Tag: biodiversity

Streamlined import of omics metadata from the European Nucleotide Archive (ENA) into an OMICS Data Paper manuscript

Pensoft creates a specialised data paper article type for the omics community within Biodiversity Data Journal to reflect the specific nature of omics data. The scholarly publisher and technology provider established a manuscript template to help standardise the description of such datasets and their most important features.

By Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Lyubomir Penev

Data papers are scientific papers which describe a dataset rather than present and discuss research results. The concept was introduced to the biodiversity community by Chavan and Penev in 2011 as the result of a joint project of GBIF and Pensoft.

Since then, Pensoft has implemented the data paper in several of its journals (Fig. 1). The recognition gained through data papers is an important incentive for researchers and data managers to author better quality metadata and to make it Findable, Accessible, Interoperable and Re-usable (FAIR). High quality and FAIRness of (meta)data are promoted through providing peer review, data audit, permanent scientific record and citation credit as for any other scholarly publication. One can read more on the different types of data papers and how they help to achieve these goals in the Strategies and guidelines for scholarly publishing of biodiversity data  (https://doi.org/10.3897/rio.3.e12431). 

Fig. 1 Number of data papers published in Pensoft’s journals since 2011.

The data paper concept was initially based on the standard metadata descriptions, using the  Ecological Metadata Language (EML). Apart from distinguishing a specialised place for dataset descriptions by creating a data paper article type, Pensoft has developed multiple workflows for streamlined import of metadata from various repositories and their conversion into data paper a manuscripts in Pensoft’s ARPHA Writing Tool (AWT). You can read more about the EML workflow in this blog post.

Similarly, we decided to create a specialised data paper article type for the omics community within Pensoft’s Biodiversity Data Journal to reflect the specific nature of omics data. We established a manuscript template to help standardise the description of such datasets and their most important features. This initiative was supported in part by the IGNITE project.

How can authors publish omics data papers?

There are two ways to do publish omics data papers – (1) to write a data paper manuscript following the respective template in the ARPHA Writing Tool (AWT) or (2) to convert metadata describing a project or study deposited in EMBL-EBI’s European Nucleotide Archive (ENA) into a manuscript within the AWT.

The first method is straightforward but the second one deserves more attention. We focused on metadata published in ENA, which is part of the International Nucleotide Sequence Database Collaboration (INSDC) and synchronises its records with these of the other two members (DDBJ and NCBI). ENA is linked to the ArrayExpress and BioSamples databases, which describe sequencing experiments and samples, and follow the community-accepted metadata standards MINSEQE and MIxS. To auto populate a manuscript with a click of a button, authors can provide the accession number of the relevant ENA Study of Project and our workflow will automatically retrieve all metadata from ENA, as well as any available ArrayExpress or BioSamples records linked to it (Fig. 2). After that, authors can edit any of the article sections in the manuscript by filling in the relevant template fields or creating new sections, adding text, figures, citations and so on.

An important component of the OMICS data paper manuscript is a supplementary table containing MIxS-compliant metadata imported from BioSamples. When available, BioSamples metadata is automatically converted to a long table format and attached to the manuscript. The authors are not permitted to edit or delete it inside the ARPHA Writing Tool. Instead, if desired, they should correct the associated records in the sourced BioSamples database. We have implemented a feature allowing the automatic re-import of corrected BioSamples records inside the supplementary table. In this way, we ensure data integrity and provide a reliable and trusted source for accessing these metadata. 

Fig. 2 Automated generation of omics data paper manuscripts through import and conversion of metadata associated with the Project ID or Study ID at ENA

Here is a step-by-step guide for conversion of ENA metadata into a data paper manuscript:

  1. The author has published a dataset to any of the INSDC databases. They copy its ENA Study or Project accession number.
  2. The author goes to the Biodiversity Data Journal (BDJ) webpage, clicks the “Start a manuscript” buttоn and selects OMICS Data Paper template in the ARPHA Writing Tool (AWT). Alternatively, the author can also start from the AWT website,  click “Create a manuscript”, and select “OMICS Data Paper” as the article type, the Biodiversity Data Journal will be automatically marked by the system. The author clicks the “Import a manuscript” button at the bottom of the webpage.
  3. The author pastes the ENA Study or Project accession number inside the relevant text box (“Import an European Nucleotide Archive (ENA) Study ID or Project ID”) and clicks “Import”.
  4. The Project or Study metadata is converted into an OMICS data paper manuscript along with the metadata from ArrayExpress and BioSamples if available. The author can start making changes to the manuscript,  invite co-authors and then submit it for technical evaluation, peer review and publication. 

For a detailed description of authoring an OMICS data paper, please refer to the Author Guidelines: https://bdj.pensoft.net/about#OmicsDataPapers

Our innovative workflow makes authoring omics data papers much easier and saves authors time and efforts when inserting metadata into the manuscript. It takes advantage of existing links between data repositories to unify biodiversity and omics knowledge into a single narrative. This workflow demonstrates the importance of standardisation and interoperability to integrate data and metadata from different scientific fields. 

We have established a special collection for OMICS data papers in the Biodiversity Data Journal. Authors are invited to describe their omics datasets by using the novel streamlined workflow for creating a manuscript at a click of a button from metadata deposited in ENA or by following the template to create their manuscript via the non-automated route.

To stimulate omics data paper publishing, the first 10 papers will be published free of charge. Upon submission of an omics data paper manuscript, do not forget to assign it to the collection Next-generation publishing of omics data.

Shining like a diamond: a new species of diamond frog from northern Madagascar

Despite the active ongoing taxonomic progress on the Madagascar frogs, the amphibian inventory of this hyper-diverse island is still very far from being complete. More new species are constantly being discovered, often within already well-studied areas. So, in one of the relatively well-studied parks in northern Madagascar, a new species of diamond frog, Rhombophryne ellae, was found in 2017. Now, the discovery is published in the open-access journal Zoosystematics and Evolution.

Despite the active ongoing taxonomic progress on Madagascar’s frogs, the amphibian inventory of this hyper-diverse island is still very far from being complete. The known diversity of the diamond frog genus Rhombophryne in Madagascar has increased significantly (more than doubled!) over the last 10 years, but still there are several undescribed candidate species awaiting description. New species are constantly being discovered in Madagascar, often even within already well-studied areas. One such place is the Montagne d’Ambre National Park in northern Madagascar.

Montagne d’Ambre National Park is widely known for its endemic flora and fauna, waterfalls and crater lakes, and considered to be a relatively well-studied area. Yet, only two studies have been published so far on the reptiles and amphibians of the Park.

Rhombophryne ellae was captured just as Cyclone Ava began to make itself felt across Madagascar with high winds and heavy rain. The camp where Dr. Scherz and his team were based became flooded, with rivers running through the kitchen and sleeping area. Miserable weather for humans, but a time of increased activity for some of the more elusive amphibians of the forest.
Credit: Mark D. Scherz
License: CC-BY 4.0

Serving the pursuit of knowledge of the herpetofauna in the region, Germany-based herpetologist Dr. Mark D. Scherz (Bavarian State Collection of Zoology, Technical University of Braunschweig, University of Konstanz) published a description of a new diamond frog species: Rhombophryne ellae, in the open-access journal Zoosystematics and Evolution.

Rhomobphryne ellae
Credit: Mark D. Scherz
License: CC-BY 4.0

“As soon as I saw this frog, I knew it was a new species. The orange flash-markings on the legs and the large black spots on the hip made it immediately obvious to me. During my Master’s and PhD research, I studied this genus and described several species, and there are no described species with such orange legs, and only few species have these black markings on the hip. It’s rare that we find a frog and are immediately able to recognise that it is a new species without having to wait for the DNA sequence results to come back, so this was elating”,

shares Dr. Scherz.

The new species is most closely related to a poorly-known and still undescribed species from Tsaratanana in northern Madagascar, but is otherwise quite different from all other diamond frogs. With the orange colouration on its legs, Rhombophryne ellae joins the growing list of frogs that have red to orange flash-markings. The function of this striking colouration remains unknown, despite having evolved repeatedly in frogs, including numerous times in Madagascar’s narrow-mouthed frogs alone.

The new species, Rhombophryne ellae, is well camouflaged among the rainforest leaflitter
Credit: Mark D. Scherz
License: CC-BY 4.0

“The discovery of such a distinctive species within a comparatively well-studied park points towards the gaps in our knowledge of the amphibians of the tropics. It also highlights the role that bad weather, especially cyclones, can play in bringing otherwise hidden frogs out of hiding—Rhombophryne ellae was caught just as Cyclone Ava was moving in on Madagascar, and several other species my colleagues and I have recently described were also caught under similar cyclonic conditions”,

says Dr. Scherz.
Rhombophryne ellae is a small, probably semi-fossorial (sub-terranean-dwelling) species of diamond frog, at home amongst the leaf litter of Montagne d’Ambre National Park, north Madagascar
Credit: Mark D. Scherz
License: CC-BY 4.0

The species is known so far only from a single specimen, making it difficult to estimate its conservation status. Yet, based on the status of other, related frogs from the same area, it will probably be Red-listed as Near Threatened due to its presumably small range and micro-endemicity.

Original source:

Scherz MD (2020) Diamond frogs forever: a new species of Rhombophryne Boettger, 1880 (Microhylidae, Cophylinae) from Montagne d’Ambre National Park, northern Madagascar. Zoosystematics and Evolution 96(2): 313-323. https://doi.org/10.3897/zse.96.51372


Scientists unravel the evolution and relationships for all European butterflies in a first

For the first time, a complete time-calibrated phylogeny for a large group of invertebrates is published for an entire continent. A German-Swedish team of scientists provide a diagrammatic hypothesis of the relationships and evolutionary history for all 496 European species of butterflies currently in existence. Their study provides an important tool for evolutionary and ecological research, meant for the use of insect and ecosystem conservation.

For the first time, a complete time-calibrated phylogeny for a large group of invertebrates is published for an entire continent. 

The figure shows the relationships of the 496 extant European butterfly species in the course of their evolution during the last 100 million years.
Image by Dr Martin Wiemers

In a recent research paper in the open-access, peer-reviewed academic journal ZooKeys, a German-Swedish team of scientists provide a diagrammatic hypothesis of the relationships and evolutionary history for all 496 European species of butterflies currently in existence. Their study provides an important tool for evolutionary and ecological research, meant for the use of insect and ecosystem conservation.

In order to analyse the ancestral relationships and history of evolutionary divergence of all European butterflies currently inhabiting the Old continent, the team led by Martin Wiemers – affiliated with both the Senckenberg German Entomological Institute and the Helmholtz Centre for Environmental Research – UFZ, mainly used molecular data from already published sources available from NCBI GenBank, but also contributed many new sequences, some from very local endemics for which no molecular data had previously been available.

The phylogenetic tree also includes butterfly species that have only recently been discovered using molecular methods. An example is this Blue (Polyommatus celina), which looks similar to the Common Blue. It used to be mistaken for the Common Blue in the Canary Islands and the southwestern part of the Mediterranean Region.
Photo by Dr Martin Wiemers

Butterflies, the spectacular members of the superfamily Papilionoidea, are seen as an important proponent for nature conservation, as they present an excellent indicator group of species, meaning they are capable of inferring the environmental conditions of a particular habitat. All in all, if the local populations of butterflies are thriving, so is their habitat.

Furthermore, butterflies are pollinating insects, which are of particular importance for the survival of humans. There is no doubt they have every right to be recognised as a flagship invertebrate group for conservation.

While many European butterflies are seriously threatened, this one: Madeiran Large White (Pieris wollastoni) is already extinct. The study includes the first sequence of this Madeiran endemic which was recorded in 1986 for the last time. The tree demonstrates that it was closely related to the Canary Island Large White (Pieris cheiranthi), another threatened endemic butterfly, which survives only on Tenerife and La Palma, but is already extinct on La Gomera.
Photo by Dr Martin Wiemers

In recent times, there has been a steady increase in the molecular data available for research, however, those would have been only used for studies restricted either to a selected subset of species, or to small geographic areas. Even though a complete phylogeny of European butterflies was published in 2019, also co-authored by Wiemers, it was not based on a global backbone phylogeny and, therefore, was also not time-calibrated.

In their paper, Wiemers and his team point out that phylogenies are increasingly used across diverse areas of macroecological research, such as studies on large-scale diversity patterns, disentangling historical and contemporary processes, latitudinal diversity gradients or improving species-area relationships. Therefore, this new phylogeny is supposed to help advance further similar ecological research.

The study includes molecular data from 18 localised endemics with no public DNA sequences previously available, such as the Canary Grayling (Hipparchia wyssii), which is only found on the island of Tenerife (Spain).
Photo by Dr Martin Wiemers

Original source: 

Wiemers M, Chazot N, Wheat CW, Schweiger O, Wahlberg N (2020) A complete time-calibrated multi-gene phylogeny of the European butterflies. ZooKeys 938: 97-124. https://doi.org/10.3897/zookeys.938.50878

A new character for Pokémon? Novel endemic dogfish shark species discovered from Japan

A new endemic deep-water dogfish shark: Squalus shiraii, was discovered in the tropical waters of Southern Japan by an international team of scientists led by Dr. Sarah Viana from South African Institute for Aquatic Biodiversity. The finding brings the amount of spurdogs shark species inhabiting Japanese waters to six. The discovery is published in the open-access journal Zoosystematics and Evolution.

Newly discovered creatures can often be as impressive and exciting as the ones from the Japanese movies and shows. Many of those fictional characters, including inhabitants of the famous Pokémon universe, might have their analogues among the real animals native to Japan. Maybe, a new species of the dogfish shark published in the open-access journal Zoosystematics and Evolution is also “a real Pokémon” to be?

A new deep-water dogfish shark: Squalus shiraii, was discovered in the tropical waters of Southern Japan by an international team of scientists, led by Dr. Sarah Viana from South African Institute for Aquatic Biodiversity. 


 Map of the North-western Pacific Ocean, showing the geographical distribution of Squalus shiraii
Credit: Sarah Viana
License: CC-BY 4.0

The new shark has the body length of 59-77 cm and some unique characteristics such as tall first dorsal fin and caudal fin with broad white margins. Currently, the species is known exclusively as a Japanese endemic, occurring in the tropical shallow waters of Southern Japan in the North-western Pacific.


Squalus shiraii lateral view
Credit: Sarah Viana
License: CC-BY 4.0

Spurdogs represent commercially important for the world fish trade taxa. They are caught for a range of purposes: consumption of meat, fins and liver oil. Despite their high occurrence, the accurate identification data of species is scarce, population threats and trends remain unknown.

Japan currently represents one of the world’s leading shark fish trade countries, though, during the last decades the amount of shark catches is decreasing and over 78 elasmobranch species traded in Japanese shark fin markets are now evaluated as threatened.

The new species Squalus shiraii previously used to be massively misidentified with shortspine spurdog, due to the resembling shape of body, fins and snout length. However, there are some differences, defining the specificity of the new species.

“Squalus shiraii has body brown in colour, postventral and preventral caudal margins whitish, dorsal and ventral caudal tips broadly white and black upper caudal blotch evident in adults. S. mitsukurii has body conspicuously black to dark grey and caudal fins black throughout with post-ventral caudal margin fairly whitish and black upper caudal blotch not evident in adults”, shares lead author Dr. Viana.

Scientists propose the name for the newly described species as Shirai’s spurdog in honour to Dr. Shigeru Shirai, the former Japanese expert of the group.

Original source:
Viana STFL, Carvalho MR (2020) Squalus shiraii sp. nov. (Squaliformes, Squalidae), a new species of dogfish shark from Japan with regional nominal species revisited. Zoosystematics and Evolution 96(2): 275-311. https://doi.org/10.3897/zse.96.51962

Contact:
Dr. Sarah Viana
Email: stviana@gmail.com


‘Social distancing’ saves frogs: New approach to identify individual frogs noninvasively

aitik Patel and Dr Abhijit Das of the Wildlife Institute of India came up with one of the very first non-invasive approaches to identify individual frogs using photos from their natural habitats, which are then processed with the animal recognition software HotSpotter. Their unique method is described in the open-access, peer-reviewed scientific journal Herpetozoa.

A Beautiful stream frog (Amolops formosus) in a Himalayan torrent stream
Photo by Naitik Patel

Globally, 41% amphibian species are regarded as threatened with extinction. However, when it comes to the case of India, the majority of the species falls in the Data Deficient group, according to the criteria of the International Union for Conservation of Nature‘s (IUCN) Red List of Threatened Species.

This means that we hardly have any population data for Indian amphibians, which leads to a serious conservation bottleneck, especially when you are dealing with elusive herpiles. Therefore, there is the pressing priority to obtain demographic trends to prompt and support conservation actions for endemic and habitat-dependent species.

While demographics of natural populations is best estimated with the mark-recapture technique, used in animals, where individuals have distinct body markings, such as the stripes in a tiger, the dots in a whale shark and the fingerprints in a human. In the meantime, while frogs are well known for their individual-specific markings and colour patterns, this kind of technique has never been used in amphibians, even though they have long been recognised as some of the most vulnerable animals on Earth.

On the other hand, it is hardly possible to capture and mark individual frogs in the wild. So, Naitik Patel and Dr Abhijit Das of the Wildlife Institute of India came up with one of the very first non-invasive approaches to identify individual frogs using photos from their natural habitats, which are then processed with the animal recognition software HotSpotter. Their unique method is described in the open-access, peer-reviewed scientific journal Herpetozoa.

“Capturing each frog is not possible in the field, so to address this problem, we conducted a short study on Beautiful stream frogs (Amolops formosus), a species that, just like many other amphibians, has variable body markings amongst individuals. As this species inhabits the Himalayan torrent stream, which is difficult to access, we tried our best to photograph each frog from a distance to avoid any kind of physical contact,”

explains Naitik Patel, a PhD student at the Wildlife Institute of India.

A Beautiful stream frog (Amolops formosus)
Photo by Abhijit Das

Having concluded their study with a success rate of 94.3%, the research team is hopeful that their protocol could be effectively implemented in rapid population estimation for many endangered species of frogs.

“We conducted photographic documentation to capture the unique markings of each frog, and then compared them, using computer-assisted individual identification. With this method, the number of individuals can be counted to estimate the population structure. This study is exceptional, owing to the minimal disturbance it causes to the frogs. Such a technique has rarely been tried on amphibians and is a promising method to estimate their numbers. It can also be used in citizen science projects,”

comments senior scientist Dr Abhijit Das.

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Original source:

Patel NG, Das A (2020) Shot the spots: A reliable field method for individual identification of Amolops formosus (Anura, Ranidae). Herpetozoa 33: 7-15. https://doi.org/10.3897/herpetozoa.33.e47279

Special ZooKeys memorial volume open to submissions to commemorate our admirable founding Editor-in-Chief Terry Erwin

In recognition of the love and devotion that Terry expressed for the study of the World’s biodiversity, ZooKeys invites contributions to this memorial issue, covering all subjects falling within the area of systematic zoology. Titled “Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020)”.

In tribute to our beloved friend and founding Editor-in-Chief, Dr Terry Erwin, who passed away on 11th May 2020, we are planning a special memorial volume to be published on 11 May 2021, the date Terry left us. Terry will be remembered by all who knew him for his radiant spirit, charming enthusiasm for carabid beetles and never-ceasing exploration of the world of biodiversity! 

In recognition of the love and devotion that Terry expressed for study of the World’s biodiversity, ZooKeys invites contributions to this memorial issue, titled “Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020)”, to all subjects falling within the area of systematic zoology. Of special interest are papers recognising Terry’s dedication to collection based research, massive biodiversity  surveys and origin of biodiversity hot spot areas. The Special will be edited by John Spence, Achille Casale, Thorsten Assmann, James Liebherr and Lyubomir Penev.

Article processing charges (APCs) will be waived for: (1) Contributions to systematic biology and diversity of carabid beetles, (2) Contributions from Terry’s students and (3) Contributions from his colleagues from the Smithsonian Institution. The APC for articles which do not fall in the above categories will be discounted at 30%.

The submission deadline is 31st December 2020.

Contributors are also invited to send memories and photos which shall be published in a special addendum to the volume.

The memorial volume will also include a joint project of Plazi, Pensoft and the Biodiversity Literature Repository aimed at extracting of taxonomic data from Terry Erwin’s publications and making it easily accessible to the scientific community.

Ten years of ecosystem services matrix: Review of a (r)evolution

In recent years, the concept of Ecosystem Services (ES): the benefits people obtain from ecosystems, such as pollination provided by bees for crop growing, timber provided by forests or recreation enabled by appealing landscapes, has been greatly popularised, especially in the context of impeding ecological crises and constantly degrading natural environments. 

Hence, there has been an increasing need for robust and practical methodologies to assess ES, in order to provide key stakeholders and decision-makers with crucial information. One such method to map and assess ES: the ES Matrix approach, has been increasingly used in the last decade.

The ES Matrix approach is based on the use of a lookup table consisting of geospatial units (e.g. types of ecosystems, habitats, land uses) and sets of ES, meant to be assessed for a specific study area, which means that the selection of a particular study area is the starting point in the assessment. Only then, suitable indicators and methods for ES quantification can be defined. Based on this information, a score for each of the ES considered is generated, referring to ES potential, ES supply, ES flow/use or demand for ES. 

Originally developed in a 2009 paper by a team, led by Prof Dr Benjamin Burkhard (Leibniz University Hannover and Leibniz Centre for Agricultural Landscape Research ZALF), the ES Matrix allows the assessment of the capacity of particular ecosystem types or geospatial units to provide ES.

Ten years later, a research led by Dr C. Sylvie Campagne (Leibniz University Hannover, Germany), Dr Philip Roche (INRAE, France), Prof Dr Felix Muller (University of Kiel, Germany) and Prof Dr Benjamin Burkhard conducted a review of 109 published studies applying the ES matrix approach to find out how the ES matrix approach was applied and whether this was done in an oversimplified way or not.

In their recent paper, published in the open-access, peer-reviewed journal One Ecosystem, the review confirms the method’s flexibility, appropriateness and utility for decision-making, as well as its ability to increase awareness of ES. Nevertheless, the ES matrix approach has often been used in a “quick and dirty” way that urges more transparency and integration of variability analyses, they conclude.

“We analysed the diversity of application contexts, highlighted trends of uses and proposed future recommendations for improved applications of the ES matrix. Amongst the main patterns observed, the ES matrix approach allows for the assessment of a higher number of ES than other ES assessment methods. ES can be jointly assessed with indicators for ecosystem condition and biodiversity in the ES matrix,”

explains Campagne.

“Although the ES matrix allows us to consider many data sources to achieve the assessment scores for the individual ES, these were mainly used together with expert-based scoring (73%) and/or ES scores that were based on an already-published ES matrix or deduced by information found in related scientific publications (51%),”

she elaborates. 

In 29% of the studies, an already existing matrix was used as an initial matrix for the assessment and in 16% no other data were used for the matrix scores or no adaptation of the existing matrix used was made. 

“Nevertheless, we recommend to use only scores assessed for a specific study or, if one wishes to use pre-existing scores from another study, to revise them in depth, taking into account the local context of the new assessment,”

she points out.

The researchers also acknowledge the fact that 27% of the reviewed studies did not clearly explain their methodology, which underlines the lack of method elucidation on how the data had been used and where the scores came from. Although some studies addressed the need to consider variabilities and uncertainties in ES assessments, only a minority of studies (15%) did so. Thus, the team also recommends to systematically report and consider variabilities and uncertainties in each ES assessment.

“We emphasise the need for all scientific studies to describe clearly and extensively the whole methodology used to score or evaluate ES, in order to be able to rate the quality of the scores obtained. The increasing number of studies that use the ES matrix approach confirms its success, appropriateness, flexibility and utility to generate information for decision-making, as well as its ability to increase awareness of ES, but the application of the ES matrix has to become more transparent and integrate more variability analyses,”

concludes the research team.

Original source:
Campagne CS, Roche P, Müller F, Burkhard B (2020) Ten years of ecosystem services matrix: Review of a (r)evolution. One Ecosystem 5: e51103. https://doi.org/10.3897/oneeco.5.e51103

Latest results of myriapod research from the 18th International Congress of Myriapodology

Last year, the 18th International Congress of Myriapodology brought together 92 of the world’s top experts on the curious, yet still largely unknown multi-legged centipedes, millipedes, pauropods, symphylans (collectively referred to as myriapods) and velvet worms (onychophorans).

Held between 25th and 31st August 2019 at the Hungarian Natural History Museum in Budapest and co-organised by the Hungarian Biological Society, the biennial event saw the announcement of the latest findings related to the diversity, distribution and biology of these creatures. Now, the public gets the chance to learn about a good part of the research presented there on the pages of the open-access scholarly journal ZooKeys.


Find all articles published in ZooKeys here
?

The special issue in ZooKeys, “Proceedings of the 18th International Congress of Myriapodology (25-31 August 2019, Budapest, Hungary)“, features a total of 11 research articles reporting on species new to science, updates on the distribution and conservation of already known myriapods and discoveries about the biology, ecology and evolution of individual species. Together, the publications reveal new insights into the myriapod life on four continents: Europe, Asia, Africa and Australia.

Amongst the published research outputs worth mentioning is the comparison between regional and global Red Listings of Threatened Species that worryingly identifies a missing overlap between the myriapod species included in the global IUCN Red List and the regional ones. This first-of-its-kind overview of the current conservation statuses of myriapods from around the world highlights the lack of dedicated funding for the conservation of hundreds of threatened myriapods. As a result, the scientists behind the study urge for the establishment of a Myriapoda Specialist Group in the Species Survival Commission of the IUCN.

Meanwhile, to give us a hint about how many millipedes are out there unbeknownst to the world and any conservation authorities, at the congress, three research teams revealed a total of seven new to science species: three giant pill-millipedes from Vietnam, another three from the biodiversity hotspot Madagascar and a spirostreptid millipede inhabiting Sao Tome and Principe.

Amongst the rest of the papers is the curious discovery of two Tasmanian species of flat-backed millipedes of the genus Tasmaniosoma whose neighbouring populations have seemingly come to their own terms to keep distance between each other, save for a little stretch of land, for no obvious reason. Not a single site where both species occur together was found by Dr Bob Mesibov, the millipede expert behind the study. How is the parapatric boundary maintained? How, when and where did the parapatry originate? These are the big mysteries that the already retired Australian scientist leaves for his successors to resolve.

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All articles published in the “Proceedings of the 18th International Congress of Myriapodology (25-31 August 2019, Budapest, Hungary” special issue, edited by Dr. Zoltan Korsos (now University of Veterinary Medicine Budapest) and Dr. Laszlo Danyi (Hungarian Natural History Museum), are publicly available in the online, open-access, peer-reviewed scholarly journal ZooKeys.

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Follow ZooKeys journal on Twitter and Facebook. Use #Myriapoda2019 to learn more about the studies published in the special issue.

New species of moths discovered in the Alps named after three famous alpinists

David Lama (1990 – 2019), a legendary alpinist, recognised by the study’s author also for his commitment to conservation.
Photo by MoserB / Copyrighted free use

The discovery of new, still unnamed animal species in a well-researched European region like the Alps is always a small sensation. All the more surprising is the description of a total of three new to science species previously misidentified as long-known alpine moths.

During a genetic project of the Tyrolean State Museums in Innsbruck (Austria), Austrian entomologist and head of the Natural Science Collections Peter Huemer used an integrative research approach that relies on molecular methods to study four European moths. Despite having been known for decades, those species remained quite controversial, because of many unknowns around their biology.

At the end, however, it turned out that the scientist was not dealing with four, but seven species. The three that were not adding up were indeed previously unknown species. Therefore, Huemer described the moths in a paper in the open-access, peer-reviewed journal Alpine Entomology. Curiously, all three species were given the names of legendary alpinists: Reinhold Messner, Peter Habeler and David Lama.

Habitat of Caryocolum lamai (Lama’s Curved-horn moth), Italy, Alpi Cozie, Colle Valcavera.
Photo by Peter Huemer

Tribute to three legends in alpinism

“The idea to name the new species in honour of three world-renowned climbers was absolutely no coincidence,”

explains Huemer.

One of the newly described species, Caryocolum messneri, or Messner’s Curved-horn moth, is dedicated to Reinhold Messner. Messner is a famous alpinist who was the first to reach Mount Everest without additional oxygen, but also the first climber to ascend all fourteen peaks over 8,000 metres. For decades, he has been inspiring followers through lectures and books. His is also the Messner Mountain Museum project, which comprises six museums located at six different locations in South Tyrol, northern Italy, where each has the task to educate visitors on “man’s encounter with mountains” by showcasing the science of mountains and glaciers, the history of mountaineering and rock climbing, the history of mythical mountains, and the history of mountain-dwelling people.

“So what could have been a better fit for a name for the species that flutters on the doorstep of his residence, the Juval Castle in South Tyrol?”

says Huemer.

The second new species, Caryocolum habeleri, or Habeler’s Curved-horn moth, honours another extraordinary mountaineer: Peter Habeler. Having joined Messner on his expedition to Mount Everest, he also climbed this mountain without additional oxygen in a first for history. Another achievement is his climbing the famous Eiger North Face in mere 10 hours. Additionally, together with the study’s author, he sits on the advisory board of the nature conservation foundation “Blühendes Österreich“. However, the species’ name is also a nod to Peter Habeler’s cousin: Heinz Habeler, recognised as “the master of butterfly and moth research in Styria”. His collection is now housed in the Tyrolean State Museums.

The third alpinist, whose name is immortalised in a species name, is David Lama, specially recognised by Huemer for his commitment to conservation. Once, in order to protect endangered butterflies along the steep railway embankments in Innsbruck, Lama took care to secure volunteers in a remarkable action. Nevertheless, Lama earned his fame for his spectacular climbing achievements. His was the first free ascent of the Compressor route on the south-eastern flank of Cerro Torre.

“Unfortunately, David lost his life far too soon in a tragic avalanche accident on 16 April 2019 in Banff National Park, Canada. Now, Caryocolum lamai (Lama’s Curved-horn moth) is supposed to make him ‘immortal’ also in the natural sciences,”

says Huemer.

Many unresolved questions

The newly described moth species are closely related and belong to the genus Caryocolum of the so-called Curved-horn moths (family Gelechiidae).

A Curved-horn moth of the genus Caryocolum feeding on a carnation plant. This genus feeds exclusively on plants in the carnation family (Caryophyllaceae).
Photo by P. Buchner / Tiroler Landesmuseen

As caterpillars, the species of this genus live exclusively on carnation plants. Even though the biology of the new moths is still unknown, because of their collection localities, it could be deduced that plants such as the stone carnation are likely their hosts. All species are restricted to dry and sunny habitats and sometimes inhabit altitudes of up to 2,500 m. So far, they have only been observed with artificial light at night.

While Messner’s Curved-horn moth occurs from northern Italy to Greece, the area of Habeler’s Curved-horn Moth is limited to the regions between southern France, northern Switzerland and southeastern Germany. On the other hand, Caryocolum lamai, only inhabits a small area in the western Alps of Italy and France.

Research on alpine butterflies and moths has been an important scientific focus at the Tyrolean state museums for decades. In 30 years, Peter Huemer discovered and named over 100 previously unknown to science species of lepidopterans. All these new discoveries have repeatedly shown the gaps in the study of biodiversity, even in Central Europe.

“How could we possibly protect a species that we don’t even have a name for is one of the key questions for science that derives from these studies,”

says Huemer in conclusion.

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Original source:

Huemer P (2020) Integrative revision of the Caryocolum schleichi species group – a striking example of a temporally changing species concept (Lepidoptera, Gelechiidae). Alpine Entomology 4: 39-63. https://doi.org/10.3897/alpento.4.50703

Novel research on African bats pilots new ways in sharing and linking published data

A colony of what is apparently a new species of the genus Hipposideros found in an abandoned gold mine in Western Kenya
Photo by B. D. Patterson / Field Museum

Newly published findings about the phylogenetics and systematics of some previously known, but also other yet to be identified species of Old World Leaf-nosed bats, provide the first contribution to a recently launched collection of research articles, whose task is to help scientists from across disciplines to better understand potential hosts and vectors of zoonotic diseases, such as the Coronavirus. Bats and pangolins are among the animals already identified to be particularly potent vehicles of life-threatening viruses, including the infamous SARS-CoV-2.

The article, publicly available in the peer-reviewed scholarly journal ZooKeys, also pilots a new generation of Linked Open Data (LOD) publishing practices, invented and implemented to facilitate ongoing scientific collaborations in times of urgency like those we experience today with the COVID-19 pandemic currently ravaging across over 230 countries around the globe.

In their study, an international team of scientists, led by Dr Bruce Patterson, Field Museum‘s MacArthur curator of mammals, point to the existence of numerous, yet to be described species of leaf-nosed bats inhabiting the biodiversity hotspots of East Africa and Southeast Asia. In order to expedite future discoveries about the identity, biology and ecology of those bats, they provide key insights into the genetics and relations within their higher groupings, as well as further information about their geographic distribution.

“Leaf-nosed bats carry coronaviruses–not the strain that’s affecting humans right now, but this is certainly not the last time a virus will be transmitted from a wild mammal to humans. If we have better knowledge of what these bats are, we’ll be better prepared if that happens,”

says Dr Terrence Demos, a post-doctoral researcher in Patterson’s lab and a principal author of the paper.
One of the possibly three new to science bat species, previously referred to as Hipposideros caffer or Sundevall’s leaf-nosed bat
Photo by B. D. Patterson / Field Museum

“With COVID-19, we have a virus that’s running amok in the human population. It originated in a horseshoe bat in China. There are 25 or 30 species of horseshoe bats in China, and no one can determine which one was involved. We owe it to ourselves to learn more about them and their relatives,”

comments Patterson.

In order to ensure that scientists from across disciplines, including biologists, but also virologists and epidemiologists, in addition to health and policy officials and decision-makers have the scientific data and evidence at hand, Patterson and his team supplemented their research publication with a particularly valuable appendix table. There, in a conveniently organized table format, everyone can access fundamental raw genetic data about each studied specimen, as well as its precise identification, origin and the natural history collection it is preserved. However, what makes those data particularly useful for researchers looking to make ground-breaking and potentially life-saving discoveries is that all that information is linked to other types of data stored at various databases and repositories contributed by scientists from anywhere in the world.

Furthermore, in this case, those linked and publicly available data or Linked Open Data (LOD) are published in specific code languages, so that they are “understandable” for computers. Thus, when a researcher seeks to access data associated with a particular specimen he/she finds in the table, he/she can immediately access additional data stored at external data repositories by means of a single algorithm. Alternatively, another researcher might want to retrieve all pathogens extracted from tissues from specimens of a specific animal species or from particular populations inhabiting a certain geographical range and so on.

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The data publication and dissemination approach piloted in this new study was elaborated by the science publisher and technology provider Pensoft and the digitisation company Plazi for the purposes of a special collection of research papers reporting on novel findings concerning the biology of bats and pangolins in the scholarly journal ZooKeys. By targeting the two most likely ‘culprits’ at the roots of the Coronavirus outbreak in 2020: bats and pangolins, the article collection aligns with the agenda of the COVID-19 Joint Task Force, a recent call for contributions made by the Consortium of European Taxonomic Facilities (CETAF), the Distributed System for Scientific Collections (DiSSCo) and the Integrated Digitized Biocollections (iDigBio).

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Original source:

Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240