Pensoft blog - Part 96

How to import data papers from GBIF, DataONE and LTER metadata

On October 13, 2015, we published a blog post about the novel functionalities in ARPHA that allow streamlined import of data papers from EML.

Now, this process has been described in the Tips and Tricks section of the ARPHA Authoring Tool. Here, we’ll list the individual workflows:

We want to stress at this point that the import functionality itself is agnostic of the data source and any metadata file in EML 2.1.1 or 2.1.0 can be imported. We have listed these three most likely sources of metadata to illustrate the workflow.

In the remainder of the post, we will go through the original post from October 13, 2015 and highlight the latest updates.

At the time of the writing of the original post, the Biodiversity Information Standards conference, TDWG 2015, was taking place in Kenya. Data sharing, data re-use, and data discovery were 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, the Global Biodiversity Information Facility (GBIF), or the Long Term Ecological Research Network 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 (Note: In the meantime, DataONE has updated their search interface).

Since butterflies are neat, let’s search for datasets about butterflies on 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 to the ARPHA writing platform and the information stored in it would be used to create a data paper! Go to the ARPHA web-site, 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 even if they are 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 the 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 using 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:

To finish it up, we want to leave you with some caveats and topics for further discussion. 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 further develop this functionality. In an upcoming version of their search interface, DataONE will provide infographics on the prevalence of the metadata standards on their site (as illustrated below), so there is still work to be done, but if there is a positive feedback from the community, we will definitely keep elaborating this feature.

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.

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.

Additional information:

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. 642241 for a PhD project titled Technological Implications of the Open Biodiversity Knowledge Management System.

How to import occurrence records into manuscripts from GBIF, BOLD, iDigBio and PlutoF

On October 20, 2015, we published a blog post about the novel functionalities in ARPHA that allows streamlined import of specimen or occurrence records into taxonomic manuscripts.

Recently, this process was reflected in the “Tips and Tricks” section of the ARPHA authoring tool. Here, we’ll list the individual workflows:

Based on our earlier post, we will now go through our latest updates and highlight the new features that have been added since then.

Repositories and data indexing platforms, such as GBIF, BOLD systems, iDigBio, or PlutoF, hold, among other types of data, specimen or occurrence records. It is now possible to directly import specimen or occurrence records into ARPHA taxonomic manuscripts from these platforms [see Fig. 1]. We’ll refer to specimen or occurrence records as simply occurrence records for the rest of this post.

Import_specimen_workflow_ — [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, iDigBio, or PlutoF, 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 in the ARPHA Writing Tool. To import records, the author needs to:

Locate an occurrence record or records in one of the supported data portals;
Note the ID(s) of the records that ought to be imported into the manuscript (see Tips and Tricks for screenshots);
Enter the ID(s) of the occurrence record(s) in a form that is to be seen in the “Materials” section of the species treatment;
Select 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.

We will illustrate this workflow by creating a fictitious treatment of the red moss, Sphagnum capillifolium, in a test manuscript. We have started a taxonomic manuscript in ARPHA and know that the occurrence records belonging to S. capillifolium can be found on 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. 2].

In this example, type or paste the UUID (b9ff7774-4a5d-47af-a2ea-bdf3ecc78885), select the iDigBio source 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. 3].

taxon-treatments- 3 — [Fig. 3] Materials after they have been imported

This workflow can be used for a number of purposes. An interesting future application is the rapid re-description of species, but even more exciting is the description of new species from BIN’s. BIN’s (Barcode Identification Numbers) delimit Operational Taxonomic Units (OTU’s), created algorithmically at BOLD Systems. If a taxonomist decides that an OTU is indeed a new species, then he/she can import all the type information associated with that OTU for the purposes of describing it as a new species.

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, iDigBio and PlutoF. 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. 642241.

Scientist collects 30 sawfly species not previously reported from Arkansas

Sawflies and wood wasps form a group of insects that feed mainly on plants when immature. Field work by Dr. Michael Skvarla, which was conducted during his Ph.D. research at the University of Arkansas, Fayetteville, USA, has uncovered 30 species of these plant-feeding wasps that were previously unknown in the state. The study is published it in the open access journal Biodiversity Data Journal.

After collecting sawflies in tent-like Malaise traps or hanging funnel traps, Dr. Michael Skvarla sent the specimens to retired sawfly expert Dr. David Smith for identification.

In total, 47 species were collected, 30 of which had not been found in Arkansas before. While many of the species are widespread in eastern North America, eight species were known only from areas hundreds of kilometers away.

“I knew that many insect groups had not yet been surveyed in Arkansas, but I was surprised that 66% of the sawfly species we found were new to the state,” Skvarla says.

“In addition, over a quarter of the newly recorded species represent large range extensions of hundreds of miles; Monophadnoides conspiculatus, for instance, was previously known only from the Appalachian Mountains. This work highlights how much basic natural history is left to discover about insects.”

Sawflies and wood wasps comprise the wasp suborder Symphyta and derive their common names from the serrated or saw-shaped ovipositor many species use to lay eggs into plant tissue, and because some species bore into wood.

While some sawfly and woodwasp species can be pests on crops or ornamental plants, most do not pose an economic concern, and all are harmless to people.

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Original source:

Skvarla M, Smith D, Fisher D, Dowling A (2016) Terrestrial arthropods of Steel Creek, Buffalo National River, Arkansas. II. Sawflies (Insecta: Hymenoptera: “Symphyta”). Biodiversity Data Journal 4: e8830. doi: 10.3897/BDJ.4.e8830

From a bulletin to a modern open access journal: Italian Botanist in Pensoft’s portfolio

Established in the distant 1888, the Italian Botanical Society has gone a long way towards publishing its achievements and research. Originated as a bulletin within an Italian journal, they have been growing ever since to now form a new international journal in its own right. Covering both Italian and international research in botany and mycology, the online open access journal Italian Botanist, published by Pensoft, is now officially launched via its first papers.

Although what was later to become Italian Botanist, published its first issue as an independent journal, called Informatore Botanico Italiano in 1969, the publications were still rather bulletin-style. It consisted of a mixture of administrative and scientific proceedings of the Society, the yearbook of the members, as well as scientific notes.

Nevertheless, such a major transition has been set to change everything fundamentally. Establishing its name, the journal started picking up, so that it was not long before the scientific contributions were prevailing. Impressively, for the Society’s centenary the journal published a celebratory 331-page contribution.

Gradually, its scope was expanded to cover several scientific fields. It hosted several themed columns, including cytotaxonomic contributions on the Italian flora, relevant new floristic records for Italy, conservational issues concerning the Italian flora and mycology.

However, the Directive Council of the Italian Botanical Society has not seemed to be ready to give up on their journal’s evolution. Last year, the botanists decided that they need to transform the journal to an an online, open access journal written in English and called Italian Botanist, in order to boost the scientific value and international visibility of Informatore Botanico Italiano.

Under the name Italian Botanist, the journal has now joined Pensoft’s portfolio of peer-reviewed open access journals, all of which take advantage of the advanced technologies and innovations developed by the publisher.

The new journal’s scope ranges from molecular to ecosystem botany and mycology. The geographical coverage of Italian Botanist is specially focused on the Italian territory, but studies from other areas are also welcome.

Staying faithful to its spirit and philosophy, it keeps its column-format, with each issue to contain five columns, namely Chromosome numbers for the Italian flora, Global and Regional IUCN Red List Assessments, Notulae to the Italian flora of algae, briophytes, fungi and lichens, Notulae to the Italian native vascular flora and Notulae to the Italian alien vascular flora.

“Our hope is that this renewed version of the journal will serve the Italian – and foreign – botanical community more efficiently and provide readers worldwide with an easier access to knowledge concerning the Italian flora,” says Italian Botanist‘s Editor-in-Chief Lorenzo Peruzzi.

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Original source:

Peruzzi L, Siniscalco C (2016) From Bullettino della Società Botanica Italiana to Italian Botanist, passing through Informatore Botanico Italiano. A 128 years-long story. Italian Botanist 1: 1-4. doi: 10.3897/italianbotanist.1.8646

The first long-horned beetle giving birth to live young discovered in Borneo

A remarkably high diversity of the wingless long-horned beetles in the mountains of northern Borneo is reported by three Czech researchers from the Palacký University, Olomouc, Czech Republic. Apart from the genera and species new to science, the entomologists report the first case of reproduction by live birth in this rarely collected group of beetles. The study was published in the open access journal ZooKeys.

Generally, insects are oviparous, which means that their females lay eggs and the embryonic development occurs outside the female’s body. On the other hand, ovoviviparous species retain their eggs in their genital tracts until the larvae are ready to hatch. Such mode of reproduction is a relatively rare phenomenon in insects and even rarer within beetles, where it has been reported for a few unrelated families only.

The long-horned beetles are a family, called Cerambycidae, comprising about 35,000 known species and forming one of the largest beetle groups.

“We studied the diversity of the rarely collected wingless long-horned beetles from Borneo, which is one of the major biodiversity hotspots in the world,” says main author and PhD student Radim Gabriš. “The mountains of northern Borneo, in particular, host a large number of endemic organisms.”

The scientists focused on the group which nobody had studied in detail for more than 60 years. They found surprisingly high morphological diversity in this lineage, which resulted in the descriptions of three genera and four species new to science.

“During a dissection of female genitalia in specimens belonging to the one of the newly described genera, named Borneostyrax, we found out that two females contained large larvae inside their bodies,” recalls Radim Gabriš. “This phenomenon have been known in a few lineages of the related leaf beetles, but this is the first case for the long-horned beetles.”

However, according to the authors, the modes of reproduction remain unknown for many beetle lineages besides Cerambycidae, so the ovoviviparity might be, in fact, much more common. Further detailed studies are needed for better understanding of the reproductive strategy in this group.

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Original source:

Gabriš R, Kundrata R, Trnka F (2016) Review of Dolichostyrax Aurivillius (Cerambycidae,Lamiinae) in Borneo, with descriptions of three new genera and the first case of (ovo)viviparity in the long-horned beetles. ZooKeys 587: 49-75. doi: 10.3897/zookeys.587.7961

New immigrant: Shiny Cowbirds noted from a recording altitude of 2,800 m in Ecuador

Two juveniles of Shiny Cowbird, a parasitic bird that lays its eggs in the nests of other birds, were spotted in the Andean city of Quito, Ecuador, for the first time. This finding represents an altitudinal expansion of approximately 500 m.

Breeding populations might have been prompted by forest fragmentation and/or climate change, suggest the research team, led by Dr Verónica Crespo-Pérez, professor at Pontificia Universidad Católica del Ecuador (PUCE). Resultingly, the ‘immigrants’ could be threatening native birds. The study is published in the open access Biodiversity Data Journal.

“The Shiny Cowbird is native to the lowlands of South America but within the last 100 years, it has been expanding its distribution to higher altitudes and latitudes” says the lead author.

The bird had already been noted from high altitudes in Bolivia and Perú, and in some localities in the Ecuadorian Andes. Since 2000, Juan Manuel Carrión, co-author and director of the Zoo in Quito, recalls observing Shiny cowbirds near his home in a valley near Quito at 2,300 m above sea level (asl). However, one has never before been reported from an altitude as high as 2,800 m asl.

Moreover, the fact that the observed individuals were juveniles means that the species is already breeding in the city.

“Such a significant expansion of reproductive birds, of approximately 500 m, could be related to human disturbances, like forest fragmentation or climate change,” adds Crespo-Pérez.

The observations took place at the PUCE campus about a year ago. Two juvenile Shiny cowbirds were seen parasitizing two different pairs of Rufous-collared Sparrow, one of the most common birds in Quito. The cowbirds displayed food-begging behaviors to adult sparrows, including chasing the sparrows on the ground and chanting intensely on bushes and tree branches.

“These observations mean that the birth mother of the cowbird laid her eggs in the nests of the sparrows, who inadvertently, became the cowbird’s foster parents and incubated, fed and cared for the it as if it were its own, even though the cowbird is almost twice as big,” says Miguel Pinto, co-author and professor at Escuela Politécnica Nacional, and former postdoctoral fellow at the Smithsonian Institution.

“The sparrows were not feeding fledglings of their own species, which suggests that the Cowbird could be having some negative effect on the Sparrow, at least on their ability to reproduce,” points out Tjitte de Vries, co-author and professor at PUCE.

There are several published reports of negative effects of Cowbirds on other birds, especially on species that are already endangered or have restricted distribution ranges. Therefore, this report of an expansion of the Shiny Cowbird towards higher altitudes may be of concern, mainly for native, endemic or endangered bird species.

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Original source:

Crespo-Pérez V, Pinto C, Carrión J, Jarrín E R, Poveda C, de Vries T (2016) The Shiny Cowbird, Molothrus bonariensis (Gmelin, 1789) (Aves: Icteridae), at 2,800 m asl in Quito, Ecuador.Biodiversity Data Journal 4: e8184. doi: 10.3897/BDJ.4.e8184

Hollywood star Brad Pitt shares a name with a new wasp species from South Africa

Not only did an international research team discover two new endoparasitic wasp species in South Africa and India, and significantly expanded their genera’s distributional range, but they also gave a celebrity name to a special one of them.

While thinking of a name for the new wasp, Dr Buntika A. Butcher, Chulalongkorn University, Thailand, recalled her long hours of studying in her laboratory right under the poster of her favourite film actor. This is how a parasitic wasp from South Africa was named after Hollywood star Brad Pitt. The researchers have published their findings in the open access journal ZooKeys.

The new wasp species, called Conobregma bradpitti, belongs to a large worldwide group of wasps parasitising in moth or butterfly caterpillars. These wasps lay their eggs into a host, which once parasitised starts hardening. Thus, the wasp cocoon can safely develop and later emerge from the ‘mummified’ larva. Despite their macabre behaviour, many of these wasp species are considered valuable in agriculture because of their potential as biological control.

Brad Pitt’s flying namesake is a tiny creature measuring less than 2 mm. Its body is deep brown, nearly black in colour, while its head, antennae and legs are brown-yellow. The wings stand out with their much brighter shades.

Interestingly, the wasp with celebrity name unites two, until now, doubtful genera. Being very similar, they had already been noted to have only four diagnostic features that set them apart. However, C. bradpitti shared two of those with each. Thus, the species prompted the solution of the taxonomic problem and, as a result, the two were synonymised.

In their paper, the authors from Chulalongkorn University, Thailand and the University of Calicut, India, also describe another new species of parasitic wasp. It is the first from its subtribe spotted in the whole of India, while its closest ‘relative’ lives in Nepal.

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Original source:

Butcher BA, Quicke DLJ, Shreevihar S, Ranjith AP (2016) Major range extensions for two genera of the parasitoid subtribe Facitorina, with a new generic synonymy (Braconidae, Rogadinae, Yeliconini). ZooKeys 584: 109-120. doi: 10.3897/zookeys.584.7815

Curious new bush species growing ‘bleeding’ fruits named by a US class of 150 7th graders

A class of 150 US 7th graders has helped select a name for a newly discovered plant, which amazes with its fruits that appear to be bleeding once they are cut open. Bucknell University biology professor Chris Martine and life science teacher Bradley Catherman challenged the students to come up with ideas for what to call the new Australian species last spring.

Looking for a way to engage local youngsters in biodiversity science, Martine scheduled a presentation to the collective 7th grade life science classes at Donald H. Eichhorn Middle School. As the day of his assembly approached, he started to think that the best way to generate interest might be to somehow allow the students to participate in the actual research he was doing in his lab at the time. Only, he knew there were few things he could do with 150 13- and 14-year olds sitting in a gymnasium.

“I emailed Mr. Catherman and I said, ‘How about we ask them to name a new species for me?’ explained Martine. “And then I showed up with live plants, preserved specimens, and my notes from the Outback – and we said, ‘Go ahead, tell us what to call this thing.'”

Nearly a year later, Martine and his co-authors, including two undergraduate students, have published the new species in the open access journal PhytoKeys. The news is coming just in time for the National Teacher Appreciation Day, thus giving tribute to Bradley Catherman, a life science teacher who is not afraid to step beyond the standard curriculum and make that extra step to actually engage his students with their studies.

“I was really impressed with Mr. Catherman’s willingness to work outside of the typical curriculum on this,” said Martine, “In an age when K-12 teachers are increasingly pressured to ‘teach to the test’ he is still willing to think creatively and try something unusual.”

Curiously, the new flowering bush species ‘behaves’ nothing like an ordinary plant. While its unripened fruits are greenish white on the inside when cut open, they start ‘bleeding’ in no more than two minutes. The scientists have even filmed a video short showing how their insides turn bloody scarlet at first, before growing darker, appearing just like clotting blood.

A week after the presentation, each of the students submitted an essay in which they suggested a name, explained the meaning, and translated it into Latin (the language that scientific names are required to be in). Catherman and Martine then selected the two best essays for the inaugural Discovery Prize, a new middle school science award established by Martine and his wife, Rachel.

“As you might imagine, the suggestions ran the gamut from the silly to the scientific,” said Martine. “But for every request to name the species after a favorite food, family pet, or Taylor Swift, there were many suggestions based on the data the students had been provided.”

According to Martine, a number of the students suggested names based on two characteristics of the plant’s berries: the ‘bleeding’ unripened fruits and the dry and bone-hard mature ones. Based on this, the plant will now be known as Solanum ossicruentum, best translated to Australian blood bone tomato, with “ossi” meaning “bone” and “cruentum” meaning “bloody”. The species belongs to the genus of the tomato.

The species is native to the sub-arid tropical zone of northern Australia. Martine collected the seeds, he grew his research plants from, during a 2014 expedition to Western Australia and the Northern Territory. However, specimens of the plant had actually been gathered for years before then.

“This is just one of thousands of unnamed Australian species that have been collected by dedicated field biologists and then stored in museums,” said Martine, who studied specimens of the new species in the Northern Territory Herbarium before hunting for it in the bush.

“There is a wealth of museum material just waiting to be given names – and, of course, the organisms represented by those specimens await that recognition, as well as the attention and protection that come with it.”

Luckily for Solanum ossicruentum, attention and protection are not too much of an issue.

“Not only is it widespread and fairly abundant,” said Martine, “but one of the healthiest populations occurs in Mirima National Park, a popular and easily-accessible natural area just outside the Western Australian town of Kununurra.”

“Plus, middle schoolers can be tough to deal with. I don’t think anyone in their right mind would mess with this plant, now,” the botanist joked.

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Original source:

Martine CT, Cantley JT, Frawley ES, Butler AR, Jordon-Thaden IE (2016) New functionally dioecious bush tomato from northwestern Australia, Solanum ossicruentum, may utilize “trample burr” dispersal. PhytoKeys 63: 19-29. doi: 10.3897/phytokeys.63.7743

Flightless survivors: Incredible invertebrate diversity in Los Angeles metropolitan area

Urban wildlife is surprisingly understudied. We tend to know more about animals in exotic places than about those that live in our cities.

This is why researchers Emile Fiesler, president of Bioveyda Biological Inventories, Surveys, and Biodiversity Assessments, USA, and Tracy Drake, manager of the Madrona Marsh Preserve, looked into the fauna of the Madrona Marsh Preserve, California, a small nature preserve in one of the world’s largest metropolitan areas.

Consequently, they published the astonishing number of 689 species of invertebrates, which have managed to survive decades of farming and oil exploration, followed by development pressures, in the open access Biodiversity Data Journal. The study was minimally invasive as the live animals have been recorded with macro-photography.

Even though it is the insects that first developed the ability to fly, long before the dinosaurs became birds, the latter have always received the most of our attention. This major evolutionary breakthrough, which has occurred more than once in the past, is also a reason why insects are currently the most diverse animals on earth in terms of number of species.

“Insects and other invertebrates have filled all ecological niches and all corners of our planet,” explain the authors. “No surprise that these small creatures conquered our cities and invaded our homes as well.”

Most of the urban dwellers, however, have been introduced – accidentally or deliberately – by humans.

“The remainder – native ‘wild’ species – are able to survive in the city mainly due to their adaptivity,” they point out. “It is therefore surprising to find a number of flightless species in a small area surrounded by urbanization.”

The Madrona Marsh Preserve is located in Torrance, which is part of the Los Angeles metropolitan area. The greater Los Angeles Metropolitan area is one of the world’s largest, with a human population of more than 17 million.

The Madrona Marsh Preserve, boasting seasonal wetlands, is well known as a birdwatchers’ paradise. Besides birds, its other vertebrates (mammals, reptiles, amphibians, and fishes), as well as its flowering plants, are relatively well known. The invertebrate fauna of the Preserve, on the other hand, aside from butterflies and dragonflies, was virtually unknown.

Interestingly, night surveys revealed the presence of a ‘second shift’ diversity, or creatures seemingly complementary to those active during the day.

Among the long-time survivors are wingless camel crickets as well as velvet ants, which are wasps whose flightless females look like furry ants. Another curiosity that intrigued the researchers is an obscure flightless female bradynobaenid wasp.

The researchers were especially surprised by their encounter with a large Solifugid [image 3] – also known as Camel Spider or Wind Scorpion. Solifugids are little-known arachnids that are neither spiders, nor scorpions, and can grow up to 15 cm (6 in). Their order’s name Solifugae translates from Latin as “those that flee from the sun”.

All in all, the biodiversity study resulted in 689 species without a backbone, belonging to 13 classes, 39 orders, and 222 families, found on this island surrounded by urbanization.

“Not unlike the moas and dodos, these ‘island’ inhabitants stayed grounded through the ages,” acknowledge the researchers.

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Original source:

Fiesler E, Drake T (2016) Macro-invertebrate Biodiversity of a Coastal Prairie with Vernal Pool Habitat. Biodiversity Data Journal 4: e6732. doi: 10.3897/BDJ.4.e6732

About the authors:

Emile Fiesler is president of Bioveyda Biodiversity Inventories, Surveys, and Studies, and Tracy Drake is manager of the Madrona Marsh Preserve.

A new scorpion from California reveals hidden biodiversity in the Golden State

California is known for its high biological diversity. The state encompasses a wide variety of habitats, from temperate coastal scrub and cool redwood forests to high-elevation conifer forests and grasslands that are home to an equally diverse variety of plants and animals. Biologists have been intensively studying and characterizing the biodiversity of California for centuries.

Recent fieldwork by researchers Warren Savary and Rob Bryson uncovered a new species of scorpion in the foothills of the Sierra Nevada in northeastern California. It is related to several species in the genusPseudouroctonus, and is only the fourth new species of scorpion to be described from California in the past twenty years. The description is published in the open access journal ZooKeys.

The lead author, Warren Savary, is a field associate of the California Academy of Sciences and has been studying the scorpion diversity of California since the 1970s. He and a collaborator described a new species endemic to the White and Inyo Mountains in eastern California in 1991.

“California is home to a remarkable variety of scorpions,” says Savary. “However, the more I study them, the more I realize that we’ve only just scratched the surface. A lot of scorpion diversity remains to be described.” He and co-author Rob Bryson, a researcher at the University of Washington, have started using DNA to help better understand scorpion diversity.

“Scorpions have been around for a long time — over 400 million years — and many are quite similar in general appearance,” comments Bryson. “We can use DNA sequences to help us piece together how scorpions have evolved and how they are related. Despite looking similar, DNA often reveals that even assumed close relatives can be quite divergent.”

Savary and Bryson are working on publishing the descriptions of several other new species of scorpions from California. “2016 will be an exciting year for scorpion discoveries,” they promise.

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Original source:

Savary WE, Bryson Jr RW (2016) Pseudouroctonus maidu, a new species of scorpion from northern California (Scorpiones, Vaejovidae). ZooKeys 584: 49-59. doi: 10.3897/zookeys.584.6026