts, those parts that present the greatest number of problems could be removed to produce a simplified or canonical version of the name. Thanks to such tools, name-matching was improved to almost 85%, and in some cases to 100%.

The study confirms the potential for the use of names to link distributed data and to make small data big. Nonetheless, it is clear that we need to continue to invest more and better names-management software specially designed to address the problems in the biodiversity sciences.


Original source:

Patterson D, Mozzherin D, Shorthouse D, Thessen A (2016) Challenges with using names to link digital biodiversity information. Biodiversity Data Journal, doi: 10.3897/BDJ.4.e8080.

Additional information:

The study was supported by the National Science Foundation.