Tag: biodiversity

Guest blog post: Operation desert: crab and dwarf spider discovered on sand dunes in military area, Slovakia

Guest blog post by Pavol Purgat

For the first time in Slovakia, the dwarf spider Walckenaeria stylifrons and crab spider Spiracme mongolica were discovered on sand dunes in Záhorie Protected Landscape Area, on  localities that serve as a military complex, used by the native Slovak army. Moreover, the spider W. stylifrons was found in a wine-growing region near the historical town of Modra.

Scientists Pavol Purgat, Dr Peter Gajdoš, Natália Hurajtová, Institute of Landscape Ecology-Slovak Academy of Sciences, Slovakia, and Dr Katarína Krajčovičová, Dr Adrián Purkart, Ľubomír Volnár, Faculty of Natural Sciences-Comenius University in Bratislava, Slovakia have published their paper, where they introduce two new spider species for Slovakia, in the open-access journal CheckList, the journal of biodiversity data.

Dwarf spider, Walckenaeria stilifrons

European continental sand dunes, characterized by high ground temperature, high temperature fluctuations and movement of sand masses, belong to the rare, climatically extreme areas resembling deserts. In Europe, lowland sandy grassland habitats are considered to be among the most endangered and are often the subject of nature conservation.

The researchers decided to understand the spider assemblages living in such extreme habitats in Western Slovakia. During 2018–2019, the study sites were chosen and co-called pitfall traps hidden in the ground were used to collect spiders.

Among other collected species, two spiders were found for the first time in Slovakia. The dwarf spider W. stilifrons is recorded from 15 European countries and it is known from Eastern England to Eastern Germany in the north, and from the Iberian Peninsula to the Crimea and Cyprus in the south. Within Central Europe, the species has so far been known from Austria, Germany and Switzerland. The crab spider S. mongolica is known from Serbia to the European part of Russia. Its distribution in Asia extends from Central Asian part of Russia, Azerbaijan, Kazakhstan to Mongolia and China. In China it is known only from Western Inner Mongolia and Xinjiang region.

Crab spider, Spiracme mongolica

Upon the detailed examination of male copulatory organs, the researchers found out that one of the species shares characters typical for the genus Spiracme, in consideration of that a new combination Spiracme mongolica for the spider previously known as Xysticus mongolicus was suggested.

In conclusion, the authors assume that W. stilifrons can live elsewhere in Europe. The rarity of the species may be related to the occurrence of adults, especially in the winter months, as most researchers are focused only on the growing seasons. The occurrence of S. mongolica in sand dunes in Slovakia confirms this species preference for dry habitats. The new finding of S. mongolica is the most known westernmost.

Research article:
Purgat P, Gajdoš P, Purkart A, Hurajtová N, Volnár Ľ, Krajčovičová K (2021) Walckenaeria stilifrons and Spiracme mongolica (Araneae, Linyphiidae, Thomisidae), two new species to Slovakia. Check List 17 (6): 1601-1608. doi: 10.15560/17.6.1601

First moth species on Alpenrose discovered

Discovery of the first moth species to mine the leaves of the highly poisonous Alpine rose

 Rust-red alpine rose, one of the most popular alpine plants. Photo by Ingrid Huemer

An Austrian-Swiss research team was able to find a previously unknown glacial relic in the Alps, the Alpine rose leaf-miner moth. It is the first known species to have its caterpillars specializing on the rust-red alpine rose, a very poisonous, widely distributed plant that most animals, including moths and butterflies, strictly avoid. The extraordinary record was just published in the peer-reviewed scientific journal Alpine Entomology.

Poisonous host plant

The rust-red alpine rose (Rhododendron ferrugineum) is among the best-known and most attractive plants due to its flowering splendor – at least for humans. It is, in fact, a highly poisonous plant, strictly avoided by grazing animals. For insects, the alpine rose is attractive at most as a nectar plant; insect larvae, on the other hand, develop on it only in exceptional cases. This also applies to Alpine butterflies and moths, which leave Alpine roses largely untouched despite their wide distribution. Therefore, the discovery of a highly specialized species in the Alps came as a complete surprise.

Chance find

Alpine rose leaf-miner moth adults resting on leaves of the host-plant in Ardez, Graubünden, Switzerland. Photos by Jürg Schmid

Since alpine roses are unattractive to caterpillars and no insect the entire Alpine region was previously known to specialize on them, butterfly and moth experts had considered them rather uninteresting and ignored them in their research. The discovery of the alpine rose leaf-miner wasn’t the result of a targeted search: it was a pure stroke of luck.

During a cloudy spell in July this year, researchers surveying the butterflies in Ardez in the Engadine valley, Switzerland, happened to take a break exactly at an infested alpine rose bush. 

“The accidental sighting of the first caterpillar in an alpine rose leaf was an absolute adrenaline rush, it was immediately clear that this must be an extraordinary species,”

Peter Huemer, researcher and head of the natural sciences department of the Tyrolean State Museums

Peter Huemer, researcher and head of the natural sciences department of the Tyrolean State Museums, and Swiss butterfly and moth expert Jürg Schmid came back in late July and early August to look for caterpillars and pupae and find out more about this curious insect. The extended search yielded evidence of a stable population of a species that was initially a complete enigma. 

Life in the leaf

Leaf-mines of the alpine rose leaf-miner moth on Rhododendron ferrugineum in Ardez, Graubünden, Switzerland. Photos by Peter Huemer

The alpine rose leaf-miner moth drills through the upper leaf skin and into the leaf interior immediately after the caterpillar hatches. The caterpillar then spends its entire life until pupation between the intact leaf skins, eating the leaf from the inside. Thanks to this behavior, the caterpillar is just as well protected from bad weather as from many predators such as birds, spiders, or some carnivore insects. The feeding trail, called a leaf mine, begins with a long corridor and ends in a large square-like mine section. The feces are deposited inside this mine. When the time comes for pupation, the caterpillar leaves the infested leaf and makes a typical web on the underside or a nearby leaf. With the help of several fine silk threads, it produces an elaborate “hammock”, in which the pupation finally takes place. In the laboratory, after about 10 days, the successful breeding to a moth succeeded, with a striking result.

Enigmatic glacial relic

Final instar larva of the alpine rose leaf-miner moth on Rhododendron ferrugineum in Ardez, Graubünden, Switzerland. Photo by Jürg Schmid

Huemer and Schmid were surprised to find out that the moths belonged to a species that was widespread in northern Europe, northern Asia and North America – the swamp porst leaf-miner butterfly Lyonetia ledi. By looking at its morphological features, such as wing color and pattern, and comparing its DNA barcodes to those of northern European specimens, they were able to confirm its identity.

Habitat of the alpine rose leaf-miner moth in Engadine/Switzerland with Rhododendron ferrugineum. Photo by Jürg Schmid

The Engadine population, however, is located more than 400 km away from the nearest other known populations, which are on the border of Austria and the Czech Republic. Furthermore, the species lives in northern Europe exclusively on swamp porst and Gagel bush – two shrubs that are typical for raised bogs and absent from the Alps. However, the researchers suggest that in earlier cold phases – some 22,000 years ago – the swamp porst and the alpine rose did share a habitat in perialpine lowland habitats north of the Alps. It is very likely that after the last cold period and the melting of the glaciers, some populations of the species shifted their host preference from the swamp porst to the alpine rose. The separation of the distribution areas of the two plants caused by subsequent warm phases inevitably led to the separation of the moth populations. 

Extinction risk

Characteristic cocoon with final instar larva and pupa of the alpine rose leaf-miner moth on Rhododendron ferrugineum in Ardez, Graubünden, Switzerland. Photos by Jürg Schmid

The Alpine Rose Leaf-miner Moth is so far only known from the Lower Engadine. It lives in a steep, north-exposed, spruce-larch-pine forest at about 1,800 m above sea level. The high snow coverage in winter and the largely shady conditions in summer mean that alpine roses don’t get to bloom there. The scientists suspect that the moth species can still be discovered in places with similar conditions in the northern Alps, such as in neighboring Tyrol and Vorarlberg. Since the moth is likely nocturnal and flies late in the year, probably hibernating in the adult stage, the search for the caterpillars and pupae is more promising. However, the special microclimate of the Swiss location does not suggest that this species, which has so far been overlooked despite 250 years of research, is widespread. On the contrary, there are legitimate concerns that it could be one of the first victims of climate change.

Research article:

Huemer P, Schmid J (2021) Relict populations of Lyonetia ledi Wocke, 1859 (Lepidoptera, Lyonetiidae) from the Alps indicate postglacial host-plant shift to the famous Alpenrose (Rhododendron ferrugineum L.). Alpine Entomology 5: 101-106. https://doi.org/10.3897/alpento.5.76930

Trigonopterus corona, the new species of tiny beetle named after the coronavirus

… and 27 other new species of beetles discovered on Sulawesi Island

Many curious animals can be found on the Indonesian Island of Sulawesi – such as the deer-hog and the midget buffalo. But the island’s tropical forests hide a diversity of tiny insects that still remains largely unexplored. Museum scientists from Indonesia and Germany have just discovered 28 new species of beetles, all belonging to the weevil genus Trigonopterus.

Twenty-four newly discovered species of the genus Trigonopterus from Sulawesi. Image by Alexander Riedel

Most of the new species were collected by Raden Pramesa Narakusumo, curator of beetles at the Museum Zoologicum Bogoriense, from two localities of Central Sulawesi Province: Mt. Dako and Mt. Pompangeo. In fact, the forests on their slopes had never been searched for small weevils before.

A view from a ridge over the cloudy slopes of Mt. Pompangeo. Photo by Raden Pramesa Narakusumo

His research partner, Alexander Riedel of the Natural History Museum Karlsruhe, had been studying this genus for the past 15 years and was planning for a research trip to Papua New Guinea, when the COVID-19 pandemic hit. Finding himself grounded, he decided to work on the specimens from Sulawesi together with Narakusumo instead.

After diagnosing the new species, it was a challenge to find suitable names for them. One obvious choice was Trigonopterus corona, which reflects the large impact of the COVID-19 pandemic on this project. However, T. corona is by far not the first insect species with a pandemic-inspired name. In the last year, we’ve seen the species descriptions of the caddisfly Potamophylax coronavirus and the wasps Stethantyx covida and Allorhogas quarentenus.

Trigonopterus corona.
Trigonopterus ewok.

While some of the newly described species go by rather ‘standard’ names that derive from either the localities they have been collected from or their distinct characters, others were given a free pass to the Hall of Fame. Two of them were named after Indonesian movie characters (T. gundala and T. unyil), while T. ewok is another addition based on the Star Wars universe – perfectly in line with T. chewbacca, T. yoda and T.porg, all described between 2016 and 2019 by teams involving Riedel. The two-millimeter-long, rust-coloured Trigonopterus ewok was found at 1900–2000 m on Mt Pompangeo, hiding among the leaf litter in the forest.

But how come the critters have remained overlooked for so long? Almost all of these beetles measure only 2-3 millimeters, while most entomologists have a preference for the larger and strikingly looking stag beetles or jewel beetles. 

A second factor is the superficial resemblance of many species: they are most easily diagnosed by their DNA sequences. Besides the publication in the open-access journal ZooKeys, high-resolution photographs of each species were uploaded to the Species ID website, along with a short scientific description. This provides a face to the species name, an important prerequisite for future studies.

R.P. Narakusumo during fieldwork at the top of Mt. Dako. Photo by Raden Pramesa Narakusumo

This is the duo’s second published paper on Trigonopterus weevils from Sulawesi – the first one describing the whopping 103 new species from the area. Currently, the known Trigonopterus species on the island amount to 132, which is likely a mere fraction of the real diversity. The numerous mountains of Sulawesi have a distinct fauna of endemics that have evolved over the past millions of years, and these wingless, flightless weevils, highly isolated in their habitats, are a good example of this diversification. Their evolution is interwoven with the island´s geological history. Riedel wants to increase the number of sampled localities: 

“Once we have enough locality coverage and understand the weevils’ evolution, we can draw conclusions on the geological processes that formed the island of Sulawesi. This is a fascinating subject, because this island was formed by the fusion of different fragments millions of years ago.” The new species thus fill an important gap required for solving the island´s geological puzzle.

For the Indonesian side, it is equally important to obtain an inventory of species: “A large percentage of Indonesian biodiversity is yet unknown and we need names and diagnoses of species, so we can use these in further studies on conservation and bioprospecting,” says R. Pramesa Narakusumo. “Two of the newly described species came from our museum collection, and this underlines the importance of museums as a source for biological discoveries,” he added.

With many more new species of this genus to be expected, it is a lucky coincidence that the number of Star Wars characters is equally long. May the Force be with these researchers!

Research article:

Narakusumo RP, Riedel A (2021) Twenty-eight new species of Trigonopterus Fauvel (Coleoptera, Curculionidae) from Central Sulawesi. ZooKeys 1065: 29-79. https://doi.org/10.3897/zookeys.1065.71680

NeoBiota invites risk analysis studies in a new Special Issue on advancements in the screening of freshwater and terrestrial non-native species

The “Recent advancements in the risk screening of freshwater and terrestrial non-native species” Special Issue in the open-access, peer-reviewed scholarly journal NeoBiota is now open for submissions. The deadline for submission is 30 April 2022, with the issue scheduled for publication in August 2022.

The “Recent advancements in the risk screening of freshwater and terrestrial non-native species” Special Issue in the open-access, peer-reviewed scholarly journal NeoBiota is now open for submissions.

The issue is managed by the international team of guest editors of Dr Daniela Giannetto (Mugla Sitki Kocman University, Turkey), Prof. Marina Piria (University of Zagreb, Croatia), Prof. Ali Serhan Tarkan (Mugla Sitki Kocman University, Turkey) and Dr Grzegorz Zięba (University of Lodz, Poland).

Update: The deadline for submission has been extended to 30 April 2022, with the issue expected to be published in August 2022. 

The new special issue is expected to collate prominent contributors from the field of invasive ecology, thereby addressing existing gaps in the knowledge about both freshwater and terrestrial non-native species and their management.

The editors note that despite the current efforts and measures to monitor and tackle the spread of non-native species, and especially those posing imminent threat to local biodiversity and ecosystems, further expansion of such populations has increasingly been recorded in recent years. Of special concern are developing countries, where legislation for controlling non-native species is still lacking.

A major problem is that – as of today – we are still missing on risk screening studies needed to provide evidence for the invasiveness potential of many non-native species across several taxonomic groups, which would then be used to support specific conservation efforts. Unfortunately, this is particularly true for species inhabiting the world’s biodiversity hotspots, point out the editors.

Risk-based identification of non-native species is an essential process to inform policy and actions for conservation and management of biodiversity. Previously published papers on risk screening of aquatic non-native species, and especially those using the most widely-employed ‘-ISK’ decision-support toolkits, have attracted mounting interest from the wider scientific community.

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Visit NeoBiota’s journal website at: https://neobiota.pensoft.net/ 

Follow NeoBiota on Twitter and Facebook.

Journal Alpine Entomology calls for contributions in a new topical collection

“Trends in Arthropods of Alpine Aquatic Ecosystems” is the first topical collection for the journal of the Swiss Entomological Society

“Trends in Arthropods of Alpine Aquatic Ecosystems” is the first topical collection for the journal of the Swiss Entomological Society

The open-access, peer-reviewed scholarly journal Alpine Entomology, published by Pensoft on behalf of the Swiss Entomological Society, announced its very first topical collection of articles, which will be focusing on arthropods associated with aquatic ecosystems in mountainous regions.

The journal is currently inviting scientists, working on aquatic fauna from alpine habitats, to openly publish their research articles and short notices that provide evidence how arthropods’ biogeography, species communities, distribution, behaviour and morphology have changed in recent times. 

“Aquatic invertebrates are key indicators of global or local changes. Furthermore, many aquatic ecosystems are closely linked to mountains because they originate in them. Many valuable unpublished datasets on aquatic arthropod fauna may therefore be available from mountainous regions,”

explain the rationale behind the newly opened topical article collection guest editors Dr. Jean-Luc Gattolliat (Museum of Zoology, Lausanne and University of Lausanne, Switzerland) and Dr. David Muranyi (Eszterházy Károly Catholic University, Hungary).

The aim of the “Trends in Arthropods of Alpine Aquatic Ecosystems” collection is to bring together data and findings about what many agree is the most impacted type of environment on Earth: aquatic ecosystems, especially running waters.

The collection will remain open for submissions for the next two years. In the meantime, the accepted manuscripts will be published on a rolling basis, as soon as they are ready for publication.

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Visit the journal’s website at: https://alpineentomology.pensoft.net/ 
Follow Alpine Entomology on Twitter and Facebook.

New BiCIKL project to build a freeway between pieces of biodiversity knowledge

Within Biodiversity Community Integrated Knowledge Library (BiCIKL), 14 key research and natural history institutions commit to link infrastructures and technologies to provide flawless access to biodiversity data.

In a recently started Horizon 2020-funded project, 14 European institutions from 10 countries, representing both the continent’s and global key players in biodiversity research and natural history, deploy and improve their own and partnering infrastructures to bridge gaps between each other’s biodiversity data types and classes. By linking their technologies, they are set to provide flawless access to data across all stages of the research cycle.

Three years in, BiCIKL (abbreviation for Biodiversity Community Integrated Knowledge Library) will have created the first-of-its-kind Biodiversity Knowledge Hub, where a researcher will be able to retrieve a full set of linked and open biodiversity data, thereby accessing the complete story behind an organism of interest: its name, genetics, occurrences, natural history, as well as authors and publications mentioning any of those.

Ultimately, the project’s products will solidify Open Science and FAIR (Findable, Accessible, Interoperable and Reusable) data practices by empowering and streamlining biodiversity research.

Together, the project partners will redesign the way biodiversity data is found, linked, integrated and re-used across the research cycle. By the end of the project, BiCIKL will provide the community with a more transparent, trustworthy and efficient highly automated research ecosystem, allowing for scientists to access, explore and put into further use a wide range of data with only a few clicks.

“In recent years, we’ve made huge progress on how biodiversity data is located, accessed, shared, extracted and preserved, thanks to a vast array of digital platforms, tools and projects looking after the different types of data, such as natural history specimens, species descriptions, images, occurrence records and genomics data, to name a few. However, we’re still missing an interconnected and user-friendly environment to pull all those pieces of knowledge together. Within BiCIKL, we all agree that it’s only after we puzzle out how to best bridge our existing infrastructures and the information they are continuously sourcing that future researchers will be able to realise their full potential,” 

explains BiCIKL’s project coordinator Prof. Lyubomir Penev, CEO and founder of Pensoft, a scholarly publisher and technology provider company.

Continuously fed with data sourced by the partnering institutions and their infrastructures, BiCIKL’s key final output: the Biodiversity Knowledge Hub, is set to persist with time long after the project has concluded. On the contrary, by accelerating biodiversity research that builds on – rather than duplicates – existing knowledge, it will in fact be providing access to exponentially growing contextualised biodiversity data.

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Learn more about BiCIKL on the project’s website at: bicikl-project.eu

Follow BiCIKL Project on Twitter and Facebook. Join the conversation on Twitter at #BiCIKL_H2020.

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The project partners:

The first Field Identification Guide of Seychelles’ deeper reefscapes

The deep ocean is the last frontier on our planet. It is home to creatures beyond our imagination and filled to the brim with life. Coastal communities have known the value of a healthy ocean for centuries, yet much of its life remains unknown, sitting beyond the reach of most research programs due to the hostility of its depth and vastness. With current research and monitoring activities in the region mostly focussing on shallow reefs, our Field Identification Guide, published in the peer-reviewed, open-access Biodiversity Data Journal, aims to showcase the benthic organisms that inhabit the Seychelles’ deeper reefscapes. The research cruise that gathered the imagery data used to create the guide, Nekton’s “First Descent: Seychelles Expedition”, was the first of its kind to systematically survey deeper reefs in Seychelles waters, bringing to light previously little-known ecosystems and their inhabitants.

Guest blog post by Nico Fassbender, Zoleka Filander, Carlos Moura, Paris Stefanoudis and Lucy Woodall

 “We cannot protect something we do not love, we cannot love what we do not know, and we cannot know what we do not see.”

These compelling words by author Richard Louv perfectly describe the importance of taxonomy in today’s conservation efforts.

A fan coral of the genus Annella surrounded by various smaller fans and encrusting benthic organisms. Photograph taken at 60m depth. © Nekton.

The deep ocean is the last frontier on our planet. It is home to creatures beyond our imagination and filled to the brim with life. Coastal communities have known the value of a healthy ocean for centuries, yet much of its life remains unknown, sitting beyond the reach of most research programs due to the hostility of its depth and vastness. 

More recently, the importance of deeper ecosystems started moving into the focus of modern marine research as many scientists across the globe are now working to unriddle the mysteries and processes that drive the patterns of life down in the deep.

Deeper reef habitats, starting at ~30m depth beyond SCUBA diving limits, are of crucial importance for coastal communities and adjacent ecosystems alike. They have been found to not only support coral and fish larval supply, aiding shallower reefs, but also to act as a refuge for many species in times of disturbance. Yet, going back to the start of this post – you cannot protect what you don’t know – and we currently know very little about these deeper reefs, especially ones in the Western Indian Ocean region.

We are many nations, but together we are one ocean.

Zoleka Filander – Department of Forestry, Fisheries and Environment, Branch Oceans and Coasts, Cape Town, South Africa

With current research and monitoring activities in the region mostly focussing on shallow reefs, our Field Identification Guide, published in the peer-reviewed, open-access Biodiversity Data Journal, aims to showcase the benthic organisms that inhabit the Seychelles’ deeper reefscapes. The research cruise that gathered the imagery data used to create the guide, Nekton’s “First Descent: Seychelles Expedition”, was the first of its kind to systematically survey deeper reefs in Seychelles waters, bringing to light previously little-known ecosystems and their inhabitants.

All species play relevant roles in trophic relations, in the functioning of ecosystems, and all have a potential biotechnological interest.

Carlos Moura – OKEANOS/DOP, University of the Azores, Horta, Portugal
A grouper (Cephalopholis miniate) hovering above encrusting benthic communities at Aldabra, dominated by the scleractinian coral Pachyseris. Photograph taken at 30m depth. © Nekton.

Our Field Identification Guide is one of the first efforts to describe the mesophotic and sub-mesophotic reefs in the Western Indian Ocean. To effectively protect these ecosystems, stakeholders need to be able to visualise them and scientists need to be able to identify and classify the organisms they observe. Displaying the diversity of the benthic organisms we encountered is only the first step in a complex and long process, allowing us to categorize, study, monitor and thus effectively protect these habitats. 

The correct identification of life is a fundamental building block of ecological knowledge. This international collaboration provided an important place to start from when considering the life on deeper reefs in Seychelles and the wider Western Indian Ocean region.

Lucy Woodall – University of Oxford, and Nekton

To survey the benthic flora and fauna of the Seychelles, we used a variety of methods, including submersibles, remotely operated vehicles and SCUBA diving teams equipped with stereo-video camera systems. We then recorded benthic communities during transect surveys conducted at 10 m, 30 m, 60 m, 120 m, 250 m and 350 m depths. This way, we ended up with 45 h of video footage and enough images to be able to present a photographic guide for the visual identification of the marine macrophytes, corals, sponges and other common invertebrates that inhabit Seychelles’ reefs.

We encountered coral fan gardens on steep slopes, boulders entirely encrusted with sponges of all colours and textures, corals of all shapes and sizes, and an amazing variety of critters. The images in our guide cannot do justice to the beauty of these habitats, and more than one tear was shed encountering these intact ecosystems teeming with life. Especially in times of increasingly frequent disturbance events and quickly shifting baselines (i.e., what we would see as a pristine, healthy reef in the 21st century), intact reef systems become increasingly rare. So much so that they are often confined to extremely remote and/or long and heavily protected areas. Finding these deeper reefs intact and with little to no signs of anthropogenic disturbance means hope – hope that there are yet undiscovered and unexplored reefs in the Western Indian Ocean region that show similar traits; and hope that we will discover even more novel habitats worth protecting.

An overview of how habitat composition changes across depths at Astove Island. © Nekton.

We hope that this guide will help the public to discover the beauty of Seychelles’ deeper reefs and aid current and future monitoring and research activities in Seychelles and the Western Indian Ocean region.

Currently, there are few formalised training materials available to new marine researchers working in mesophotic and deeper reef habitats, especially for the Indian Ocean. The present benthic field ID guide will hopefully be of use to marine researchers, managers, divers and naturalists with the identification of organisms as seen in marine imagery or live in the field.

Paris Stefanoudis – University of Oxford, and Nekton

Taxonomic paper:

Fassbender N, Stefanoudis PV, Filander ZN, Gendron G, Mah CL, Mattio L, Mortimer JA, Moura CJ, Samaai T, Samimi-Namin K, Wagner D, Walton R, Woodall LC (2021) Reef benthos of Seychelles – A field guide. Biodiversity Data Journal 9: e65970. https://doi.org/10.3897/BDJ.9.e65970

The journal Biosystematics and Ecology moves to ARPHA Platform

The scholarly publisher and technology provider Pensoft and its self-developed publishing platform ARPHA welcome Biosystematics and Ecology – a journal by the Austrian Academy of Sciences – to its growing open-access scholarly portfolio. By moving to ARPHA, Biosystematics and Ecology now enjoys a long list of high-tech perks, which dramatically enhance the entire publishing process, from submission to publication, distribution and archiving.

The Austrian Academy of Sciences’ journal Biosystematics and Ecology now boasts an improved publishing infrastructure after moving to the technologically advanced ARPHA Platform and signing with publisher and technology provider Pensoft. The publisher, well-established in the domain of biodiversity-themed journals, is eager to welcome this latest addition to its growing open-access portfolio.

Biosystematics and Ecology is a continuation and replaces the established print-only Biosystematics and Ecology Series of the Austrian Academy of Sciences’s Commission for Interdisciplinary Ecological Studies. It publishes research focused on biodiversity in Central Europe and around the world, a domain of rapidly growing importance as а global biodiversity crisis is looming. A great advantage of Biosystematics and Ecology, in contrast to its predecessor, is the ability to simply update existing checklists and therefore to account for new scientific findings about taxonomic groups or regions. 

The peer-reviewed outlet includes contributions on a wide range of ecology and biosystematics topics, aiming to provide biodiversity data, such as catalogi, checklists and interdisciplinary research to the scientific community, while offering the maximum in accessibility, usability, and transparency. The journal is currently indexed in Crossref and archived in CLOCKSS, Portico and Zenodo.

Having already acquired its own glossy and user-friendly website provided by ARPHA, the journal also takes advantage of the platform’s signature fast-track publishing system, which offers an end-to-end publishing solution from submission to publication, distribution and archiving. The platform offers a synergic online space for authoring, reviewing, editing, production and archiving, ensuring a seamlessly integrated workflow at every step of the publishing process.

Thanks to the financial support of the Academy, Biosystematics and Ecology will publish under Diamond Open Access, which means that it is free to read and publish. Opting for ARPHA’s white-label publishing solution, the journal is published under the Academy’s branding and imprint, while benefiting from all signature high-tech features by ARPHA.

Biosystematics and Ecology also makes use of ARPHA Preprints, another platform developed by Pensoft, where authors can post a preprint in a matter of seconds upon submitting a manuscript to the journal. Once the associated manuscript gets published, the preprint is conveniently linked to the formal paper, displaying its citation details.

ARPHA’s easy-to-use, open-access publishing platform offers high-end functionalities such as diverse paper formats (PDF, machine-readable JATS XML, and semantically enriched HTML), automated data export to aggregators, web-service integrations with major global indexing databases, advanced semantics publishing, and automated email notifications and reminders. Features like these make it easy for both humans and machines all over the world to discover, access, cite, and reuse published research.

From an amateur nature video to a unique study on Antarctic jellyfish

Sometimes research emerges from the strangest turns of events. In this case, an online video created by an amateur videographer on life under the sea ice in McMurdo Sound, Antarctica, resulted in a unique taxonomic study on Antarctic jellyfish and an image-based training set for machine learning. This study was published in the open-access Biodiversity Data Journal.

Sometimes, scientific discoveries emerge from the strangest turns of events.

It all started in 2018, when Dr. Emiliano Cimoli, postdoctoral researcher at the University of Tasmania, joined a field campaign to McMurdo Sound in the Ross Sea, Antarctica – to study not jellyfish, but rather the algal communities that thrive beneath the ice. 

This crystal-like comb jelly species, Callianira cristata, has been reported for the first time in the Ross Sea by the team of researchers. Photo by Dr. Emiliano Cimoli

“These algae are like the plants of the under-ice world and are very important for the Antarctic food chain,” Dr. Cimoli says.  The research team he was part of focused on the development of new sensing technologies to monitor these algal communities (e.g. optical techniques and chemical microsensors).

“We usually have a nice large tent to be able to work and operate such instruments in the harsh Antarctic environment. The cool part is that inside this tent, we have a massive 2 x 2 m hole in the sea ice that allows us to deploy these instruments to the under-ice world.”

It’s kind of like a magic portal to another world filled with mysterious and wondrous jellyfish-like creatures that live down there.

Besides working as an engineer and remote sensing scientist, Dr. Cimoli is also a passionate amateur nature and wildlife photographer and videographer, and in his free time he decided to document all sightings of these creatures with his camera. The researcher used a combination of macro photography equipment and a set of light sources, along with underwater robots for filming underwater. 

This brownish-orange comb jelly of the genus Beroe is likely one of the five undescribed species characterized by the team of researchers. Photo by Dr. Emiliano Cimoli

“Finally, I ended up having a massive amount of jellyfish footage, did not know what to do with it, then lockdown hit and suddenly I found myself working on a trippy video composition of all these creatures,” he adds.

The value of his video was soon picked up by biologist Dr. Gerlien Verhaegen, postdoctoral researcher at the Japan Agency for Marine-Earth Science and Technology (JAMSTEC):

“When I came across Emiliano’s video, I was amazed by the image quality of his underwater footage. You could clearly distinguish some key morphological features.” Unlike hard-bodied animals, the fragile body of jellyfishes and comb jellies (i.e. “sea gooseberries”) are easily destroyed when sampled with nets, which is why photography and videography of specimens are crucial to describing them taxonomically.

“Life Beneath the Ice”, a short musical film about light and life beneath the Antarctic sea-ice by Dr. Emiliano Cimoli

The two postdocs soon joined forces to produce a collaborative study. 

“I think I underestimated the time needed to produce a jellyfish taxonomic paper,” laughs Dr. Verhaegen. “Most of the original descriptions of Antarctic jellies date back to the so-called Heroic Age of Antarctic Exploration in the early 20th century, and are written in English, French, and German. Furthermore, due to the high-water content of jellies, it is extremely difficult to fix and preserve them in formalin or ethanol. We therefore could not compare our specimens to physical specimens preserved in museums but had to rely on the century old descriptions and drawings. Luckily, we were in good hands with my project host, Dr. Dhugal Lindsay, senior scientist at JAMSTEC, a jellyfish taxonomist expert, and last author of our paper”.

Filming creatures in their natural environment can yield valuable information on their trophic interactions with other organisms. For example, this picture of a Diplulmaris antarctica jellyfish shows it feeds on comb jellies, with a Beroe present in its stomach, whereas numerous hyperiid amphipods (small parasitic crustaceans) are observed scattered around on the bell of the jellyfish. Photo by Dr. Emiliano Cimoli

Despite the small geographical and temporal scale of this study, which was published in the open-access Biodiversity Data Journal, a total of 12 species were reported, with two jellyfish and three comb jellies likely representing undescribed species.

Besides revealing new morphological traits for every species, including some behavior and trophic traits, this study was also the first to include a training image set for video annotation of Antarctic jellyfish through machine learning. 

“Machine learning is being applied to numerous fields nowadays, from voice recognition software and translation through to detection of typhoon formation,” comments Dr. Lindsay.

“In marine biology, annotating species from underwater videos can be both time-consuming and financially costly, with very few experts able to give names to the high diversity of species invariably encountered. Machine learning techniques could help solve these issues by enabling automatic first-pass annotation of videos. However, taxonomically accurate image-based datasets are needed to train these learning algorithms, and this study is a valuable first step.”

Watch the video “Life Beneath the Ice” by Dr. Emiliano Cimoli on YouTube and Vimeo.

Original source

Verhaegen, G., Cimoli, E., & Lindsay, D. J. (2021). Life beneath the ice: jellyfish and ctenophores from the Ross Sea, Antarctica, with an image- based training set for machine learning. Biodiversity Data Journal, 9, e69374. https://doi.org/10.3897/BDJ.9.e69374

One water bucket to find them all: Detecting fish, mammals, and birds from a single sample

Revolutionary environmental DNA analysis holds great potential for the future of biodiversity monitoring, concludes a new study.

Revolutionary environmental DNA analysis holds great potential for the future of biodiversity monitoring, concludes a new study

Collection of water samples for eDNA metabarcoding bioassessment.
Photo by Till-Hendrik Macher.

In times of exacerbating biodiversity loss, reliable data on species occurrence are essential, in order for prompt and adequate conservation actions to be initiated. This is especially true for freshwater ecosystems, which are particularly vulnerable and threatened by anthropogenic impacts. Their ecological status has already been highlighted as a top priority by multiple national and international directives, such as the European Water Framework Directive.

However, traditional monitoring methods, such as electrofishing, trapping methods, or observation-based assessments, which are the current status-quo in fish monitoring, are often time- and cost-consuming. As a result, over the last decade, scientists progressively agree that we need a more comprehensive and holistic method to assess freshwater biodiversity.

Meanwhile, recent studies have continuously been demonstrating that eDNA metabarcoding analyses, where DNA traces found in the water are used to identify what organisms live there, is an efficient method to capture aquatic biodiversity in a fast, reliable, non-invasive and relatively low-cost manner. In such metabarcoding studies, scientists sample, collect and sequence DNA, so that they can compare it with existing databases and identify the source organisms.

Furthermore, as eDNA metabarcoding assessments use samples from water, often streams, located at the lowest point, one such sample usually contains not only traces of specimens that come into direct contact with water, for example, by swimming or drinking, but also collects traces of terrestrial species indirectly via rainfalls, snowmelt, groundwaters etc. 

In standard fish eDNA metabarcoding assessments, these ‘bycatch data’ are typically left aside. Yet, from a viewpoint of a more holistic biodiversity monitoring, they hold immense potential to also detect the presence of terrestrial and semi-terrestrial species in the catchment.

In their new study, reported in the open-access scholarly journal Metabarcoding and Metagenomics, German researchers from the University of Duisburg-Essen and the German Environment Agency successfully detected an astonishing quantity of the local mammals and birds native to the Saxony-Anhalt state by collecting as much as 18 litres of water from across a two-kilometre stretch along the river Mulde.

After water filtration the eDNA filter is preserved in ethanol until further processing in the lab.
Photo by Till-Hendrik Macher.

In fact, it took only one day for the team, led by Till-Hendrik Macher, PhD student in the German Federal Environmental Agency-funded GeDNA project, to collect the samples. Using metabarcoding to analyse the DNA from the samples, the researchers identified as much as 50% of the fishes, 22% of the mammal species, and 7.4% of the breeding bird species in the region. 

However, the team also concluded that while it would normally take only 10 litres of water to assess the aquatic and semi-terrestrial fauna, terrestrial species required significantly more sampling.

Unlocking data from the increasingly available fish eDNA metabarcoding information enables synergies among terrestrial and aquatic biodiversity monitoring programs, adding further important information on species diversity in space and time. 

“We thus encourage to exploit fish eDNA metabarcoding biodiversity monitoring data to inform other conservation programs,”

says lead author Till-Hendrik Macher. 

“For that purpose, however, it is essential that eDNA data is jointly stored and accessible for different biodiversity monitoring and biodiversity assessment campaigns, either at state, federal, or international level,”

concludes Florian Leese, who coordinates the project.

Original source:

Macher T-H, Schütz R, Arle J, Beermann AJ, Koschorreck J, Leese F (2021) Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species. Metabarcoding and Metagenomics 5: e66557. https://doi.org/10.3897/mbmg.5.66557