Non-native forest tree species can reduce native species diversity if they are planted in uniform stands. In contrast, the effects of introduced species on soil properties are small. This was found by an international review study with the participation of the Swiss Federal Institute for Forest, Snow and Landscape Research WSL.
Curse or blessing? Opinions are divided on non-native tree species. In addition to native species, many foresters also plant non-native species that can withstand the increasing summer drought. In various parts of Europe, the latter are already important suppliers of timber. However, conservationists fear ecological damage, for example if native species are displaced or tree pathogens and insect pests are introduced.
In Switzerland, Douglas fir is partly used for afforestation. However, large pure stands, such as those found in Germany, are prohibited there. Photo by Thomas Reich
Now a team of European researchers, led by Thomas Wohlgemuth of WSL, has looked at the state of knowledge on the ecological consequences of alien tree species in Europe. They analysed the results of 103 studies on seven such species. All of these studies had investigated how stands dominated by non-native tree species affected biodiversity or soil condition under the trees compared to stands of native tree species. The organisms studied included plants, mosses, microorganisms and insects from the forest floor to the treetops.
Of the seven alien species studied, only the Douglas fir is currently planted in larger numbers in the Swiss forests. While foresters used to value its fast, straight growth and its versatile wood, today they appreciate its higher drought tolerance compared to spruce. Other species are problematic because they can spread uncontrollably. The North American Robinia, for example, is invasive and can displace native species. It was already introduced in Europe 400 years ago and used in Switzerland, among other things, to stabilise soils.
Robinia can spread rapidly and form stands as here in Valais. Photo by Thomas Reich
Negative effects on biodiversity predominate
Across the 103 studies, the consequences of non-native species for biodiversity were negative. Comparisons from 20 studies show, for example, that on average fewer insect species live on and in Douglas fir than in spruce or beech stands. Robinia also reduces the diversity of insects, eucalyptus that of birds. This is hardly surprising, says Wohlgemuth, head of the WSL Forest Dynamics Research Unit. Because: “These results apply to comparisons between pure stands.” In continuous, uniform plantations, many alien species clearly have worse impacts than native species.
Proportion of cases with increasing (green), decreasing (red) or non-significant (grey) effects of tree species non-native to Europe on diversity attributes (abundance, species richness or diversity) of different taxonomic groups in comparison to native vegetation. Numbers of cases are shown next to the NNTs names, below the diversity attributes and above the bars.
But alien species do not only have negative impacts. Most of them do not affect soil properties. The easily degradable needles of Douglas firs can even make more nutrients available than the poorly degradable spruce needles. “When it comes only to soil properties, the Douglas fir has no negative impact,” Wohlgemuth says. In general, an equal number of studies found positive and negative effects of the seven non-native species on the soil.
Douglas firs are attractive for forestry because of their fast growth, good wood properties and – in regard to climate change – their drought resistance. Photo by Thomas Reich
Furthermore, it makes a difference whether the alien species are more closely or more distantly related to European tree species. “Tree species without closer relatives, such as eucalyptus and acacia from Australia, reduce species diversity more strongly across all studies than closely related species, such as Douglas fir and wild black cherry from North America,” adds Martin Gossner, head of the WSL Forest Entomology Group and second author of the study.
Management has a significant influence on whether Douglas fir or other tree species are good or bad for a forest overall. Uniform and dense Douglas fir stands are unsuitable habitats for many organisms. However, the same is true for spruces, which have been planted extensively for timber production in lowland areas of Central Europe over the last 100 years. On the other hand, Douglas firs in stands of native forest trees, individually or in small groups, would hardly disturb the ecosystem, Wohlgemuth says: “We conclude that the impact on native biodiversity is low with mixed-in Douglas firs.”
Should foresters plant non-native tree species or not? Despite certain negative aspects, Wohlgemuth does not recommend total renunciation. “Particularly in the case of Douglas fir, the facts show that moderate admixture in stands has little impact on native biodiversity, while at the same time preserving ecosystem services such as the production of construction timber. This is especially true when other, less drought-resistant conifers are increasingly lacking with regard to unchecked climate change.”
Research article:
Wohlgemuth T, Gossner MM, Campagnaro T, Marchante H, van Loo M, Vacchiano G, Castro-Díez P, Dobrowolska D, Gazda A, Keren S, Keserű Z, Koprowski M, La Porta N, Marozas V, Nygaard PH, Podrázský V, Puchałka R, Reisman-Berman O, Straigytė L, Ylioja T, Pötzelsberger E, Silva JS (2022) Impact of non-native tree species in Europe on soil properties and biodiversity: a review. NeoBiota 78: 45-69. https://doi.org/10.3897/neobiota.78.87022
The enigmatic animals with beautiful shells are facing population declines and, possibly, even extinctions due to the activity of unregulated fisheries.
Guest blog post by Dr Gregory Barord, marine biology instructor at Central Campus and conservation biologist at the conservation organization Save the Nautilus
Nautiloids were once quite plentiful throughout the oceans, based upon the fossil record. Today, they are represented by just a handful of species, including the newly described Nautilus vitiensis of Fiji, Nautilus samoaensis of American Samoa, and Nautilus vanuatuensis of Vanuatu. These descriptions highlight the concept of allopatric speciation, or biogeographic isolation, where populations are geographically separated from other populations, resulting in a barrier to gene flow. Over time, these populations may eventually evolve into distinct species.
Nautilus samoaensis.
Nautilus trap construction. Photo by Gregory Barord
But what does it take to be able to collect the evidence needed to determine if three different populations of nautiluses are in fact three different species? For me, this is the best/worst part of the overall process, because nautilus fishing is not easy. For our team, it starts with building large, steel traps that are about a meter cubed. Then, we wrap the steel frame (ouch), with chicken wire (ouch) mesh (ouch), create an entry hole (ouch), attach it to a surface buoy with about 300 meters of fishing line, and bait it with (ouch) raw meat, usually chicken! Trap construction may take place on a nice beach or a bit inland in the rain or in a warm warehouse. Wherever it takes place, you will have some memories, I mean little scars, on your hands from working with the chicken wire. Looking down at my hands right now, I can remember where I was by looking at each of those scars… worth it!
Tossing the traps into the sea at dusk is the easy part. Load them on the boat, find the right depth, and tip them over the side of the boat. The hard part is retrieving the traps the next day, after about 12 hours of the raw chicken scent moving through the currents. There are a number of methods we’ve used to pull the traps up, from mechanical winches, hand-powered winches, float systems, boat pulls, and of course, just pulling with one hand at a time. Invariably, something happens in each location where we are just pulling the trap up from 300 meters one meter at a time, which takes a good half hour at least. But, at least you are getting a VERY good work-out. Eventually, you see the trap and these white little orbs in it and you know you’ve caught some nautiluses and the pulling is almost done, for now.
Nautilus trap in water with nautiluses in it. Photo by Gregory Barord
The next step might be my favorite. One of us jumps in the water and free dives about 5 meters to carefully (ouch, that chicken wire) reach for the nautiluses in the trap and bring them to the surface. You are face to face with these uniquely, misunderstood organisms who seem like this is just another day for them. For me, this is exhilarating! Once on the boat, they are placed in chilled seawater and from then on, the data collection happens fast. With the living organism in hand, you can start to glean even more of the differences between the species, examining the hood ornaments, or lack thereof. After some photos, measurements, and non-lethal tissue samples, the nautiluses are released and burped.
Nautilus vanuatuensis.
Maybe nautilus burping is my favorite part. To do this, we either dive with SCUBA or free dive with the nautiluses, and ensure there are no air bubbles trapped in the shell that may cause them to be positively buoyant. Imagine, you have one nautilus in each hand and you start swimming down, your feet and the nautilus tentacles pointed toward the surface. At a sufficient depth, you release them and observe their buoyancy. As the nautiluses compose themselves and jet back down to their nektobenthic habitat 300 meters below, you realize you may never see that individual nautilus again, and that nautilus may never see another human, well, maybe they will…
For me, the impetus for this publication in ZooKeysis rooted in nautilus conservation efforts. Over the last 20 years, I have studied nautiluses from many angles and for over 10 years now, have worked with an international team of folks to address nautilus conservation issues. For many nautiluses, probably millions, they were caught in much the same way that our team collected nautiluses. However, their first meeting with humans was their last as they were pulled from the trap, ripped from their protective shell, and tossed back in the ocean, used as bait, or, rarely, consumed. The shell is the attractive piece for shell traders and the living body has no value. It is like shark finning in that sense. As a direct result of these unregulated fisheries, populations of nautiluses have crashed, some have reportedly gone extinct, and international and country level legislation and regulations has been enacted.
A nautilus shell shop. Photo by Gregory Barord
Nautilus vitiensis.
Currently, there are no known fisheries in Fiji, American Samoa, or Vanuatu so the risk of these populations decreasing from fisheries is low, at the moment. Now, what is the risk to these same populations from ocean acidification, increased sedimentation, eutrophication, warming seas, and over-fishing of other species connected to the ecosystem nautiluses reside in? Right now, we simply do not know. Our conservation efforts started with simply counting how many nautiluses were left in different areas across the Indo-Pacific, then recording them in their natural habitat, then tracking their migrations, and now describing new species. There are still many questions to address regarding where they lay eggs, what they eat, and how they behave.
All nautiluses have long been grouped together when describing their natural history, but as we continue to uncover the nautilus story, it is increasingly obvious that each population of nautiluses is different, as exemplified by these three new species descriptions. This is certainly an exciting time for nautilus research, as we uncover more and more information about the secret life of nautiluses. I just hope that this is also an exciting time for nautiluses as well, and they continue doing their nautilus thing as they have done for millions of years.
A number of serious management and compliance issues were revealed on lion farms in the Free State province, South Africa, by a joint team of researchers from MONITOR, Blood Lions, and World Animal Protection. Potentially fraudulent activities relating to the use of microchips, operating without valid permits, and incomplete, inconsistent, and unclear record keeping were some of the irregularities found on commercial facilities that keep and trade captive lions and other predators.
Lions on a commercial lion farm in South Africa. Photo by Blood Lions
African lions are legally farmed in South Africa for commercial uses in interactive tourism activities, such as cub petting, voluntourism, or the “canned” hunting industry (where captive-bred lions are released into a confined space to be killed for sport). Other reasons include trade in live animals, or selling their body parts for the needs of traditional Asian Medicine.
All lions born and kept on commercial farms in South Africa should be registered with the provincial authority and fitted with a unique identification microchip, in order for each animal to be followed from birth to death through the system and to avoid the laundering of wild-caught and/or non-registered captive-bred lions.
Lions on a commercial lion farm in South Africa. Photo by Blood Lions
A multinational team of researchers used permit data legally obtained from provincial authorities to summarise such uses of lions on farms in the Free State and found multiple instances of violation of national and provincial regulations.
It is known that the Free State province is at the heart of the commercial lion industry, with about a third of all lion facilities across the country located on its territory. These farms in the Free State predominantly breed, keep and euthanise lions, as well as trade with other provinces to supply “canned” hunting farms and tourism facilities. They also prepare lion body parts for export, such as taxidermy for trophies, and skeletons for the bone trade with Southeast Asia.
Lion cubs on a commercial lion farm in South Africa. Photo by Blood Lions
Data legally obtained from the Free State Department of Small Business Development, Tourism and Environmental Affairs show hundreds of reused microchip numbers across permits for keeping, euthanising and transporting captive lions, indicating potential non-compliance with national and provincial regulations.
During a four-year period (2017-2020), more than 500 unique microchips (11% of the total microchip numbers) could not be followed through the system. For euthanasia permits, the number of potentially fraudulently used microchip numbers of lions was as many as 15%, and in some cases a microchip number had been reused up to four times.
This raises serious concerns that lion farm owners may deliberately be reusing microchip numbers to launder wild-caught and/or unregistered captive-bred lions.
A lion. Photo by Matthias Appel under a CC0 1.0 license
“Although some of these inconsistencies may have legitimate explanations, the number of times microchip numbers were reused is worrisome and requires further investigation by the authorities”, states Dr Sarah Heinrich of MONITOR, one of the researchers behind the study, which was published in the journal Nature Conservation.
The laundering of lions and/or other predators through the fraudulent use of microchips has implications beyond South Africa’s borders, in particular, in the trade in lion bones for traditional medicine, where bones, claws, skeletons, and skulls are exported to Southeast Asia. “Looking at live lion exports through the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), it is unclear what happens to these animals once they arrive at their international destinations. It is possible that some of these live exports circumvent the zero CITES lion bone export quota and are eventually euthanised at their import destinations to feed the persisting demand for lion bones”, said Dr Jennah Green of World Animal Protection.
CITES is the main regulatory mechanism governing the commercial international trade in certain wildlife species, including lions, their body parts, and derivatives. Under CITES, (African) lions are listed in Appendix II. A screenshot from Speciesplus.net, taken 31 January 2023.
Lions that were euthanised in the Free State in 2019 and 2020, during a CITES zero export quota for lion bones, most likely became part of a growing and largely unregulated stockpile of lion bones that exists in South Africa, which warrants further investigation.
Ensuring regulatory compliance in all areas of the commercial captive lion industry is more important now than ever. In 2021, Minister Barbara Creecy of the Department of Forestry, Fisheries and the Environment (DEFE), stated that the South African government intends to effectively end the commercial captive lion industry through a mandatory phase-out, which eventually was changed to a voluntary scheme.
In its current state, the lion farming industry is governed by a patchwork of contrasting legislation across multiple provincial and national authorities, with disparities and legal loopholes, which create opportunity for harmful and fraudulent activity.
“Our research highlights many areas of grave concern and these issues need the urgent attention of the Minister and the DFFE, as well as the nine provincial nature conservation authorities, to put stricter enforcement of the TOPS Regulations in place”, concludes Dr Louise de Waal, Director of Blood Lions.
Original source:
Heinrich S, Gomez L, Green J, de Waal L, Jakins C, D’Cruze N (2022) The extent and nature of the commercial captive lion industry in the Free State province, South Africa. Nature Conservation 50: 203-225. https://doi.org/10.3897/natureconservation.50.85292
In Thailand, more than 1,000 caddisfly species occur, and a recent study shows that their diversity in the country is even greater than previously suggested.
Caddisflies are an order of aquatic insects with high diversity. In Thailand, more than 1,000 caddisfly species are known to occur, and a recent study in the journal Check Listshows that their diversity in the country is even greater than previously suggested.
Scientists Rungnapa Somnark from Khon Kaen University and Narumon Sangpradub from the Center of Biodiversity Excellence, Chulalongkorn University recorded, for the first time, two caddisfly species that were previously not documented as part of Thailand’s fauna. They were able to catch the insects using black-light traps set up along water streams. The field study took place in the summer of 2017 at Thap Lan National Park, which is a part of Dong Phayayen–Khao Yai Forest Complex, a Natural World Heritage site in the north-eastern Thailand.
The two newly-recorded caddisfly species are Diplectrona erinya, a brown insect previously only known from Tam Dao in Vietnam, and Diplectrona extrema, yellowish-brown in colour and distributed in Borneo, Sumatra, and Java.
They both belong to the genus Diplectrona, which now has 10 documented representatives in Thailand.
The researchers suggest they are probably rare in the country.
“Our study suggests that two newly reported species occur at low densities, which highlights the continuing need for efforts to conserve the [Thap Lan National] park and to conduct more studies on the caddisfly fauna,” they say in conclusion.
Research article:
Somnark R, Sangpradub N (2023) New records of the caddisflies Diplectrona erinya Malicky, 2002 and Diplectrona extrema Banks, 1920 (Trichoptera, Hydropsychidae) from Thailand. Check List 19(1): 13-20. https://doi.org/10.15560/19.1.13
Five new drop-dead-gorgeous tree-dwelling snake species were discovered in the jungles of Ecuador, Colombia, and Panama. Conservationists Leonardo DiCaprio, Brian Sheth, Re:wild, and Nature and Culture International chose the names for three of them in honor of loved ones while raising awareness about the issue of rainforest destruction at the hands of open-pit mining operations. The research was conducted by Ecuadorian biologist Alejandro Arteaga, an Explorers Club Discovery Expedition Grantee, and Panamanian biologist Abel Batista.
The mountainous areas of the upper-Amazon rainforest and the Chocó-Darién jungles are world-renowned for the wealth of new species continually discovered in this region. However, it is becoming increasingly clear that they also house some of the largest gold and copper deposits in the world. During the COVID-19 pandemic, the proliferation of illegal open-pit gold and copper mining operations in the jungles of Ecuador, Colombia, and Panama reached a critical level and is decimating tree-dwelling snake populations.
Illegal mining activity in the upper Ecuadorian Amazon doubled between 2021 and 2022. Photo by Jorge Anhalzer
Neotropical snail-eating snakes (genera Sibon and Dipsas) have a unique lifestyle that makes them particularly prone to the effects of gold and copper mining. First, they are arboreal, so they cannot survive in areas devoid of vegetation, such as in open-pit mines. Second, they feed exclusively on slugs and snails, a soft-bodied type of prey that occurs mostly along streams and rivers and is presumably declining because of the pollution of water bodies.
“When I first explored the rainforests of Nangaritza River in 2014, I remember thinking the place was an undiscovered and unspoiled paradise,” says Alejandro Arteaga, author of the research study on these snakes, which was published in the journal ZooKeys. “In fact, the place is called Nuevo Paraíso in Spanish, but it is a paradise no more. Hundreds of illegal gold miners using backhoe loaders have now taken possession of the river margins, which are now destroyed and turned into rubble.”
Biologist Alejandro Arteaga examines a snail-eating snake in the museum. Photo by Jorge Castillo
The presence of a conservation area may not be enough to keep the snail-eating snakes safe. In southeastern Ecuador, illegal miners are closing in on Maycu Reserve, ignoring landowner rights and even making violent threats to anyone opposed to the extraction of gold. Even rangers and their families are tempted to quit their jobs to work in illegal mining, as it is much more lucrative. A local park ranger reports that by extracting gold from the Nangaritza River, local people can earn what would otherwise be a year’s salary in just a few weeks. “Sure, it is illegal and out of control, but the authorities are too afraid to intervene,” says the park ranger. “Miners are just too violent and unpredictable.”
Gold mining activities in Napo, Ecuador. Photo by Ivan Castaneira
In Panama, large-scale copper mining is affecting the habitat of two of the new species: Sibon irmelindicaprioae and S. canopy. Unlike the illegal gold miners in Ecuador and Colombia, the extraction in this case is legal and at the hands of a single corporation: Minera Panamá S.A., a subsidiary of the Canadian-based mining and metals company First Quantum Minerals Ltd. Although the forest destruction at the Panamanian mines is larger in extent and can easily be seen from space, its borders are clearly defined and the company is under the purview of local environmental authorities.
Sibon irmelindicaprioae, named after Leonardo DiCaprio’s mother, is the rarest of the lot. It occurs in the Chocó-Darién jungles of eastern Panama and western Colombia. Photo by Alejandro Arteaga of Khamai Foundation.
“Both legal and illegal open-pit mines are uninhabitable for the snail-eating snakes,” says Arteaga, “but the legal mines may be the lesser of two evils. At the very least they respect the limit of nearby protected areas, answer to a higher authority, and are presumably unlikely to enact violence on park rangers, researchers, and conservationists.”
Gold mining activities in Napo province, Ecuador. Photo by Ivan Castaneira
Sibon canopy, one of the newly described species, appears to have fairly stable populations inside protected areas of Panama, although elsewhere nearly 40% of its habitat has been destroyed. At Parque Nacional Omar Torrijos, where it is found, there has been a reduction in the number of park rangers (already very few for such a large protected area). This makes it easier for loggers and poachers to reach previously unspoiled habitats that are essential for the survival of the snakes.
Sibon canopy is named in honor of the Canopy Family system of reserves, particularly its Canopy Lodge in Valle de Antón, Coclé province, Panama. Photo by Alejandro Arteaga
Lack of employment and the high price of gold aggravate the situation. No legal activity can compete against the “gold bonanza.” More and more often, farmers, park rangers, and indigenous people are turning to illegal activities to provide for their families, particularly during crisis situations like the COVID-19 pandemic, when NGO funding was at its lowest.
An Ecuadorian miner shows the gold she has collected and that she will use to pay for any family emergency. Photo by Ivan Castaneira
“These new species of snake are just the tip of the iceberg in terms of new species discoveries in this region, but if illegal mining continues at this rate, there may not be an opportunity to make any future discoveries,” concludes Alejandro Arteaga.
A gold mine in Nangaritza. Photo by Alejandro Arteaga
Fortunately, three NGOs in Ecuador and Panama (Khamai, Nature and Culture International, and Adopta Bosque) have already made it their mission to save the snake’s habitat from the emerging gold mining frenzy. Supporting these organizations is vital, because their quest for immediate land protection is the only way to save the snakes from extinction.
Research article:
Arteaga A, Batista A (2023) A consolidated phylogeny of snail-eating snakes (Serpentes, Dipsadini), with the description of five new species from Colombia, Ecuador, and Panama. ZooKeys 1143: 1-49. https://doi.org/10.3897/zookeys.1143.93601
Invasive land snail species can displace native species and harm human health. A recent study by the Leibniz Institute for Biodiversity Change Analysis (LIB) compiles an overview of the exponential increase and dynamic spread of land snail species introduced to Europe and the Mediterranean from other continents.
To date, there is a lack of information for the spread of alien species, especially invertebrates such as snails. “Despite efforts to compile lists of alien species, there is not even a well-documented inventory of alien invertebrate species for Europe,” emphasizes Prof. Dr. Bernhard Hausdorf, section leader Mollusca at LIB. His study, just published in the journal NeoBiota, provides a basis for decisions on further measures to control or eradicate introduced populations.
Alien land snail species in the Western Palaearctic Region: Zonitoides arboreus, Hawaiia minuscula, Guppya gundlachii, Polygyra cereolus
Land snails play a supporting role in ecosystems. They decompose decaying plants and thus play an important role in nutrient cycling and soil formation. However, more and more species are being spread beyond their native range, usually by humans, sometimes intentionally, but often unintentionally by goods or travellers.
The study examines 22 land snail species introduced to Europe and the Mediterranean from other continents. Most of them are small, live on decaying plant parts and apparently cause few problems. In contrast, carnivorous species can threaten native species; and species that feed on living plants can cause damage to agriculture. Some even serve as hosts and vectors of parasites that can cause brain encephalitis, for example, and thus can indirectly harm human health.
Alien land snail species in the Western Palaearctic Region: Paralaoma servilis and Helicodiscus parallelus.
Harmful species include the Laevicaulis species recently introduced to the Mediterranean from tropical Africa and the African giant snail Lissachatina fulica. They can cause economic damage on irrigated farmland or in greenhouses by destroying or contaminating crops, making them unsaleable.
Hausdorf’s study compiles records of land snail species introduced to the Western Palearctic region, Europe and the Mediterranean, from other regions after 1492 and established in the wild. In doing so, he observes that the number of alien species has increased steadily since the 19th century, even exponentially from the 1970s onward, and that the introduced species have become more widespread.
Within Europe, alien species generally spread from south to north and from west to east. Thirteen of the 22 species studied were from North America, three from sub-Saharan Africa, two from the Australian region, three probably from the Oriental region, and one from South America.
Alien land snail species in the Western Palaearctic Region: llopeas clavulinum, Allopeas gracile, Lissachatina fulica, Paropeas achatinaceum, and Discocharopa aperta.
Even if trade relations and the spread of species can be correlated, Hausdorf believes that the prevailing climate is primarily decisive: “The spread of many of the introduced species, especially the tropical species dispersing in Mediterranean, is probably favored by climate change.”
Bernhard Hausdorf, “Distribution patterns of established alien land snail species in the Western Palaearctic Region”, NeoBiota, Pensoft https://doi.org/10.3897/neobiota.81.96360
As an experienced science communicator and open-science publisher, Pensoft is joining this promising project on its mission within its acronym: Trust, Integrity, and Efficiency in Research, through next-level Reproducibility
Recent years have seen perceptions of a “reproducibility crisis” grow in various disciplines. Scientists see poor levels of reproducibility as a severe threat to scientific self-correction, the efficiency of research processes, and societal trust in research results.
Now, a newly launched Horizon Europe-funded project: TIER2 brings together 10 major European organisations and proponents of open science to dig deeper into the issues surrounding reproducibility in research work with the aim to improve practices and policies across diverse scientific fields.
In its capacity as an experienced science communicator and open-science publisher, Pensoft is joining this promising project on its mission within its acronym: Trust, Integrity, and Efficiency in Research, through next-level Reproducibility (TIER2).
TIER2’s interdisciplinary, expert project team will use co-creative methods to work with researchers in social, life and computer sciences, research funders, and publishers to further understand and address the causes of poor reproducibility.
The project will produce and test new tools, connect initiatives, engage communities, and test novel interventions to increase reuse and overall quality of research results.
“It is very exciting to take part in such significant work for the benefit of scientific rigor and integrity. As an open-access publisher, the goals of Pensoft and TIER2 are very much aligned – increasing the trust and efficiency of the research apparatus on a large scale. We are looking forward to collaborating on this mutual goal.”
said Teodor Metodiev, TIER2 Principal Investigator for Pensoft.
The project
TIER2 launched in early January 2023 and will be running until December 2025 with the support of EUR 2 millions in funding, provided by the European Union’s Horizon Europe program and the United Kingdom’s Research & Innovation.
TIER2 will study reproducibility in diverse contexts by selecting three broad research areas (i.e. social, life and computer sciences) and two cross-disciplinary stakeholder groups (i.e. research publishers and funders). Reaching different contexts will allow the project team to systematically investigate the causes and implications of the lack of reproducibility across the research spectrum. Together with curated co-creation communities of these groups, the project will design, implement, and assess systematic interventions – addressing critical levers of change (tools, skills, communities, incentives, and policies) in the process.
In 3 years’ time, TIER2-led activities will have significantly boosted knowledge on reproducibility, created valuable tools, engaged communities, and implemented interventions and policies across science. As a result, the reuse of resources and the quality of research results in the European research landscape and beyond will be improved and increased, and so will trust, integrity, and efficiency in research overall.
The website – including its design and software development – is itself one of Pensoft’s communication contributions to TIER2.
Stay up to date with the project’s activities and progress on Twitter: @TIER2Project.
International consortium
The interdisciplinary TIER2 consortium comprises ten members from universities and research centers across Europe to bring together a range of expertise spanning open science, research integrity, AI, data analytics, policy research, science infrastructures, stakeholder engagement, and core knowledge in social, life, and computational sciences. They share a long history of successful cooperation and have extensive experience in completed EU projects, especially in the fields of Open Science, Research Integrity, and Science Policy.
Nestled amongst a chain of islands in the southern reaches of Southeast Asia, Timor-Leste occupies the eastern half of the island of Timor, the largest of the Lesser Sunda Islands that also include Bali and Komodo, the latter of which is home to the Komodo Dragon. In May 2002, Timor-Leste (officially the Democratic Republic of Timor-Leste) became the first sovereign nation in the 21st century and is currently the 4th youngest country in the world.
A view from the road between Dili and Baucau, Timor-Leste. Photo by Graham Crumb shared under a CC BY-SA 2.0 license.
Even though the country lies in the highly biodiverse region of Wallacea, its biodiversity is relatively poorly known, partly because decades of pre-independence violence and conflict have hindered biological surveys. In August 2022, a partnership between the Lee Kong Chian Natural History Museum (Singapore), Conservation International, and the Ministry of Agriculture and Fisheries of Timor-Leste conducted preliminary biological surveys across the eastern part of the island. The surveys specifically targeted remote and underexplored areas, such as the isolated mountain of Mundo Perdido (“Lost World” in Portuguese) and Nino Konis Santana National Park (NKS)—the first and largest national park in Timor-Leste.
An aerial view of Nino Konis Santana National Park, Timor-Leste. Photo by UN Photo/Martine Perret under a CC BY-NC-ND 2.0 license
NKS is an enormous park that covers 1,236 square kilometers of land and is mainly characterized by lowland tropical forests. In it, there are several limestone caves of archaeological importance, and it was in one of those caves that a new gecko species was found.
While surveying the Lene Hara cave during the day, a member of the research team caught a glimpse of a lizard scurrying on the ground before disappearing into a crevice. Dr. Chan Kin Onn, a herpetologist at the Lee Kong Chian Natural History Museum and the lead author of a study published in ZooKeys, sprung into action. Soon, he found himself wedged into a tight crevice in hopes of capturing the lizard.
Lene Hara cave, where the new species was found. Photo by Tan Heok Hui
“I couldn’t get to the lizard because the crack was too narrow, but I saw the rear half of its body and could tell that it was a bent-toed gecko from the genus Cyrtodactylus. New species of bent-toed geckos are being discovered all across Southeast Asia and due to the remoteness of the cave, the potential for this gecko to be a new species was high,” explained Dr. Chan.
Several hours later, under the cover of darkness, the team was back in the cave, this time equipped with flashlights. “Bent-toed geckos are usually nocturnal and can be skittish during the day. Our best chance at capturing them would be at night,” says Dr. Chan.True enough, after just one hour of looking, they collected ten specimens. A few weeks later, the gecko from Lena Hara cave was confirmed to be a new species based on DNA analysis and external morphological characteristics.
The new species of bent-toed gecko, Cyrtodactylus santana. Photo by Chan Kin Onn
The new species is named Cyrtodactylussantana, in reference to Nino Konis Santana National Park. The park’s name honors Nino Konis Santana, a freedom fighter who led the Falintil militia against the Indonesian occupation of Timor-Leste.
Even though past surveys have documented several populations of bent-toed geckos in Timor-Leste, none of them had been identified to the species level and thus, remain unnamed. Cyrtodactylussantana is the first bent-toed gecko in Timor-Leste formally described as a species.
The expedition also discovered several interesting plants and crabs that are currently being examined, all of which have the potential to be new species. “We have barely scratched the surface of Timor-Leste’s biodiversity. New discoveries can have profound impacts, because Timor-Leste is a substantial landmass bounded by deep sea trenches and is located at the fringe of the Wallacean Biodiversity Hotspot and Weber’s Line, a transitional zone between Oriental and Australasian fauna” remarked the researchers. Understanding the biodiversity of Timor-Leste could provide key insights into the divergence, evolution, and distribution of species, they believe.
Research article:
Chan KO, Grismer LL, Santana F, Pinto P, Loke FW, Conaboy N (2023) Scratching the surface: a new species of Bent-toed gecko (Squamata, Gekkonidae, Cyrtodactylus) from Timor-Leste of the darmandvillei group marks the potential for future discoveries. ZooKeys 1139: 107-126. https://doi.org/10.3897/zookeys.1139.96508
A new insect species from Kosovo challenges the idea of the intelligence and cleverness of humankind, compared to other organisms, with its scientific name.
Type locality of the new species. Photo by Halil Ibrahimi
Lying at the center of the Balkan Peninsula, Kosovo harbors a diversity of ecosystems and conditions, which have favored processes leading to the existence of many endemic and rare species. In the past few years, several new species of aquatic insects have been discovered from the small Balkan country, making it unique in terms of biodiversity. Unfortunately, as elsewhere in the Balkans, many of these ecosystems have deteriorated heavily.
A team of scientists from Kosovo, led by Professor Halil Ibrahimi of the University of Prishtina, recently found a new species of aquatic insect, a caddisfly, from the Sharr Mountains in Kosovo, and named it Potamophylax humoinsapiens.
The species epithet humoinsapiens is a combination of two Latin words, “humo”, which in English means “to cover with soil, to bury,” and “insapiens,” meaning “unwise”. The researchers explain this name refers to the unwise and careless treatment of the habitats of the new species: hydropower plant, illegal logging and pollution have greatly degraded the area in the past years. “In some segments, whole parts of the Lepenc River are “buried” in large pipes,” they write in their study, which was published in the open-access Biodiversity Data Journal.
Potamophylax humoinsapiens. Photo by Halil Ibrahimi
“The species name ‘humoinsapiens’ ironically sounds like Homo insapiens, and this new species is right in calling us unwise,” thinks Prof. Ibrahimi. “With its actions, humankind has caused the extinction of many species of insects and other organisms during the past decades and has degraded greatly all known ecosystems in the planet. The debate on questioning wise nature of humans is already ongoing.
In the past few years, Professor Halil Ibrahimi and his team have found several new species of aquatic insects from the Balkans, Middle East and North Africa. In an attempt to raise awareness for this group of vulnerable creatures, endangered greatly by human activities, the team of scientists has given their species unique names. One of their previous discoveries was named Potamophylax coronavirus in order to raise the attention to the silent and dangerous “pandemic” humans have caused in freshwater ecosystems in the Balkans.
The research team behind the discovery. Photo by Halil Ibrahimi
“By combining classical taxonomy and modern molecular analysis techniques with the unique names, we are making insect species talk to our collective consciousness. It is in humankind’s capacity to earn the name Homo sapiens again,” the researchers conclude.
Ibrahimi H, Bilalli A, Gashi A, Grapci Kotori L, Slavevska Stamenkovič V, Geci D (2023) Potamophylax humoinsapiens sp. n. (Trichoptera, Limnephilidae), a new species from the Sharr Mountains, Republic of Kosovo. Biodiversity Data Journal 11: e97969. https://doi.org/10.3897/BDJ.11.e97969
EIVE 1.0 is the most comprehensive system of ecological indicator values of vascular plants in Europe to date. It can be used as an important tool for continental-scale analyses of vegetation and floristic data.
Geographic coverage of the 31 ecological indicator value systems that entered the calculation of the consensus system of EIVE 1.0 (image from the original article).
It took seven years and hundreds of hours of work by an international team of 34 authors to develop and publish the most comprehensive system of ecological indicator values (EIVs) of vascular plants in Europe to date.
EIVE 1.0 provides the five most-used ecological indicators, M – moisture, N – nitrogen, R – reaction, L – light and T – temperature, for a total of 14,835 vascular plant taxa in Europe, or between 13,748 and 14,714 for the individual indicators. For each of these taxa, EIVE contains three values: the EIVE niche position indicator, the EIVE niche width indicator and the number of regional EIV systems on which the assessment was based. Both niche position and niche width are given on a continuous scale from 0 to 10, not as categorical ordinal values as in the source systems.
Evidently, EIVE can be an important tool for continental-scale analyses of vegetation and floristic data in Europe.
It will allow to analyse the nearly 2 million vegetation plots currently contained in the European Vegetation Archive (EVA; Chytrý et al. 2016) in new ways.
Since EVA apart from elevation, slope inclination and aspect hardly contains any in situ measured environmental variables, the numerous macroecological studies up to date had to rely on coarse modelled environmental data (e.g. climate) instead. This is particularly problematic for soil variables such as pH, moisture or nutrients, which can change dramatically within a few metres.
Here, the approximation of site conditions by mean ecological indicator values can improve the predictive power substantially (Scherrer and Guisan 2019). Likewise, in broad-scale vegetation classification studies, mean EIVE values per plot would allow a better characterisation of the distinguished vegetation units. Lastly, one should not forget that most countries in Europe do not have a national EIV system, and here EIVE could fill the gap.
Violin plots showing largely continuous value distributions of the niche position and niche width values of the five indicators in EIVE 1.0 (image from the original article).
Almost on the same day as EIVE 1.0 another supranational system of ecological indicator values in Europe has been published by Tichý et al. (2023) with a similar approach.
Thus, it will be important for vegetation scientists in Europe to understand the pros and cons of both systems to allow the wise selection of the most appropriate tool:
EIVE 1.0 is based on 31 regional EIV systems, while Tichý et al. (2023) uses 12.
Both systems provide indicator values for moisture, nitrogen/nutrients, reaction, light and temperature, while Tichý et al. (2023) additionally has a salinity indicator.
Tichý et al. (2023) aimed at using the same scales as Ellenberg et al. (1991), which means that the scales vary between indicators (1–9, 0–9, 1–12), while EIVE has a uniform interval scale of 0–10 for all indicators.
Only EIVE provides niche width in addition to niche position. Niche width is an important aspect of the niche and might be used to improve the calculation of mean indicator values per plot (e.g. by weighting with inverse niche width).
The taxonomic coverage is larger in EIVE than in Tichý et al. (2023): 14,835 vs. 8,908 accepted taxa and 11,148 vs. 8,679 species.
EIVE provides indicator values for accepted subspecies, while Tichý et al. (2023) is restricted to species and aggregates. Separate indicator values for subspecies might be important for two reasons: (a) subspecies often strongly differ in at least one niche dimension; (b) many of the taxa now considered as subspecies have been treated at species level in the regional EIV systems.
Tichý et al. (2023) added 431 species not contained in any of the source systems based on vegetation-plot data from the European Vegetation Archive (EVA; Chytrý et al. 2016) while EIVE calculated the European indicator values only for taxa occurring at least in one source system.
While both systems present maps that suggest a good coverage across Europe, Tichý et al. (2023)’s source systems largely were from Central Europe, NW Europe and Italy, but, unlike EIVE, these authors did not use source systems from the more “distal” parts of Europe, such as Sweden, Faroe Islands, Russia, Georgia, Romania, Poland and Spain, and they used only a small subset of indicators of the EIV systems of Ukraine, Greece and the Alps.
In a validation with GBIF-derived data on temperature niches, Dengler et al. (2023) showed that EIVE has a slightly stronger correlation than Tichý et al. (2023)’s indicators (r = 0.886 vs. 0.852).
The correlation of EIVE-T values of species with GBIF-derived temperature niche data was high and even higher when restricting the calculation to those species whose consensus value was based on at least four sources (image from the original article).
How did EIVE manage to integrate all EIV systems in Europe that contained at least one of the selected indicators for vascular plants, while Tichý et al. (2023) used only a small subset?
This difference is mainly due to a more complex workflow in EIVE (which also was one of the reasons why the preparation took so long). First, Tichý et al. (2023) restricted their search to EIV systems and indicators that had the same number of categories as the “original” Ellenberg system.
Second, from these they discarded those that showed a too low correlation with Ellenberg. By contrast, EIVE’s workflow allowed the use of any system with an ordinal (or even metric) scale, irrespective of the number of categories or the initial match with Ellenberg et al. (1991).
EIVE also did not treat one system (Ellenberg) as the master to assess all others but considered each of them equally valid. While indeed the individual EIV systems are often quite inconsistent, i.e. even if they refer to Ellenberg, the same value of an indicator in one system might mean something different in another system, our iterative linear optimisation enabled us to adjust all 31 systems for the five indicators to a common basis.
This in turn allowed deriving EIVE as the consensus system of all the source systems. The fact that in our validation of the temperature indicator, EIVE performed better than Tichý et al. (2023) and much better than most of the regional EIV systems might be attributable to the so-called “wisdom of the crowd”, going back to the statistician Francis Galton who found that averaging numerous independent assessments (even by laymen) of a continuous quantity can leads to very good estimates of the true value.
Apart from the indicator values themselves, EIVE has a second main feature that might not be so obvious at first glance, but which actually took the EIVE team, including several taxonomists, more time than the workflow to generate the indicator values themselves: the taxonomic backbone. EIVE for vascular plants is fully based on the taxonomic concept (including the synonymic relationships) of the Euro+Med Plantbase.
However, since Euro+Med lacks an important part of taxa that are frequently recorded in vegetation plots, to make our backbone fully usable to vegetation science, we expanded it beyond Euro+Med to something called “Euro+Med augmented”. We particularly added hybrids, neophytes and aggregates, three groups of plants hitherto only very marginally covered in Euro+Med. All additions were done by experts consistently with the taxonomic concept of Euro+Med and are fully documented. Likewise, many additional synonym relationships had to be added that were missing in Euro+Med.
Finally, we implemented the so-called “concept synonymy” (see Jansen and Dengler 2010), which allows the assignment of the same name from different sources to different accepted names (“taxonomic concepts”). This applies mainly to nested taxa that are treated at different levels in different sources, e.g. once as species with several subspecies, once as aggregate with several species. However, there are also some cases of misapplied names (i.e. names that were not used in agreement with their nomenclatural type in certain EIV systems). Such cases generally cannot be solved by the various tools for automatic taxonomic cleaning, but require experts who make a case-by-case decision.
The whole taxonomic workflow of EIVE is fully transparent with an R code that “digests”:
(a) the names as they are in the source systems,
(b) the official Euro+Med database and
(c) tables that document our additions and modifications (with reasons and references).
This comprehensive documentation will allow continuous and efficient improvement in the future, be it because of taxonomic novelties adopted in Euro+Med or because EIVE’s experts decide to change certain interpretations. That way, “Euro+Med augmented” and the accompanying R-based workflow can also be a valuable tool for other projects that wish to harmonise plant taxonomic information from various sources at a continental scale, e.g. in vegetation-plot databases such as GrassPlot (Dengler et al. 2018) and EVA (Chytrý et al. 2016).
The publication of EIVE 1.0 is not the endpoint, but rather a starting point for future developments in a community-based approach.
Together with interested colleagues from outside, the EIVE core team plans to prepare better and more comprehensive releases of EIVE in the future, including updates to its taxonomic backbone.
Future releases of EIVE will be published in fixed versions, typically together with a paper that describes the changes in the content.
As steps for the next two years, we anticipate that we will first add further taxa (bryophytes, lichens, macroalgae) and some additional indicators, both of which are relatively easy with our established R-based workflow. Then we plan EIVE 2.0 that will use the approx. 2 million vegetation plots in EVA (Chytrý et al. 2016) to re-calibrate EIVE for all taxa (see http://euroveg.org/requests/EVA-data-request-form-2022-02-10-Dengleretal.pdf).
We invite you to get into contact with us if you have:
(a) a new or overlooked indicator value system for any taxonomic group in Europe and adjacent areas (including comprehensive datasets of measured environmental data in vegetation plots);
(b) suggestions for improvements of our taxonomic backbone;
(c) a paper idea in the EIVE context that you would like to realise together with the EIVE core team (since everything is OA, you can, of course, use EIVE 1.0 for any possible purpose without notifying us as long as you cite EIVE properly).
Last but not least, any test of the validity and performance of EIVE, alone or in comparison with Tichý et al. (2023), with in situ measured environmental variables, locally or even continentally, would be most welcome.
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This Behind the paper post refers to the article Ecological Indicator Values for Europe (EIVE) 1.0 by Jürgen Dengler, Florian Jansen, Olha Chusova, Elisabeth Hüllbusch, Michael P. Nobis, Koenraad Van Meerbeek, Irena Axmanová, Hans Henrik Bruun, Milan Chytrý, Riccardo Guarino, Gerhard Karrer, Karlien Moeys, Thomas Raus, Manuel J. Steinbauer, Lubomir Tichý, Torbjörn Tyler, Ketevan Batsatsashvili, Claudia Bita-Nicolae, Yakiv Didukh, Martin Diekmann, Thorsten Englisch, Eduardo Fernandez Pascual, Dieter Frank, Ulrich Graf, Michal Hájek, Sven D. Jelaska, Borja Jiménez-Alfaro, Philippe Julve, George Nakhutsrishvili, Wim A. Ozinga, Eszter-Karolina Ruprecht, Urban Šilc, Jean-Paul Theurillat, and François Gillet published in Vegetation Classification and Survey (https://doi.org/10.3897/VCS.98324).
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Brief personal summaries:
Jürgen Dengler is a Professor of Vegetation Ecology at the Zurich University of Applied Science (ZHAW) in Wädenswil, Switzerland. Among others, he cofounded the European Vegetation Database (EVA), the global vegetation-plot database “sPlot” and the “GrassPlot” database of the Eurasian Dry Grassland Group. His major research interests are grassland ecology, grassland conservation, biodiversity patterns, macroecology, vegetation change, broad-scale vegetation classification, methodological developments in vegetation ecology and ecoinformatics.
Florian Jansen is a Professor of Landscape Ecology at the University of Rostock, Germany. His research interests are vegetation ecology and dynamics, mire ecology including greenhouse gas emissions, and numerical ecology with R. He (co-)founded the German Vegetation Database vegetweb.de, the European Vegetation Database (EVA), and the global vegetation-plot database “sPlot”. He wrote the R package eHOF for modelling species response curves along one-dimensional ecological gradients.
François Gillet is an Emeritus Professor of Community Ecology at the University of Franche-Comté in Besançon, France. His major research interests are vegetation diversity, ecology and dynamics, grassland and forest ecology, integrated synusial phytosociology, numerical ecology with R, dynamic modelling of social-ecological systems.
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References:
Chytrý, M., Hennekens, S.M., Jiménez-Alfaro, B., Knollová, I., Dengler, J., Jansen, F., Landucci, F., Schaminée, J.H.J., Aćić, S., (…) & Yamalov, S. 2016. European Vegetation Archive (EVA): an integrated database of European vegetation plots. Applied Vegetation Science 19: 173–180.
Dengler J, Wagner V, Dembicz I, García-Mijangos I, Naqinezhad A, Boch S, Chiarucci A, Conradi T, Filibeck G, … Biurrun I (2018) GrassPlot – a database of multi-scale plant diversity in Palaearctic grasslands. Phytocoenologia 48: 331–347.
Dengler, J., Jansen, F., Chusova, O., Hüllbusch, E., Nobis, M.P., Van Meerbeek, K., Axmanová, I., Bruun, H.H., Chytrý, M., (…) & Gillet, F. 2023. Ecological Indicator Values for Europe (EIVE) 1.0. Vegetation Classification and Survey 4: 7–29.
Ellenberg H, Weber HE, Düll R, Wirth V, Werner W, Paulißen D (1991) Zeigerwerte von Pflanzen in Mitteleuropa. Scripta Geobotanica 18: 1–248.
Jansen F, Dengler J (2010) Plant names in vegetation databases – a neglected source of bias. Journal of Vegetation Science 21: 1179–1186.
Midolo, G., Herben, T., Axmanová, I., Marcenò, C., Pätsch, R., Bruelheide, H., Karger, D.N., Acic, S., Bergamini, A., Bergmeier, E., Biurrun, I., Bonari, G., Carni, A., Chiarucci. A., De Sanctis, M., Demina, O., (…), Dengler, J., (…) & Chytrý, M. 2023. Disturbance indicator values for European plants. Global Ecology and Biogeography 32: 24–34.
Scherrer D, Guisan A (2019) Ecological indicator values reveal missing predictors of species distributions. Scientific Reports 9: Article 3061.
Tichý, L, Axmanová, I., Dengler, J., Guarino, R., Jansen, F., Midolo, G., Nobis, M.P., Van Meerbeek, K., Aćić, S., (…) & Chytrý, M. 2023. Ellenberg-type indicator values for European vascular plant species. Journal of Vegetation Science 34: e13168.
