Tag: taxonomy

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.

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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.

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.

Poorly known South African mountain endemic appears to be a very valuable keystone species

Mountain ecosystems are valuable providers of key resources including water. These ecosystems comprise diverse species, some of which appear to be especially important to the ecosystem’s functioning. In poorly studied mountain environments in biodiversity-rich countries, these keystone species can often be overlooked and undervalued.

Macowania is a group of yellow daisy shrubs occurring in the alpine-like regions of the Drakensberg and highlands of Ethiopia, Eritrea and Yemen. Doctoral student Joanne Bentley, University of Cape Town, studied the genetic relationships between the various Macowaniaspecies and relatives during her Masters degree studies. Her research led to the first collection of the poorly known species Macowania revoluta (known also as the Amathole Macowania) in about 40 years.

The story of Macowania revoluta is published in the open access journal PhytoKeys.

The Amathole Macowania appears to be an exceptionally important keystone species. This is because it forms one of the dominant members of the valuable mountain wetland communities and, thus, likely plays a very important role in wetland functioning and soil protection.

It appears to be somewhat tolerant of woody alien species and a valuable pioneer species protecting its native co-habitants. Plants like this one buffer more sensitive plants from sudden changes in environment (such as forestry, alien invasion and fire), and provide an opportunity for the ecosystem to ‘bounce back’.

113693 Restricted to the Amathole mountains in the Eastern Cape Province, South Africa, the Amathole Macowania was first collected sometime before 1870 by the pioneer botanist Peter MacOwan, and was well documented until around 1949. After that, except for one record in 1976, the plant quietly disappeared.

“This was the first Macowania species that we found during our fieldtrip across the greater Drakensberg. We had combed several of the localities where it had been collected before; mostly from several decades ago, some from more than a century ago!” says Joanne Bentley. “We became increasingly doubtful about finding the plant, given the heavily transformed plantation landscape.”

“Ready to throw in the towel, we came across a peaty area on the margins of the forest and decided on one last investigation. We were lucky: it was growing prolifically! It was a very special moment.”

As it often happens, exciting discoveries come in bulk. Joanne’s discovery of the plant in July 2010 was followed by another record in October 2010, by the Curator of the Schonland Herbarium, Tony Dold. In 2014 at least three additional localities were recorded along the popular Amathole Hiking Trail by Dr Ralph Clark, Rhodes University. A further record was added in 2015 by Vathi Zikishe, South African National Biodiversity Institute. The verdict: this is a very localised but patchily abundant species, and an ecologically valuable component of the Amathole flora.

Listed as ‘Data Deficient’ in the Threated Plants List for South Africa, this string of modern records of the species also provided the first opportunity to get an idea of its ecology and abundance, as well as the first photographs.

“The practical value of this species in local land restoration projects still needs to be explored, but the opportunities are exciting,” says Dr Clark. “The discovery that this obscure endemic mountain plant is not only abundant, but is, in fact, fulfilling an extremely important ecological role, highlights the value of detailed mountain biodiversity research in southern Africa.”

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Original source

Clark VR, Bentley J, Dold AP, Zikishe V, Barker NP (2016) The rediscovery of the Great Winterberg endemic Lotononis harveyi B.-E.van Wyk after 147 years, and notes on the poorly known Amathole endemic Macowania revoluta Oliv. (southern Great Escarpment, South Africa). PhytoKeys 62: 1-13. doi: 10.3897/phytokeys.62.8348

Dragons out of the dark: 6 new species of Dragon millipedes discovered in Chinese caves

Six new species of Chinese dragon millipedes, including species living exclusively in caves, are described as a result of an international cooperation of research institutes from China, Russia and Germany. These cave species have unusually long legs and antennae, with one of them resembling a stick insect, only with a lot more legs. Others appear ghostly white and semi-transparent. The study is published in the open-access journal ZooKeys.

Underresearched in many tropical countries, numerous millipede species are still awaiting discovery and description in China as well. In the present study, three researchers from South China Agricultural University, the Russian Academy of Sciences, and Zoological Research Museum Alexander Koenig describe six particularly extraordinary new species of so-called ‘dragon millipedes’ from the two southern Chinese regions of Guangdong and Guangxi Zhuang. Both areas host a large number of spectacular caves, which have only recently been thoroughly surveyed. Four of the species never leave their underground homes.

Dragon millipedes, a genus of millipedes living in southeastern Asia, are characterised with their ‘armour’ of unusual spine-like projections. Furthermore, some of these species produce toxic hydrogen cyanide to ward off predators.

Among the public, the genus gained particular attention when the “Shocking pink dragon millipede” was discovered in Thailand in 2007. This discovery highlighted a large number of unknown millipede species in the Mekong region and worldwide. While the newly described cave dragon millipedes from China lack the “shocking” warning colour of their surface-living relatives, they are no less spectacular.

One of the new millipedes has received a formal name translating to the “stick insect dragon millipede” because of its extremely long legs and antennae. Therefore, it looks a lot like a stick insect, only with much more legs. Another two of the species have fully lost their colours, which is a common characteristic among exclusively cave-living animals. As a result, they appear ghostly white and even semi-transparent.

Miss Liu Weixin, PhD candidate at the South China Agricultural University in Guangzhou, China, and co-author of the present study, has conducted the research at the Centre of Taxonomy at the Research Museum Koenig (ZFMK), Leibniz Institute for Animal Biodiversity in Bonn, Germany as a part of her PhD, which focuses on Chinese cave millipedes. She worked along with her advisor and lead author Prof. Tian Mingyi, and renowned millipede expert Dr. Sergei Golovatch from the Russian Academy of Sciences, Moscow.

Over the course of her PhD, Miss Liu Weixin has explored more than 200 Chinese caves, where she has discovered over 20 new millipede species. The dragon millipedes are among her most spectacular discoveries as they exhibit extreme cave adaptations including loss of pigmentation and extremely elongated legs and antennae.

Still on her guest research year in Germany, Liu is currently busy describing additional batch of more than two dozen millipede species, she collected from the Chinese caves, literally bringing to light an unknown world.

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Original source:

Liu WX, Golovatch SI, Tian MY (2016) Six new species of dragon millipedes, genus Desmoxytes Chamberlin, 1923, mostly from caves in China (Diplopoda, Polydesmida, Paradoxosomatidae).ZooKeys 577: 1-24. doi: 10.3897/zookeys.577.7825

Top 50 most wanted fungi: New search function zooms in on the dark fungal diversity

There are many millions of undescribed fungi, and public DNA sequence databases contain thousands of fungal sequences that cannot be assigned to any known fungal group with confidence. Many of these sequences have defied robust taxonomic assignment for more than 10 years.

Frustrated at this situation, an international group of researchers presents a search functionin the UNITE database for molecular identification of fungi. Its aim is to highlight the fungi we know the least about, and invite the scientific community to resolve their taxonomic affiliation. The effort seeks to bridge the substantial knowledge gap between fungal taxonomy and molecular ecology through a list, the authors refer to as the “50 Most Wanted Fungi”. Their work is presented in a new research paper published in the open-access journal MycoKeys.

Some 100,000 species of fungi have been described formally, although current estimates put the number of extant fungal species to at least 6 million. There is clearly no shortage of research venues in the study of fungi – but are there other shortages? The vast dark fungal diversity unravelled with molecular techniques hints that the interaction between fungal taxonomy and DNA sequencing of environmental substrates such as soil and water is not necessarily optimal.

“There is no taxonomic feedback loop in place to highlight the presence of these enigmatic lineages to the mycological community, and they often end up in sequence databases for years without attracting significant research interest,” explain the authors. “More than 10 years in some cases, as a matter of fact.”

Therefore, the researchers, led by Dr Henrik Nilsson, University of Gothenburg, now present a search function that produces lists of approximately genus-level clusters of fungal DNA sequences whose taxonomic affiliation we know next to nothing about. These lists are recomputed on a monthly basis, accounting for any updates and additions contributed by the scientific community in between each iteration. Community participation is encouraged, and the UNITE database has extensive support for third-party annotation.

By putting the spotlight on these fungal lineages, Dr Nilsson and colleagues hope to speed up the study and formal description of the underlying species. To support researchers focusing on select groups of fungi or environments, a set of keyword-filtered lists is provided. This allows researchers to zoom in on unknown fungi recovered, for example, from the built environment or aquatic habitats.

Commenting on their choice of a name for the list, the researchers clarify that the underlying fungi are not guilty of any crime. “Indeed, nothing can be said of the way they make a living. It is simply not known. We make no claim as to the importance of these fungi from whatever point of view – ecological, economic, or otherwise,” they stress. “We do make claim to their uniqueness, though, because it is frustrating, in the year 2016, not to be able to assign a name to a fungal sequence even at the phylum level.”

“We hope that the present publication will serve to put the spotlight on these uncharted parts of the fungal tree of life, and we invite the reader to examine them through our online tools or otherwise,” they conclude.

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Original source:

Nilsson RH, Wurzbacher C, Bahram M, Coimbra VRM, Larsson E, Tedersoo L, Eriksson J, Duarte Ritter C, Svantesson S, Sánchez-García M, Ryberg M, Kristiansson E, Abarenkov K (2016) Top 50 most wanted fungi. MycoKeys 12: 29-40. doi: 10.3897/mycokeys.12.7553

Single no more: First females of a Madagascan chameleon described with modern technologies

The first females of a scarcely known chameleon species from Northeast Madagascar have been described. Because of lack of genetic data, X-ray micro-computed tomography scans of the chameleon’s head were used for species assignment. Regrettably, the habitats of this and many other chameleon species are highly threatened by the ongoing deforestation in Madagascar. The study is published in the open-access journal Zoosystematics and Evolution.

Chameleons belong to the most popular animals of Madagascar and have been quite intensively studied in the past. However, many new species are still being discovered and described, and several species are only known by a single or a few specimens. Likewise, the chameleon species Calumma vatosoa from northeastern Madagascar was described in 2001 based on a single male. The identity of females of this species has been unclear until now.

Recently, the PhD student David Proetzel of the herpetology section of the Zoologische Staatssammlung Munchen (ZSM), Germany, found specimens of female chameleons in the collection of the Senckenberg Museum, Frankfurt am Main, Germany, that looked similar to Calumma vatosoa. The problem was, how to prove this? The specimens from Frankfurt were collected back in 1933 and therefore, the extraction of DNA for genetic analysis was not possible anymore.

Researchers of the ZSM have been using X-ray micro-computed tomography scans for a few years to study the internal morphology of organisms in a non-invasive way.

“With the help of Micro-CT you can investigate even the skeleton of very valuable samples like holotypes without destroying them,” explains David Proetzel.

“In chameleons the morphology of the skeleton, especially the skull, contains important characteristics that distinguish different species,” explains the researcher. “Here, the comparison of the skulls of the male and the female showed that they belong to the same chameleon species. With the help of modern technology we could describe females of Calumma vatosoa for the first time, and add another distribution locality of this species.”

“The habitats of many chameleon species, and not only, are highly threatened by the ongoing deforestation in Madagascar and we need rapidly to expand our knowledge about the biodiversity, so that suitable conservation measures can be taken,” he stresses.

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Original source:

Proetzel D, Ruthensteiner B, Glaw F (2016) No longer single! Description of female Calumma vatosoa (Squamata, Chamaeleonidae) including a review of the species and its systematic position. Zoosystematics and Evolution, 92 (1): 13-21. doi: 10.3897/zse.92.6464

The lizard of consistency: New iguana species which sticks to its colors found in Chile

During a field trip at 3000 metres above sea level, a group of scientists, led by Jaime Troncoso-Palacios, Universidad de Chile, discovered a new endemic iguana species, in the mountains of central Chile, scientists. Noticeably different in size and scalation, compared to the rest of the local lizards, what initially grabbed the biologists’ attention was its colouration. Not only was it unlike the already described ones, but also appeared surprisingly consistent within the collected individuals, even regardless of their sex. Eventually, it was this peculiar uniformity that determined the lizard’s name L. uniformis. The study is published in the open-access journal ZooKeys.

The researchers found the lizards quite abundant in the area, which facilitated their observations and estimations. Apart from a thorough description of the new iguana along with its comparisons to its related species, the present paper also provides an in-depth discussion about the placement of the new taxon, which had been confused with other species in the past.

While most of the other lizards from the area and its surroundings often vary greatly in colouration and pattern between populations and sexes, such thing is not present in the new species. Both males and females from the observed collection have their bodies’ upper side in brown, varying from dark on the head, through coppery on the back and light brown on the tail. The down side of the body is mainly yellowish, while the belly – whitish. The only variables the scientists have noticed in their specimens are slight differences in the shade with two females demonstrating unusual olive hues on their snouts. These differences in morphology were also strongly supported by the molecular phylogeny through the analysis of mitochondrial DNA, which was performed by Dr. Alvaro A. Elorza, from Universidad Andres Bello.

Accustomed to life in highland rocky habitats with scarce greenery, these lizards spend their active hours, estimated to take place between 09:00 h and 18:00 h hidden under stones. However, they might not be too hard to find due to their size of about 8.5 cm for the males and their abundance in the studied area. The females are more slender and measure 7 cm in length on average.

Having caught one of their specimens while holding a yellow flower in its mouth, the scientists conducted further examination of the stomach contents of the studied individuals and concluded that the species is omnivorous, feeding mainly on plants as well as insects and roundworms.

In conclusion, the researchers showed that there is still a huge gap in the knowledge of the close relatives of the newly described species and their “challenging taxonomy”.

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Original source:

Troncoso-Palacios J, Elorza AA, Puas GI, Alfaro-Pardo E (2016) A new species of Liolaemusrelated to L. nigroviridis from the Andean highlands of Central Chile (Iguania, Liolaemidae).ZooKeys 555: 91-114. doi: 10.3897/zookeys.555.6011

The tip of an iceberg: Four new fungus gnat species from the Scandinavian north

One may think that the extreme north of Europe is low in insect life, except for the notorious blood-sucking flies. However, while it is a generally accepted truth that both plant and animal species’ count is higher the closer one gets to the Equator, some insects display anomalous diversity gradient. Such is the case for European fungus gnats, for example, a highly diverse group of true flies. No less than about 1000 species are known to occur in the Scandinavian Peninsula, representing about 83% of the continent’s total. Furthermore, undescribed fly species are continuously being discovered from North Europe.

In a recent paper published in Biodiversity Data Journal, four new species are described. These species have been collected from mires and old-growth forests of Finnish Lapland between 2012 and 2014. One of the species has a wider range, known from Sweden, Norway and Canada.

‘I must admit that it was a pleasure to give names to these species’ says Dr. Jukka Salmela, conservation biologist at Parks & Wildlife Finland (Metsahallitus). ‘These four species are really interesting, because they are rather distant to other known members of the genus Boletina. I am also confident that these species are very rare and may be dependent on old-growth forests or small water bodies such as springs and wetlands.’

The names of the new species all reflect northern nature in one way or another. Boletina valteri is named after Professor Valter Keltikangas, a forest researcher who made very demanding and physically tough field excursions to Finnish Lapland in the 1920’s and the ’30’s.

Boletina kullervoi derives from Kalevala, a Finnish national epic. It tells the story of an orphan, called Kullervo, who eventually kills his foster father and commits suicide. The violent story of Kullervo has also inspired composer Jean Sibelius for his first symphony, “Kullervo”.

Boletina hyperborea is self-explanatory, meaning far north. The species occurs in Yukon and in northern Scandinavia. Similarly, Boletina nuortti is named after the River Nuortti. In north Sami language nuorti means east. The gorgeous and wild River Nuortti flows from Finland to Russia.

No less than 100 Fennoscandian (Scandinavian) fungus gnat species await their formal description. ‘The boreal and Arctic nature still holds many secrets. Entomologists with simple gear such as sweep nets, Malaise traps and microscopes can still make notable discoveries even in rather well-studied regions such as Finland and Sweden. Samples collected from northern mires and boreal forests are never boring if one studies neglected groups such as small flies,’ says Jukka Salmela. “These four newly described taxa just represent a small fraction of the numerous undescribed northern fly species, so they are like a tip of an iceberg.”

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Original source:

Salmela J, Suuronen A, Kaunisto K (2016) New and poorly known Holarctic species of Boletina Staeger, 1840 (Diptera, Mycetophilidae). Biodiversity Data Journal 4: e7218. doi:10.3897/BDJ.4.e7218

1,541 snout moth species and counting in the United States and Canada

The present snout moth list contains a ten-percent increase in the number of species since 1983. For the last thirty-three years snout moth specialists in the United States and Canada have been describing species new to science and recording species new to these two countries. Scientists have also published studies resulting in major changes to the classification above the species level, for example by studying snout moth “ears” (tympanal organs) and utilizing genes to study their relationships.

This check list was compiled over a three-year period by Dr. Brian Scholtens and Dr. M. Alma Solis. Brian Scholtens is a professor at the College of Charleston, South Carolina, and M. Alma Solis is a research entomologist at the Agriculture Research Service’s Systematic Entomology Laboratory, and curator of the U.S. National Pyraloidea Collection located at the Smithsonian Institution, National Museum of Natural History, Washington, D.C. Their results have been published in the open-access journal ZooKeys.

“A check list is one of the most important pieces of research, with many applications,” says Dr. Solis. “Knowing the fauna of a geographic area makes it possible to track species and, in this case, potential invasive species. The caterpillars of snout moths are economically important worldwide as pests of planted crops for food or biofuel, of forest trees, and of stored products such as wheat and nuts.”

“Many species, for example, the stored product pests, occur worldwide, but others, such as pest species of grasses including corn, can be restricted or only exist in certain geographic areas,” the scientist further explains. “It is important to be able to recognize as soon as possible that a particular species is not native to the United States or Canada.”

Scientists use Latin scientific names as “unique tags” to communicate about the morphological or molecular identity and habits of a species. One of the functions of taxonomists is to determine if a species is new or if it has already been described. Historically, confusion is created when the same species is described more than once (called a synonym) in other parts of the world.

A regional check list such as this one and a worldwide check list can work together to reinforce precision in the definition and communication about species, especially decreasing confusion about synonyms. Most worldwide check lists exist as online databases that can be updated. Dr. Solis said that they had cited new discoveries relevant to the North American snout moth fauna found in GLOBIZ, or the Global Information System on Pyraloidea, an electronic list of over 15,500 snout moth species names for which she is a collaborator.

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Original source:

Scholtens, B. & M. A. Solis. 2015. Annotated check list of the Pyraloidea (Lepidoptera) of America North of Mexico. Zookeys.535:1-1136. doi: 10.3897/zookeys.535.6086.