Out of the dark: historical cave snail collection rediscovered in the attic

Stored in the attic for decades, the shell collection of Dominik Bilimek at BOKU University hides a plethora of untold narratives.

Guest blog post by Petra Lukeneder and Adrienne Jochum

During the past years, interest in the processing and preservation of historical, scientific collections has increased significantly. Fascinating and obscure treasures are stored along with their individual stories while splendid and exciting specimens eke out an existence in boxes and cellars. The scientific curation of the Dominik Bilimek (1813-1884) Collection at BOKU University (Vienna, Austria) is one such example. Stored in the attic for many decades, later stashed in the basement, surviving two floods, a plethora of untold narratives unfolded as the specimens were unpacked. For example, the story of the young, aspiring, Slovenian collector and researcher, Heinrich Hauffen (1836-1866), with his special interests in speleology and the fauna inhabiting the subterranean realm come to light.

A grainy black-and-white photograph of a bearded man. — The only known photograph of collector and naturalist Heinrich Hauffen (1836-1866) (Digital Library of Slovenia; reference number 5S74D58Z).

At first, it was just a label type in the collection that differed from the others. It was a multidisciplinary process to assign it to Hauffen. At that time, only few scientists were concerned with the genus Carychium, including Georg von Frauenfeld (1807-1873), Heinrich Freyer (1802-1866), and Meinrad Thaurer von Gallenstein (1811-1872), all of whom were names that were closely linked to Bilimek and his collection. Fortunately, Hauffen’s handwriting could be identified by using original manuscripts from the Archive of the National Museum of Slovenia.

In our work published in Subterranean Biology, we present our results on the rediscovery of historical material of Heinrich Hauffen, which turned out to be original material, that he used to describe the cave snail taxa Carychium reticulatum and Carychium reticulatum bidentatum. Today, the eastern Alpine and the Dinaric subterranean members of the genus Carychium are assigned to their own genus, Zospeum, based on their troglobiontic characteristics such as lack of eyes, colourless bodies, genetic data, and their totally different shell morphology.

A photograph of a tiny white snail attached to a rocky surface, with a yellow arrow to indicate the location of the snail — Live animal, indicated by the yellow arrow, of the genus *Zospeum* from Krska jama cave in Slovenia. The snail’s shell appears almost to be translucent.

This interdisciplinary work not only includes historical aspects, but also a collaboration with the Natural History Museum Vienna and the Department of Evolutionary Biology (University of Vienna) in conjunction with the taxonomic expertise from the Natural History Museum Bern (Bern, Switzerland), the Senckenberg Research Institute and Natural History Museum (Frankfurt am Main, Germany) and from the Zoologische Staatssammlung München (Münich, Germany). By using light microscopy, X-ray Micro-CT data and SEM in sync with Hauffen’s original figures and handwritten documents, the morphological analysis of C. reticulatum illustrates the degree of phenotypic variation on the shells of individuals from two different cave populations of the species Zospeum spelaeum. The species Carychium bidentatum is considered a junior synonym of Zospeum costatum.

Photographs of people taking samples from caves. — Cave snail collection during field work in Slovenia and Spain.

The genus Zospeum constitutes a radiation of minute, glassy troglobitic snails (Ellobioidea) endemic to the Eastern Alps and the Dinaric Alps, extending as far west as Lake Garda in Italy and as far south as Montenegro. So far, 38 species of Zospeum have been described. Morphologically, the most informative diagnostic characters are apertural form and the degree of coiling and the shape of the columella (inner spindle) as well as the presence and configuration of the lamella in relation to it. In the Pre-Micro-CT era, one had to poke windows into the shells to view these signatory structures. Valuable material could become damaged, and many taxonomists shied from risky mishaps to assess the tiny shells (< 1.5 mm). This present work demonstrates the efficacy of fine-resolution imagery to assess valuable historic material.

A photograph of a woman walking past drawers of specimens — Archive of the Institute of Applied Geology (BOKU University), where the Bilimek Collection including Hauffen’s material, is being stored and processed. Photo by Radek Polách, Muzea Novojičínska.

Hauffen died at the age of 30 as part of the Austrian volunteer corps in Mexico – with the prospect of a permanent position at the Mexican National Museum. According to current knowledge, this is the reason why the Hauffen collection was passed on to Bilimek, who returned to Europe in 1867. There are still abundant specimens, often from localities that cannot longer be sampled nowadays, from Hauffen within the Bilimek collection. In the future, this part can hopefully be separated and scientifically processed as well.

Research article:

Lukeneder P, Ottner F, Harzhauser M, Winkler V, Metscher B, Ruthensteiner B, Jochum A (2024) Lost & Found – Rediscovery of H. Hauffen’s Carychium material in the Dominik Bilimek Collection, BOKU University, including a contemporary assessment within the genus Zospeum (Gastropoda, Ellobioidea, Carychiinae). Subterranean Biology 49: 97-116. https://doi.org/10.3897/subtbiol.49.130692

From science to literature: New arachnid taxa named after Gabriela Mistral and Pablo Neruda

A taxonomic revision describes 22 new species, with two of the names honoring prominent figures of Chilean culture.

Guest blog post by Willians Porto and Abel Pérez González

The third-largest group of arachnids, in terms of number of known species, is the harvestmen, with nearly 7,000 described species, ranking just behind spiders and mites. Despite this number, a considerable portion of their diversity is unknown, and many species still remain undescribed.

An individual of Fresiax spinulosa in a natural setting. — Fresiax spinulosa. Photo by Abel Pérez-González

The harvestmen of the family Triaenonychidae comprise 404 known species and have a peculiar distribution. They are found in temperate regions of the southern hemisphere, with representatives in Australia, New Zealand, South Africa, Madagascar, and southern South America— a typical temperate Gondwana distribution. In the America continent, the diversity is concentrated in the Southern Cone of South America, mainly in the Chilean Valdivian Forest, where 26 species were previously recorded.

A map of Chile showing the distribution of 16 harvestman species. — Distribution maps for 27 harvestman species in Chile.

A map of Chile showing the distribution of Lautaria ceachei. — Distribution maps for 27 harvestman species in Chile.

In our latest work published in ZooKeys, we present the result of a taxonomic and systematic revision of the South American triaenonychids previously included in the mainly New Zealand genus Nuncia. After examining hundreds of specimens, we redescribed all the four previously known species and described 22 new ones. All these species were included in six genera─one resurrected and five new to science─regarding the genus Nuncia as exclusively to New Zealand. The new systematic arrangement was supported by a comprehensive new phylogenetic analysis based on molecular (UCE + Sanger) data.

An individual of Laftrachia robin in a natural environment. — Laftrachia robin, one of the new species described in the study. Photo by Abel Pérez-González

The proposed phylogenetic hypothesis reveals the relationships between South American Triaenonychidae and their counterparts from the rest of the world, indicating that the diversity of triaenonychids in the Southern Cone is polyphyletic, reflecting an ancient diversification predating the Gondwana breakup.

A brown spider in a natural environment. — A species of the newly described Nerudiella genus. Photo by Abel Pérez-González

A bust of Chilean poet Pablo Neruda. — A bust of Pablo Neruda. Photo by Wally Gobetz under a CC BY-NC-ND 2.0 license

Our work represents the most comprehensive contribution to the taxonomy and systematic of South American triaenonychids, almost doubling the number of previously known species. For naming the new taxa, we select names derived from geography, historical figures, and recognized intellectuals. Since most of the newly discovered fauna is distributed across various regions of Chile, the authors decided to honor two prominent figures of Chilean literature. The poet Gabriela Mistral (1889-1957), Nobel laureate in literature in 1945, was honored with the new genus Mistralia, and Pablo Neruda (1904-1973), Nobel laureate in literature in 1971, was honored with the new genus Nerudiella. In addition to tributes to globally renowned Chilean poets, the new species also include dedications to members of the arachnological scientific community and researchers who collaborated on this work.

The taxonomic revision includes hundreds of images that are extremely important for species identification. These images consist of various optical microscopy, stereomicroscopy, and numerous scanning electron microscopy micrographs.

Scanning electron microscope image showing detailed views of the male genitalia of Mistralia verrucosa. — Scanning electron microscope image showing various detailed views of the male genitalia of Mistralia verrucosa.

This work is one of the products of years of collaboration between the Arachnology Division of the Museo Argentino de Ciencias Naturales Bernardino Rivadavia (MACN) and the Giribet Lab in Harvard University and Museum of Comparative Zoology (MCZ). It also represents a continuation of the collaboration initiated in the 20th century by the late Argentinean arachnologist Emilio Maury (MACN) with the Chilean zoologist Tomás Nicolás Cekalovic (Museo de Zoología de la Universidad de Concepción) and the American Museum of Natural History.

Research article:

Porto W, Derkarabetian S, Giribet G, Pérez-González A (2024) Systematic revision of the South American “Nuncia” (Opiliones, Laniatores, Triaenonychidae). ZooKeys 1207: 1-149. https://doi.org/10.3897/zookeys.1207.120068

Low-cost, high-volume imaging for entomological digitization

The flexibility of the imaging rig could benefit many potential users who are looking for an accessible method for larger collections of specimens

Guest blog post by Corey Feng and Dirk Steinke

The demand for the digitization of natural history collections has increased with the advancement of imaging technologies. Large collections composed of millions of insect specimens are exploring efficient strategies and new technologies to digitize them. However, many of these new systems are quite elaborate and expensive, creating a need for more affordable and easy-to-use equipment.

75-by-47-cm foam platform with pinned insects in dorsal and lateral positions.

Creating a digital image for every specimen is an essential part of the DNA barcoding workflow at the Centre for Biodiversity Genomics (CBG). A newly designed imaging rig has enabled the CBG to quickly and efficiently image specimens at high quality while controlling the specimen’s orientation to emphasize key morphological characters. This system allowed the CBG to take some 190,000 images over the past year.

The SLR rig is placed on a heavy-base table to minimize vibration. The inset shows the actual rig area with specimens on the styrofoam base.

Our new ZooKeys study describes this imaging rig, which was mainly created for pinned specimens. It is inexpensive and easy to install as it uses a camera mounted to a CNC machine rig to photograph specimens at high capacity. By using a foam board to array specimens, the user can choose their orientation, which contrasts some existing methods that do not provide such flexibility. This setup produces 95 high quality images within half an hour.

Panel of example images taken with the SLR rig.

The flexibility of the imaging rig could benefit many potential users who are looking for an accessible method for larger collections of specimens. By alternating various parameters, such as the distance between the camera and specimens or the type of camera and lens used, users can adapt their system to specimens of varying sizes. With further changes to the array, the imaging rig can also be adapted to support imaging specimens on slides, within vials, or other storage solutions.

Research article:

Steinke D, McKeown JTA, Zyba A, McLeod J, Feng C, Hebert PDN (2024) Low-cost, high-volume imaging for entomological digitization. ZooKeys 1206: 315-326. https://doi.org/10.3897/zookeys.1206.123670

Arctic botany amongst the fjords: a new annotated species checklist for Agguttinni Territorial Park

A team of museum botanists and guides travelled across the park on foot and by helicopter seeking out every plant and lichen species within the park.

Guest blog post by Paul C. Sokoloff, Lynn J. Gillespie, Geoffrey A. Levin

On northern Baffin Island, Nunavut – the northernmost territory of Canada and Inuit homeland since time immemorial – the tips of long fjords weave around towering peaks and harbour shrubby plants, mounds of lichens, and carpets of mosses and other bryophytes, all set in a majestic landscape known and stewarded by Inuit past, present, and future. This is Agguttinni, Nunavut’s newest and largest territorial park. A new study published in Check List and led by Dr. Lynn Gillespie from the Canadian Museum of Nature, documents the 141 vascular plant, 69 bryophyte, and 93 lichen species collected from this unique protected area.

Arviqtujuq Kangiqtua fjord and Atagulisaktalik valley, location of one of the team’s base camps. *Credit:* Paul Sokoloff © Canadian Museum of Nature

The backdrop to this study is the Canadian Arctic ecozone. This vast region comprises approximately 40% of Canada’s landmass and a broad array of unique habitats, from expansive flat tundra to glacial peaks to rich wetlands. The plants that grow here are well-adapted to their environment. Most grow low, soaking up heat from sun-warmed soil and staying out of cold, drying winds. Many are covered in insulating hairs and can go from bud to flower to fruit quickly during the short Arctic summers. And while woody, spreading shrubs can dominate in the low Arctic, they become rarer further north; conversely bryophyte and lichen species become increasingly important components of the biomass. In this context, the 303 species found in Agguttinni represent a wide swath of Arctic floristic diversity.

Arctic Pyrola (Pyrola grandiflora). Credit: Lynn Gillespie © Canadian Museum of Nature
Arctic cinquefoil (Potentilla hyparctica). Credit: Lynn Gillespie © Canadian Museum of Nature
Black crowberry (Empetrum nigrum). Credit: Paul Sokoloff © Canadian Museum of Nature
Whiteworm lichen (Thamnolia subuliformis). Credit: Paul Sokoloff © Canadian Museum of Nature
Nodding catchfly (Silene uralensis subsp. arctica). Credit Lynn Gillespie © Canadian Museum of Nature

In 2021, Dr. Gillespie’s team travelled to Kanngiqtugaapik (Clyde River) to conduct a botanical inventory of Agguttinni Territorial Park, in partnership with Nunavut Parks and Special Places and with the support of Polar Knowledge Canada. Over the course of five weeks, the team, a fearless five including museum botanists and guides from Kanngiqtugaapik, travelled across the park on foot and by helicopter seeking out every habitat and plant and lichen species within the park. The team established four base camps at the heads of fjords, within mountain passes, and in sheltered harbours, where all necessities were slung in by helicopter, including sleeping tents, kitchen shelters, a field lab for processing samples, and even a solar panel to take advantage of the 24-hour sunlight. Through the weeks on the land, the team found an efficient tempo of collecting specimens in the field and pressing back at camp.

Paul Sokoloff and Lynn Gillespie pressing Alpine fireweed (*Chamaenerion latifolium*) at Atagulisaktalik. *Credit:* Geoffrey Levin © Canadian Museum of Nature

While 2021 was a cold, wet year on northern Baffin Island, the challenging conditions were offset with good company, good food, and warming long hikes. The team searched through hummocky tundra, over gravel scree, in river valleys and on esker ridges, documenting the flora of every terrain within Agguttinni, while our guides from Clyde River, Jaypiti Inutiq and Leeno Apak, provided us with valuable insight into their lands and kept us safe in numerous ways. These wanders, and helicopter excursions from Kanngiqtugaapik, allowed us to thoroughly inventory and compare various habitats within the park.

Geoff Levin collecting Holmen’s dandelion (Taraxacum holmenianum) — *Credit:* Lynn Gillespie © Canadian Museum of Nature

*Credit:* Lynn Gillespie © Canadian Museum of Nature

The sheltered valleys and heads of fjords, far inland from the coast of Baffin Bay, were the most floristically diverse in the study area. At these sites, willow shrubs grow tall (well, at up to 1.5 m high, tall for Baffin Island), and a diverse patchwork of geology and topography is home to species found nowhere else in the park, including new northern-most Canadian records of Lapland Diapensia (Diapensia lapponica) and Flame-tipped Lousewort (Pedicularis flammea), as well as species rare on Baffin Island, such as Dwarf Hawksbeard (Askellia pygmaea) and Hartz’s Bluegrass (Poa hartzii).

Flame-tipped lousewort (*Pedicularis flammea*) at the head of Kangiqtualuk Uqquqtifiord. This species was found only in warmer inland valleys; our collections represent the northernmost confirmed records of the species in Canada. *Credit:* Lynn Gillespie © Canadian Museum of Nature

Conversely, coastal habitats and inland valleys and plateaus proved to be less floristically diverse. Immediately adjacent to the Barnes Ice Cap, the recently-unglaciated zone harboured few vascular plant species and no lichens – a lesson in succession. However, amid this scour, large mounds of blackened moss, likely covered during the Little Ice Age, could be seen regenerating – new green growth amongst bare rock.

Even so, we encountered fascinating new botanical records in these environments, including the first records of Bruggemann’s Alkaligrass (Puccinellia bruggemannii) and Skult’s Shield Lichen (Parmelia skultii) for Baffin Island. On the Barnes Plateau, collections of Powdered Matchstick Lichen (Pilophorus caerulus), Starke’s Fork Moss (Kiaeria starkei) and Sprig Moss (Aongstroemia longipes) are newly reported for Nunavut.

Acutetip aulacomnium moss (Aongstroemia longipes), growing in the recently deglaciated zone in front of the Barnes icecap. This species is rare in eastern North America and was not previously reported for Nunavut. Credit: Lynn Gillespie © Canadian Museum of Nature

While these new records provide important new knowledge about the Arctic flora, commonly encountered species also provide important context about species important to ecosystem health and functioning, and some species proved to be unusually common in the area. For example, Mountain Woodrush (Luzula confusa), Four Angled-Mountain Heather (Cassiope tetragona), Hairy Rock-Moss (Racomitrium lanuginosum), and Orange Chocolate Chip Lichen (Solorina crocea) were encountered throughout the park. Arctic Mushroom Scales Lichen (Lichenomphalia hudsoniana) was also encountered in many locations throughout the park, despite its relative under-collection elsewhere in Nunavut.

Four-angled mountain heather (*Cassiope tetragona*), one of the most common plants in Agguttinni Territorial Park. *Credit:* Lynn Gillespie © Canadian Museum of Nature

The 1007 collections made by Dr. Gillespie’s team in 2021, deposited at the National Herbarium of Canada (CAN), serve as the biodiversity backbone of this current study. The authors examined an additional 386 existing herbarium specimens at CAN, Agriculture and Agrifoods Canada (DAO), and the Université de Montréal (MT), and from other institutions accessed through the Global Biodiversity Information Facility (GBIF). The vast majority of these existing specimens were collected during the Baird Expedition to Baffin Island in 1950. Seventy-four years later, these specimens still provide valuable insight into the biodiversity of Agguttinni.

This powerful combination of old and new specimens, brought together in this paper, more than doubles the number of plant and lichen species known from the park (from 136 to 299), and triples the number of known vascular plants from 45 to 137. It therefore provides a vital biodiversity reference to help in the management and conservation of Agguttinni Territorial Park. More broadly, it expands our understanding of plant diversity in northern Canada, a vast area that includes many under-explored areas. Studies like this also provide important baseline data for assessing future impacts of climate change.

With Thanks

We are grateful to the community of Kanngiqtugaapik for hosting us and this research on their land, Nunavut Parks and Special Places and Polar Knowledge Canada for supporting this work, Jaypiti Inutiq and Leeno Apak for their knowledge and protection on the land, Stéphane Caron and Louis André Grégoire for keeping us up in the air, Patrick Graillon and Linda Vaillancourt from Nunavut Parks for facilitating this work, Martha Raynolds, Helga Bültmann, Yemisi Dare and Julian Starr for excellent recent collections that were included in the study, and herbarium specialists at CAN, DAO, and MT.

Original Study

Gillespie LJ, Sokoloff PC, Levin GA, Doubt J, McMullin RT (2024) Vascular plant, bryophyte, and lichen biodiversity of Agguttinni Territorial Park, Baffin Island, Nunavut, Canada: an annotated species checklist of a new Arctic protected area. Check List 20(2): 279-443. https://doi.org/10.15560/20.2.279

Microplastic contamination of Black Sea fish threatens marine ecosystems

Five commercially important fish species from the Bulgarian Black Sea coast were found to be contaminated with microplastics.

Guest blog post by Stephany Toschkova, Sevginar Ibryamova, Darina Ch. Bachvarova, Teodora Koynova, Elitca Stanachkova, Radoslav Ivanov, Nikolay Natchev, Tsveteslava Ignatova-Ivanova

One of the main problems of the world’s oceans, reported by many scientific studies, is microplastic pollution. It is also one of the main sources of pollution in the Black Sea. Our new study in BioRisk details microplastic contamination in five fish species important for commercial fishing (Garfish, Мullet, Knout goby, Pontic shad, and Mediterranean horse mackerel). The fish were collected from the Sozopol area of the Bulgarian Black Sea coast.

Mediterranean horse mackerel. Photo by Donald Davesne
Knout Goby. Photo by Aleksandr_Levon
Мullet. Photo by Roberto Pillon

Our results show a wide variety of micropollutants originating from commonly used items such as plastic cups, stirrers, bags, soft drink bottles, fishing nets, packaging, аnd personal hygiene products. These objects systematically enter the Black Sea and degrade into microplastic particles. Microplastics (MPs) were found in all studied tissues of the fish in the form of pellets, fibers and fragments. Pellets were found most frequently, followed by irregularly shaped fragments, while fibers were the least numerous.

Stereomicroscope picture of morphological types of microplastics (arrowheads) recognized in the studied specied from: A) Garfish; B) Mullet C) Pontic shad and D) Mediterranean horse mackerel.

The bulk of the isolated plastics are made of polyethylene (PE) and polyethylene terephthalate (PET). PE is found in plastic bottles, cups, stirrers, and plastic bags. This polymer is very light and floats on the surface of the sea because its density is lower than that of water. PET, on the other hand, is denser than water and more likely to sink and accumulate in it and in organisms living on the seafloor. These polymers are widely used in fabrics, nets, ropes, and strings used for fishing, one of the main economic activities in the Black Sea. The predominant polymer type, PE, corresponds to the content of manufactured plastics all around Europe, as almost half of the plastics produced in Europe are reported as PE.

The sinking and sedimentation of plastics relate to the fact that the upper layer of the Black Sea is less dense than that of other seas. Furthermore, the weight of these particles increases due to the accumulation of marine plants and nutrients on them, and this can affect the distribution of plastics and their sedimentation on the seabed.

A satellite image of the Black Sea. Photo by NASA/GSFC/MODIS

Judging by the obtained results and the amount and type of polymers found in the study and the literature, the source of contamination, in our opinion, can be mainly attributed to domestic wastewater discharges coming from the washing of synthetic fabrics. In Bulgaria, wastewater is discharged – directly or after purification – into marine and freshwater ecosystems, as is the case in other neighbouring countries along the Black Sea coast. However, detailed studies are needed to prove this hypothesis.

Considering the wide variety of MP types detected in the digestive tracts of the fish, we assume that they regularly ingested MPs during feeding. Many nutrients are also held on the plastic particles, which deceives the fish into perceiving them as food.

microplastics under a microscope — Microplastics under a microscope. Photos by GTM NERR

Microplastics under a microscope. Photos by GTM NERR

It has been reported that plastics smaller than 1000 μm can reach the digestive tract or the gills of fish, and in turn can cause adverse effects such as a weak immune response or reduced fertility.

MPs can also accumulate in predatory fish species. Unfortunately, very limited research was performed on bioaccumulation and biomagnification in food webs, therefore more studies are needed to reach this conclusion.

MPs enter seawater food chains in different pathways and threaten entire ecosystems through their ability to transport pollutants, pathogenic microorganisms, and alien species. Bearing in mind the intensifying economic activity on the Black Sea coast and the consequent influence on the riverine water quality, river mouths can be considered potential sources of MPs. Particularly concerning is the area near the Kamchia River mouth, which is the biggest intra-territorial river in Bulgaria, entering directly into the Black Sea, with a catchment area of more than 5 300 km². This catchment and the entire Black Sea coast, where agriculture is well developed is a potential source of MPs, which have the ability to absorb and release toxic chemicals of organic and inorganic origin such as bisphenol A, PCBs and DDT, creating an additional potential risk to human health.

A satellite image showing the Kamchia River mouth.

Humans are exposed to BPA in the environment they live in, from the air we breathe to the food and drinks we consume. So, even if BPA intake is below accepted limits, this does not guarantee that the additive will not accumulate and cause more pronounced effects and chronic toxicity in the food chain, given its tendency to accumulate.

It is important that future research determines the toxicological side effects of plastic ingestion for fish communities in both benthic and pelagic habitats. However, even if we stop introducing plastics into the water system, both groups of fish will continue to be impacted, since the number of microplastics can increase due to the breakdown of larger plastics in the environment.

Invasive species as biomonitors of microplastics in freshwater ecosystems?

This study shows the need to carry out further studies of microplastics using different types of microscopic and spectral analysis. Even though microplastics may not pose a risk to humans who consume fish, these contaminants pose a potential risk to marine food webs and endangered species. We found particles of different sizes, types and colours in different fish species, and believe the variability of polymer types in fish can indicate the polymer types in water to some extent. Our results show that fish are important as ecological bioindicators and serve as a basis for future studies on microplastic pollution in tourist sandy beaches.

Research article:

Toschkova S, Ibryamova S, Bachvarova DCh, Koynova T, Stanachkova E, Ivanov R, Natchev N, Ignatova-Ivanova T (2024) The assessment of the bioaccumulation of microplastics in key fish species from the Bulgarian aquatory of the Black Sea. BioRisk 22: 17-31. https://doi.org/10.3897/biorisk.22.117668

Integration of ecosystem services in urban planning tools can directly contribute to the sustainability of ecosystems

Integrated ecosystem services can be a potent tool to inform and guide spatial decision-making.

Guest blog post by Zeynep Türkay

Ecosystem services’ (ES) integration into global policies is widely recognized as a hope for environmental sustainability, as they provide a robust framework for representing natural values. The role of healthy ecosystems in combating climate change-related risks and ensuring the sustainability of ecosystem services that are critical for human-natural life is well understood, and in this context, the protection and sustainability of Integrated ES areas, which represent the highest ecological functional areas in this sense, need to be highlighted. Integrated ES can be a potent tool to inform and guide spatial decision-making. However, presently, there is a need to improve the content of related conventional tools on how to introduce and involve their roles in decision-making processes.

A map of Istanbul showing the integrated ecosystem services potential of the current situation.

Our paper, published in the journal One Ecosystem, investigates the incorporation of this problem, underlines ES significance as the Integrated ES, and transfers this information into spatial decision-making. The content of the paper discusses the potential contributions and limitations of the integration. It provides solid suggestions on how Integrated ES can be operationalized in Istanbul’s high-level plans.

Research article:

Türkay Z, Tezer A (2024) Contribution of integrated ecosystem services to urban planning tools: Can it be more functional for the sustainability of ecosystems? One Ecosystem 9: e121553. https://doi.org/10.3897/oneeco.9.e121553

Entangled “her”stories – How to create an open multi-linked dynamic dataset of plant genera named for women

Which plant genera do you know that are named for women? Who were/are they?

Guest blog post by Siobhan Leachman, Sabine von Mering, Heather Lindon & Carmen Ulloa Ulloa

How it all began

A post on social media asked about plant genera named for women and sparked a lively discussion with many contributors. This simple question was not as easily answered as initially thought. The resulting informal working group tackled this topic remotely during the COVID-19 pandemic and beyond. The team was motivated by the desire to amplify the contribution of women to botany through eponymy. The work of this team has so far resulted in a paper in Biodiversity Data Journal, presentations at several conferences, and a linked open dataset.

Prior to our international collaboration, no dataset was available to answer these simple questions and the required information was scattered in many different data sources. We set out to bring these data together and in doing so developed and refined our workflow. Our data paper documents this innovative workflow bringing together the various data elements needed to answer our research questions. Ultimately we created a Linked Open Data (LOD) dataset that amplified the names of women and female mythological beings celebrated through generic names of flowering plants.

🙋🏻‍♀️Inspired by the melastome plant genus 𝘔𝘦𝘳𝘪𝘢𝘯𝘪𝘢: which plant genera do you know that honor women? Who were/are they? 🌺 ¿Qué géneros de plantas dedicados a mujeres conoces? ¿Quienes fueron/son? 🧵👇🏽 #WomenInSTEM https://t.co/QWpyaMfihT pic.twitter.com/XBCYD6hmx1
— Carmen Ulloa (@meriania) May 14, 2021

Linking the Data

During our research process we focused on pulling data from a wide variety of sources while at the same time proactively sharing the data generated as widely as possible. This was done by adding and linking it to multiple public databases and sources (push-pull) including the International Plant Name Index (hereafter IPNI), Tropicos®, Wikidata, Bionomia and the Biodiversity Heritage Library (hereafter BHL).

*Visualisation of our workflow to create a working list of flowering plant genera named for women.*

For our list of genera, each of the protologues were reviewed to confirm the etymology or eponymy. To find the generic prologues, we searched botanical databases such as IPNI and Tropicos, openly accessible providers of digital publications and other digital libraries and websites that provide free access to such publications. Here the BHL was invaluable as the majority of protologues and many other relevant publications were openly accessible through this digital library. Where no digital publication was available we accessed scientific literature through our affiliated institutions.

For the women, our starting point was the “Index of Eponymic Plant Names – Extended Edition” by Lotte Burkhardt (2018). We manually extracted all genera honouring women. This dataset was supplemented with other sources including IPNI (2023), Mari Mut (2017-2021), a 2022 updated version of Burkhardt’s document (Burkhardt 2022), as well as suggestions received from colleagues and generated from our own research.

We collected the following information as structured data: information on the woman honoured, the genera named in honour of the woman, the year and place of the protologue or original publication (the nomenclatural reference), the author(s) of the genus name, and the link to the protologue or original publication if available online.

Wikidata

Wikidata was the central data repository and linking mechanism for this project as it provided structured data that can be read and edited by humans and machines and it acts as a hub for other identifiers. As such Wikidata played a central role in semantic linking and enriching of our data.

Wikidata items for the plant genera were created or enriched with information about the name, the author(s) of the genus and the year of publication. Those statements were referenced using the original publication. If the protologue was available on BHL, the BHL bibliographic or page number was added to that reference, thus creating a digital link improving access to the protologue. While undertaking this work we also collated a list of all those public domain publications that appeared to be absent from BHL. We passed on this list to BHL and requested these texts be scanned and added to BHL for the benefit of everyone.

We then added a named after statement to the Wikidata item for the appropriate plant genera linking that item to the Wikidata item for the woman honoured. Wikidata items for the women honoured were newly created or enriched. We researched each person and her contributions, plus information on mythological figures where necessary, and added this information to Wikidata items. Our work also included disambiguating the woman from other people with identical or similar names.

To amplify the women’s contributions to science and to enrich the wider (biodiversity) data ecosystem, we linked to other Wikidata items and websites or databases by adding other relevant identifiers. For example if the women were botanists, botanical collectors or other naturalists, we used the author property to link the women to publications written by them. In addition, we added the women to Bionomia and attributed specimens collected or identified by them to their profiles.

Our work also included enriching Wikidata items of taxon authors. IPNI and Tropicos were searched for these author names, and websites such as BHL, the Global Biodiversity Information Facility (GBIF) or other specialist databases were consulted. Corrections or newly researched information on taxon authors was placed not just in Wikidata but was also sent together with the corresponding references to IPNI and Tropicos. This information was then used by those organizations to update these databases accordingly.

As a result of our data being placed in Wikidata it is available to be queried via the Wikidata Query Service.

Our Goal Achieved

As a result of our project, we published a dataset of 728 genera honouring women or female beings. This was a nearly twenty-fold increase in the number of genera linked to women in Wikidata. Our analysis paper on this data is forthcoming.

Notable Women

Monsonia L.

All of us came away from this research with a favourite story. One that stood out was Ann Monson, for whom Linnaeus named Monsonia. Linnaeus wrote a delightful letter to her about their creating, platonically of course, a kind of plant love-child between them, in the form of this new genus.

Translated from Latin : “….Lock these [seeds] in a pot, and place them in the window of the chamber towards the sun, when it bursts forth in February, and in the first summer the sun blooms and lasts the most beautiful Alstromeria, which no one has seen in England, and you bring forth no flowers. If it should come to pass, as I wish, if you offer our flames, I would only wish to beget with you an only child, as a pledge of my love, little Monsonia, by which you may perpetuate the fame of Lady in the kingdom of Flora, who was the Queen of Women.”

Fittonia Coem.

Two eponymous women with an interesting story are Sarah Mary Fitton and her sister Elizabeth. They wrote Conversations on Botany in 1817 accompanied by colour engravings of flowers which popularised botany with women. The genus Fittonia was named in their honour.

Chanekia Lundell

Another woman honoured in a plant genus was Mercedes Chanek, a Mayan plant collector who worked in the 1930’s for Cyrus Longworth Lundell and collected for the University of Michigan in British Honduras, today Belize. Very little is known about her life and work. However, her collections are detailed in Tropicos and Bionomia, and you can see the genus named for her by Lundell in IPNI under Chanekia.

Medusa Lour. and other genera

An example of a mythological female being honoured in several plant names is that of Medusa, who has the most genera named after her, six, more than any real woman!

We hope that our data paper inspires others to use the methodology and workflow described to create other linked open datasets, e.g. celebrating and amplifying the contributions of underrepresented or marginalised groups in science.

Data paper:

von Mering S, Gardiner LM, Knapp S, Lindon H, Leachman S, Ulloa Ulloa C, Vincent S, Vorontsova MS (2023) Creating a multi-linked dynamic dataset: a case study of plant genera named for women. Biodiversity Data Journal 11: e114408. https://doi.org/10.3897/BDJ.11.e114408

A new dawn for biological collections: The AI revolution in museums and herbaria

There are numerous uses for machine learning in digital collections, including an enormous potential to extract traits of organisms.

Guest blog post by Quentin Groom

Imagine having access to all the two billion biological collections of the world from your desktop! Not only to browse, but to search with artificial intelligence. We recently published a paper where we envisage what might be possible, such as searching all specimen labels for a person’s signature, studying the patterns of butterflies’ wings, or reconstructing a historic expedition.

Numbers of digital images from biodiversity collections are increasing exponentially. Herbariums have led the way with tens of millions of images available, but images of pinned insects will soon overtake plants.

Numbers of accessible images of specimens are increasing exponentially. Plants lead the way, but insects are increasing at the fastest rate. This graph was created from snapshots of the Global Biodiversity Information Facility and is undoubtedly an underestimate of the actual number of specimens for which images exist. See how this was created in Groom et al. (2023).

At one time, if you wanted access to biological collections, you had to travel. Now we are used to visiting collections online, where we can view images of specimens and their details on our desktops. Nevertheless, biological collection images are still dispersed and this limits their effective use, not just for people, but also for computers. One of the promises of making specimens digital is being able to apply machine learning to these images. Yet the real benefits of machine access to specimens can only be realised through massive access to collection images and the ability to apply these techniques to hundreds of collections and millions of specimens.

Imagine examining collections globally for the variation and evolution of wing coloration in butterflies, or studying the size and shape of leaves in research that transverses habitats and gradients of latitude and altitude.

In our paper in Biodiversity Data Journal, we examined some of the numerous uses for machine learning in digital collections. These include an enormous potential to extract traits of organisms, from the size and shape of different organs, to their colours, patterns, and phenology. Imagine examining collections globally for the variation and evolution of wing coloration in butterflies, or studying the size and shape of leaves in research that transverses habitats and gradients of latitude and altitude. We would not only be able to study the intricacies of evolution, but also practical subjects, such as the mechanics of pollination in insects, adaptations to drought in plants, and adaptations to weediness in invasive species.

Machine access to these images will also provide an unparalleled view of the history of the biological sciences, the specimens used to describe species, the evidence for evolution, the people involved and institutions that contributed. Such transparency may reveal some amazing stories of scientific exploration, but will undoubtedly also shed light on some of the less exemplary actions of colonialism. Yet if we are to redress the injustices of the past we need to have a balanced view of collections, and we should do this openly.

Specimen labels provide numerous clues to their history often in the form of stamps and emblems. A BR0000013433048 Meise Botanic Garden (CC-BY-SA 4.0). B USCH0030719, A.C. Moore Herbarium at the University of South Carolina (public domain). C E00809288, Royal Botanic Garden Edinburgh (public domain). D USCH0030719, University of South Carolina (public domain). E E00919066, Royal Botanic Garden Edinburgh (public domain). F BR0000017682725, Meise Botanic Garden (CC-BY-SA 4.0). G P00605317, Museum National d’Histoire Naturelle, Paris (CC-BY 4.0). H LISC036829, Instituto de Investigação Científica Tropical (CC-BY-NC 4.0). l PC0702930, Muséum National d’Histoire Naturelle, Paris (CC-By 4.0). J same specimen as (B). K PC0702930 Muséum National d’Histoire Naturelle, Paris (CC-BY 4.0). L 101178648, Missouri Botanical Garden (CC-BY-SA 4.0).

With such unparalleled access to collections, we could travel vicariously to times and places that are hard to reach in any other way. Fieldwork is expensive and time-consuming, and can’t provide the historic perspective of collections, let alone the geographic extent. Furthermore, digital resources have the potential to democratise collections, allowing anyone the opportunity to study these collections irrespective of location.

Is such a vision of integrated digital collections possible? It certainly is! The technologies already exist, not just for machine learning, but also to create the infrastructure to provide access to millions of digital images and their metadata. Initiatives, such as DiSSCo in Europe and iDigBio in the USA are moving in this direction. Yet, we conclude that the main challenge to realising this vision of the future is a sociopolitical one. Can so many institutions and funders work together to pool their resources? Can collections in rich countries share the sovereignty of their collections with the countries where many of the specimens originated?

If you too share the dream, we encourage you to support or contribute to initiatives working in this direction, whether through funding, collaboration, or sharing knowledge. If the full potential of digital collections is to be realised, we need to think big and work together.

Research article:

Groom Q, Dillen M, Addink W, Ariño AHH, Bölling C, Bonnet P, Cecchi L, Ellwood ER, Figueira R, Gagnier P-Y, Grace OM, Güntsch A, Hardy H, Huybrechts P, Hyam R, Joly AAJ, Kommineni VK, Larridon I, Livermore L, Lopes RJ, Meeus S, Miller JA, Milleville K, Panda R, Pignal M, Poelen J, Ristevski B, Robertson T, Rufino AC, Santos J, Schermer M, Scott B, Seltmann KC, Teixeira H, Trekels M, Gaikwad J (2023) Envisaging a global infrastructure to exploit the potential of digitised collections. Biodiversity Data Journal 11: e109439. https://doi.org/10.3897/BDJ.11.e109439

For peace in Colombia: a new genus and five new species of pseudoscorpions

Looking into biological collections, pseudoscorpion researcher Catalina Romero-Ortiz found five new species and a new genus of these interesting creatures.

Guest blog post by Catalina Romero-Ortiz

Colombia is a South American country full of beautiful landscapes, indigenous cultures, delicious food, and warm people. In its territory, the country hosts an amazing diversity of birds, amphibians, vascular plants, fishes, among other biological groups, which makes it one of the biodiversity hotspots on Earth. The nation’s recent steps toward peace have allowed for the exploration of regions previously off-limits due to conflict.

A map showing the location of Colombia. Screenshot from OpenStreetMap.

Of all this diversity in Colombia, pseudoscorpions, little arachnids that resemble scorpions, are very little known. They can get mistaken for mites or fleas due to their size, but are entirely harmless to humans, with their venom glands only used for hunting and self-defense. Their cryptic behaviors make them difficult to find, which in turn makes them difficult to study. For a biodiversity hotspot like Colombia, researchers expect that there are more species out there than the 63 that are already known to science.

Looking into biological collections, pseudoscorpion researcher Catalina Romero-Ortiz found five new species and a new genus of these interesting creatures. Together with Dr. Mark Harvey from the Western Australian Museum and Dr. Carlos Sarmiento from the Instituto de Ciencias Naturales of the National University of Colombia, they recently described those findings in the scientific journal ZooKeys. They also proposed a new classification for a species that was only known by its description, contributing to the broader understanding of pseudoscorpions in Colombia. The star of their research is the newfound genus Paciwithius.

Newly described pseudoscorpion species: A Paciwithius chimbilacus, B Cystowithius florezi, C Parawithius bromelicola, D Oligowithius achagua. Scale bars: 0.5 mm.

A peculiar name

To understand the meaning of the genus name, which refers to the Latin for peace, pax, we should look at the history of this beautiful country. Since the early 20th century, Colombia has grappled with an ongoing civil conflict, particularly in rural areas. Starting in 1946 with the rise of the Guerrilla, this historic period named “La Violencia” claimed millions of lives. Over the years, the dynamics of the conflict evolved, but violence persisted. The 1980s witnessed the rise of the narco-era, plunging the entire nation into a vortex of violence. With the emergence of paramilitary forces vying for control of the drug trade, violent clashes with guerrillas further escalated the bloodshed.

In 2012, peace negotiations began in Colombia, and in 2016 the Peace agreement with the biggest Guerrilla group was established. Prior to this, a process of reconciliation was initiated with paramilitary groups. With the perception that for a true peace there has to be a comprehensive understanding of past events in order to forgive, the “Comisión de la verdad” (Truth commission) was created. This Commission did incredible work gathering testimonials of the war from all sides and making them accessible to the public. Remembering is essential to healing and moving on.

The signed peace agreement. Photo by FAOAmericas used under a CC BY-NC-SA 2.0 license

In the end, peace for this country has a lot to do with people, territory, and biodiversity. Areas that were previously unexplored due to violence are now accessible, and although war is far from over, this is a good path to follow. A long one, but, we hope, full of life.

Research article:

Romero-Ortiz C, Sarmiento CE, Harvey MS (2023) A new genus and five new species of pseudoscorpions (Arachnida, Pseudoscorpiones, Withiidae) from Colombia. ZooKeys 1184: 301-326. https://doi.org/10.3897/zookeys.1184.106698

Listen to the trees: a detective work on the origin of invasive species

An attempt to explore the history of the spread of four non-indigenous invasive tree species in one of the most important Hungarian forest-steppe forests of high conservation value.

Guest blog post by Arnold Erdélyi, Judit Hartdégen, Ákos Malatinszky, and Csaba Vadász

Today, almost everyone is familiar with the term “biological invasion”. Countless studies have been carried out to describe the various processes, and explore the cause and effect, and several methods have been developed in order to control certain invasive species. However, one of the biggest puzzles is always the question of how it all happened. It is not always easy to answer, and, in general, the smaller the area, the more difficult or even impossible it is to answer. In the course of our work, we attempted to explore the history of the spread of four, non-indigenous invasive tree species in one of the most important Hungarian forest-steppe forests of high conservation value, the Peszér Forest (approximately 1000 ha). Last week, we published our study in the journal One Ecosystem.

An open formation of the Eurosiberian steppic woods with Quercus spp., a priority natural habitat type of Community interest under the European Union’s Habitats Directive

The Far Eastern tree of heaven (Ailanthus altissima), as well as the North American black cherry (Prunus serotina), the box elder (Acer negundo) and the common hackberry (Celtis occidentalis) are among the worst invasive plant species in Hungary. They are also responsible for serious conservation and economic problems in the Peszér Forest.

Invasion of tree of heaven (top left) and common hackberry (top right) in poplar stands, carpet of seedlings of black cherry (bottom left), and monodominant stand of box elder, regrown from stump after cutting (bottom right)

Historical reconstructions of the spread of invasive species are most often based on only one, or sometimes a few aspects. We used six approaches simultaneously:

we reviewed the published and grey literature,
extracted tree species data from the National Forest Database since 1958,
conducted a field survey with full spatial coverage (16,000 survey units (25×25 m quadrats)) – instead of sampling,
recorded all the largest (and presumably the oldest) individuals for annual ring counts,
performed hotspot analyses on the field data
collected local knowledge.

Cutting down the oldest common hackberry trees in order to count the annual rings from trunk discs

Our results show that each approach provided some new information, and without any of them the story revealed would have been much shorter and more uncertain. We have also highlighted that at the local level, the use of one or two aspects can be not only inadequate but also misleading.

From the literature it was possible to determine the exact place and date of the first occurrence of the tree of heaven and the black cherry. However, in the case of black cherry, for example, it was only possible to piece together the circumstances of the first plantings by combining three different sources. The first occurrences of box elder were found in forestry data. Finally, in the case of the common hackberry, searching for old individuals and determining their age gave the best results.

Common hackberry in the Peszér forest according to the recent forestry data (2016) and the field survey (2017-2019). The difference is clear: in the official forestry database, the tree species is underrepresented several times over

A well-explored story of a biological invasion can go a long way in making more and more people understand that controlling these non-indigenous species can only be beneficial. On the other hand, it can also help to strengthen conservation efforts, for example by increasing the volunteer workforce, which can be a major factor in the reduction of certain species. We hope that our work and the approaches we have taken will serve as a good model for exploring other invasion stories around the world.

Winter snapshot from the Peszér Forest, a diverse forest edge habitat along an inner road.

Research article:

Erdélyi A, Hartdégen J, Malatinszky Á, Vadász C (2023) Historical reconstruction of the invasions of four non-native tree species at local scale: a detective work on Ailanthus altissima, Celtis occidentalis, Prunus serotina and Acer negundo. One Ecosystem 8: e108683. https://doi.org/10.3897/oneeco.8.e108683