Citizen science data crucial to understand wildlife roadkill

In a first for science, researchers set out to analyze over 10 years of roadkill records in Flanders, Belgium, using data provided by citizen scientists.

The road is a dangerous place for animals: they can easily get run over, which can seriously affect wildlife diversity and populations in the long term. There is also a human economic cost and possible injury or even death in these accidents, while crashing into heavier animals or trying to avoid them on the road.

Making roads safer for both animals and people starts with a simple first step: understanding when, where, and how many animals get run over. This knowledge can help protect specific species, for example by using warning signs, preventing access to the roads for animals, creating overpasses and underpasses, or closing roads. Wildlife roadkill data can also help monitor other trends, such as population dynamics, species distribution, and animal behavior.

Thanks to citizen science platforms, obtaining this kind of data is no longer a task reserved for scientists. There are now dozens of free, easy-to-use online systems, where anyone can record wildlife collision accidents or roadkill, contributing to a fuller picture that might later be used to inform policy measures.

One such project is the Flemish Animals under wheels, where users can register the roadkill they saw, adding date, time and geolocation online or by using the apps. The data is stored in the online biodiversity database Waarnemingen.be, the Flemish version of the international platform Observation.org

Between 2008 and 2020, the project collected almost 90,000 roadkill records from Flanders, Belgium, registered by over 4,000 citizen scientists. Roadkill recording is just a small part of their nature recording activities – the multi-purpose platform which also allows the registration of living organisms. This is probably why the volunteers have remained engaged with the project for over 6 years now.

In a first for science, researchers from Natuurpunt Studie, the scientific institute linked to the largest Nature NGO in Flanders, with support from the Department of Environmental and Spatial Development, set out to analyze over 10 years of roadkill records in the region, using data provided by citizen scientists. In their study, published in the peer-reviewed journal Nature Conservation, they focused on 17 key species of mammals and their fate on the roads of Flanders. 

The researchers analyzed data on 145,000 km of transects monitored, which resulted in records of 1,726 mammal and 2,041 bird victims. However, the majority of the data – over 60,000 bird and mammal roadkill records – were collected opportunistically, where opportunistic data sampling favors larger or more “enigmatic” species. Hedgehogs, red foxes and red squirrels were the most frequently registered mammal roadkill victims.  

In the last decade, roadkill incidents in Flanders have diminished, the study found, even though search effort increased. This might be the result of effective road collision mitigation, such as fencing, crossing structures, or animal detection systems. On the other hand, it could be a sign of declining populations among those animals that are most prone to being killed by vehicles. More research is needed to understand the exact reason. Over the last 11 years, roadkill records of the European polecat showed a significant relative decrease, while seven species, including the roe deer and wild boar, show a relative increase in recorded incidents.

There seems to be a clear influence of the COVID-19 pandemic on roadkill patterns for some species. Restrictions in movement that followed likely led simultaneously to fewer casualties and a decrease in the search effort. 

The number of new observations submitted to Waarnemingen.be continues to increase year after year, with data for 2021 pointing to about 9 million. Even so, the scientists warn that those recorded observations “are only the tip of the iceberg.”

 “Citizen scientists are a very valuable asset in investigating wildlife roadkill. Without your contributions, roadkill in Flanders would be a black box,”

the researchers conclude.

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Research paper:

Swinnen KRR, Jacobs A, Claus K, Ruyts S, Vercayie D, Lambrechts J, Herremans M (2022) ‘Animals under wheels’: Wildlife roadkill data collection by citizen scientists as a part of their nature recording activities. In: Santos S, Grilo C, Shilling F, Bhardwaj M, Papp CR (Eds) Linear Infrastructure Networks with Ecological Solutions. Nature Conservation 47: 121-153. https://doi.org/10.3897/natureconservation.47.72970

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The research article is part of the Special Issue: “Linear Infrastructure Networks with Ecological Solutions“, which collates 15 research papers reporting on studies presented at the IENE2020 conference.

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New, possibly arboreal rice rat species discovered in Ecuador

Three expeditions led an international research team to the nearly inaccessible Cordillera de Kutukú in southeastern Ecuador to find just a single specimen of the previously unknown species

New rat species of the little known and rare genus Mindomys described: Three expeditions led an international research team with participation from the Leibniz Institute for the Analysis of Biodiversity Change (LIB) to the Cordillera de Kutukú, an isolated mountain range in Ecuador, to find just one specimen of the previously unknown species. The find in the Amazonian side of the Andes underlines the valuable biological role of this mountainous region.

Drawing of the new species Mindomys kutuku. © Glenda Pozo

“In total, the expeditions to the Kutukú region in southeastern Ecuador involved 1,200 trap nights, but only one specimen of the new species Mindomys kutuku was found,” says Dr. Claudia Koch, curator of herpetology at the LIB, Museum Koenig Bonn, explaining the effort that went into locating the rare animal. From the collected specimen, the dry skin, skeleton and tissue were preserved for the collections. Preservation will allow future research to detect environmental changes, learn more about the ecology of the animals and plants – and securely document the new species description, which was published in late February in the prestigious journal Evolutionary Systematics.

The rice rat genus Mindomys was previously considered monotypic and included only the type species Mindomys hammondi. This species is known from only a few specimens, all of which were collected in the foothill forests of the Andes in northwestern Ecuador.

Using computed tomography images obtained for the new species at LIB and for the holotype (specimen from which a species was described) of M. hammondi at the Natural History Museum in London, the researchers Jorge Brito of the Instituto Nacional de la Biodiversidad (INABIO), Claudia Koch, Nicolás Tinoco from the Pontificia Universidad Católica del Ecuador (PUCE) and Ulyses Pardiñas from the Instituto de Diversidad y Evolución del Sur (IDEAus-CONICET) were able to compare the skulls of the two species in great detail in a 3D model and distinguish between the two species.

According to Jorge Brito, INABIO’s mammal curator, the new species is easily distinguished from Mindomys hammondi by a number of anatomical features: “These include larger jugals, “wings” of the parietal bone extending to the zygomatic roots, larger otic capsules, narrow zygomatic plates almost without upper free borders, a posteriorly oriented foramen magnum (large occipital hole), larger molars and an accessory root of the first upper molar.”

The adult male of M. kutuku measures just under 35 cm from snout to tip of tail, of which the tail makes up about 20 cm. It has a dark reddish-brown dorsal coloration and a pale yellow ventral fur.

Since the only specimen found was captured with the help of a ground trap set, it could not be observed in its habitat. Thus, as with its sister species M. hammondi, which was described in 1913, virtually nothing is known about the natural history of the new species. The scientists suspect that both of them could be arboreal species. A tail that is significantly longer than the body length and also covered with long hairs could be two features that indicate an arboreal lifestyle. However, aboreality is the least studied way of life within the New World mice and a reliable study of the anatomical aspects typical of this way of life is still lacking.

Previously, Mindomys records were restricted to the western Andean foothills of Ecuador. The Kutukú material now shows that the genus also occurs on the Amazonian side of the Andes and underscores the valuable biological importance of the isolated mountain ranges in eastern Ecuador.

Research article:

Brito J, Koch C, Tinoco N, Pardiñas UFJ (2022) A new species of Mindomys (Rodentia, Cricetidae) with remarks on external traits as indicators of arboreality in sigmodontine rodents. Evolutionary Systematics 6(1): 35-55. https://doi.org/10.3897/evolsyst.6.76879

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First-ever fish species described by a Maldivian scientist

Though there are hundreds of species of fish found off the coast of the Maldives, a mesmerizing new addition is the first-ever to be formally described by a Maldivian researcher.

Named after the country’s national flower, the species is added to the tree of life as part of the California Academy of Sciences’ global Hope for Reefs initiative

Originally published by the California Academy of Sciences

Though there are hundreds of species of fish found off the coast of the Maldives, a mesmerizing new addition is the first-ever to be formally described—the scientific process an organism goes through to be recognized as a new species—by a Maldivian researcher.

The new-to-science Rose-Veiled Fairy Wrasse (Cirrhilabrus finifenmaa), described in the journal ZooKeys, is also one of the first species to have its name derived from the local Dhivehi language, ‘finifenmaa’ meaning ‘rose’, a nod to both its pink hues and the island nation’s national flower.

Scientists from the California Academy of Sciences, the University of Sydney, the Maldives Marine Research Institute (MMRI), and the Field Museum collaborated on the discovery as part of the Academy’s Hope for Reefs initiative aimed at better understanding and protecting coral reefs around the world.

“It has always been foreign scientists who have described species found in the Maldives, even those that are endemic, without much involvement from local scientists. This time, it is different and getting to be part of something for the first time has been really exciting, especially having the opportunity to work alongside top ichthyologists on such an elegant and beautiful species,”

says study co-author and Maldives Marine Research Institute biologist Ahmed Najeeb.

First collected by researchers in the 1990s, C. finifenmaa was originally thought to be the adult version of a different species, Cirrhilabrus rubrisquamis, which had been described based on a single juvenile specimen from the Chagos Archipelago, an island chain 1,000 kilometers (621 miles) south of the Maldives. 

In this new study, however, the researchers took a more detailed look at both adults and juveniles of the multicolored marvel, measuring and counting various features, such as the color of adult males, the height of each spine supporting the fin on the fish’s back and the number of scales found on various body regions. These data, along with genetic analyses, were then compared to the C. rubrisquamis specimen to confirm that C. finifenmaa is indeed a unique species. 

Importantly, this revelation greatly reduces the known range of each wrasse, a crucial consideration when setting conservation priorities.  

“What we previously thought was one widespread species of fish, is actually two different species, each with a potentially much more restricted distribution. This exemplifies why describing new species, and taxonomy in general, is important for conservation and biodiversity management,”

says lead author and University of Sydney doctoral student Yi-Kai Tea. 

Despite only just being described, the researchers say that the Rose-Veiled Fairy Wrasse is already being exploited through the aquarium hobbyist trade. 

“Though the species is quite abundant and therefore not currently at a high risk of overexploitation, it’s still unsettling when a fish is already being commercialized before it even has a scientific name. It speaks to how much biodiversity there is still left to be described from coral reef ecosystems,”

says senior author and Academy Curator of Ichthyology Luiz Rocha, PhD, who co-directs the Hope for Reefs initiative.

Last month, Hope for Reefs researchers continued their collaboration with the MMRI by conducting the first surveys of the Maldives’ ‘twilight zone’ reefs—the virtually unexplored coral ecosystems found between 50- to 150-meters (160- to 500-feet) beneath the ocean’s surface—where they found new records of C. finifenmaa along with at least eight potentially new-to-science species yet to be described. 

This new-to-science Rose-Veiled Fairy Wrasse (Cirrhilabrus finifenmaa) became the first Maldivian fish to ever be described by a local researcher.
Photo by Yi-Kai Tea.

For the researchers, this kind of international partnership is pivotal to best understand and ensure a regenerative future for the Maldives’ coral reefs. 

“Nobody knows these waters better than the Maldivian people. Our research is stronger when it’s done in collaboration with local researchers and divers. I’m excited to continue our relationship with MMRI and the Ministry of Fisheries to learn about and protect the island nation’s reefs together,”

says Rocha says

“Collaborating with organizations such as the Academy helps us build our local capacity to expand knowledge in this field. This is just the start and we are already working together on future projects. Our partnership will help us better understand the unexplored depths of our marine ecosystems and their inhabitants. The more we understand and the more compelling scientific evidence we can gather, the better we can protect them,”

adds Najeeb.

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Research article:

Tea Y-K, Najeeb A, Rowlett J, Rocha LA (2022) Cirrhilabrus finifenmaa (Teleostei, Labridae), a new species of fairy wrasse from the Maldives, with comments on the taxonomic identity of C. rubrisquamis and C. wakanda. ZooKeys 1088: 65-80. https://doi.org/10.3897/zookeys.1088.78139

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Image recognition to the rescue of natural history museums by enabling curators to identify specimens on the fly

New Research Idea, published in RIO Journal presents a promising machine-learning ecosystem to unite experts around the world and make up for lacking taxonomic expertise.

In their Research Idea, published in Research Ideas and Outcomes (RIO Journal), Swiss-Dutch research team present a promising machine-learning ecosystem to unite experts around the world and make up for lacking expert staff

Guest blog post by Luc Willemse, Senior collection manager at Naturalis Biodiversity Centre (Leiden, Netherlands)

Imagine the workday of a curator in a national natural history museum. Having spent several decades learning about a specific subgroup of grasshoppers, that person is now busy working on the identification and organisation of the holdings of the institution. To do this, the curator needs to study in detail a huge number of undescribed grasshoppers collected from all sorts of habitats around the world. 

The problem here, however, is that a curator at a smaller natural history institution – is usually responsible for all insects kept at the museum, ranging from butterflies to beetles, flies and so on. In total, we know of around 1 million described insect species worldwide. Meanwhile, another 3,000 are being added each year, while many more are redescribed, as a result of further study and new discoveries. Becoming a specialist for grasshoppers was already a laborious activity that took decades, how about knowing all insects of the world? That’s simply impossible. 

Then, how could we expect from one person to sort and update all collections at a museum: an activity that is the cornerstone of biodiversity research? A part of the solution, hiring and training additional staff, is costly and time-consuming, especially when we know that experts on certain species groups are already scarce on a global scale. 

We believe that automated image recognition holds the key to reliable and sustainable practises at natural history institutions. 

Today, image recognition tools integrated in mobile apps are already being used even by citizen scientists to identify plants and animals in the field. Based on an image taken by a smartphone, those tools identify specimens on the fly and estimate the accuracy of their results. What’s more is the fact that those identifications have proven to be almost as accurate as those done by humans. This gives us hope that we could help curators at museums worldwide take better and more timely care of the collections they are responsible for. 

However, specimen identification for the use of natural history institutions is still much more complex than the tools used in the field. After all, the information they store and should be able to provide is meant to serve as a knowledge hub for educational and reference purposes for present and future generations of researchers around the globe.

This is why we propose a sustainable system where images, knowledge, trained recognition models and tools are exchanged between institutes, and where an international collaboration between museums from all sizes is crucial. The aim is to have a system that will benefit the entire community of natural history collections in providing further access to their invaluable collections. 

We propose four elements to this system: 

  1. A central library of already trained image recognition models (algorithms) needs to be created. It will be openly accessible, so any other institute can profit from models trained by others.
Mock-up of a Central Library of Algorithms.
  1. A central library of datasets accessing images of collection specimens that have recently been identified by experts. This will provide an indispensable source of images for training new algorithms.
Mock-up of a Central Library of Datasets.
  1. A digital workbench that provides an easy-to-use interface for inexperienced users to customise the algorithms and datasets to the particular needs in their own collections. 
  2. As the entire system depends on international collaboration as well as sharing of algorithms and datasets, a user forum is essential to discuss issues, coordinate, evaluate, test or implement novel technologies.

How would this work on a daily basis for curators? We provide two examples of use cases.

First, let’s zoom in to a case where a curator needs to identify a box of insects, for example bush crickets, to a lower taxonomic level. Here, he/she would take an image of the box and split it into segments of individual specimens. Then, image recognition will identify the bush crickets to a lower taxonomic level. The result, which we present in the table below – will be used to update object-level registration or to physically rearrange specimens into more accurate boxes. This entire step can also be done by non-specialist staff. 

Mock-up of box with grasshoppers mentioned in the above table

Results of automated image recognition identify specimens to a lower taxonomic level.

Another example is to incorporate image recognition tools into digitisation processes that include imaging specimens. In this case, image recognition tools can be used on the fly to check or confirm the identifications and thus improve data quality.

Mock-up of an interface for automated taxon identification. 

Using image recognition tools to identify specimens in museum collections is likely to become common practice in the future. It is a technical tool that will enable the community to share available taxonomic expertise. 

Using image recognition tools creates the possibility to identify species groups for which there is very limited to none in-house expertise. Such practises would substantially reduce costs and time spent per treated item. 

Image recognition applications carry metadata like version numbers and/or datasets used for training. Additionally, such an approach would make identification more transparent than the one carried out by humans whose expertise is, by design, in no way standardised or transparent.

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Research publication:

Greeff M, Caspers M, Kalkman V, Willemse L, Sunderland BD, Bánki O, Hogeweg L (2022) Sharing taxonomic expertise between natural history collections using image recognition. Research Ideas and Outcomes 8: e79187. https://doi.org/10.3897/rio.8.e79187

Endangered new orchid discovered in Ecuador

The plant – unique with its showy, intense yellow flowers – was described by Polish orchidologists in collaboration with an Ecuadorian company operating in orchid research, cultivation and supply.

An astounding new species of orchid has been discovered in the cloud rainforest of Northern Ecuador. Scientifically named Maxillaria anacatalina-portillae, the plant – unique with its showy, intense yellow flowers – was described by Polish orchidologists in collaboration with an Ecuadorian company operating in orchid research, cultivation and supply. 

A specimen of the newly described orchid species Maxillaria anacatalina-portillae in its natural habitat. Photо by Alex Portilla

Known from a restricted area in the province of Carchi, the orchid is presumed to be a critically endangered species, as its rare populations already experience the ill-effects of climate change and human activity. The discovery was aided by a local commercial nursery, which was already cultivating these orchids. The study is published in the open-access journal PhytoKeys.

During the past few years, scientists from the University of Gdańsk (Poland) have been working intensely on the classification and species delimitations within the Neotropical genus Maxillaria – one of the biggest in the orchid family. They have investigated materials deposited in most of the world’s herbarium collections across Europe and the Americas, and conducted several field trips in South America in the search of the astonishing plants.

The newly described orchid species Maxillaria anacatalina-portillae. Photо by Hugo Medina

The first specimens of what was to become known as the new to science Maxillaria anacatalina-portillae were collected by Alex Portilla, photographer and sales manager at Ecuagenera, an Ecuadorian company dedicated to orchid research, cultivation and supply, on 11th November 2003 in Maldonado, Carchi Province (northern Ecuador). There, he photographed the orchid in its natural habitat and then brought it to the greenhouses of his company for cultivation. Later, its offspring was offered at the commercial market under the name of a different species of the same genus: Maxillaria sanderiana ‘xanthina’ (‘xanthina’ in Latin means ‘yellow’ or ‘red-yellow’). 

In the meantime, Prof. Dariusz L. Szlachetko and Dr. Monika M. Lipińska would encounter the same intriguing plants with uniquely colored flowers on several different occasions. Suspecting that they may be facing an undescribed taxon, they joined efforts with Dr. Natalia Olędrzyńska and Aidar A. Sumbembayev, to conduct additional morphological and phylogenetic analyses, using samples from both commercial and hobby growers, as well as crucial plants purchased from Ecuagenera that were later cultivated in the greenhouses of the University of Gdańsk.

As their study confirmed that the orchid was indeed a previously unknown species, the scientists honored the original discoverer of the astonishing plant by naming it after his daughter: Ana Catalina Portilla Schröder.

Research paper:

Lipińska MM, Olędrzyńska N, Portilla A, Łuszczek D, Sumbembayev AA, Szlachetko DL (2022) Maxillaria anacatalinaportillae (Orchidaceae, Maxillariinae), a new remarkable species from Ecuador. PhytoKeys 190: 15-33. https://doi.org/10.3897/phytokeys.190.77918

Rare, protected orchid thrives in a military base in Corsica

Counting over 155,000 individuals, the population is a world precedent. Globally, this orchid can only be found in the south of France, Italy, and along the east coast of the Adriatic.

In Corsica, away from the eyes of locals and tourists, hides a population of unprecedented proportions of a rare and protected orchid: the neglected Serapias (Serapiasneglecta). In a closed military base in the east of the island, researchers discovered 155,000 individuals of the plant.

Globally, this orchid can only be found in the south of France (including Corsica), Italy, and along the east coast of the Adriatic, but none of its known populations has been as abundant as the one documented in Solenzara.

High density of Serapias neglecta on the air base. Photo by Margaux Julien (Ecotonia)

Margaux Julien, Dr Bertrand Schatz, Simon Contant, and Gérard Filippi, researchers from the Center of Functional Ecology and Evolution (CEFE) and Ecotonia consultancy,came across this population while studying plant diversity in the Solenzara air base. Their research, published in Biodiversity Data Journal, documented impressive plant richness, including 12 other orchid species.

The maintenance of the closed military area turned out to be really favourable to the development of orchids. The flower was abundant around the edges of runways and on lawns near military buildings.

Serapias neglecta. Photo by Margaux Julien (Ecotonia)

“Мilitary bases are important areas for biodiversity because they are closed to the public, are not heavily impacted and these areas have soils that are often poorly fertilised and untreated due to old installations, so they often have high biodiversity,” the researchers say in their study.

The meadows around the airport are regularly mowed for security reasons, which allows orchids to thrive in a low vegetation environment with little competition. In addition, the history of the land with its position on the old Travo river bed favours low vegetation, providing rocky ground just a few centimetres beneath the soil.

“The case of S. neglecta is particularly remarkable, because this species benefits from a national protection status and it is a sub-endemic species with a very localised distribution worldwide,” the research team writes. Moreover, the species is classified as near threatened in the World and European Red Lists of the International Union for Conservation of Nature.

The Ecotonia consultancy also did several inventories on the air base, finding biodiversity of rare richness: 552 species of plants, including 19 with protected status in France. Within only 550 ha, they found 23% of the plant species distributed in Corsica. Among these are some very rare plants, as well as endangered species such as the gratiole (Gratiola officinalis) and Anthemis arvensis subsp. incrassate, a subspecies of the corn chamomile.

Serapias neglecta. Photo by Bertrand Schatz

The Solenzara military base hides rich floristic diversity thanks to its history, management, and the lack of public access. While the Corsican coastline is suffering from urbanisation, this sector is a testament to the local flora, featuring several species with conservation status.

The protection of this richness is crucial. “If logistical developments are carried out on this base, they will have to favour the conservation of this exceptional floristic biodiversity, and, in particular of this particularly abundant orchid. Military bases are a great opportunity for the conservation of species and would benefit from enhancing their natural heritage,” the researchers conclude.

Research article:

Julien M, Schatz B, Contant S, Filippi G (2022) Flora richness of a military area: discovery of a remarkable station of Serapias neglecta in Corsica. Biodiversity Data Journal 10: e76375. https://doi.org/10.3897/BDJ.10.e76375

Frog with tapir-like nose found in Amazon rainforest

The people of Peru’s Comunidad Nativa Tres Esquinas have long known about a tiny, burrowing frog with a characteristically long snout. Yet, until now, this species has remained elusive to biologists.

The people of Peru’s ​​Comunidad Nativa Tres Esquinas have long known about a tiny, burrowing frog with a long snout; one local name for it is rana danta, “tapir frog” for its resemblance to the large-nosed Amazonian mammal. But until now, this frog has remained elusive to biologists. Thanks to the help of local guides, an international team of researchers was able to find the frog and give it an official scientific name and description.

It’s an example of the Amazon’s hidden diversity, and it’s important to document it to understand how important the ecosystem functions.

Michelle Thompson, researcher in the Keller Science Action Center at Chicago’s Field Museum

“These frogs are really hard to find, and that leads to them being understudied,” says Michelle Thompson, a researcher in the Keller Science Action Center at Chicago’s Field Museum and one of the authors of a study describing the frog in Evolutionary Systematics. “It’s an example of the Amazon’s hidden diversity, and it’s important to document it to understand how important the ecosystem functions.”

“Frogs of this genus are spread throughout the Amazon, but since they live underground and can’t get very far by digging, the ranges each species is distributed in are fairly small. Since we found this new species in Amazon peatland, it wouldn’t be strange for it to be restricted to this environment. Its body shape and general look seems to be adapted to the soft soil of the peatland, rather than the robust and wider shape of species in other environments,”says Germán Chávez, a researcher at Peru’s Instituto Peruano de Herpetología and the study’s first author.

Synapturanus danta. Photo provided by Field Museum

The tapir frog’s appearance is striking. “It looks like a caricature of a tapir, because it has a big blobby body with this tiny little pointy head,” says Thompson. But despite its goofy appearance, it was very difficult to find. “The frogs are tiny, about the size of a quarter, they’re like brown, they’re underground, and they’re quick,” she says. “You know these little frogs are somewhere underground, but you just don’t see them hopping around.”

But while the frogs are hard to see, they’re not hard to hear. “We just kept hearing this beep-beep-beep coming from underground, and we suspected it could be a new species of burrowing frog because there had recently been other species in its genus described,” says Thompson. “But how do we get to it?”

Local guides who were familiar with the frogs led the researchers to peatland areas– wetlands carpeted with nutrient-rich turf made of decaying plant matter. The team searched by night, when the frogs were most active. 

“After 15 to 20 minutes of digging and looking for them, I heard Michelle screaming, and to me that could only mean that she and David had found the first adult,” says Chavez.

“We could hear them underground, going beep-beep-beep, and we’d stop, turn off our lights, and dig around, and then listen for it again,” says Thompson. “After a few hours, one hopped out of his little burrow, and we were screaming, ‘Somebody grab it!’”

Synapturanus danta. Photo by Germán Chávez

In addition to finally finding adult specimens of the frogs, the team recorded their calls. “I am obsessed with recording frog calls, so I decided to record the call first and then continue digging,” says Chávez.

The researchers used the physical specimens of the frogs, along with the recordings of their calls and an analysis of the frogs’ DNA, to confirm that they were a new species. They named them Synapturanus danta– Synapturanus is the name of the genus they belong to, and danta is the local word for “tapir.”

The frogs’ burrowing behavior that made them hard to find likely makes them an important part of their peatland home. “They’re part of the underground ecosystem,” says Thompson. “They’re moving down there, they’re eating down there, they’re laying their eggs down there. They contribute to nutrient cycling and changing the soil structure.”

“Beside the important role of this new species in the food chain of its habitat, we believe that it could be an indicator of healthy peatlands,” says Chávez. “First, we have to confirm whether it’s restricted to this habitat, but its body adaptations seem to point in that direction. For instance, if the habitat is too dry, the soil would become too hard for a non-robust frog like this one to dig. This would leave our frog with far fewer chances to find a shelter and eventually, it would be hunted by a bigger predator. So I think possibilities that this frog would be a wetlands specialist are high, but still need to go further in this research to confirm it.”

Panoramic view of the type locality. Photo by Alvaro del Campo

And the study’s implications go beyond the description of one little frog. S. danta was found during a rapid inventory led by Field Museum scientists, a program in which biologists and social scientists spend a few weeks in a patch of the Amazon to learn what species live there, how the people in the area manage the land, and how they can help make a case for the area to be protected. “Even though it’s called a rapid inventory, it could take a year or more to plan these things, and then it could take a year or a decade to do the conservation follow-up,” says Thompson. “The rapid part is where you spend a month in the field. And it’s a total whirlwind.”

A view of the landscape in the Amazonian Peatlands inhabited by Synapturanus danta. Photo by Luis Montenegro

Peru’s Putumayo Basin, where this rapid inventory took place, is part of a larger conservation scheme by the Keller Science Action Center and its partners. “The Putumayo Corridor spans from Ecuador, Colombia, Peru, and down to Brazil, following the Putumayo River,” says Thompson. “There’s very little deforestation, and it’s also one of the last free flowing rivers that has no current dams. There’s like a huge conservation opportunity to conserve the whole corridor, watershed and surrounding areas. This tapir frog is another piece of evidence of why scientists and local people need to work together to protect this region.”

Research article:

Chávez G, Thompson ME, Sánchez DA, Chávez-Arribasplata JC, Catenazzi A (2022) A needle in a haystack: Integrative taxonomy reveals the existence of a new small species of fossorial frog (Anura, Microhylidae, Synapturanus) from the vast lower Putumayo basin, Peru. Evolutionary Systematics 6(1): 9-20. https://doi.org/10.3897/evolsyst.6.80281

Simplified method to survey amphibians will aid conservation

Researchers developed a method to determine which amphibians inhabit a specific area. The new technique will resolve some of the issues with conventional methods, such as capture and observational surveys.

Ryukyu Sword Tailed Newt, or Firebellied Newt. Photo by Neil Dalphin via Creative Commons CC0.

An international collaborative research group of members from seven institutions has developed a method to determine which amphibians (frogs, newts and salamanders) inhabit a specific area. Their work was published in the open-access, peer-reviewed journal Metabarcoding and Metagenomics (MBMG).

To do so, the scientists amplified and analysed extra-organismal DNA (also known as environmental DNA or eDNA) found in the water. This DNA ends up in the water after being expelled from the amphibian’s body along with mucus and excrement. 

The research group included Postdoctoral Researcher Sakata K. Masayuki and Professor Minamoto Toshifumi (Kobe University), Associate Professor Kurabayashi Atsushi (Nagahama Institute of Bio-Science and Technology), Nakamura Masatoshi (IDEA Consultants, Inc.) and Associate Professor Nishikawa Kanto (Kyoto University). 

The newly developed technique will resolve some of the issues with conventional methods, such as capture and observational surveys, which require a specialist surveyor who can visually identify species. Conventional surveys are also prone to discrepancies due to environmental factors, such as climate and season.

The researchers hope that the new method will revolutionise species monitoring, as it will enable anyone to easily monitor the amphibians that inhabit an area by collecting water samples.  

While monitoring in general is crucial to conserve the natural ecosystems, the importance of surveying amphibians is even more pressing, given the pace of their populations’ decline.

Amongst major obstacles to amphibian monitoring, however, are the facts that they are nocturnal; their young (e.g. tadpoles) and adults live in different habitats; and that specialist knowledge is required to capture individuals and identify their species. These issues make it particularly difficult to accurately survey amphibians in a standardised way, and results of individual efforts often contradict each other.

On the other hand, eDNA analysis techniques have already been established in programmes targeted at monitoring fish species, where they are already commonplace. So, the researchers behind the present study joined forces to contribute towards the development of a similar standardised analysis method for amphibians.

First of all, the researchers designed multiple methods for analysing the eDNA of amphibians and evaluated their performance to identify the most effective method. Next, they conducted parallel monitoring of 122 sites in 10 farmlands across Japan using the developed eDNA analysis along with the conventional methods (i.e. capture surveys using a net and observation surveys). 

As a result, the newly developed method was able to detect all three orders of amphibians: Caudata (the newts and salamanders), Anura (the frogs), and Gymnophiona (the caecilians). 

Furthermore, this novel eDNA analysis method was able to detect more species across all field study sites than the conventional method-based surveys, indicating its effectiveness.

Research Background

Amphibian biodiversity is continuing to decline worldwide and collecting basic information about their habitats and other aspects via monitoring is vital for conservation efforts. Traditional methods of monitoring amphibians include visual and auditory observations, and capture surveys.

However, amphibians tend to be small in size and many are nocturnal. The success of surveys varies greatly depending on the climate and season, and specialist knowledge is required to identify species. Consequently, it is difficult to monitor a wide area and assess habitats. The last decade has seen the significant development of environmental DNA analysis techniques, which can be used to investigate the distribution of a species by analysing external DNA (environmental DNA) that is released into the environment along with an organism’s excrement, mucus and other bodily fluids. 

The fundamentals of this technique involve collecting water from the survey site and analysing the eDNA contained in it to find out which species inhabit the area. In recent years, the technique has gained attention as a supplement for conventional monitoring methods. Standardised methods of analysis have already been established for other species, especially fishes, and diversity monitoring using eDNA is becoming commonplace. 

However, eDNA monitoring of amphibians is still at the development stage. One reason for this is that the proposed eDNA analysis method must be suitable for the target species or taxonomic group, and there are still issues with developing and implementing a comprehensive method for detecting amphibians. If such a method could be developed, this would make it possible for monitoring to be conducted even by people who do not have the specialised knowledge to identify species nor surveying experience.

Hopefully, this would be established as a unified standard for large-scale monitoring surveys, such as those on a national scale. This research group’s efforts to develop and evaluate analysis methods will hopefully lay the foundations for eDNA analysis to become a common tool for monitoring amphibians, as well as fish. 

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Follow Metabarcoding and Metagenomics (MBMG) journal on Twitter and Facebook.

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Research article: 

Sakata MK, Kawata MU, Kurabayashi A, Kurita T, Nakamura M, Shirako T, Kakehashi R, Nishikawa K, Hossman MY, Nishijima T, Kabamoto J, Miya M, Minamoto T (2022) Development and evaluation of PCR primers for environmental DNA (eDNA) metabarcoding of Amphibia. Metabarcoding and Metagenomics 6: e76534. https://doi.org/10.3897/mbmg.6.76534

Natural History Museum of Berlin’s journal Fossil Record started publishing on ARPHA Platform

Fossil Record – the paleontological scholarly journal of the Natural History Museum of Berlin (Museum für Naturkunde Berlin) published its first articles after moving to the academic publisher Pensoft and its publishing platform ARPHA Platform in late 2021. The renowned scientific outlet – launched in 1998 – joined two other historical journals owned by the Museum: Deutsche Entomologische Zeitschrift and Zoosystematics and Evolution, which moved to Pensoft back in 2014.

Fossil Record – the paleontological scholarly journal of the Natural History Museum of Berlin (Museum für Naturkunde Berlin) published its first articles after moving to the academic publisher Pensoft and its publishing platform ARPHA in late 2021. The renowned scientific outlet – launched in 1998 – joined two other historical journals owned by the Museum: Deutsche Entomologische Zeitschrift and Zoosystematics and Evolution, which moved to Pensoft back in 2014.

Published in two issues a year, the open-access scientific outlet covers research from all areas of palaeontology, including the taxonomy and systematics of fossil organisms, biostratigraphy, palaeoecology, and evolution. It deals with all taxonomic groups, including invertebrates, microfossils, plants, and vertebrates.

As a result of the move to ARPHA, Fossil Record utilises the whole package of ARPHA Platform’s services, including its fast-track, end-to-end publishing module, designed to appeal to readers, authors, reviewers and editors alike. A major advantage is that the whole editorial process, starting from the submission of a manuscript and continuing into peer review, editing, publication, dissemination, archiving and hosting, happens within the online ecosystem of ARPHA. 

As soon as they are published, the articles in Fossil Record are available in three formats: PDF, machine-readable JATS XML and semantically enriched HTML for better and mobile-friendly reader experience. 

The publications are equipped with real-time metrics on both article and sub-article level that allow easy access to the number of visitors, views and downloads for every article and each of it’s figures, tables or supplementary materials. In their turn, the semantic enhancements do not only allow for easy navigation throughout the text and quick access to cited literature and the article’s own citations, but also tag each taxon that appears in the paper to provide links to further information concerning its occurrences, genomics, nomenclature, treatments and more as available from various databases.      

The first five papers – now available on the brand new journal website powered by ARPHA – already demonstrate the breadth of topics covered by Fossil Record, including systematics, paleobiogeography, palaeodiversity and morphology, as well as the international appeal of the scholarly outlet. The articles are co-authored by collaborative research teams representing ten countries and spanning three continents: Europe, Asia and Africa.

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About the Natural History Museum of Berlin:

The “Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science” is an integrated research museum within the Leibniz Association. It is one of the most important research institutions worldwide in the areas of biological and geological evolution and biodiversity.

The Museum’s mission is to discover and describe life and earth – with people, through dialogue. As an excellent research museum and innovative communication platform, it wants to engage with and influence the scientific and societal discourse about the future of our planet, worldwide. Its vision, strategy and structure make the museum an excellent research museum. The Natural History Museum of Berlin has research partners in Berlin, Germany and approximately 60 other countries. Over 700,000 visitors per year as well as steadily increasing participation in educational and other events show that the Museum has become an innovative communication centre that helps shape the scientific and social dialogue about the future of our earth. 

Cultivated and wild bananas in northern Viet Nam threatened by а devastating fungal disease

For over 100 years, Fusarium, one of the most important fungal plant pathogens, has affected banana production worldwide.

Fusarium is one of the most important fungal plant pathogens, affecting the cultivation of a wide range of crops. All over the world, thousands of farmers suffer agricultural losses caused by Fusarium oxysporum f. sp. cubense (referred to as Foc for short), which directly affects their income, subsistence, and nourishment.

As a soil-borne fungus, Foc invades the root system, from where it moves into the vascular tissue that gradually deteriorates, until eventually the plant dies. What makes it particularly hard to deal with is that, even 20 years after all infected plants and tissue are removed, spores of it still remain in the soil.

One industry significantly affected by Foc is global banana export, largely dependent on the cultivation of members of the Cavendish subgroup, which are highly susceptible to some of the Foc strains.

For over 100 years, the fungus has affected banana production worldwide. Researchers predict it will continue spreading intensively in Asia, affecting important banana-producing countries such as China, the Philippines, Pakistan, and Viet Nam.

For Viet Nam, predictions on the impact of Foc for the future are dramatic: an estimated loss in the banana production area of 8% within the next five years, and up to 71% within the next 25 years. In particular, the recent rise of the novel TR4 strain has resulted in worldwide anxiety about the future of the well-known Cavendish banana and many other cultivars. Fusarium oxysporum f. sp. cubense is, however, not limited to TR4 or other well-known strains, like Race 1 or Race 2; it is a species complex that plant pathologists are yet to fully disentangle. 

In Viet Nam, like in the rest of Asia, Africa, Latin America, and the Caribbean, most bananas are consumed and traded locally, supporting rural livelihood. This means that any reduction in crop harvest directly affects local people’s income and nourishment. 

It has thus become necessary to find out what are the individual species causing the Fusarium wilt among Vietnamese bananas. Only by understanding which species are infecting the cultivated bananas can concrete measures be taken to control the future spreading of the disease to other regions.

Using DNA analyses and morphological characterization, an international team of researchers from Viet Nam (Plant Resources Center, Vietnam National University of Agriculture), Belgium (Meise Botanic Garden, KU Leuven, Bioversity Leuven, MUCL) and the Netherlands (Naturalis Biodiversity Center) investigated the identity of the Fusarium wilt infections. They recently published their joint research in the open-access, peer-reviewed journal MycoKeys.

The study shows that approximately 3 out of 4 Fusarium infections of the northern Vietnamese bananas are caused by the species F. tardichlamydosporum, which can be regarded as the typical Race 1 infections. Interestingly, Foc TR4 is not yet a dominant strain in northern Viet Nam, as the species causing the disease – F. odoratissimum – only accounts for 10% of the Fusarium infections. A similar proportion of Fusarium infections is caused by the species Fusarium cugenangense – considered to cause Race 2 infections among bananas.More importantly, Fusarium wilt was not only found in cultivated bananas: the disease seemed to also affect wild bananas. This finding indicates that wild bananas might function as a sink for Fusarium wilt from where reinfections towards cultivars could take place.

Research article:

Le Thi L, Mertens A, Vu DT, Vu TD, Anh Minh PL, Duc HN, de Backer S, Swennen R, Vandelook F, Panis B, Amalfi M, Decock C, Gomes SIF, Merckx VSFT, Janssens SB (2022) Diversity of Fusarium associated banana wilt in northern Viet Nam. MycoKeys 87: 53-76. https://doi.org/10.3897/mycokeys.87.72941