Tag: biology

Notice me! Neglected for over a century, Black sea spider crab re-described

After the revision of available type specimens from all available collections in the Russian museums and the Senckenberg Museum in Frankfurt-on-Main, as well as newly collected material in the Black Sea and the North-East Atlantic, a research team of scientists, led by Dr Vassily Spiridonov from Shirshov Institute of Oceanology of Russian Academy of Sciences, re-described Macropodia czernjawskii and provided the new data on its records and updated its ecological characteristics.

Even though recognised in the Mediterranean Sea, the Macropodia czernjawskii spider crab was ignored by scientists (even by its namesake Vladimir Czernyavsky) in the regional faunal accounts of the Black Sea for more than a century. At the same time, although other species of the genus have been listed as Black sea fauna, those listings are mostly wrong and occurred either due to historical circumstances or misidentifications.Now, scientists re-describe this, most likely, only species of the genus occurring in the Black Sea in the open-access journal Zoosystematics and Evolution.

The studied spirder crab species Macropodia czernjawskii in the wild, Tuaphat (near Gelendzhik), Caucasus, Black Sea.
Photo by Sergey Anosov

The spider crab genus Macropodia was discovered in 1814 and currently includes 18 species, mostly occurring in the Atlantic and the Mediterranean. The marine fauna of the Black Sea is predominantly of Mediterranean origin and Macropodia czernjawskii was firstly discovered in the Black Sea in 1880, but afterwards, its presence there was largely ignored by the scientists.

After the revision of available type specimens from all available collections in the Russian museums and the Senckenberg Museum in Frankfurt-on-Main, as well as newly collected material in the Black Sea and the North-East Atlantic, a research team of scientists, led by Dr Vassily Spiridonov from Shirshov Institute of Oceanology of Russian Academy of Sciences, re-described Macropodia czernjawskii and provided the new data on its records and updated its ecological characteristics.

“The analysis of the molecular genetic barcode (COI) of the available material of Macropodia species indicated that M. czernjawskii is a very distinct species while M. parva should be synonimised with M. rostrata, and M. longipes is a synonym of M. tenuirostris”,

states Dr Spiridonov sharing the details of the genus analysis.

All Macropodia species have epibiosis and M. czernjawskii is no exception: almost all examined crabs in 2008-2018 collections had significant epibiosis. It normally consists of algae and cyanobacteria and, particularly, a non-indigenous species of red alga Bonnemaisonia hamifera, officially reported in 2015 at the Caucasian coast of the Black Sea, was found in the epibiosis of M. czernjawskii four years earlier.

“It improves our understanding of its invasion history. Museum and monitoring collections of species with abundant epibiosis (in particular inachid crabs) can be used as an additional tool to record and monitor introduction and establishments of sessile non-indigenous species,”

suggests Dr Spiridonov.
The spider crab species Macropodia czernjawskii in the wild, Tuaphat (near Gelendzhik), Caucasus, Black Sea.
Photo by Sergey Anosov

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Original source:

Spiridonov VA, Simakova UV, Anosov SE, Zalota AK, Timofeev VA (2020) Review of Macropodia in the Black Sea supported by molecular barcoding data; with the redescription of the type material, observations on ecology and epibiosis of Macropodia czernjawskii (Brandt, 1880) and notes on other Atlanto-Mediterranean species of Macropodia Leach, 1814 (Crustacea, Decapoda, Inachidae). Zoosystematics and Evolution 96(2): 609-635. https://doi.org/10.3897/zse.96.48342

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.

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

Plazi and Pensoft join forces to let biodiversity knowledge of coronaviruses hosts out

Pensoft’s flagship journal ZooKeys invites free-to-publish research on key biological traits of SARS-like viruses potential hosts and vectors; Plazi harvests and brings together all relevant data from legacy literature to a reliable FAIR-data repository

To bridge the huge knowledge gaps in the understanding of how and which animal species successfully transmit life-threatening diseases to humans, thereby paving the way for global health emergencies, scholarly publisher Pensoft and literature digitisation provider Plazi join efforts, expertise and high-tech infrastructure. 

By using the advanced text- and data-mining tools and semantic publishing workflows they have developed, the long-standing partners are to rapidly publish easy-to-access and reusable biodiversity research findings and data, related to hosts or vectors of the SARS-CoV-2 or other coronaviruses, in order to provide the stepping stones needed to manage and prevent similar crises in the future.

Already, there’s plenty of evidence pointing to certain animals, including pangolins, bats, snakes and civets, to be the hosts of viruses like SARS-CoV-2 (coronaviruses), hence, potential triggers of global health crises, such as the currently ravaging Coronavirus pandemic. However, scientific research on what biological and behavioural specifics of those species make them particularly successful vectors of zoonotic diseases is surprisingly scarce. Even worse, the little that science ‘knows’ today is often locked behind paywalls and copyright laws, or simply ‘trapped’ in formats inaccessible to text- and data-mining performed by search algorithms. 

This is why Pensoft’s flagship zoological open-access, peer-reviewed scientific journal ZooKeys recently announced its upcoming, special issue, titled “Biology of pangolins and bats”, to invite research papers on relevant biological traits and behavioural features of bats and pangolins, which are or could be making them efficient vectors of zoonotic diseases. Another open-science innovation champion in the Pensoft’s portfolio, Research Ideas and Outcomes (RIO Journal) launched another free-to-publish collection of early and/or brief outcomes of research devoted to SARS-like viruses.

Due to the expedited peer review and publication processes at ZooKeys, the articles will rapidly be made public and accessible to scientists, decision-makers and other experts, who could then build on the findings and eventually come up with effective measures for the prevention and mitigation of future zoonotic epidemics. To further facilitate the availability of such critical research, ZooKeys is waiving the publication charges for accepted papers.

Meanwhile, the literature digitisation provider Plazi is deploying its text- and data-mining expertise and tools, to locate and acquire publications related to hosts of coronaviruses – such as those expected in the upcoming “Biology of pangolins and bats” special issue in ZooKeys – and deposit them in a newly formed Coronavirus-Host Community, a repository hosted on the Zenodo platform. There, all publications will be granted persistent open access and enhanced with taxonomy-specific data derived from their sources. Contributions to Plazi can be made at various levels: from sending suggestions of articles to be added to the Zotero bibliographic public libraries on virus-hosts associations and hosts’ taxonomy, to helping the conversion of those articles into findable, accessible, interoperable and reusable (FAIR) knowledge.

Pensoft’s and Plazi’s collaboration once again aligns with the efforts of the biodiversity community, after the natural science collections consortium DiSSCo (Distributed System of Scientific Collections) and the Consortium of European Taxonomic Facilities (CETAF), recently announced the COVID-19 Task Force with the aim to create a network of taxonomists, collection curators and other experts from around the globe.

Tiny fly from Los Angeles has a taste for crushed invasive snails

Living individual of Draparnaud’s glass snail
Photo by Kat Halsey

As part of their project BioSCAN – devoted to the exploration of the unknown insect diversity in and around the city of Los Angeles – the scientists at the Natural History Museum of Los Angeles County (USA) have already discovered numerous insects that are new to science, but they are still only guessing about the lifestyles of these species.

“Imagine trying to find a given 2 mm long fly in the environment and tracking its behavior: it is the smallest imaginable needle in the largest haystack. So when researchers discover new life histories, it is something worth celebrating,”

explains Dr. Brian Brown, lead author of a recent paper, published in the scholarly open-access Biodiversity Data Journal.

However, Brown and Maria Wong, former BioSCAN technician, while doing field work at the L.A. County Arboretum, were quick to reveal a curious peculiarity about one particular species discovered as part of the project a few years ago. They successfully lured female phorid flies by means of crushing tiny, invasive snails and using them as bait. In comparison, the majority of phorid flies, whose lifestyles have been observed, are parasitoids of social insects like ants.

Within mere seconds after the team crushed tiny invasive snails (Oxychilus draparnaudi), females representing the fly species Megaselia steptoeae arrived at the scene and busied themselves feeding. Brown and Wong then collected some and brought them home alive along with some dead snails. One of the flies even laid eggs. After hatching, the larvae were observed feeding upon the rotting snails and soon they developed to the pupal stage. However, none was reared to adulthood.

Female phorid fly feeding on a crushed Draparnaud’s glass snail
Photo by Kat Halsey

Interestingly, the host species – used by the fly to both feed on and lay eggs inside – commonly known as Draparnaud’s glass snail, is a European species that has been introduced into many parts of the world. Meanwhile, the studied fly is native to L.A. So far, it is unknown when and how the mollusc appeared on the menu of the insect.

To make things even more curious, species of other snail genera failed to attract the flies, which hints at a peculiar interaction worth of further study, point out the scientists behind the study, Brown and Jann Vendetti, curator of the NHM Malacology collection. They also hope to lure in other species of flies by crushing other species of snails.

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In recent years, the BioSCAN project led to other curious discoveries from L.A., also published in Biodiversity Data Journal. In 2016, a whole batch of twelve previously unknown scuttle fly species was described from the heart of the city. A year later, another mysterious phorid fly was caught ovipositing in mushroom caps after Bed & Breakfast owners called in entomologists to report on what they had been observing in their yard.

Original source:

Brown BV, Vendetti JE (2020) Megaselia steptoeae (Diptera: Phoridae): specialists on smashed snails. Biodiversity Data Journal 8: e50943. https://doi.org/10.3897/BDJ.8.e50943

Research on bats and pangolins – potential vectors of zoonotic pandemics like COVID-19 – invited to a free-to-publish special issue in ZooKeys

Captively bred pangolins. 
Photo by Hua L. et al., taken from their study on the current status, problems and future prospects of captive breeding of pangolins, openly accessible in ZooKeys at: https://doi.org/10.3897/zookeys.507.6970

Accepted papers will be published free of charge in recognition of the emergency of the current global situation

Was it the horseshoe bat or could it rather be one of the most traded mammal in the world: the pangolin, at the root of the current devastating pandemic that followed the transmission of the zoonotic SARS-CoV-2 virus to a human host, arguably after infected animal products reached poorly regulated wet markets in Wuhan, China, last year? 

To make matters worse, the current situation is no precedent. Looking at the not so distant past, we notice that humanity has been repeatedly falling victim to viral deadly outbreaks, including Zika, Ebola, the Swine flu, the Spanish flu and the Plague, where all are linked to an animal host that at one point, under specific circumstances transferred the virus to people. 

Either way, here’s a lesson humanity gets to learn once again: getting too close to wildlife is capable of opening the gates to global disasters with horrific and irreversible damage on human lives, economics and ecosystems. What is left for us to understand is how exactly these transmission pathways look like and what are the factors making certain organisms like the bat and the pangolin particularly efficient vectors of diseases such as COVID-19 (Coronavirus). This crucial knowledge could’ve been easier for us to grasp had we only obtained the needed details about those species on time.

Aligning with the efforts of the biodiversity community, such as the recently announced DiSSCo and CETAF COVID-19 Task Force, who intend to create an efficient network of taxonomists, collection curators and other experts from around the globe and equip them with the tools and large datasets needed to combat the unceasing pandemic, the open-access peer-reviewed scholarly journal ZooKeys invites researchers from across the globe to submit their work on the biology of bats and pangolins to a free-to-publish special issue. 

The effort will be coordinated with the literature digitisation provider Plazi, who will extract and liberate data on potential hosts from various journals and publishers. In this way, these otherwise hardly accessible data will be re-used to support researchers in generation of new hypotheses and knowledge on this urgent topic.

By providing further knowledge on these sources and vectors of zoonotic diseases, this collection of publications could contribute with priceless insights to make the world better prepared for epidemics like the Coronavirus and even prevent such from happening in the future. 

Furthermore, by means of its technologically advanced infrastructure and services, including expedite peer review and publication processes, in addition to a long list of indexers and databases where publications are registered, ZooKeys will ensure the rapid publication of those crucial findings, and will also take care that once they get online, they will immediately become easy to discover, cite and built on by any researcher, anywhere in the world. 

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The upcoming “Biology of bats and pangolins” special issue is to add up to some excellent examples of previous research on the systematics, biology and distribution of pangolins and bats published in ZooKeys. 

In their review paper from 2015, Chinese scientists looked into the issues and prospects around captive breeding of pangolins. A year later, their colleagues at South China Normal University provided further insights into captive breeding, in addition to new data on the reproductive parameters of Chinese pangolins.

Back in 2013, a Micronesian-US research studied the taxonomy, distribution and natural history of flying fox bats inhabiting the Caroline Islands (Micronesia). A 2018 joint study on bat diversity in Sri Lanka focused on chiropteran conservation and management; while a more recent article on the cryptic diversity and range extension of the big-eyed bats in the genus Chiroderma. 

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For more information, visit ZooKeys website. 

Follow ZooKeys on Twitter and Facebook.

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References:

Buden D, Helgen K, Wiles G (2013) Taxonomy, distribution, and natural history of flying foxes (Chiroptera, Pteropodidae) in the Mortlock Islands and Chuuk State, Caroline Islands. ZooKeys 345: 97-135. https://doi.org/10.3897/zookeys.345.5840

Edirisinghe G, Surasinghe T, Gabadage D, Botejue M, Perera K, Madawala M, Weerakoon D, Karunarathna S (2018) Chiropteran diversity in the peripheral areas of the Maduru-Oya National Park in Sri Lanka: insights for conservation and management. ZooKeys 784: 139-162. https://doi.org/10.3897/zookeys.784.25562

Hua L, Gong S, Wang F, Li W, Ge Y, Li X, Hou F (2015) Captive breeding of pangolins: current status, problems and future prospects. ZooKeys 507: 99-114. https://doi.org/10.3897/zookeys.507.6970

Lim BK, Loureiro LO, Garbino GST (2020) Cryptic diversity and range extension in the big-eyed bat genus Chiroderma (Chiroptera, Phyllostomidae). ZooKeys 918: 41-63. https://doi.org/10.3897/zookeys.918.48786

Zhang F, Wu S, Zou C, Wang Q, Li S, Sun R (2016) A note on captive breeding and reproductive parameters of the Chinese pangolin, Manis pentadactyla Linnaeus, 1758. ZooKeys 618: 129-144. https://doi.org/10.3897/zookeys.618.8886

Citizen scientists discover a new snail and name it after Greta Thunberg

A new to science species of land snail was discovered by a group of citizen scientists working together with scientists from Taxon Expeditions, a company that organises scientific field trips for teams consisting of both scientists and laypeople. Having conducted a vote on how to name the species, the expedition participants and the local staff of the National Park together decided to name the mollusc Craspedotropis gretathunbergae. The species name honors the young Swedish activist Greta Thunberg for her efforts to raise awareness about climate change. The study is published in the open-access journal Biodiversity Data Journal.

“The newly described snail belongs to the so-called caenogastropods, a group of land snails known to be sensitive to drought, temperature extremes and forest degradation”,

says snail expert and co-founder of Taxon Expeditions, Dr. Menno Schilthuizen.

All individuals were found very close to the research field station (Kuala Belalong Field Studies Centre) at the foot of a steep hill-slope, next to a river bank, while foraging at night on the green leaves of understorey plants.

Citizen scientist J.P. Lim, who found the first specimen of Greta Thunberg’s snail says:

“Naming this snail after Greta Thunberg is our way of acknowledging that her generation will be responsible for fixing problems that they did not create. And it’s a promise that people from all generations will join her to help”.


Taxon Expeditions participant J.P. Lim collecting snails.
Credit: Taxon Expeditions – Pierre Escoubas
License: CC-BY 4.0

The expedition team approached Ms. Thunberg who said that she would be “delighted” to have this species named after her. 

Video about Taxon Expeditions & Greta Thunberg snail
Credit: Taxon Expeditions

However, this is not the first time that Taxon Expeditions team names a species in honour of an environmental advocate. In 2018, they named a new species of beetle after famous actor and climate activist Leonardo DiCaprio. Mr. DiCaprio temporarily changed his profile photo on Facebook to the photo of “his” beetle to acknowledge this honour.


View of the Ulu Temburong National Park in Brunei from the canopy bridge.
Credit: Taxon Expeditions – Pierre Escoubas
License: CC-BY 4.0

Original source:

Schilthuizen M, Lim JP, van Peursen ADP, Alfano M, Jenging AB, Cicuzza D, Escoubas A, Escoubas P, Grafe U, Ja J, Koomen P, Krotoski A, Lavezzari D, Lim L, Maarschall R, Slik F, Steele D, Ting Teck Wah D, van Zeeland I, Njunjić I (2020) Craspedotropis gretathunbergae, a new species of Cyclophoridae (Gastropoda: Caenogastropoda), discovered and described on a field course to Kuala Belalong rainforest, Brunei. Biodiversity Data Journal 8: e47484. https://doi.org/10.3897/BDJ.8.e47484

Field research in Turkmenistan’s highest mountain reveals high biological diversity

Camera trap image of male Markhor Capra falconeri at the Koytendag State Nature Reserve
Photo by Koytendag State Nature Reserve

New open-access book presents a comprehensive report on the remarkable ecosystems of the Koytendag nature reserve

Situated in the extreme south-east of Turkmenistan: on the border with Uzbekistan and close to the border with Afghanistan, Koytendag presents one of the most distinct landscapes in Central Asia. Reaching elevations of up to 3,137 m, this is also the highest mountain in Turkmenistan.

Location of Koytendag
Image by Atamyrat Veyisov

Koytendag State Nature Reserve and its three Wildlife Sanctuaries: Hojapil, Garlyk and Hojaburjybelent, were established between 1986 and 1990 to protect and preserve the mountain ecosystem of the Koytendag region and maintain the ecological balance between the environment and increasing economic activities.

Since 2013, a series of scientific expeditions and assessments were coordinated and funded by the Royal Society for the Protection of Birds (RSPB) to pave the way for the protection and preservation of the unique landscape and rare wildlife the site is recognised for.

As a result, the efforts of the conducted field studies of multidisciplinary international research teams are brought together in a comprehensive report, which is now openly available as an Advanced Book from the scientific publisher and technology provider Pensoft, edited by Geoff Welch (RSPB) and Prof. Pavel Stoev (National National Museum of Natural History of Bulgaria and Pensoft). Soon, the book will also be available in Russian.

The book is split into eight sections focused on different areas within the study of biodiversity: Flora, Surface dwelling invertebrates, Cave fauna, Fish, Amphibians, Reptiles, Birds and Mammals. An additional chapter is dedicated to the hydrogeology of the site because of its key role in supporting both the cave fauna and the local communities.

Entrance to the newly discovered record-breaking underground lake at the Koytendag State Nature Reserve
Photo by Mikhail Pereladov

In the summary of the report, the authors make a list of the most significant findings made during the research. These include the discovery of a cave hosting the largest underground lake in the whole North Eurasia (4,400 m2) and a total of 48 species of higher plants that can only be found in Koytendag. In terms of Koytendag’s surface-dwelling fauna, the report lists a number of species new to science: a scorpion (most likely yet unnamed species currently recognised as a species complex) and a spider. Meanwhile, a total of seven previously unknown species were found underground, including the very first exclusively subterranean animal found in the country: the insect-like ‘marvellous’ dipluran named Turkmenocampa mirabilis, and a strongly adapted to the underground waters of a desert sinkhole Gammarus troglomorphus. Additionally, the annual monitoring, conducted since 1995 by the reserve staff, report an encouraging increase in the populations of the rare markhors and mouflons. An intact predator-prey community was also identified as a result of observations of numerous Eurasian lynxes and grey wolves, as well as prey species.

Entrance of the cave Kaptarhana, (Lebap Province, Eastern Turkmenistan), where scientists discovered the first ever exclusively subterranean dweller for the country (find more here).
Photo by Aleksandr Degtyarev

Stephanie Ward, RSPB Central Asia Partner Development Officer, says:

“RSPB has been working in Turkmenistan under a Memorandum of Understanding with the Government since 2004. In that time we have had the privilege of working with a team of talented and dedicated national experts across the diverse and inspiring nature of this fascinating country. Our work in Koytendag has captured the attention and interest of many international scientists who hope that their contemporary biodiversity research will help to deepen the understanding and therefore ensure protection of the unique wonders of this mountain ecosystem. As a potential UNESCO World Heritage Site, we will continue to collaborate with the Turkmen people on the research and promotion of Koytendag State Nature Reserve.

Book editor and member of the research team Prof. Pavel Stoev adds:

“Koytendag Mountain is among the least explored and, simultaneously, one of the most biologically diverse regions in Central Asia. The rapid assessments of its flora and fauna revealed a high number of highly specialised species, all of which have undergone a long evolution to adapt to the harsh environments of the mountain. The establishment of Koytendag State Nature Reserve and the associated wildlife sanctuaries is a step in the right direction for the protection of this unique biota.”

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Cover of the book, available as an open-access Advanced book from: https://doi.org/10.3897/ab.e37858.

Original source:

Welch G, Stoev P (2019) A report of RSPB-supported scientific research at Koytendag State Nature Reserve, East Turkmenistan. Advanced Books. https://doi.org/10.3897/ab.e37858

Additional information:

This work was carried out under the Memorandum of Understanding between the Ministry of Agriculture and Environment Protection of Turkmenistan and the RSPB, within the Project on “Improvement of the status of birds and other biodiversity in Turkmenistan”.

About Koytendag State Nature Reserve:

Koytendag State Nature Reserve was established in 1986 to protect and preserve the mountain ecosystem of the Koytendag region and maintain the ecological balance between the environment and the increasing anthropogenic activities. Of particular importance was the protection of rare species, such as the markhor; important habitats, including pistachio and juniper forests; and the impressive dinosaur trackways at Hojapil.

Advanced Books publishing by Pensoft:

Launched by Pensoft and powered by the scholarly publishing platform ARPHA, the Advanced Books approach aims to issue new books or re-issue books previously only available in print or PDF. In the Advanced Books format, the publications are semantically enhanced and available in HTML and XML as well, in order to accelerate open access, data publication, mining, sharing and reuse. The Advanced books builds on the novel approaches developed by the Pensoft’s journals.



Extraordinary treefrog discovered in the Andes of Ecuador

An adult of the newly described species, Hyloscirtus hillisi. Photo by Gustavo Pazmiño, BIOWEB Ecuador.

A new treefrog species was discovered during a two-week expedition to a remote tabletop mountain at Cordillera del Cóndor, a largely unexplored range in the eastern Andes.

“To reach the tabletop, we walked two days along a steep terrain. Then, between sweat and exhaustion, we arrived to the tabletop where we found a dwarf forest. The rivers had blackwater and the frogs were sitting along them, on branches of brown shrubs similar in color to the frogs’ own. The frogs were difficult to find, because they blended with their background,” Alex Achig, one of the field biologists who discovered the new species comments on the hardships of the expedition.

Curiously, the frog has an extraordinary, enlarged claw-like structure located at the base of the thumb. Its function is unknown, but it could be that it is used either as a defence against predators or as a weapon in fights between competing males.

Having conducted analyses of genetic and morphologic data, scientists Santiago R. Ron, Marcel Caminer, Andrea Varela, and Diego Almeida from the Catholic University of Ecuador concluded that the frog represented a previously unknown species. It was recently described in the open-access journal ZooKeys.

Unlike other frogs, the new species has a claw at the base of the thumb. Photo by Gustavo Pazmiño, BIOWEB Ecuador.

The species name, Hyloscirtus hillisi, honors Dr. David Hillis, a member of the National Academy of Sciences of the United States of America, who discovered three closely related frog species in the same genus in the 1980s, while conducting a series of field trips to the Andes of southern Ecuador. Throughout his career, Dr. Hillis has made significant contributions to the knowledge of Andean amphibians and reptiles.

Despite being newly described, Hyloscirtus hillisi is already at risk of extinction. It has a small distribution range near a large-scale mining operation carried out by a Chinese company. Habitat destruction in the region has been recently documented by the NGO Amazon Conservation.

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Original source:

Ron SR, Caminer MA, Varela-Jaramillo A, Almeida-Reinoso D (2018) A new treefrog from Cordillera del Cóndor with comments on the biogeographic affinity between Cordillera del Cóndor and the Guianan Tepuis (Anura, Hylidae, Hyloscirtus). ZooKeys 809: 97-124. https://doi.org/10.3897/zookeys.809.25207

A metamorph of the new species, Hyloscirtus hillisi. Photo by Darwin Núñez, BIOWEB Ecuador.

Towards untangling the ‘antennal grabbing’ phenomenon in mating cuckoo bees

Scientists report this behavior for the first time in the genus Nomada, following both lab and field observations in Germany

One can seldom spot a cuckoo bee, whose peculiar kleptoparasitic behaviour includes laying eggs in the nests of a certain host bee species, let alone a couple mating.

Nevertheless, German scientists – Dr. Matthias Schindler, University of Bonn, Michaela Hofmann and Dr. Susanne S. Renner of the University of Munich, and Dr. Dieter Wittmann, recently managed to record copulation in three different cuckoo bee species in the genus Nomada.

Intriguingly, in field and lab settings alike, the observed couples demonstrated the phenomenon the researchers called “antennal grabbing” where the male cuckoo bee winds his antennae around

Insertion phase of copulation in a couple of the species Nomada flavoguttata. Note the male’s antennae spirally entangling the female’s.

the female’s during copulation, thus transferring pheromones. Even though such behaviour is relatively common in Hymenoptera, this is the first known record for the genus Nomada.

While the particular biological reason for the “antennal grabbing” in different species remains unsettled, the scientists discuss the phenomenon in view of both previous hypotheses and their own observations in a new paper published in the open access Journal of Hymenoptera Research.

The courtship in Nomada cuckoo bee starts with the ‘swarming’ of males at willow shrubs and gooseberry or their patrolling in groups with males of the Andrena or Melitta species that will “foster” their offspring.

Two males of the species Nomada flavoguttata patrolling at a blossom of a common dandelion.

There is no aggression among the males. They were observed to rub their bellies and heads against the grass, in order to leave sexual pheromones, thus marking the “dating spot” for potential mates.

Earlier chemical studies of Nomada bees noted that the mandibular glands of males produce chemical compounds identical with those of their Andrena or Melitta hosts, leading to the suggestion that the males transfer pheromones that help the females mimic the odor of the host bee, and later enter its nest unnoticed to lay its eggs. An alternative explanation for the “antennal grabbing” is that males are spraying a substance onto the females to make them unattractive to other potential mates.

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Original source:

Schindler M, Hofmann MM, Wittmann D, Renner SS (2018) Courtship behaviour in the genus Nomada – antennal grabbing and possible transfer of male secretions. Journal of Hymenoptera Research 65: 47-59. https://doi.org/10.3897/jhr.65.24947