As a South American herpetologist, it is inevitable to be absolutely buzzed every time I hear “Germán, you have to go to the Amazon jungle”. Going to the Amazon forest in Peru is perhaps the most joyful way to do your work. The chances to find so many frogs, lizards, snakes, turtles, and even caimans are really high, so one can’t help but get excited.
The Agua Blanca forest. Photo by Germán Chávez
The thing is, to someone like me who focuses their work on describing new species, the expectations shouldn’t be that high. The Amazon has always been a place full of mysteries, so many explorers, seduced by its enigmatic atmosphere, have gone deeper and deeper into the Amazonia. This has resulted in the description of so many species and very few unexplored places left.
So, when Wilmar Aznaran and I found this new species in the Amazon lowlands of central Peru, a well-visited area, we were quite surprised and kind of speechless. I have to confess that my reaction was “Bloody hell!” Externally, the frog is clearly different from any other similar species, and that was evident for us at the very moment we caught it. Indeed, the first option for the title of our new paper in Evolutionary Systematics was “Expect the unexpected: a new treefrog from the Amazon lowlands of Peru.” We could not believe that a medium-sized arboreal frog had passed in front of other researchers’ eyes, and remained unseen.
Scinax pyroinguinis. Photo by Germán Chávez
Soon we found out that it is not a common species in the area: after catching two individuals, we were unable to find more. Not ready to give up, we went once more time to that site a few months later and our efforts to find it were unsuccessful, so we suggest it is not a common frog.
At that point, we knew that we had a new species on hands, but describing it with only two specimens was challenging. Luis A. García-Ayachi went to the area and his efforts were also unsuccessful. That is when Alessandro Catenazzi joined us, so we decided to add an integrative approach to our work, basing our research on morphological and genetic differences. I can only say thanks to all our co-authors: from then on, everything started to work out.
Scinax pyroinguinis. Photo by Germán Chávez
We noticed there were wildfires in the area, are a serious threat to the frog’s habitat. So it is really curious that the orange pattern on the groins, thighs and shanks of the new species, resembles flames, like those threatening its habitat. No better name for our frog than Scinax pyroinguinis, which literally means “groins of fire”.
Scinax pyroinguinis. Photo by Germán ChávezA wildfire in the frog’s habitat. Photo by Luis A. García-Ayachi
We hope that this discovery encourages people and institutions to protect these remnant forests in central Peru, because they may yet harbour unknown species. If these forests disappear, we will probably lose a diversity that we do not even know now yet, and may never will. It is sort of a race against deforestation and habitat loss, but this doesn’t mean there’s nothing we can do. Research like ours is really important to help put the focus on this place, at least in the short term, and try to attract people to join forces in the conservation of Scinax pyroinguinis and its habitat.
Research article:
Chávez G, Aznaran W, García-Ayachi LA, Catenazzi A (2023) Rising from the ashes: A new treefrog (Anura, Hylidae, Scinax) from a wildfire-threatened area in the Amazon lowlands of central Peru. Evolutionary Systematics 7(1): 183-194. https://doi.org/10.3897/evolsyst.7.102425
To bridge the gap between authors and their readers or fellow researchers – whether humans or computers – Knowledge Pixels and Pensoft launched workflows to link scientific publications to nanopublications.
A new pilot project by Pensoft and Knowledge Pixels breaks scientific knowledge into FAIR and interlinked snippets of precise information
As you might have already heard, Knowledge Pixels: an innovative startup tech company aiming to revolutionise scientific publishing and knowledge sharing by means of nanopublications – recently launched a pilot project with the similarly pioneering open-science journal Research Ideas and Outcomes (RIO), in a first of several upcoming collaborations between the software developer and the open-access scholarly publisher Pensoft.
“The way how science is performed has dramatically changed with digitalisation, the Internet, and the vast increase in data, but the results are still shared in basically the same form and language as 300 years ago: in narrative text, like a story. These narratives are not precise and not directly interpretable by machines, thereby not FAIR. Even the latest impressive AI tools like ChatGPT can only guess (and sometimes ‘hallucinate’) what the authors meant exactly and how the results compare,”
said Philipp von Essen and Tobias Kuhn, the two founders of Knowledge Pixels in a press announcement.
So, in order to bridge the gap between authors and their readers and fellow researchers – whether humans or computers – the partners launched several workflows to bi-directionally link scientific publications from RIO Journal to nanopublications. We will explain and demonstrate these workflows in a bit.
Now, first, let’s see what nanopublications are and how they contribute to scientific knowledge, researchers and scholarship as a whole.
Basically, a nanopublication – unlike a research article – is just a tiny snippet of a scientific finding (e.g. medication X treats disease Y), which exists as a complete and straightforward piece of information stored on a decentralised server network in a specially structured format, so that it is readable for humans, but also “understandable” and actionable for computers and their algorithms.
A nanopublication may also be an assertion related to an existing research article meant to support, comment, update or complement the reported findings.
In fact, nanopublications as a concept have been with us for quite a while now. Ever since the rise of the Semantic Web, to be exact. At the end of the day, it all boils down to providing easily accessible information that is only a click away from additional useful and relevant content. The thing is, technological advancement has only recently begun to catch up with the concept of nanopublications. Today, we are one step closer to another revolution in scientific publishing, thanks to the emergence and increasing adoption of what we call knowledge graphs.
Second time I hear about nanopublications in biodiversity in 3 days -1st by @rdmpage + now by @Pensoft#ECN2016
“As pioneers in the semantic open access scientific publishing field for over a decade now, at Pensoft we are deeply engaged with making research work actually available at anyone’s fingertips. What once started as breaking down paywalls to research articles and adding the right hyperlinks in the right places, is time to be built upon,”
said Prof. Lyubomir Penev, founder and CEO at Pensoft: the open-access scholarly publisher behind the very first semantically enhanced research article in the biodiversity domain, published back in 2010 in the ZooKeys journal.
Why nanopublications?
Apart from enabling computer algorithms with wholesome access to published research findings, nanopublications allow for the knowledge snippets that they are intended to communicate to be fully understandable and actionable. With nanopublications, each byte of knowledge is interconnected and traceable back to its author(s) and scientific evidence.
Nanopublications present a complete and straightforward piece of information stored on a decentralised server network in a specially structured format, so that it is readable for humans, but also “understandable” and actionable for computers and their algorithms. Illustration by Knowledge Pixels.
By granting computers the capability of exchanging information between users and platforms, these data become Interoperable (as in the Iin FAIR), so that they can be delivered to the right user, at the right time, in the right place.
Another issue nanopublications are designed to address is research scrutiny. Today, scientific publications are produced at an unprecedented rate that is unlikely to cease in the years to come, as scholarship embraces the dissemination of early research outputs, including preprints, accepted manuscripts and non-conventional papers.
By linking assertions to a publication by means of nanopublications allows the original authors and their fellow researchers to keep knowledge up to date as new findings emerge either in support or contradiction to previous information.
A network of interlinked nanopublications could also provide a valuable forum for scientists to test, compare, complement and build on each other’s results and approaches to a common scientific problem, while retaining the record of their cooperation each step along the way.
A scientific issue that would definitely benefit from an additional layer of provenance and, specifically, a workflow allowing for new updates to be linked to previous publications is the biodiversity domain, where species treatments, taxon names, biotic interactions and phylogenies are continuously being updated, reworked and even discarded for good. This is why an upcoming collaboration between Pensoft and Knowledge Pixels will also involve the Biodiversity Data Journal (stay tuned!)
What can you do in RIO?
Now, let’s have a look at the *nano*opportunities already available at RIO Journal.
The integration between RIO and Nanodash: the environment developed by Knowledge Pixels where users edit and publish their nanopublications is available at any article published in the journal.
Add reaction to article
This function allows any reader to evaluate and record an opinion about any article using a simple template. The opinion is posted as a nanopublication displayed on the article page, bearing the timestamp and the name of the creator.
All one needs to do is go to a paper, locate the Nanopubs tab in the menu on the left and click on the Add reaction command to navigate to the Nanodash workspace accessible to anyone registered on ORCiD.
To access the Nanodash workspace, where you can fill in a ready-to-use, partially filled in nanopublication template, simply go to the Nanopubs tab in the menu of any article published in RIO Journal and click Add reaction to this article (see example).
Within the simple Nanodash workspace, the user can provide the text of the nanopublication; define its relation to the linked paper using the Citation Typing Ontology (CiTO); update its provenance and add information (e.g. licence, extra creators) by inserting extra elements.
To do this, the Knowledge Pixels team has created a ready-to-use nanopublication template, where the necessary details for the RIO paper and the author that secure the linkage have already been pre-filled.
Post an inline comment as a nanopublication
Another opportunity for readers and authors to add further meaningful information or feedback to an already published paper is by attaching an inline comment and then exporting it to Nanodash, so that it becomes a nanopublication. To do this, users will simply need to select some text with a left click, type in the comment, and click OK. Now, their input will be available in the Comment tab designed to host simple comments addressing the authors of the publication.
While RIO has long been supporting features allowing for readers to publicly share comments and even CrossRef-registered post-publication peer reviews along the articles, the nanopublications integration adds to the versatile open science-driven arsenal of feedback tools. More precisely, the novel workflow is especially useful for comments that provide a particularly valuable contribution to a research topic.
To make a comment into a nanopublication the user needs to locate the comment in the tab, and click on the Post as Nanopub command to access the Nanodash environment.
Add a nanopublication while writing your manuscript
A functionality available from ARPHA Writing Tool – the online collaborative authoring environment that underpins the manuscript submission process at several journals published by Pensoft, including RIO Journal – allows for researchers to create a list of nanopublications within their manuscripts.
By doing so, not only do authors get to highlight their key statements in a tabular view within a separate pre-designated Nanopublications section, but they also make it easier for reviewers and scientific editors to focus on and evaluate the very foundations of the paper.
By incorporating a machine algorithm-friendly structure for the main findings of their research paper, authors ensure that AI assistants, for example, will be more likely to correctly ‘read’, ‘interpret’ and deliver the knowledge reported in the publication for the next users and their prompts. Furthermore, fellow researchers who might want to cite the paper will also have an easier time citing the specific statement from within the cited source, so that their own readers – be it human, or AI – will make the right links and conclusions.
Within a pre-designated article template at RIO – regardless of the paper type selected – authors have the option to either paste a link to an already available nanopublication or manage their nanopublication via the Nanodash environment by following a link. Customised for the purposes of RIO, the Nanodash workspace will provide them with all the information needed to guide them through the creation and publication of their nanopublications.
Why Research Ideas and Outcomes, a.k.a. RIO Journal?
Why did Knowledge Pixels and Pensoft opt to run their joint pilot at no other journal within the Pensoft portfolio of open-access scientific journals but the Research Ideas and Outcomes (RIO)?
Well, one may argue that there simply was no better choice than an academic outlet that was initially designed to serve as “the open-science journal”: something it has been honourably recognised for by SPARC in 2016, only one year since its launch.
Innovative since day #1, back in 2015, RIO surfaced as an academic outlet to publish a whole lot of article types, reporting on scientific work from across the research process, starting from research ideas, grant proposals and workshop reports.
After all, back in 2015, when it was only a handful of funders who required Data and Software Management Plans to be made openly and publicly, RIO was already providing a platform to publish those as easily citable research outputs, complete with DOI and registration on Crossref. In the spirit of transparency, RIO has always operated an open and public by default peer review policy.
More recently, RIO introduced a novel collections workflow which allows, for example, project coordinators, to provide a one-stop access point for publications and all kinds of valuable outputs resulting from their projects regardless of their publication source.
Bottom line is, RIO has always stood for innovation, transparency, openness and FAIRness in scholarly publishing and communication, so it was indeed the best fit for the nanopublication pilot with Knowledge Pixels.
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We encourage you to try the nanopublications workflow yourself by going to https://riojournal.com/articles, and posting your own assertion to an article of your choice!
Don’t forget to also sign up for the RIO Journal’s newsletter via the Email alert form on the journal’s website and follow it on Twitter, Facebook, Linkedin and Mastodon.
The latest issue published in African Invertebrates is a special one: it honours the career and achievements of South African entomologist Dr Jason G. H. Londt. In celebration of Londt’s prolific and inspiring work, the issue was published to coincide with his 80th birthday in 2023.
For more than 50 years, Londt has made a notable impact on South African and international entomology, collecting large numbers of Diptera and other insect orders. He has made outstanding contributions to the entomological research on flies, especially assassin or robber flies (Diptera, Asilidae), on hangingflies (Mecoptera, Bittacidae), and field collections of insects, primarily in South Africa.
Throughout his career, he has described more species of Afrotropical Asilidae and Bittacidae (Mecoptera) than any other author.
“Today, some 952 Asilidae species are recognised from southern Africa and thanks to Jason’s exceptional collecting efforts and detailed revisionary taxonomic publications these species can be easily identified,“ write African Invertebrates editors John Midgley and Torsten Dikow in the editorial to the Festschrift.
The Festschrift includes nine articles celebrating Dr Londt’s career by authors from three continents, covering the broad contributions that he has made to Afrotropical entomology. It also introduces five new species described in his honour, one hangingfly and four true flies.
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For updates about African Invertebrates and its latest publications, follow the journal on Twitter and Facebook. You can also sign up for the journal’s newsletter from the Email alert panel accessible from the homepage.
As an expert in science communication, dissemination and exploitation, Pensoft joins TRANSPATH for transformative changes at consumer, producer and organisational levels.
As an expert in science communication, dissemination and exploitation, Pensoft joins the Horizon-funded project TRANSPATH to identify leverage points and interventions for triggering transformative changes at consumer, producer and organisational levels.
Why TRANSPATH?
The magnitude of biodiversity loss and climate crisis has grown exponentially in recent years, which will inevitably lead to serious consequences at a global scale. Although reversing the degradation of ecosystems and reducing greenhouse gas emissions are top priorities for the European Union, science and policy communities are united in the belief that conventional policies alone are not enough to halt biodiversity loss or mitigate climate change.
In order to achieve climate neutrality by 2050, whilst simultaneously reshaping people’s relations with nature, we need transformative changes in our economies and societies urgently.
How?
TRANSPATH (short for TRANSformative PATHways for synergising just biodiversity and climate actions) – a new European Union-funded project, plans to satisfy this need by accelerating diverse transformative pathways towards biodiversity-positive and climate-proofed societies, with sensitivity to social-cultural contexts and rights.
TRANSPATH will identify leverage points and interventions for triggering transformative changes at consumer, producer and organisational levels. A research team, consisting of leading academics, science-policy experts, and early-career professionals, will directly engage with diverse stakeholders, who affect and are affected by trade regimes and associated ‘greening’ mechanisms.
As a leader of WP5: Dissemination, outreach and catalysing transformative pathways, Pensoft is responsible for providinga dissemination and communication strategy, as well as taking care of the project branding and website. In addition, the Pensoft team is to organise joint activities with other projects or initiatives on transformative change and related topics.
What?
Funded by the European Union’s Horizon Europe research and innovation programme, TRANSPATH was launched on 1st November 2022 and will be running until October 2026. The official kick-off of the project took place online and was followed by an in-person kick-off meeting of all consortium members on the 2nd and 3rd February 2023 in Wageningen, the Netherlands.
For the next four years TRANSPATH will be focussing on the design and integrated assessment of a suite of transformative pathways that hold potential to accelerate shifts in unsustainable patterns of extraction, production, consumption and trade. The project’s mission will be achieved by four objectives:
Set up a Policy Board and Science-policy-practitioner Labs at multiple scales to engage and jointly deliberate on implications of diverse visions and pathways of change.
Identify and characterise leverage points for diverse contexts that lead to positive synergies between biodiversity, climate and trade domains.
Integrate and customise European and global pathways by considering coupled biodiversity-climate actions and critical leverage points.
Identify and test alternative interventions at global and European scales that can trigger transformative change at the level of consumers, producers and organisations.
TRANSPATH will bring together and advance several strands of recent research, which hold potential for triggering and accelerating transformative changes that can restrain biodiversity loss and climate change.
The project will draw on diverse contexts in Eastern and Western Europe, Africa and Latin America, to engage with policy makers and practitioners, individuals, Civil Society Organisations (CSOs), small- and medium-sized enterprises (SMEs) and multinational corporations.
In addition, policy packages and other interventions will be designed to facilitate the emergence of leverage points at different scales of action in ways that change the decision-making framework of everyday choices.
These interventions take into account the synergies and trade-offs of actions across multiple individuals and locations, as well as the role of incentives and political obstacles to implementation.
The EU project will provide a suite of Transformative Pathways along with a Toolbox of Transformative Interventions to trigger and enable these pathways. The Transformative Navigation Toolkit assists practitioners in enabling and navigating these pathways, acknowledging that determining what constitutes a ‘transformative pathway’ is also a product of an iterative and adaptive process that emerges and evolves over time.
Whom?
The TRANSPATH project brings together leading academics, science-policy experts, and young professionals from different social-cultural origins across Eastern and Western Europe, Africa and Latin America. Represented by nine countries and twelve nationalities, the consortium comprises a diverse range of scientific disciplines in environments, economics, and social sciences.
Dedicated to ensuring sufficient engagement from local to global levels in this project, the experts are focused on integrated and inclusive deliberation that is essential for identifying, legitimising, and navigating transformative pathways.
You can find more about the project on the TRANSPATH website: transpath.eu. Stay up to date with the project’s progress on Twitter (@TRANSPATH_EU) and Linkedin (/transpath-project).
MINNEAPOLIS/ST. PAUL (05/11/2023) — Researchers at the University of Minnesota have discovered a new species of tiny parasitic wasp that might prove beneficial to managing soybean gall midge, a recently emerged pest in Midwest soybean fields that can have devastating impacts on plant production.
Synopeas maximum. Credit: Elijah Talamas, Florida Department of Agriculture and Consumer Services
Since the appearance of the midge in 2018, growers have struggled to manage this insect, prompting researchers to seek effective and environmentally-friendly ways to help soybean farmers protect their crop. One approach is biological control, using natural enemies to kill pests. However, because soybean gall midge is new, very little is known about which species might prove to be good allies to growers in the fight against this damaging insect.
Amelia Lindsey, an assistant professor in the Department of Entomology, and Robert Koch, an associate professor in the Department of Entomology and an Extension entomologist, led the team at the University of Minnesota. They focused on searching for parasitoids — insects that lay their eggs in or on another insect — of soybean gall midge. Juveniles of the parasitoid develop inside the other insect, eventually killing them.
To find such parasitic insects, a graduate student in the Lindsey and Koch labs, Gloria Melotto, collected soybean gall midge-infested plants from a Minnesota farm and waited to see which adult insects emerged from the plants.
The researchers found:
In addition to a lot of soybean gall midges, there were a number of tiny parasitoid wasps.
In collaboration with two taxonomists who specialize in this group of insects—Jessica Awad, doctoral researcher, State Museum of Natural History Stuttgart, and Elijah Talamas, Florida Department of Agriculture and Consumer Services—it became clear that there was no information on this wasp anywhere in the scientific record. It is a new-to-science species.
The team used DNA sequencing data and physical characteristics of the wasps to formally describe the specimens and give them a scientific name: Synopeas maximum.
The findings point toward this newly described parasitoid wasp species being a likely natural enemy of soybean gall midge.
The head of Synopeas maximum.
“Unidentified and undescribed parasitoid micro-wasps are all around us. Although they are tiny, they play a huge role in regulating the populations of other insects, including pests. It’s really exciting to discover a new parasitoid species in such an important crop system,” said Awad.
“Effective management of soybean gall midge has proven challenging. Identification of a new species of parasitic wasp attacking this pest is an exciting breakthrough,” said Koch.
Ongoing work from the team includes a deeper dive into the biology of the wasp and the soybean gall midge to see how often this wasp attacks the pest, and how widespread this potential beneficial insect is across the midwest. Ultimately, the goal is to develop strategies for incorporating the natural enemy into management plans for safe and effective control of soybean gall midge infestations.
This research was supported by the Minnesota Rapid Agricultural Response Fund.
Mangrove forests are an essential component of the coastal zones in tropical and subtropical areas, providing a wide range of goods and ecosystem services that play a vital role in ecology. They are also threatened, disappearing, and degraded across the globe.
One way to stimulate effective mangrove conservation and encourage policies for their protection is to carefully assess mangrove habitats and how they change, and identify fragmented areas. But obtaining this kind of information is not always an easy task.
“Since mangrove forests are located in tidal zones and marshy areas, they are hardly accessible,” says Dr. Neda Bihamta Toosi, postdoc at Isfahan University of Technology in Iran working on landscape pattern changes using remote sensing. In a recent study in the journal Nature Conservation, together with a team of authors, she explored ways to classify these fragile ecosystems using machine learning.
Comparing the performance of different combinations of satellite images and classification techniques, the researchers looked at how good each method was at mapping mangrove ecosystems.
“We developed a novel method with a focus on landscape ecology for mapping the spatial disturbance of mangrove ecosystems,” she explains. “The provided disturbance maps facilitate future management and planning activities for mangrove ecosystems in an efficient way, thus supporting the sustainable conservation of these coastal areas.”
The results of the study showed that object-oriented classification of fused Sentinel images can significantly improve the accuracy of mangrove land use/land cover classification.
“Assessing and monitoring the condition of such ecosystems using model-based landscape metrics and principal component analysis techniques is a time- and cost-effective approach. The use of multispectral remote sensing data to generate a detailed land cover map was essential, and freely available Sentinel-2 data will guarantee its continuity in future,” explains Dr. Bihamta Toosi.
The research team hopes this approach can be used to provide information on the trend of changes in land cover that affect the development and management of mangrove ecosystems, supporting better planning and decision-making.
“Our results on the mapping of mangrove ecosystems can contribute to the improvement of management and conservation strategies for these ecosystems impacted by human activities,“ they write in their study.
Research article:
Soffianian AR, Toosi NB, Asgarian A, Regnauld H, Fakheran S, Waser LT (2023) Evaluating resampled and fused Sentinel-2 data and machine-learning algorithms for mangrove mapping in the northern coast of Qeshm island, Iran. Nature Conservation 52: 1-22. https://doi.org/10.3897/natureconservation.52.89639
Mention fungi, and most people will probably think of the mushrooms they pick in fall, or maybe the yeast they add when baking or making wine. Others will perhaps recall last week’s mouldy bread – or cucumbers gone bad in the refrigerator. Indeed, mycologists have studied these fungi as sources of food and fermentation but also decay and disease for centuries.
Sampling soil and sediments for fungal diversity not far from Göteborg, Sweden. Photo by Henrik Nilsson
But while we’re used to thinking of fungi as organisms that form physical structures such as fruiting bodies, or yeast-like life forms that we can grow in our kitchens or laboratories, it is gradually becoming clear that fungi don’t readily assort into only these two groups. DNA sequencing studies of environmental substrates such as soil are finding massive evidence of large groups of fungi that do not seem to form fruiting bodies and that we seem unable to grow in the lab – but that are there nonetheless. These groups are often called “dark fungi,” in analogy with the concept of “dark matter” in astronomy – something we know is out there, but that we cannot directly observe right now.
A new study in MycoKeys contrasts the accumulation of fungal species recovered using traditional mycological approaches with those recovered using environmental DNA sequencing over time. Even when allowing for various kinds of biases, the authors found that species discovery through environmental sequencing vastly outpaces traditional species recovery in a strongly increasing trend over the last five years. The authors conclude that dark fungi form a defining feature of the fungal kingdom.
Field work on the Tibetan Plateau. Photo by Wengang Kang
“And that’s where it gets interesting”, Henrik Nilsson at the University of Gothenburg, Sweden, and the lead author of the study, says. “Under the current rules of nomenclature, these fungi cannot be given scientific names – they cannot be described formally. And species and groups that cannot be named formally, well, they tend to fall between the cracks. They’re typically not considered in nature conservation initiatives. They are often left out from efforts to estimate the evolutionary history of fungi, and their ecological roles and associations are largely overlooked when we try to figure out how mass and energy flow in ecosystems. They’re essentially treated as if they didn’t exist.”
Examining minute fungal fruiting bodies not far from Stockholm, Sweden. Photo by Kristina Stenmarck
Second author Martin Ryberg at the University of Uppsala, Sweden chimes in, “And it’s not like we’re adding the few missing pieces to an otherwise nearly complete jigsaw puzzle. It seems to be the other way around. We’re talking about tens of large groups of fungi – and thousands upon thousands of species, some of which seem to be so common that we have yet to find a soil sample from which they’re absent. Indeed, we’re talking about what could well prove to be the dominant life style in the fungal kingdom.”
The mycological community has been debating whether the rules of fungal nomenclature should be modified to allow formal description of these dark fungi. So far, the matter has not been resolved in the affirmative. “I think our study shows that it’s time to stop that debate, like, right away,” Nilsson says. “What we should be debating is how we should describe them. What criteria must be fulfilled for a dark fungus to be given a formal scientific name? Clearly, formation of a fruiting body or growth in the laboratory can’t be part of those criteria.”
Field work in New Caledonia. Photo by Sten Anslan
Co-author Alice Retter of the University of Vienna, Austria explains, “We figured we’d kickstart the how debate by listing criteria that we think make sense – criteria that would be stringent enough to allow for only particularly well-vetted dark fungi to be described, upholding a high level of scientific rigor and reproducibility in the process. We blended our own observations with suggestions from the mycological community, culled from depositing a preprint of the manuscript at bioRxiv. We’re certainly not claiming that our suggestions form the final word in the debate. It’s more like they’re the first. We’re thinking that the mycological community will jointly be able to come up with a set of sound guiding principles on the matter – and here comes an initial set of well-meaning observations for nucleation.”
Field work in the German Alps. Photo by Vanessa Schulz
The authors advocate gentle modifications to the nomenclatural rules governing the naming of fungi to allow giving formal names to at least the most well-documented species and groups of dark fungi. The suggested modifications would, at present, exclude many rare or otherwise less well-documented dark fungi from formal description.
“But you don’t have to have a theory of everything to have a theory of something,” senior author Kessy Abarenkov of the Tartu Natural History Museum, Estonia asserts. “By establishing rules for what’s needed to describe dark fungi, and specifying when we’ll have to refrain from describing such species at present, mycologists can do what they do best: doggedly gather enough research data to warrant naming of the dark fungi, group by group, and species by species. It’s what mycology has excelled at for hundreds of years. It’s just the setting that’s a bit new.”
Drying soil samples immediately upon collection under field conditions in Norway. Photo by Sten Anslan
Sten Anslan, University of Tartu, continues: “Much is at stake, obviously. The current rules governing the naming of fungi have served mycology well for a long time. We don’t want to upend or overthrow them. But we fear that if they’re not updated in this particular regard, there’s a risk that they grow increasingly obsolete over time. Having a book of rules that govern maybe only some few percent of the organisms it was originally conceived to govern – the fungal kingdom – would seem untenable in the long run.”
Getting ready for DNA extraction from soil samples. Photo by Sten Anslan
Marisol Sanchez-Garcia of the Swedish Agricultural University concludes: “The nomenclatural aspects of dark fungi will presumably be discussed at some length at next year’s international mycological congress in Maastricht, the Netherlands. We’re hopeful that the mycological community will reach meaningful agreement on integration of the dark fungi into the rules of nomenclature. After all, mycologists are used to negotiating and solving non-trivial questions on a day-to-day basis, and this one is hardly any different. Being part of tackling a huge, more or less unknown group of organisms where precious little is set in stone and where the rules will have to be adapted over time for the endeavour to stay attuned to recent developments, well, that’s what makes being a mycologist so interesting and rewarding in my eyes.”
Research article:
Nilsson RH, Ryberg M, Wurzbacher C, Tedersoo L, Anslan S, Põlme S, Spirin V, Mikryukov V, Svantesson S, Hartmann M, Lennartsdotter C, Belford P, Khomich M, Retter A, Corcoll N, Gómez Martinez D, Jansson T, Ghobad-Nejhad M, Vu D, Sanchez-Garcia M, Kristiansson E, Abarenkov K (2023) How, not if, is the question mycologists should be asking about DNA-based typification. MycoKeys 96: 143-157. https://doi.org/10.3897/mycokeys.96.102669
Working with the scientific travel agency Taxon Expeditions, citizen scientists studed specimens, and analyse their DNA in a field camp in the heart of the forest.
Semislugs, or ‘snugs’ as they are affectionately known among mollusc researchers, are like the squatters of the snail world: they do carry a home on their back but it is too small to live in. Still, it offers a sort of protection, while not getting in the way of the worm-like physique of the slug. For reasons unknown, on the island of Borneo, which is shared among the countries of Brunei, Malaysia, and Indonesia, most slugs are of the semislug type. The genus Microparmarion there consists of around 10 semislug species, most of which are found in the cooler forests of the mountains. So, when citizen scientists discovered a Microparmarion in the hot lowland forest of Ulu Temburong National Park, Brunei, as part of their expedition, they were surprised.
A team of citizen scientists in the Brunei forest, searching for slugs and snails.The type locality of the new species.
For the past years, the scientific travel agency Taxon Expeditions, in collaboration with Universiti Brunei Darussalam (UBD) has been organising biodiversity discovery trips for scientists, students, and laypersons to this forest. On the first trip, in 2018, during a night walk, participant Simon Berenyi, who runs an ethical pest control company in the UK, reached up to a dead leaf suspended over the trail. Everybody—the other participants, even the resident snail expert—had ducked and passed underneath this dead leaf without so much as giving it a glance. But something on its surface caught Simon’s eye. “Oi, is that a slug?” he exclaimed, and picked a slimy, well-camouflaged mollusc off it.
Microparmarion sallehi.
At the time, the team’s zoologists already suspected it was a new species – nothing like it had ever been found in this corner of the island. But that single specimen was not enough to publish its description as a new species. Over the years, successive expeditions to the same area came up with several more specimens of the same species, which made it clear that it was really a species never seen before.
On the 2022 expedition, a team composed of UBD students Nurilya Ezzwan and Izzah Hamdani and citizen scientist Harrison Wu from Virginia, USA, finished the description. Using the portable lab that Taxon Expeditions always carries with them, the team studied the animals’ shell, reproductive organs, and DNA, and prepared a paper for the open-access Biodiversity Data Journal, where it was published this week.
As usual on Taxon Expedition trips, on the last night the team voted on the scientific name for the new species. With an overwhelming majority, the ‘snug’ was named after Mr. Md Salleh Abdullah Bat, the field centre supervisor, who would retire just weeks after the team left. Mr. Salleh himself agrees that it is indeed a very fitting farewell gift.
Research article:
Schilthuizen M, Berenyi S, Ezzwan NSMN, Hamdani NIAA, Wu H, De Antoni L, Vincenzi L, de Gier W, van Peursen ADP, Njunjić I, Delledonne M, Slik F, Grafe U, Cicuzza D (2023) A new semi-slug of the genus Microparmarion from Brunei, discovered, described and DNA-barcoded on citizen-science ‘taxon expeditions’ (Gastropoda, Stylommatophora, Ariophantidae). Biodiversity Data Journal 11: e101579. https://doi.org/10.3897/BDJ.11.e101579
With expertise in science communication, dissemination and exploitation, Pensoft is involved in this project set to develop new technologies for monitoring species and their habitats across Europe
With expertise in science communication, dissemination and exploitation, Pensoft became part of this project dedicated to new technologies for species and habitat monitoring across Europe
Background
The European Union puts a great value in monitoring the health of ecosystems, as comprehensive mapping can aid policy makers’ work in adopting appropriate legislation for nature conservation. It allows for understanding the impact of human activities and making informed decisions for effective management of nature’s resources. This is particularly important for the EU, as it has set ambitious goals to halt biodiversity loss and restore degraded ecosystems by 2030, as outlined in the EU Biodiversity Strategy for 2030.
Effective biodiversity monitoring can help the EU track progress towards these goals, assess the effectiveness of conservation policies and initiatives, and identify emerging threats to biodiversity.
Despite this awareness, efforts to monitor animals and plants remain spatially and temporally fragmented. This lack of integration regarding data and methods creates a gap in biodiversity monitoring, which can negatively impact policy-making. Today, modern technologies such as drones, artificial intelligence algorithms, or remote sensing are still not widely used in biodiversity monitoring.
MAMBO project (Modern Approaches to the Monitoring of BiOdiversity) recognises this need and aims to develop, test, and implement enabling tools for monitoring conservation status and ecological requirements of species and habitats. Having started in late 2022, the project is set to run for four years until September 2026.
Pensoft – with its proven expertise in communicating scientific results – is committed to amplifying the impact of MAMBO. Pensoft supports the project through tailored approaches to communication, dissemination and exploitation so as to reach the most appropriate target audience and achieve maximum visibility of the project.
Deep-dive into the project
In order to enrich the biodiversity monitoring landscape, MAMBO will implement a multi-disciplinary approach by utilising the technical expertise in the fields of computer science, remote sensing, and social science expertise on human-technology interactions, environmental economy, and citizen science. This will be combined with knowledge on species, ecology, and conservation biology.
More specifically, the project will develop, evaluate and integrate image and sound recognition-based AI solutions for EU biodiversity monitoring from species to habitats as well as promote the standardised calculation and automated retrieval of habitat data using deep learning and remote sensing.
“Classification algorithms have matured to an extent where it is possible to identify organisms automatically from digital data, such as images or sound,”
“Technical breakthroughs in the realm of high spatial resolution remote sensing set the future of ecological monitoring and can greatly enrich traditional approaches to biodiversity monitoring.”
In order to achieve its goals, the project will test existing tools in combination with MAMBO-developed new technologies at the project’s demonstration sites geographically spread across Europe. This will contribute to an integrated European biodiversity monitoring system with potential for dynamic adaptations.
Pensoft is part of MAMBO’s Work Package 7 (WP7): “Science-policy interface and dissemination”, led by Helmholtz Centre for Environmental Research (UFZ). The work package is dedicated to providing a distinct identity of the project and its services through branding, visualisation and elaborated dissemination and communication strategy.
Within WP7, Pensoft will also be taking care after the launch of an open-science collection of research outputs in the scholarly journal Research Ideas and Outcomes(RIO).
Amongst the tasks of the partners in WP7 is also the development of different pathways for integrating new technologies and innovations into the EU Pollinators Monitoring Scheme (EU PoMS; SPRING).
You can find more about the project on the MAMBO website: mambo-project.eu. Stay up to date with the project’s progress on Twitter (@MAMBO_EU) and Linkedin (/MAMBO Project).
Tetrigidae, commonly known as pygmy grasshoppers, are an ancient and diverse family, currently numbering about 2000 species. As their name suggests, tetrigids are very small; their largest representatives are barely several centimeters long, so they might be difficult to spot on a casual stroll through tropical vegetation. However, when they are spotted, they are immediately recognizable by their elongated pronotum, a hard structure that starts behind the head and covers the entire body like a hood. They come in many shapes and colors and are often exciting to see, but this comes with a price—the taxonomy of Tetrigidae, the way they are organized into natural groups, is a mess. This is where we come in.
In our latest paper, we dealt with Choriphyllini, a small Caribbean tribe that belongs to the subfamily Cladonotinae. This subfamily had been filling up with unrelated but similar-looking tetrigids for more than a century. It had never been clearly defined so almost everything wingless and robust was assigned to Cladonotinae. We decided to put an end to this by slowly removing the superficially similar genera from the subfamily and describing tribes to group the genera that are clearly related to each other. We piloted this system just last year, when we described the tribe Valalyllini from Madagascar, with only two endemic (and endangered) genera and species.
The diversity and the distribution of the tribe Valalyllini, the Malagasy dead-leaf-like Cladonotinae. Both species are endemic to small areas and are likely endangered because of deforestation. Both species most probably inhabit rainforest leaf litter.
Put the species of Choriphyllini and Valalyllini together, mix them up, and try to guess which belongs where—this is no simple task; they are all doing their impressions of dead leaves that our primate brains struggle to differentiate. And there’s more: such leaf-like grasshoppers live in Africa and South East Asia as well, and then there are those that look like twigs and spiky tree bark.
Only now that we have an idea of what the true Cladonotinae are can we be properly amazed by the duality they represent to us. On the one hand, they are incredibly diverse with every species having its own variation on the basic shape. On the other, they are so alike that they either represent the best example of convergent evolution ever documented or they all stem from a common ancestor that is currently supposed to have lived during the Mesozoic. The evolutionary history of Cladonotinae will take many years to unravel, but the work can only begin after we define what to call by that name.
Valalyllum folium, a member of the tribe Valalyllini, subfamily Cladonotinae. This species, endemic to Madagascar, is a relative of Choriphyllini.
It only took 250 years
The first species of Choriphyllini, Phyllotettix rhombeus, was described in 1765 as Cicada rhombea, that is, as a member of an entirely different order of insects. Continuing in this manner, many authors (including the great Linnaeus himself) made many taxonomic and nomenclatural mistakes that compounded over the centuries and made these grasshoppers difficult to identify and refer to. It didn’t help that new species and new records kept being reported without being contextualized by comprehensive literature reviews. Like detectives, we followed the scattered crumbs of data and arrived at a synthesis that will make future research in the region much more pleasant.
Hancock’s plate I from the “Tettigidae of North America” shows leaf-like Caribbean species under the numbers 1), 2) and 7), but has many taxonomic and nomenclatural errors. 1) – Phyllotettix foliatus (= female holotype of Hancock’s Choriphyllum foliatum), 2) – Phyllotettix rhombeus (= Hancock’s Choriphyllum westwoodi), 7) – Choriphyllum saussurei. (= Hancock’s Phyllonotus saussurei). Source: Biodiversity Heritage Library, available at https://www.biodiversitylibrary.org/item/25899#page/10.
This is not where interesting facts about Phyllotettix rhombeus stop. While looking through the literature, we tried to extract the measurements of drawings. Most of the drawings had a scale bar printed next to them, but the archaic usage of “lines” as the standard measurement initially gave us some trouble. That is why at first we doubted one of our most fascinating discoveries: with the pronotal length measuring nearly 3 centimeters, Phyllotettix rhombeus is the largest tetrigid ever recorded! Many, many authors dealt with this species over the last 250 years, but this record was never made explicit.
It should not go unnoticed now that its proposed common name is “Jamaican Colossal Jumping Leaf”. Inspired by this, we took the measurements of the other species as well and made a figure where all the specimens are resized to a common scale, which shows the diversity of both shapes and sizes.
The genera and species of the tribe Choriphyllini. All specimens are drawn to scale.
Besides P. rhombeus, there are three more species in the genus Phyllotettix: P. plagiatus,P. foliatus, and P. compressus. All four of them are known only from Jamaica. P. foliatus and P. compressus are known from the Blue Mountains, but for the other two no precise localities are known; we still don’t know where exactly the largest tetrigid lives. The other genus of the tribe is Choriphyllum, also with four species. Three of them, C. sagrai, C. saussurei, and C. wallaceum live in Cuba, while C. bahamense is all alone on Hummingbird Cay island in the Bahamas. The easiest way to differentiate these two genera is a little strange but practical, the tallest point of the leaf-like crest in Choriphyllum species is in the front, while in Phyllotettix species it is in the back.
A map of all known Choriphyllini records. For three species, not a single precise locality is known.
Some Caribbean leaves dance and jump
For each species, we proposed a common name as a means to give these animals even more character. Names, such as “Jamaican Bitten Jumping Leaf” and “Old Cuban Dancing Leaf” may not be “official”, but they have certainly found their audience. The tweet in which we shared the collage of all the species was viewed over 17000 times; everyone was amazed by the pretty shapes and some even noted that they especially liked the crazy common names. We were very glad to see our scientific and artistic package that is Choriphyllini be so warmly received.
Another hit on Twitter, with over 20000 views, is the post showcasing the newly-described species from Cuba, Choriphyllum wallaceum. The holotype of this species has been awaiting description for a long time. We found it in Museo Nacional de Ciencias Naturales in Madrid, Spain, with a note from Ignacio Bolívar, the father of the Tetrigidae classification system. He referred to it as “Choriphyllum Seoanei” but never managed to publish it.
This “new” species presented us with the perfect opportunity to honor the 200th anniversary of Alfred Russel Wallace’s birth. Wallace is often called the “father of biogeography” but is all too often neglected when discussing the origins of the theory of evolution, with which Charles Darwin is considered synonymous. Wallace, with his independent arrival at the key concepts of the evolutionary theory, his correspondence with Darwin, and his staunch defense of Darwin’s ideas, was (and is) at the very least equal to Darwin and deserves much more recognition than he currently gets.
Choriphyllum wallaceum, a newly-described species from Cuba, named after Alfred Russel Wallace.
This is just the start
Choriphyllini are a pretty package, but one that merely introduces the real problem. The history of this tribe is long, yet we have very few specimens to work with. Although we have an understanding of how morphology varies within species, P. compressus and P. foliatus are not only suspiciously similar to each other, but they also live in the same general area of the Blue Mountains. It remains to be seen if they are in fact a single species.
Much more pressing is that we have only a vague idea of where these animals live and how their populations are impacted by various factors such as human activity and climate change—we do not have a baseline against which to assess their conservation status. Then there is the fact that there are many more islands in the Caribbean, making the possibility of discovering new Choriphyllini species on them real and exciting. We can only guess what the future holds for these neglected animals.
Old Cuban Dancing Leaf (Choriphyllum sagrai) in its natural environment among the leaf litter in Cuba, photographed by Sheyla Yong.
The stage is set; everything we know about this group is laid out in the paper and now there is no path but forward. Research is expensive, dedication to this work takes a certain kind of soul, and everything takes time. It is our sincere hope that someone someday takes this further. The pygmy jumping leaves will wait for as long as they can, on their islands, hopping without a care in the world.
References:
Deranja M, Kasalo N, Adžić K, Franjević D, Skejo J (2022) Lepocranus and Valalyllum gen. nov. (Orthoptera, Tetrigidae, Cladonotinae), endangered Malagasy dead-leaf-like grasshoppers. ZooKeys 1109: 1-15. https://doi.org/10.3897/zookeys.1109.85565
