Tag: zoology

The Venom Spider: new genus named after Tom Hardy’s Marvel character

Researchers referenced the British actor and Spider-Man villain due the unusual pattern on the Australian arachnid’s abdomen.

Tom Hardy and his Marvel character Venom have given their names to a newly discovered Australian spider. The genus Venomius and its only current species Venomius tomhardyi were described following an expedition to Tasmania.

Scientists MSc Giullia Rossi, Dr Pedro Castanheira and Dr Volker Framenau from Murdoch University ( Perth, Australia) partnered with Dr Renner Baptista from the Federal University of Rio de Janeiro (Brazil) to describe the new genus of orb-weaving spiders published in the open access journal Evolutionary Systematics.

Tom Hardy portrays Eddie Brock and his alter-ego Venom, an antihero closely associated with Spider-Man, across two Marvel films and gives his name to the sole species of the new genus. The distinctive black spots on the arachnid’s abdomen reminded the scientists of Venom’s head, inspiring them to select the unusual name.

Annotated image showing five angles of a spider. — *Venomius* *tomhardyi* male holotype. Scale bars: 2 mm (**A, B**); 0.2 mm (**C–E**).
Photos by Rossi et al.

The genus belongs to the Araneidae family of spiders, or Araneae, that build upright circular webs to capture prey. Despite resembling the related genus Phonognatha as both do not have tubercles on the abdomen, the newly described spiders are distinct in their behaviour of creating silk-lined holes in the branches of trees for shelter, as well as their different genitalia.

The holotype of the new species was discovered and subsequently preserved at the Queen Victoria Museum and Art Gallery following an expedition to Tasmania, Victoria, South Australia and Western Australia.

“This is part of a long-term research that aims to document the entire Australian spider fauna, which will be of extreme importance for conservation management plans and the continuation of the decadal plan for taxonomy and biosystematics in Australia and New Zealand.”
Dr. Pedro Castanheira, contributing author.

Distribution records of *Venomius tomhardyi*.
Image by Rossi et al.

Researchers also sourced supplementary specimens from scientific arachnology collections, with researchers examining approximately 12,000 records in Australian and overseas institutions.

“It is really important to keep describing new spiders to assess the total biodiversity of these predators in Australia,” added the study’s first author MSc Giullia Rossi.

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Original source:

Rossi GF, Castanheira PS, Baptista RLC, Framenau VW (2023) Venomius, a new monotypic genus of Australian orb-weaving spiders (Araneae, Araneidae). Evolutionary Systematics 7(2): 285-292. https://doi.org/10.3897/evolsyst.7.110022

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Psychedelic rock gecko among dozens of species in need of further conservation protection in Vietnam

Researchers recommend IUCN CPSG’s One Plan Approach to Conservation measures, which include both habitat conservation and increasing the number of threatened species in breeding stations and zoos.

Endangered psychedelic rock gecko (*Cnemaspis psychedelica*)
Photo by Thomas Ziegler. Licence: CC-BY.

Further conservation measures are required to protect Vietnamese reptiles, such as the psychedelic rock gecko (Cnemaspis psychedelica), from habitat loss and overharvesting, concludes a new report, published in the open-access scientific journal Nature Conservation.

Having identified areas of high reptile diversity and large numbers of endangered species, the study provides a list of the 50 most threatened species as a guide for further research and conservation action in Vietnam.

The study, based on the bachelor thesis of Lilli Stenger (University of Cologne, Germany), recommends IUCN CPSG’s One Plan Approach to Conservation measures, which, next to improved habitat conservation, also involves increasing the number of threatened species in breeding stations and zoos to maintain populations suitable for restocking.

Co-authors of the report are Anke Große Hovest (University of Cologne, Germany), Truong Quang Nguyen (Vietnam Academy of Science and Technology), Cuong The Pham, (Vietnam Academy of Science and Technology), Anna Rauhaus (Cologne Zoo, Germany), Minh Duc Le (Vietnam National University), Dennis Rödder (Leibniz Institute for the Analysis of Biodiversity Change, Germany) and Thomas Ziegler (University of Cologne and Cologne Zoo, Germany).

“Modern zoos, as well as local facilities, can play a crucial role in not only conducting or financially supporting in situ conservation projects, that is to say in nature, but also by protecting species from extinction through maintaining ex situ assurance colonies to reinforce in situ conservation programs,”
said Prof. Dr. Thomas Ziegler, Vietnam conservation team member and coordinator from Cologne Zoo, Germany.

Endangered Truong Son pit viper or Quang Binh pit viper (*Trimeresurus truongsonensis*).
Photo by Thomas Ziegler. Licence: CC-BY.

The scientists identified 484 reptile species known to Vietnam, aiming to provide a baseline to authorities, conservationists, rescue centers, and zoos, so they can follow up with appropriate conservation measures for endangered species. They note that the number is likely to go up, as the country is regarded as a top biodiversity hotspot, and the rate of new reptile species discoveries remains high.

According to the IUCN Red List, 74 of the identified species are considered threatened with extinction, including 34 endemic species. For more than half of Vietnam’s endemic reptiles (85 of 159), the IUCN Red List status is either missing or outdated, and further research is imperative for these species, the researchers say.

Vietnam has a high level of reptile diversity and an outstanding number of endemic species. The species richness maps in the study revealed the Central Annamites in central Vietnam to harbor the highest endemic species diversity (32 species), which highlights it as a site of particular importance for reptile conservation. Alarmingly, a protected area analysis showed that 53 of the 159 endemic species (33.2%) including 17 threatened species, have been recorded exclusively from unprotected areas, such as the Psychedelic Rock Gecko.

The Critically Endangered Annam pond turtle (*Mauremys annamensis*) is one of the most endangered turtle species in Vietnam and in the world. It is not known from any protected area. Despite likely being extinct in the wild, ex situ conservation programs have been implemented in time with a high number of individuals being kept and bred in zoos and stations and now ready for restocking actions.
Photo by Thomas Ziegler. Licence: CC-BY.

In General, Vietnam is considered a country with high conservation priority due to habitat loss and overharvesting for trade, traditional medicine and food.

Globally, reptiles are considered a group of special conservation concern, as they play an important role in almost all ecosystems and often have relatively small distribution ranges, making them especially vulnerable to human threats.

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Original source:

Stenger L, Große Hovest A, Nguyen TQ, Pham CT, Rauhaus A, Le MD, Rödder D, Ziegler T (2023) Assessment of the threat status of reptile species from Vietnam – Implementation of the One Plan Approach to Conservation. Nature Conservation 53: 183 221. https://doi.org/10.3897/natureconservation.53.106923

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Persian Gold Tarantula: a new species from Iran for Tarantula Appreciation Day 2023

Its “woolly, golden hairs” were one of the features so unique it was not necessary for additional individuals to be collected

Guest blog post by Dr Alireza Zamani (@Arachno_AZ)

In the latest issue (1174^th) of the scientific open-access journal ZooKeys, you can find our paper describing a new species of tarantula (family Theraphosidae) found in northwestern Iran.

This species belongs to Chaetopelma, a relatively small genus, distributed in Crete, Sudan, and the Middle East, and one of the only two tarantula genera inhabiting the Mediterranean region.

Our discovery is significant for several reasons. Firstly, it marks the first record of this genus in Iran and the third known species of tarantulas in this country. Additionally, it extends the known range of Chaetopelma spiders by almost 350 km eastwards.

We named this species Chaetopelma persianum, paying homage to its occurrence in Iran, which has historically been known as Persia. As a potential common name, we suggest “Persian Gold Tarantula”, where we are also making a reference to the “woolly, golden hairs’’ on its carapace.

The newly described tarantula species (*Chaetopelma persianum*) seen in a defensive posture.
Photo by Kari Kaunisto.

For the purpose of our study, we only had one specimen: a female with a leg span of almost 9 cm, available. Yet, its distinct characteristics allowed us to confidently differentiate it from other known Chaetopelma species.

This tarantula is an obligate burrower and inhabits high elevations in well-vegetated mountainous regions of the northern Zagros Mountains. The holotype specimen was collected from a self-made ground burrow on sloped rocky ground, amidst sparse low vegetation and grasses.

It all started with local nature enthusiast Mehdi Gavahyan, who photographed a wandering male and sent me the photo. When I figured it was most likely an undescribed species, I asked him to team up with Amir Hossein Aghaei, a nature enthusiast and a friend of mine, and send me specimens of these spiders for further examination. Unfortunately, they only managed to collect that one female. However, it turned out to be enough for us to describe the Persian Gold Tarantula!

Additionally, thanks to local citizen scientists and naturalists, we later also got hold of photos of another two males of the same genus, taken very close to the type locality of the new species: one in Sardasht in West Azerbaijan Province of Iran, and the other in the surroundings of Sulaymaniyah in Iraq. While it is highly probable that both these males belong to Ch. persianum, this cannot be confirmed until further examination of collected material from both sexes is conducted.

_{Burrow of Persian Gold Tarantulas in West Azerbaijan Province, Iran. The arrow in the photo on the right indicates the location of the burrow. Photos by Amir Hossein Aghaei.}

During our research, we also noted that one species of Chaetopelma described from Cameroon is misclassified and should be transferred to another genus. However, this transfer is pending until the type material undergoes examination.

Looking ahead, we believe that more comprehensive investigations employing integrative methods would greatly benefit the taxonomy of Chaetopelma.

Habitat of the newly described Persian Gold Tarantula (*Chaetopelma persianum*) in West Azerbaijan Province, Iran.
Photo by Amir Hossein Aghaei.

For example, Ch. olivaceum, a species with seven junior synonyms and one of the broadest ranges within the entire family, covering an area of approximately 1,493,978 km², might potentially have cryptic species within its range. Moreover, the disjunct distribution of Ch. olivaceum in Turkey, where it occurs both in the southern regions and as far north as Istanbul, raises the possibility of distinct species status for the latter population, which is geographically isolated from the rest of the recorded occurrences. Integrative studies incorporating molecular data could offer insights into this.

Additionally, further collection efforts in lesser-sampled or completely unexplored regions, such as Saudi Arabia, Syria, Iraq, eastern Turkey and western Iran, could lead to the discovery of additional Chaetopelma species or records. These findings would be instrumental in gaining a more comprehensive understanding of the taxonomy and distribution of this genus.

Research paper:

Zamani A, West RC (2023) A new species of Chaetopelma Ausserer, 1871 (Araneae, Theraphosidae) from Iran. ZooKeys 1174: 75-84. https://doi.org/10.3897/zookeys.1174.109135

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Southernmost crocodile newt record is a threatened new species

“Exceptional discovery” for its colors, the amphibian is also the first crocodile newt species known from the Central Highlands of Vietnam.

A spectacular crocodile newt from the Central Highlands of Vietnam was just published in the international peer-reviewed open-access academic journal ZooKeys.

“It is an exceptional discovery as it is one of the most colourful species in the genus Tylototriton. This is also the first time that a crocodile newt species is recorded from the Central Highlands of Vietnam. Occurring at elevations from 1,800 to 2,300 m above sea level, this discovery sets an elevational record for the genus in the country, with former distribution ranges between 250 m and 1,740 m.”
says discoverer and first author of the study Trung My Phung.

Furthermore, the discovery by the Vietnamese-German researcher team, which was supported by the Vietnam Academy of Science and Technology and the Cologne Zoo (Germany), represents the southernmost distribution range of the genus known to date.

The habitat of the new species is located approximately 370 air km away from the nearest Tylototriton population, which makes it an important discovery in terms of evolution and zoogeography.

The name “ngoclinhensis” refers to the type locality of the new species, Ngoc Linh Mountain. Restricted to evergreen montane forest, the Ngoc Linh Crocodile Newt is currently known only from the Ngoc Linh Nature Reserve, Kon Tum Province, in the Central Highlands of Vietnam. This is the eighth salamander taxon described from Vietnam, and is the thirty-ninth Tylototriton species officially recognized.

The newly described crocodile newt *Tylototriton* *ngoclinhensis* sp. nov.
Photo by Prof. Dr. Tao Thien Nguyen.

Crocodile newts, scientifically known as the genus Tylototriton, include nearly 40 species inhabiting montane forest areas throughout the Asian monsoon climate zone. Remarkably, 15 of these species have been described in the past five years, and there remain several unnamed taxa, which contain cryptic species that are morphologically difficult to distinguish.

Established in 1986, Ngoc Linh Nature Reserve is a key biodiversity area for rare species like the endangered Golden-winged Laughingthrush and the Truong Son Muntjac. The Ngoc Linh Crocodile Newt certainly will represent another flagship species of this protected area and its surroundings, say the researchers.

Ngoc Linh has become a hotspot of amphibian diversity, with numerous endemic species. An earlier study – published in the Nature Conservation journal in 2022 – highlighted the extraordinary endemism rate of amphibians in the Central Highlands of Vietnam.

“[The Central Highlands is] where the highest amphibian species diversity was recorded for Vietnam, with 130 species, while also containing the highest number of regionally occurring, micro-endemic amphibians, amounting for 26 species,”
explains one of the authors of this and the present study, Prof. Dr. Truong Quang Nguyen, vice director of the Institute of Ecology and Biological Resources (IEBR), Hanoi.

Scientists identify gaps in the protection of Vietnam’s amphibians

This recent discovery is another remarkable case, “demonstrating that the Central Highlands play a special role in Vietnamese amphibian diversification and evolution,” by the words of co-author Dr. Cuong The Pham from IEBR.

The Ngoc Linh Crocodile Newt belongs to the group of range-restricted, so-called micro-endemic species, which face the greatest risk of extinction because of their presumably small population size. Unfortunately, on top of its special zoogeographic situation and rarity, its particularly colorful appearance will likely make it highly attractive to illegal collectors.

“Therefore, this discovery is of high conservation relevance,”
says one of the corresponding authors, Prof. Dr. Tao Thien Nguyen from the Institute of Genome Research, Hanoi.

The species should be provisionally considered to be listed as Endangered on the IUCN Red List of threatened species, the researchers say. All the species of the genus Tylototriton are already listed in the Appendices of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) and also in the Governmental Decree No. 84/2021/ND-CP of Vietnam. The new species thus is automatically protected under these regulations.

Now, conservation activities on site have priority, but the team is already working on breeding conservation measures, which is in line with the One Plan Approach to Conservation, developed by IUCN’s Conservation Planning Specialist Group, which combines in-situ and ex-situ efforts and various expertises for the optimum protection of a species.

“This has already been successfully implemented for another recently discovered, micro-endemic crocodile newt species from Vietnam, Tylototriton vietnamensis, of which already more than 350 individuals could have successfully been reproduced at the Cologne Zoo in Germany and also at the Melinh Station for Biodiversity in Vietnam, which is a promising example for IUCN’s Reverse the Red campaign and the idea of the conservation zoo”,
says Prof. Dr. Thomas Ziegler, Vietnam conservation team member and coordinator from Cologne Zoo, Germany.

***

Research article:

Phung TM, Pham CT, Nguyen TQ, Ninh HT, Nguyen HQ, Bernardes M, Le ST, Ziegler T, Nguyen TT (2023) Southbound – the southernmost record of Tylototriton (Amphibia, Caudata, Salamandridae) from the Central Highlands of Vietnam represents a new species. ZooKeys 1168: 193-218. https://doi.org/10.3897/zookeys.1168.96091

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Miniature Snail in a Rock Sandwich

First fossil record of thorn snails in the southern United States

Researchers from the USA and Switzerland, including Senckenberg scientist and first author Dr. Adrienne Jochum, have described the first fossil Carychium land snails from Florida. The rock layer containing the snail fossils, which are only a few millimeters in size, was accidentally uncovered during construction work and dates from the Pleistocene period between 2.58 million and 11,700 years ago. In their study, published in the open-access journal ZooKeys, the scientists also describe a previously unknown carychiid fossil species.

Light microscopic images of Carychium nashuaense.

The tiny snails of the genus Carychium with a maximum height of 2.5 millimeters and a width of 1.5 millimeters are known mostly east of the Mississippi River in the USA and from eastern Canada, Mexico and Jamaica as well as in sheltered humid habitats in Central America to Panama. “However, unlike the extant species, fossilized thorn snails are rarely found east of the Mississippi River. In our recent field work we have now provided the first fossil record of the genus in the southeastern United States, as well as the first fossil record ever for the species Carychium floridanum,” explains Dr. Adrienne Jochum of the Senckenberg Research Institute and Natural History Museum in Frankfurt and the Natural History Museum in Bern.

During the construction of a track bed for the Brightline railroad, which will connect Port Canaveral with Orlando International Airport, civil engineers accidentally came across a one-meter-thick layer of fossilized non-marine gastropods between two marine shell beds. “This ‘rock sandwich’ was formed during the Pleistocene, a geologic era characterized by repeated glaciations, climate changes, and fluctuations in water level that greatly influenced and shaped the region around present-day Florida. The shell layer is sandwiched between rock layers from the Lower Pleistocene, 2.58 to 0.77 million years ago, and the Upper Pleistocene, 140,000 to 120,000 years ago, and contains 14 freshwater and 28 terrestrial snail species.”

Later stage of excavation showing middle stratum of freshwater marl (c. 1 m thick) wedged between two layers of marine shell layers (each c. 3 m thick).

Among them is the snail Carychium floridanum, whose current representatives still live in humid, forested, and undisturbed habitats in central and northern Florida. The researchers also described a new species, Carychium nashuaense, which is less than 1.6 millimeters long and was previously unknown to science.

“To dislodge the fossil miniature snails from the rock layers, we first washed them through a graduated series of sieves. Next, 32 Carychium shells were culled under a microscope from a mixture of other mollusks and rock debris. A high-resolution X-ray tomograph helped us examine the spindle structure inside the fragile fossil shells and compare them with 3D reconstructions of the inner shell of still-living thorn snail species from the southeastern U.S., Mexico, Central America, and Jamaica,” explains Jochum.

While the design of the inner shell structure of Carychium floridanum has changed little from the Pleistocene to the present, the shell structure of Carychium nashuaense suggests a relationship with Central American Carychium relatives. “We suspect that the spread of the snails occurred via birds, mammals, and reptiles, who transported the small snails in their guts, fur, or feathers to the wetlands from which the alluvial sediments in the rock layer we studied originated. The subsequent mixing with other members of the genus led to the emergence of new species,” adds Jochum in conclusion.

***

Publication:

Jochum A, Bochud E, Haberthür D, Lee HG, Hlushchuk R, Portell RW (2023) Fossil Carychiidae (Eupulmonata, Ellobioidea) from the Lower Pleistocene Nashua Formation of Florida, with the description of a new species. ZooKeys 1167: 89-107.
https://doi.org/10.3897/zookeys.1167.102840

Press release originally published by Senckenberg. Republished with permission.

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Mapping our ecosystems: Pensoft joined the Horizon Europe project MAMBO

With expertise in science communication, dissemination and exploitation, Pensoft is involved in this project set to develop new technologies for monitoring species and their habitats across Europe

With expertise in science communication, dissemination and exploitation, Pensoft became part of this project dedicated to new technologies for species and habitat monitoring across Europe

Background

The European Union puts a great value in monitoring the health of ecosystems, as comprehensive mapping can aid policy makers’ work in adopting appropriate legislation for nature conservation. It allows for understanding the impact of human activities and making informed decisions for effective management of nature’s resources. This is particularly important for the EU, as it has set ambitious goals to halt biodiversity loss and restore degraded ecosystems by 2030, as outlined in the EU Biodiversity Strategy for 2030.

Effective biodiversity monitoring can help the EU track progress towards these goals, assess the effectiveness of conservation policies and initiatives, and identify emerging threats to biodiversity.

Despite this awareness, efforts to monitor animals and plants remain spatially and temporally fragmented. This lack of integration regarding data and methods creates a gap in biodiversity monitoring, which can negatively impact policy-making. Today, modern technologies such as drones, artificial intelligence algorithms, or remote sensing are still not widely used in biodiversity monitoring.

MAMBO project (Modern Approaches to the Monitoring of BiOdiversity) recognises this need and aims to develop, test, and implement enabling tools for monitoring conservation status and ecological requirements of species and habitats. Having started in late 2022, the project is set to run for four years until September 2026.

Pensoft – with its proven expertise in communicating scientific results – is committed to amplifying the impact of MAMBO. Pensoft supports the project through tailored approaches to communication, dissemination and exploitation so as to reach the most appropriate target audience and achieve maximum visibility of the project.

Deep-dive into the project

In order to enrich the biodiversity monitoring landscape, MAMBO will implement a multi-disciplinary approach by utilising the technical expertise in the fields of computer science, remote sensing, and social science expertise on human-technology interactions, environmental economy, and citizen science. This will be combined with knowledge on species, ecology, and conservation biology.

More specifically, the project will develop, evaluate and integrate image and sound recognition-based AI solutions for EU biodiversity monitoring from species to habitats as well as promote the standardised calculation and automated retrieval of habitat data using deep learning and remote sensing.

“Classification algorithms have matured to an extent where it is possible to identify organisms automatically from digital data, such as images or sound,”
comments project coordinator Prof. Toke T. Høye, Aarhus University.

“Technical breakthroughs in the realm of high spatial resolution remote sensing set the future of ecological monitoring and can greatly enrich traditional approaches to biodiversity monitoring.”

In order to achieve its goals, the project will test existing tools in combination with MAMBO-developed new technologies at the project’s demonstration sites geographically spread across Europe. This will contribute to an integrated European biodiversity monitoring system with potential for dynamic adaptations.

Pensoft is part of MAMBO’s Work Package 7 (WP7): “Science-policy interface and dissemination”, led by Helmholtz Centre for Environmental Research (UFZ). The work package is dedicated to providing a distinct identity of the project and its services through branding, visualisation and elaborated dissemination and communication strategy.

Within WP7, Pensoft will also be taking care after the launch of an open-science collection of research outputs in the scholarly journal Research Ideas and Outcomes (RIO).

Amongst the tasks of the partners in WP7 is also the development of different pathways for integrating new technologies and innovations into the EU Pollinators Monitoring Scheme (EU PoMS; SPRING).

Full list of partners

Aarhus University (AU)
Naturalis Biodiversity Centre (Naturalis)
Helmholtz Centre for Environmental Research (UFZ)
National Institute for Research in Digital Science and Technology (INRIA)
University of Amsterdam (UvA)
The French Agricultural Research Centre for International Development (CIRAD)
Pensoft Publishers (Pensoft)
Ecostack Innovations Limited (EcoINN)
University of Reading (UREAD)
UK Centre For Ecology & Hydrology (UKCEH)

You can find more about the project on the MAMBO website: mambo-project.eu. Stay up to date with the project’s progress on Twitter (@MAMBO_EU) and Linkedin (/MAMBO Project).

Protecting marine biodiversity: we take a look at science

In light of the UN’s High Seas Treaty, we look back at deep-sea science published in our journals.

Surely, March 2023 will be remembered with the historic agreement of UN member states to protect marine biodiversity in the world’s oceans.

The so-called High Seas Treaty is a legal framework for the protection of marine biodiversity and responsible and equitable use of resources of areas beyond national jurisdiction (BBJN). Its draft, published on the 5th of March 2023, is the outcome of two decades of negotiations, and is part of the international effort to protect a third of the world’s biodiversity by 2030.

An unwavering dedication to the protection and conservation of biodiversity will be required to see the firm landing of this hopeful step.

On this occasion, we look back at some impactful studies published in our journals that have made waves, hopefully in the right direction towards impactful conservation measures and actions.

Following President Barack Obama’s expansion of the largest permanent Marine Protected Area on Earth (Papahānaumokuākea Marine National Monument) in 2016, a new species of coral-reef fish was named in his honour. The fish is the only known coral-reef species to be endemic to the Monument, and, despite its small size, it carries wide-reaching cultural and political significance as a reminder of how politics go hand in hand with science.

Former President of the United States, Barack Obama, arriving on Midway Atoll Midway on September 1, 2016 to commemorate his use of the Antiquities Act to expand the boundaries of the Papahānaumokuākea Marine National Monument. Dr. Sylvia Earle gives President Barack Obama a photograph of *Tosanoides obama* on Midway Atoll, from the film “Sea of Hope: America’s Underwater Treasures” premiered on National Geographic Channel on January 15, 2017. See also the news story on National Geographic.

Other studies from our flagship zoology journal ZooKeys have focused on the benthic megafauna and abyssal fauna of the Clarion-Clipperton Zone (CCZ) in the Pacific Ocean.

The Clarion-Clipperton Zone, managed by the International Seabed Authority, has been targeted by deep-sea mining interests. In the context of heightened concern over potential biodiversity loss, scientific research is crucial for informing policy-makers and the general public about the risks and outcomes of such initiatives.

The Clarion-Clipperton Zone, central Pacific Ocean (purple box), spanning 6 milllion km². Knowledge of marine biodiversity in the area is crucial for its protection.
Image source: A. Glover at al. (2016).

The rich biodiversity of the deep sea has also been documented in big-scale taxonomic inventories and checklists in the Biodiversity Data Journal.

Such examples are the publication of 48 new echinoderm records from the CCZ made during a single 25-day cruise, marking a ~25% increase of the echinoderm species records previously available in databases. Other notable contributions are the first image atlas of annelid, arthropod, bryozoan, chordate, ctenophore and mollusc morphospecies and the first image atlas of echinoderm megafauna morphospecies inhabiting the UK-1 exploration contract area and the eastern CCZ.

The echinoderm *Amphioplus* cf. *daleus* Lyman, 1879. Image source: A. Glover at al.

*Hymenopenaeus* cf. *nereus* observed in the UK-1 exploration contract area.
Image source: Amon et al. (2017).

Going forward, the expansion of Marine Protected Areas should also ensure the implementation of policies for the methods of resource extraction and their equitable sharing and use among the world’s nations.

Over the next few years, we hope to see an ever increasing interest in biodiversity conservation - from the general public, stakeholders and policy makers, and, of course, research institutions.

 We need to love what we protect in order to be able to protect it.

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Unraveling nature’s chorus: AI detects bird sounds in Taiwan’s montane forests

Researchers developed an AI tool which identifies 169 species native to Taiwan from the sound of their calls.

Spectacular subtropical montane forest scenery in Yushan National Park. Credit: Ms. Wen-Ling Tsai

Montane forests, known as biodiversity hotspots, are among the ecosystems facing threats from climate change. To comprehend potential impacts of climate change on birds in these forests, researchers set up automatic recorders in Yushan National Park, Taiwan, and developed an AI tool for species identification using bird sounds. Their goal is to analyze status and trends in animal activity through acoustic data.

Prof. Hsueh-Wen Chang and Ph.D. Candidate Shih-Hung Wu from National Sun Yat-Sen University, Taiwan, Dr. Ruey-Shing Lin, Assistant Researcher Jerome Chie-Jen Ko from the Endemic Species Research Institute, and Ms. Wen-Ling Tsai from Yushan National Park Headquarters have published a paper in the open access journal Biodiversity Data Journal, detailing their use of AI to detect 6 million bird songs.

Compared to traditional observation-based methods, passive acoustic monitoring using automatic recorders to capture wildlife sounds provides cost-effective, long-term, and systematic alternative for long-term biodiversity monitoring.

The authors deployed six recorders in Yushan National Park, Taiwan, a subtropical montane forest habitat with elevations ranging from 1,200 to 2,800 meters. From 2020 to 2021, they recorded nearly 30,000 hours of audio files with abundant biological information.

An automatic recorder was installed on a tree to capture the surrounding soundscape. Credit: Ph.D. Candidate Shih-Hung Wu

However, analyzing this vast dataset is challenging and requires more than human effort alone.

To tackle this challenge, the authors utilized deep learning technology to develop an AI tool called SILIC that can identify species by sound.

SILIC can quickly pinpoint the precise timing of each animal call within the audio files. After several optimizations, the tool is now capable of recognizing 169 species of wildlife native to Taiwan, including 137 bird species, as well as frogs, mammals, and reptiles.

In this study, authors used SILIC to extract 6,243,820 vocalizations from seven montane forest bird species with a high precision of 95%, creating the first open-access AI-analyzed species occurrence dataset available on the Global Biodiversity Information Facility. This is the first open-access dataset with species occurrence data extracted from sounds in soundscape recordings by artificial intelligence.

The Gray-chinned Minivet (left) displays a secondary non-breeding season peak (right) which is possibly related to flocking behavior. Credit: Shih-Hung Wu, Ph.D. Candidate

The dataset unveils detailed acoustic activity patterns of wildlife across both short and long temporal scales. For instance, in diel patterns, the authors identify a morning vocalization peak for all species. On an annual basis, most species exhibit a single breeding season peak; however, some, like the Gray-chinned Minivet, display a secondary non-breeding season peak, possibly related to flocking behavior.

As the monitoring projects continue, the acoustic data may help to understand changes and trends in animal behavior and population across years in a cost-effective and automated manner.

The sound of Gray-chinned Minivet. Credit: Ph.D. Candidate Shih-Hung Wu

The authors anticipate that this extensive wildlife vocalization dataset will not be valuable only for the National Park’s headquarters in decision-making.

“We expect our dataset will be able to help fill the data gaps of fine-scale avian temporal activity patterns in montane forests and contribute to studies concerning the impacts of climate change on montane forest ecosystems,”
they say.

Original source:

Wu S-H, Ko JC-J, Lin R-S, Tsai W-L, Chang H-W (2023) An acoustic detection dataset of birds (Aves) in montane forests using a deep learning approach. Biodiversity Data Journal 11: e97811. https://doi.org/10.3897/BDJ.11.e97811

You can also follow Biodiversity Data Journal on Twitter and Facebook.

Japanese scientists use a novel research approach to study populations of deep-sea brittle stars

Researchers designed two new sets of PCR primers for the detection of brittle stars through eDNA metabarcoding.

For the first time, researchers developed a metabarcoding technology for brittle stars.

Japanese scientists, led by Dr Masanori Okanishi of the Hiroshima Shudo University and the University of Tokyo, analyzed environmental DNA (eDNA) released from marine invertebrates in the water, and successfully identified the species they were looking for. The study is published in the open-access journal Metabarcoding and Metagenomics.

Metabarcoding allows researchers to easily and quickly identify species and determine their number in a given location on the basis of environmental DNA (that is DNA released into, for example, the water in a particular lake).

In Japan, this method has been used successfully to detect the number of species in specific locations in the sea by sampling as little as a bucket of water. Monitoring species is part of the effort for conservation of biological resources and maintenance of their economic value, and metabarcoding can be utilized as a less labor-intensive and more cost-effective tool for marine surveys of biodiversity.

The new study reports on the research team’s development of the first DNA primers for metabarcoding of brittle stars.

Brittle stars are the most abundant species in the phylum Echinodermata (approximately 2,100 species), making them promising indicator organisms for environmental DNA metabarcoding. These marine invertebrates are thought to release abundant environmental DNA due to their size, large populations, and habitats in a variety of seafloor environments.

Brittle stars collected from Sagami Sea, Japan (credit: Hisanori Kohtsuka, The University of Tokyo)

To determine the origin of DNA sequences obtained from samples and used for metabarcoding, Okanishi’s team constructed a database of reference DNA sequences based on specimens identified to 60 brittle star species from Sagami Bay.

Up until now, metabarcoding had not been used for organisms with little mobility such as brittle stars, because many reference DNA sequences had been misidentified or unidentified. The new database will aid further research and application of the technology.

“If metabarcoding becomes possible through the development of additional primers and richer databases of reference DNA sequences, it will be possible to monitor the marine environment with a precision never before thought possible,”
say the authors in conclusion.

Original source: Okanishi M, Kohtsuka H, Wu Q, Shinji J, Shibata N, Tamada T, Nakano T, Minamoto T (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics 7: e94298. https://doi.org/10.3897/mbmg.7.94298

Expert Contact: Masanori Okanishi: Hiroshima Shudo University Assistant Professor. E-mail: okahoku@gmail.com

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Interoperable biodiversity data extracted from literature through open-ended queries

OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.

The OpenBiodiv contribution to BiCIKL

Apart from coordinating the Horizon 2020-funded project BiCIKL, scholarly publisher and technology provider Pensoft has been the engine behind what is likely to be the first production-stage semantic system to run on top of a reasonably-sized biodiversity knowledge graph.

OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.

As of February 2023, OpenBiodiv contains 36,308 processed articles; 69,596 taxon treatments; 1,131 institutions; 460,475 taxon names; 87,876 sequences; 247,023 bibliographic references; 341,594 author names; and 2,770,357 article sections and subsections.

In fact, OpenBiodiv is a whole ecosystem comprising tools and services that enable biodiversity data to be extracted from the text of biodiversity articles published in data-minable XML format, as in the journals published by Pensoft (e.g. ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal), and other taxonomic treatments – available from Plazi and Plazi’s specialised extraction workflow – into Linked Open Data.

“I believe that OpenBiodiv is a good real-life example of how the outputs and efforts of a research project may and should outlive the duration of the project itself. Something that is – of course – central to our mission at BiCIKL.”
explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft.

“The basics of what was to become the OpenBiodiv database began to come together back in 2015 within the EU-funded BIG4 PhD project of Victor Senderov, later succeeded by another PhD project by Mariya Dimitrova within IGNITE. It was during those two projects that the backend Ontology-O, the first versions of RDF converters and the basic website functionalities were created,”
he adds.

At the time OpenBiodiv became one of the nine research infrastructures within BiCIKL tasked with the provision of virtual access to open FAIR data, tools and services, it had already evolved into a RDF-based biodiversity knowledge graph, equipped with a fully automated extraction and indexing workflow and user apps.

Currently, Pensoft is working at full speed on new user apps in OpenBiodiv, as the team is continuously bringing into play invaluable feedback and recommendation from end-users and partners at BiCIKL.

As a result, OpenBiodiv is already capable of answering open-ended queries based on the available data. To do this, OpenBiodiv discovers ‘hidden’ links between data classes, i.e. taxon names, taxon treatments, specimens, sequences, persons/authors and collections/institutions.

Thus, the system generates new knowledge about taxa, scientific articles and their subsections, the examined materials and their metadata, localities and sequences, amongst others. Additionally, it is able to return information with a relevant visual representation about any one or a combination of those major data classes within a certain scope and semantic context.

Users can explore the database by either typing in any term (even if misspelt!) in the search engine available from the OpenBiodiv homepage; or integrating an Application Programming Interface (API); as well as by using SPARQL queries.

On the OpenBiodiv website, there is also a list of predefined SPARQL queries, which is continuously being expanded.

*Sample of predefined SPARQL queries at OpenBiodiv.*

“OpenBiodiv is an ambitious project of ours, and it’s surely one close to Pensoft’s heart, given our decades-long dedication to biodiversity science and knowledge sharing. Our previous fruitful partnerships with Plazi, BIG4 and IGNITE, as well as the current exciting and inspirational network of BiCIKL are wonderful examples of how far we can go with the right collaborators,”
concludes Prof Lyubomir Penev.

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