Pensoft blog - Part 105

Black mouse-eared bat goes green: First case of a fruit-eating bat in the largest genus

Out of more than 110 allegedly well-studied mouse-eared bat species, there turns out to be one that has been keeping its diet a mystery. Belonging to the largest group of bats, known to be feeding on insects exclusively, the widely common Black mouse-eared bat (Myotis nigricans) is found to also seek fruits. The Brazilian team of researchers, led by biologist Roberto Leonan Morim Novaes, Fiocruz, conducted their work in the Rio de Janeiro’s reserve Reserva Ecologica de Guapiacu (REGUA), a 5,500 ha remnant of Atlantic Forest, and have their findings and discussion published in the open-access Biodiversity Data Journal.

The unexpected first documentation of fruit consumption in this group of bats happened when the researchers captured a number of bats with mist-nets and kept them alone in cotton bags for about thirty minutes before handling for identification and biometry. Thus, they managed to retrieve feces of the specimens, which showed to contain small seeds. Later, in an experiment, part of the seeds even grew into seedlings. As a result, the scientists report the first fruit consumption within the mouse-eared bat genus, called Myotis, as well as the whole subfamily Myotinae. Their finding might also mean that the examined species plays the ecological role of a seed disperser.

Although the finding is based on a single specimen of Black mouse-eared bat, the researchers reject the possibility of the cotton bags having been previously contaminated with feces of other animals. Dismissed is also the chance of the seeds having been consumed on accident while predation, since the Black mouse-eared bat hunts insects during flight.

Overall, bats are remarkable because of their varied eating habits. Commonly eating insects, there are predatory groups specialised in feeding on other invertebrates, terrestrial vertebrates, fishes or blood. Among the plant-eating, there are those specialised in fruits, flowers or leaves. A few are classified as omnivores and yet few, which are known to be using one category of food exclusively, on rare occasions include an untypical food item to compliment their diet. For example, a carnivorous bat may sporadically consume a plant and vice versa.

“The discovery of a well-studied species, previously considered strictly insectivorous, foraging on fruits shows how little we know about the biology and natural history of Neotropical bats,” conclude the authors.

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Original source:

Novaes R, Souza R, Ribeiro E, Siqueira A, Greco A, Moratelli R (2015) First evidence of frugivory in Myotis(Chiroptera, Vespertilionidae, Myotinae). Biodiversity Data Journal 3: e6841. doi:10.3897/BDJ.3.e6841

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

Counting stars: Illegal trade of Indian star tortoises is a far graver issue

Patterned with star-like figures on their shells, Indian star tortoises can be found in private homes across Asia, where they are commonly kept as pets. One can also see them in religious temples, praised as the living incarnation of the Hindu god Vishnu. How did they get there? Suspicious of a large-scale illegal international trade of these tortoises that could in fact pose a grave threat to the survival of the Indian Star tortoise, a team of researchers, led by Dr. Neil D’Cruze from Wildlife Conservation Research Unit, University of Oxford, and World Animal Protection, London, spent 17 months investigating the case focusing on India and Thailand. They have their study published in the open-access journal Nature Conservation.

The present study established that at least 55,000 Indian star tortoise individuals are being poached over the span of a year from a single trade hub in India. Helped by a number of herpetologists and wildlife enforcement officials, the researchers have tracked signals about how sophisticated criminal gangs are exploiting “legal loopholes” and people alike, taking advantage of rural communities and urban consumers in India and other Asian countries.

“We were shocked at the sheer scale of the illegal trade in tortoises and the cruelty inflicted upon them,” comments Dr. Neil D’Cruze. “Over 15 years ago wildlife experts warned that the domestic trade in Indian star tortoises needed to be contained before it could become established as an organised international criminal operation.”

“Unfortunately, it seems that our worst nightmare has come true – sophisticated criminal gangs are exploiting both impoverished rural communities and urban consumers alike,” he also added. “Neither group is fully aware how their actions are threatening the welfare and conservation of these tortoises.”

Although deemed of “Least Concern” on the IUCN Red List when last formally assessed back in 2000, the Indian star tortoise and its increasing illegal poaching and trading can easily lead to a serious risk of the species’ extinction. Other dangers of such unregulated activities include the introduction of invasive species and diseases.

Having spent a year among a rural hunter-gatherer community, researchers established the collection of at least 55,000 juvenile wild Indian star tortoises between January and December 2014. This is already between three and six times more than the last such record dating from about ten years ago.

Collectors tend to poach juvenile tortoises, but it is not rare for them to also catch adults. Based on the individual’s age and health, the tortoises are later sold to vendors at a price of between 50 and 300 Indian Rupees (INR), or between 1 and 5 USD, per animal. “Therefore, we conservatively estimate (assuming no mortalities) that the collector engagement in this illegal operation has a collective annual value of up to 16,500,000 INR (263,000 USD) for their impoverished communities,” comment the researchers.

Consumers seek the Indian star tortoise for either exotic pets or spiritual purposes. With their star-like radiating yellow patterns splashed with black on their shells, not only is this tortoise species an attractive animal, but it was also found to be considered as a good omen among the locals in the Indian state of Gujarat. During their survey, the researchers found over a hundred hatchlings in a single urban household. However, their owner claimed that none of them was kept with commercial intent, although some of the tortoises were meant for close friends and relatives.

On the other hand, there was a case where the researchers came across a Shiva temple hosting a total of eleven Indian star tortoises. Temple representatives there confirmed that the tortoise is believed to represent an incarnation of the Hindu god Vishnu, one of the three central gods in the religion, recognised as the preserver and protector of the universe.

In India vendors do not show the reptiles in public, but they are made available upon a special request. If paid for in advance, a vendor can also supply a larger quantity of the animals at a price ranging from 1,000 to 3,000 INR (15 to 50 USD) per animal. The researchers managed to see seven captive tortoises in private, including six juveniles and one adult, all in visibly poor health. Disturbingly, in order to reach these vendors, the collected tortoise are usually wrapped in cloths and packed into suitcases. Covered by a ‘mask’ of legal produce such as fruit and vegetables, they are transported to the ‘trade hubs’. They are also smuggled abroad to satisfy consumer demand among the growing middle classes in countries such as Thailand and China.

“Despite being protected in India since the 1970’s, legal ‘loopholes’ in other Asian countries such as Thailand and China appear to undermine India’s enforcement efforts,” explains Mr. Gajender Sharma, India’s Director at World Animal Protection, “They are smuggled out of the country in confined spaces, it’s clear there is little or no concern about the welfare of these reptiles.”

“World Animal Protection is concerned about the suffering that these tortoises endure,” he further notes. “We are dealing with an organised international criminal operation which requires an equally organised international approach to combat it.”

As a result of their study, the authors conclude that more research into both the illegal trafficking of Indian star tortoise and its effects as well as the consumer demand is urgently needed in order to assess, address and subsequently tackle the issue.

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Original source:

D’Cruze N, Singh B, Morrison T, Schmidt-Burbach J, Macdonald DW, Mookerjee A (2015) A star attraction: The illegal trade in Indian Star Tortoises. Nature Conservation 13: 1-19. doi:10.3897/natureconservation.13.5625

How did the stonefly cross the lake? The mystery of stoneflies recolonising a US island

Massive glaciers once covered an island in one of the Great Lakes, USA, leaving it largely devoid of life. Its subsequent recolonisation by insects triggered the curiosity of entomologist R. Edward DeWalt and graduate student Eric J. South of the Illinois Natural History Survey and Department of Entomology. Not only did they prove there were significantly fewer species, compared to the mainland, but also that smaller stonefly species appeared to be more capable of recolonizing the island. This study was published in the open-access journal ZooKeys .

Isle Royale is a large island and national park in the middle of Lake Superior, isolated from the mainland by 22 — 70 km distance. As recently as 8,000 — 10,000 years ago, glaciers completely covered the island making it almost uninhabitable.

Over the last 10 millennia mammals as large as moose and wolves, swam, floated, flew, or walked on ice bridges to the island. Therefore, it seemed logical that it was the larger size that allowed some species to cross the water. However, as far as stoneflies are concerned, the results turned out quite different.

“We sampled stoneflies (Plecoptera), mayflies (Ephemeroptera), and caddisflies (Trichoptera), because they are important water quality indicators. Our laboratory has expertise in the taxonomy and ecology of these important species and we know that national parks potentially provide us with wilderness quality conditions,” says DeWalt.

Being much better fliers, the mayflies and caddisflies did not show a particular relation between a species’ body size and their ability to recolonise the island. Conversely, stoneflies on the island were considerably smaller than their mainland counterparts.

“Stoneflies are clumsy fliers, especially the larger species. Large ones are not very aerodynamic and because of this they don’t have the energy reserves to cover the distance to the island. Few species of stoneflies can actually live in the lake, so most could not swim to the island,” explains DeWalt. “Mayflies and caddisflies, on the other hand, are known to be better fliers and tolerant of lake conditions, which would allow for more of the mainland species and similarly sized species to reach Isle Royale.

“Smaller stoneflies have probably used updrafts from the mainland and prevailing winds to get to the island,” the scientist suggests. “The wind just held them up until they reached the island.”

Future research is to use molecular techniques to identify the possible mainland origin for several species inhabiting Isle Royale National Park.

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Original source:

DeWalt RE, South EJ (2015) Ephemeroptera, Plecoptera, and Trichoptera on Isle Royale National Park, USA, compared to mainland species pool and size distribution. ZooKeys 532: 137-158.doi: 10.3897/zookeys.532.6478

World’s tiniest snail record broken with a myriad of new species from Borneo

The world’s record for the smallest land snail is broken once again. A minute shell with an average diameter of 0.7 mm was found in Malaysian Borneo by a team of Dutch and Malaysian biologists along with another 47 new species of greatly varying sizes. Called ‘dwarf’ (“nanus” meaning “dwarf” in Latin), the new snail, Acmella nana, is first-shown to the world in the open-access journal ZooKeys, where the last record-holder was announced only about a month ago.

The world’s tiniest snail has a shell of merely 0.50 – 0.60 mm width and 0.60 – 0.79 mm height. The previous holder of the title of world’s smallest snail, the Chinese Angustopila dominikae, published earlier this year, measured just 0.80 and 0.89 mm respectively.

Some of the new 48 species described in the present paper are widespread in Borneo and had been familiar to the team of snail researchers for decades. Yet, they had not got round to naming them until now. Others eke out a hidden existence on mountain tops or in rare vegetation types and, therefore, were only recently discovered by the authors. For instance, there are seven new species that can only be found on the 4,095-metre-high Mount Kinabalu. Another example, called Diplommatina tylocheilos, only lives at the entrance of the hardly accessible Loloposon Cave in Mount Trusmadi.

The new information tells us more about isolated, or endemic, species such as the new record-holder. Moving so slowly, snails can easily get stuck in very small patches of a habitat. There they can spend long enough to evolve and adapt to the particular limited area, undisturbed by the rest of the world. This makes them excellent examples of how endemic species can arise.

On the other hand, their restricted distribution makes them key targets for biodiversity conservation. “A blazing forest fire at Loloposon Cave could wipe out the entire population ofDiplommatina tylocheilos,” says co-author Schilthuizen.

The discoveries are the latest result of an ongoing research project on the snail fauna of Borneo by the authors. For more than twenty-five years, Jaap Vermeulen, Thor-Seng Liew, and Menno Schilthuizen of Naturalis Biodiversity Center and Universiti Malaysia Sabah, have been documenting Malaysia’s wonderful terrestrial molluscs. Only last year, also in ZooKeys, the team published ten new Malaysian species of the “micro-jewel” snails of the genus Plectostoma.

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Original source:

Vermeulen JJ, Liew TS, Schilthuizen M (2015) Additions to the knowledge of the land snails of Sabah (Malaysia, Borneo), including 48 new species. ZooKeys 531: 1-139. doi:10.3897/zookeys.531.6097

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.

New gorgeous coffee tree species from Honduras is critically endangered

Amid the challenging terrain of north-western Honduras, where Dr. Kelly’s team faced rugged and steep forest areas cut across here and there by a few trails, a gorgeous tree with cherry-like fruits was discovered. Being about 10 metres (33 ft) high and covered with cream-colored flowers, it was quickly sorted into the Coffee family (Rubiaceae), but it was its further description that took much longer. Eventually, it was named Sommera cusucoana, with its specific name stemming from its so far only known locality, the Cusuco National Park. The study is available in the open-access journal PhytoKeys.

During a plant diversity study in the Cusuco National Park, conducted by Drs. Kelly, Dietzch and co-workers as a part of a broader survey by Operation Wallacea, an international organisation dealing with biodiversity and conservation management research programmes.

A couple of curious findings in the past decade provide a strong incentive to further work. The place turns out to be not only of high biodiversity, but to also contain rare and hitherto unknown plant and animal species.

For instance, the tree Hondurodendron (from Greek, ‘Honduras Tree’) and the herbaceous plant Calathea carolineae are another two endemic species discovered as a result of the Operation Wallacea survey.

In 2013, two individuals of another unknown, 10-metre high (33 ft) tree with cream-colored flowers and red, cherry-like fruits were found by Daniel Kelly and Anke Dietzsch from Trinity College, University of Dublin, Ireland. The two were aided by local guide Wilmer Lopez.

The multinational collaboration did not stop then and there. Although the scientists quickly figured that the tree belonged to the Coffee family, they needed some additional help to further identify their discovery. Thus, they were joined by two leading specialist in this plant group, first Charlotte Taylor from Missouri Botanical Garden and then David Lorence from the National Tropical Botanical Garden in Hawaii.

It was actually David who was the first to recognise the unknown tree as a member of theSommera genus, a group of nine known species of trees and shrubs. Later, the team decided to name the new plant Sommera cusucoana to celebrate its singular locality, the Cusuco National Park.

“Sadly, there has been extensive logging in the vicinity in recent years, and we fear for the future of our new species,” the authors stressed. “According to the criteria of the International Union for the Conservation of Nature (IUCN), it must be regarded as Critically Endangered.”

“We hope that the publication of this and other discoveries will help to galvanize support for the conservation of this unique and beautiful park and its denizens,” they concluded.

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Original Source:

Lorence DH, Dietzsch AC, Kelly DL (2015) Sommera cusucoana, a new species of Rubiaceaefrom Honduras. PhytoKeys 57: 1-9. doi: 10.3897/phytokeys.57.5339

A data paper at the click of a button: Streamlining metadata conversion into scholarly manuscripts for GBIF and DataONE data

At the time of the writing of this post, the Biodiversity Information Standards conference, TDWG 2015, is on in Kenya and everyone around the world can listen to the live audio stream. Data sharing, data re-use, and data discovery are being brought up in almost every talk. We might have entered the age of big data twenty years ago, but it is now that scientists face the real challenge – storing and searching through the deluge of data to find what they need.

As the rate at which we exponentially generate data exceeds the rate at which data storage technologies improve, the field of data management seems to be greatly challenged. Worse, this means the more new data is generated, the more of the older ones will be lost. In order to know what to keep and what to delete, we need to describe the data as much as possible, and judge the importance of datasets. This post is about a novel way to automatically generate scientific papers describing a dataset, which will be referred to as data papers.

The common characters of the records, i.e. descriptions of the object of study, the measurement apparatus and the statistical summaries used to quantify the records, the personal notes of the researcher, and so on are called metadata. Major web portals such as DataONE or the Global Biodiversity Information Facility store metadata in conjunction with a given dataset as one or more text files, usually structured in special formats enabling the parsing of the metadata by algorithms.

To make the metadata and the corresponding datasets discoverable and citable, the concept of the data paper was introduced in the early 2000’s by the Ecological Society of America. This concept was brought to the attention of the biodiversity community by Chavan and Penev (2011) with the introduction of a new data paper concept, based on a metadata standard, such as the Ecological Metadata Language, and derived from metadata content stored at large data platforms, in this case the Global Biodiversity Information Facility (GBIF). You can read this article for an in-depth discussion of the topic.

Pensoft’s Biodiversity Data Journal (BDJ) is to the best of our knowledge the first academic journal to have implemented a one-hundred-percent online authoring system for data papers, called ARPHA. Moreover, BDJ and the other Pensoft journals, such as ZooKeys, have already published more than seventy data papers. Therefore, in the remainder of this post we will explain how to use an automated approach to publish a data paper describing an online dataset in Biodiversity Data Journal. The ARPHA system will convert the metadata describing your dataset into a manuscript for you after reading in the metadata! We will illustrate the workflow on the previously mentioned DataONE and GBIF.

The Data Observation Network for Earth (DataONE) is a distributed cyberinfrastructure funded by the U.S. National Science Foundation. It links together over twenty five nodes, primarily in the U.S., hosting biodiversity and biodiversity-related data, and provides an interface to search for data in all of them.

Since butterflies are neat, let’s search for datasets about butterflies at DataONE! Type “Lepidoptera” in the search field and scroll down to the dataset describing “The Effects of Edge Proximity on Butterfly Biodiversity.” You should see something like this:

As you can notice, this resource has two objects associated with it: metadata, which has been highlighted, and the dataset itself. Let’s download the metadata from the cloud! The resulting text file, “Blandy.235.1.xml”, or whatever you want to call it, can be read by humans, but is somewhat cryptic because of all the XML tags. Now, you can import this file into the ARPHA writing platform and the information stored in it would be used to create a data paper! Go to the ARPHA web-site, pwt.pensoft.net, and click on “Start a manuscript,” then scroll all the way down and click on “Import manuscript.”

Upload the “blandy” file and you will see an “Authors’ page,” where you can select which of the authors mentioned in the metadata must be included as authors of the data paper itself. Note that the user of ARPHA uploading the metadata is added to the list of the authors if they is not included in the metadata. After the selection is done, a scholarly article is created by the system with the information from the metadata already in respective sections of the article:

Now, the authors can add some description, edit out errors, tell a story, cite someone – all of this without leaving ARPHA – i.e. do whatever it takes to produce a high-quality scholarly text. After they are done, they can submit their article for peer-review and it could be published in a matter of hours. Voila!

Let’s look at GBIF. Go to “Data -> Explore by country” and select “Saint Vincent and the Grenadines,” an English-speaking Caribbean island. There are, as of the time of writing of this post, 166 occurrence datasets containing data about the islands. Select the dataset from the Museum of Comparative Zoology at Harvard. If you scroll down, you will see the GBIF annotated EML. Download this as a separate text file (if you are in Chrome you can view the source and then use copy-paste). Do the exact same steps as before – go to “Import manuscript” in ARPHA and upload the EML file. The result should be something like this, ready to finalize:

Now, allow us to give a disclaimer here: the authors of this blog post have nothing to do with the two datasets. They have not contributed to any of them, nor do they know the authors. The datasets have been chosen more or less randomly since the authors wanted to demonstrate the functionality with a real-world example. You should only publish data papers if you know the authors or you are the author of the dataset itself. During the actual review process of the paper, the authors that have been included will get an email from the journal!

Having said that, we want to leave you with some caveats and topics for further discussions. Till today, useful and descriptive metadata has not always been present. There are two challenges: metadata completeness and metadata standards. The invention of the EML standard was one of the first efforts to standardize how metadata should be stored in the field of ecology and biodiversity science. Currently, our import system supports the last two versions of the EML standard: 2.1.1 and 2.1.0, but we hope to expand this functionality. In an upcoming version of their search interface, DataONE will provide infographics on the prevalence of the metadata standards at their site (see figure), so there is still work to be done, but if there is a positive feedback from the community, we will definitely keep expanding this feature.

Credit: DataONE

Regarding metadata completeness, our hope is that by enabling scientists to create scholarly papers from their metadata with a single-step process, they will be incentivized to produce high-quality metadata.
This project has received funding from the European Union’s FP7 project EU BON (Building the European Biodiversity Observation Network), grant agreement No 308454, and Horizon 2020 research and innovation project BIG4 (Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow’s researchers and entrepreneurs) under the Marie Sklodovska-Curie grant agreement No. 542241 for a PhD project titled Technological Implications of the Open Biodiversity Knowledge Management System.

How small is the smallest? New record of the tiniest free-living insect provides precision

The long-lasting search and debate around the size and identity of the World’s smallest free-living insect seems to have now been ended with the precise measurement and second record of the featherwing beetle species.

Described back in 1999 based on only several specimens found in Nicaragua, as many as 85 individuals of the minute beetle species have recently been retrieved from Colombia and thoroughly examined. The smallest of them measured the astounding 0.325 mm. The finding made by Dr. Alexey Polilov, Lomonosov Moscow State University, Moscow, is available in the open access journal ZooKeys.

The World’s smallest beetle and tiniest non-parasitoid insect, called Scydosella musawasensis, is morphologically characterised by its elongated oval body, yellowish-brown colouration and antennae split into 10 segments. It is also the only representative of this featherwing beetle genus.

Not able to precisely measure its size because of the preserved specimens being embedded in preparations for microscopy studies, Dr. Polilov used new individuals, collected in Chicaque National Park, Colombia in early 2015. To conclude the length of the smallest one as 325 µm (0.325 mm) the scientist used a specialised software and digital micrographs.

The recent survey is the second record of the tiny beetle species, which also proved that the range of its distribution is actually much wider. Thereafter, so are the localities of the fungi that the insect feeds on.

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Original source:

Polilov AA (2015) How small is the smallest? New record and remeasuring of Scydosella musawasensis Hall, 1999 (Coleoptera, Ptiliidae), the smallest known free-living insect. ZooKeys526: 61-64. doi: 10.3897/zookeys.526.6531 ZooBank: urn:lsid:zoobank.org:pub:E38CA5AE-0C65-45D0-9116-E74A1E889BDE

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