How to ensure biodiversity data are FAIR, linked, open and future-proof?

Now concluded Horizon 2020-funded project BiCIKL shares lessons learned with policy-makers and research funders

Within the Biodiversity Community Integrated Knowledge Library (BiCIKL) project, 14 European institutions from ten countries, spent the last three years elaborating on services and high-tech digital tools, in order to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of various types of data about the world’s biodiversity. These types of data include peer-reviewed scientific literature, occurrence records, natural history collections, DNA data and more.

By ensuring all those data are readily available and efficiently interlinked to each other, the project consortium’s intention is to provide better tools to the scientific community, so that it can more rapidly and effectively study, assess, monitor and preserve Earth’s biological diversity in line with the objectives of the likes of the EU Biodiversity Strategy for 2030 and the European Green Deal. Their targets require openly available, precise and harmonised data to underpin the design of effective measures for restoration and conservation, reminds the BiCIKL consortium.

Since 2021, the project partners at BiCIKL have been working together to elaborate existing workflows and links, as well as create brand new ones, so that their data resources, platforms and tools can seamlessly communicate with each other, thereby taking the burden off the shoulders of scientists and letting them focus on their actual mission: paving the way to healthy and sustainable ecosystems across Europe and beyond.

Now that the three-year project is officially over, the wider scientific community is yet to reap the fruits of the consortium’s efforts. In fact, the end of the BiCIKL project marks the actual beginning of a European- and global-wide revolution in the way biodiversity scientists access, use and produce data. It is time for the research community, as well as all actors involved in the study of biodiversity and the implementation of regulations necessary to protect and preserve it, to embrace the lessons learned, adopt the good practices identified and build on the knowledge in existence.

This is why amongst the BiCIKL’s major final research outputs, there are two Policy Briefs meant to summarise and highlight important recommendations addressed to key policy makers, research institutions and funders of research. After all, it is the regulatory bodies that are best equipped to share and implement best practices and guidelines.

Most recently, the BiCIKL consortium published two particularly important policy briefs, both addressed to the likes of the European Commission’s Directorate-General for Environment; the European Environment Agency; the Joint Research Centre; as well as science and policy interface platforms, such as the EU Biodiversity Platform; and also organisations and programmes, e.g. Biodiversa+ and EuropaBON, which are engaged in biodiversity monitoring, protection and restoration. The policy briefs are also to be of particular use to national research funds in the European Union.

One of the newly published policy briefs, titled “Uniting FAIR data through interlinked, machine-actionable infrastructures”, highlights the potential benefits derived from enhanced connectivity and interoperability among various types of biodiversity data. The publication includes a list of recommendations addressed to policy-makers, as well as nine key action points. Understandably, amongst the main themes are those of wider international cooperation; inclusivity and collaboration at scale; standardisation and bringing science and policy closer to industry. Another major outcome of the BiCIKL project: the Biodiversity Knowledge Hub portal is noted as central to many of these objectives and tasks in its role of a knowledge broker that will continue to be maintained and updated with additional FAIR data-compliant services as a living legacy of the collaborative efforts at BiCIKL.

The second policy brief, titled “Liberate the power of biodiversity literature as FAIR digital objects”, shares key actions that can liberate data published in non-machine actionable formats and non-interoperable platforms, so that those data can also be efficiently accessed and used; as well as ways to publish future data according to the best FAIR and linked data practices. The recommendations highlighted in the policy brief intend to support decision-making in Europe; expedite research by making biodiversity data immediately and globally accessible; provide curated data ready to use by AI applications; and bridge gaps in the life cycle of research data through digital-born data. Several new and innovative workflows, linkages and integrative mechanisms and services developed within BiCIKL are mentioned as key advancements created to access and disseminate data available from scientific literature. 

While all policy briefs and factsheets – both primarily targeted at non-expert decision-makers who play a central role in biodiversity research and conservation efforts – are openly and freely available on the project’s website, the most important contributions were published as permanent scientific records in a BiCIKL-branded dedicated collection in the peer-reviewed open-science journal Research Ideas and Outcomes (RIO). There, the policy briefs are provided as both a ready-to-print document (available as supplementary material) and an extensive academic publication.

Currently, the collection: “Towards interlinked FAIR biodiversity knowledge: The BiCIKL perspective” in the RIO journal contains 60 publications, including policy briefs, project reports, methods papers, conference abstracts, demonstrating and highlighting key milestones and project outcomes from along the BiCIKL’s journey in the last three years. The collection also features over 15 scientific publications authored by people not necessarily involved in BiCIKL, but whose research uses linked open data and tools created in BiCIKL. Their publications were published in a dedicated article collection in the Biodiversity Data Journal.

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Visit the Biodiversity Community Integrated Knowledge Library (BiCIKL) project’s website at: https://bicikl-project.eu/.

Don’t forget to also explore the Biodiversity Knowledge Hub (BKH) for yourself at: https://biodiversityknowledgehub.eu/ and watch the BKH’s introduction video

Highlights from the BiCIKL project are also accessible on Twitter/X from the project’s hashtag: #BiCIKL_H2020 and handle: @BiCIKL_H2020.

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 (1174th) 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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Don’t forget to also keep up-to-date with the latest publications in ZooKeys by following the journal on Twitter and Facebook.

You can also sign up for the journal newsletter from the ZooKeys homepage.

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.

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.

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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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Under Extinction Pressure: Rare Australian bee found after 100 years

A widespread field search for a rare Australian native bee (Pharohylaeus lactiferus) that had not been recorded for almost a century found the species has been there all along – but is probably under increasing pressure to survive. Prior to this study, only six individuals had been found, with the last published record of this Australian endemic bee species, from 1923 in Queensland.

Male Pharohylaeus lactiferus bee. Photo by James Dorey.

A widespread field search for a rare Australian native bee (Pharohylaeus lactiferus) that had not been recorded for almost a century found the species has been there all along – but is probably under increasing pressure to survive. Prior to this study, only six individuals had been found, with the last published record of this Australian endemic bee species, from 1923 in Queensland.

“This is concerning because it is the only Australian species in the Pharohylaeus genus and nothing was known of its biology,”

Flinders University researcher and biological sciences PhD candidate James Dorey says in the new scientific paper in the peer-reviewed, open-access Journal of Hymenoptera Research.

The ‘hunt’ began after bee experts Olivia Davies and Dr Tobias Smith raised the possibility of the species’ extinction based on the lack of any recent sightings. The ‘rediscovery’ followed an extensive sampling of 225 general and 20 targeted sampling sites across New South Wales and Queensland.

Along with extra bee and vegetation recordings from the Atlas of Living Australia, which lists 500 bee species in New South Wales and 657 in Queensland, the Flinders researchers sought to assess the latest levels of true diversity, warning that habitat loss and fragmentation of Australia’s rainforests, along with wildfires and climate change, are likely to put extinction pressure on this and other invertebrate species.  

“Three populations of P. lactiferous were found by sampling bees visiting their favoured plant species along much of the Australian east coast, suggesting population isolation,”

Mr Dorey reports.

Highly fragmented habitat and potential host specialisation might explain the rarity of P. lactiferus.

Additionally, the scientists remind of previous findings that Australia has already cleared more than 40% of its forests and woodlands since European colonisation, leaving much of the remainder fragmented and degraded.

“My geographical analyses used to explore habitat destruction in the Wet Tropics and Central Mackay Coast bioregions indicate susceptibility of Queensland rainforests and P. lactiferus populations to bushfires, particularly in the context of a fragmented landscape,”

Mr Dorey says.

The study also warns the species is even more vulnerable as they appear to favour specific floral specimens and were only found near tropical or sub-tropical rainforest – a single vegetation type.

“Collections indicate possible floral and habitat specialisation with specimens only visiting firewheel trees (Stenocarpus sinuatu), and Illawarra flame trees (Brachychiton acerifolius), to the exclusion of other available floral resources.”

Known populations of P. lactiferus remain rare and susceptible to habitat destruction (e.g. caused by changed land use or events such as fires), the paper concludes.

“Future research should aim to increase our understanding of the biology, ecology and population genetics of P. lactiferus.”

Female Pharohylaeus lactiferus bee. Photo by James Dorey.

“If we are to understand and protect these wonderful Australian species, we really need to increase biomonitoring and conservation efforts, along with funding for the museum curation and digitisation of their collections and other initiatives,”  

Mr Dorey says.

Research paper:

Dorey JB (2021) Missing for almost 100 years: the rare and potentially threatened bee, Pharohylaeus lactiferus (Hymenoptera, Colletidae). Journal of Hymenoptera Research 81: 165-180. https://doi.org/10.3897/jhr.81.59365

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New tarantula species from Angola distinct with a one-of-a-kind ‘horn’ on its back

A new to science species of tarantula with a peculiar horn-like protuberance sticking out of its back was recently identified from Angola, a largely underexplored country located at the intersection of several Afrotropical ecoregions.

Collected as part of the National Geographic Okavango Wilderness Project, which aims to uncover the undersampled biodiversity in the entire Okavango catchment of Angola, Namibia and Botswana, thereby paving the way for sustainable conservation in the area, the new arachnid is described in a paper published in the open-access journal African Invertebrates by the team of Drs John Midgley and Ian Engelbrecht.

Although the new spider (Ceratogyrus attonitifer sp.n.) belongs to a group known as horned baboon spiders, the peculiar protuberance is not present in all of these species. Moreover, in the other species – where it is – the structure is completely sclerotised, whereas the Angolan specimens demonstrate a soft and characteristically longer ‘horn’. The function of the curious structure remains unknown.

The new tarantula’s extraordinary morphology has also prompted its species name: C. attonitifer, which is derived from the Latin root attonit– (“astonishment” or “fascination”), and the suffix –fer (“bearer of” or “carrier”). It refers to the astonishment of the authors upon the discovery of the remarkable species.

“No other spider in the world possesses a similar foveal protuberance,” comment the authors of the paper.

Individual of the newly described species in defensive posture in its natural habitat. Photo by Kostadine Luchansky.

During a series of surveys between 2015 and 2016, the researchers collected several female specimens from the miombo forests of central Angola. To find them, the team would normally spend the day locating burrows, often hidden among grass tufts, but sometimes found in open sand, and excavate specimens during the night. Interestingly, whenever the researchers placed an object in the burrow, the spiders were quick and eager to attack it.

The indigenous people in the region provided additional information about the biology and lifestyle of the baboon spider. While undescribed and unknown to the experts until very recently, the arachnid has long been going by the name “chandachuly” among the local tribes. Thanks to their reports, information about the animal’s behaviour could also be noted. The tarantula tends to prey on insects and the females can be seen enlarging already existing burrows rather than digging their own. Also, the venom of the newly described species is said to not be dangerous to humans, even though there have been some fatalities caused by infected bites gone untreated due to poor medical access.

In conclusion, the researchers note that the discovery of the novel baboon spider from Angola does not only extend substantially the known distributional range of the genus, but can also serve as further evidence of the hugely unreported endemic fauna of the country:

“The general paucity of biodiversity data for Angola is clearly illustrated by this example with theraphosid spiders, highlighting the importance of collecting specimens in biodiversity frontiers.”

Apart from the described species, the survey produced specimens of two other potentially new to science species and range expansions for other genera. However, the available material is so far insufficient to formally diagnose and describe them.

The newly described baboon spider species (Ceratogyrus attonitifer), showing the peculiar soft and elongated horn-like protuberance sticking out of its back. Photo by Dr Ian Enelbrecht.

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Original source:

Midgley JM, Engelbrecht I (2019) New collection records for Theraphosidae (Araneae, Mygalomorphae) in Angola, with the description of a remarkable new species of Ceratogyrus. African Invertebrates 60(1): 1-13. https://doi.org/10.3897/afrinvertebr.60.32141

Pensoft journals integrated with Catalogue of Life to help list the species of the world

While not every taxonomic study is conducted with a nature conservation idea in mind, most ecological initiatives need to be backed by exhaustive taxonomic research. There simply isn’t a way to assess a species’ distributional range, migratory patterns or ecological trends without knowing what this species actually is and where it is coming from.

In order to facilitate taxonomic and other studies, and lay the foundations for effective biodiversity conservation in a time where habitat loss and species extinction are already part of our everyday life, the global organisation Catalogue of Life (CoL) works together with major programmes, including GBIFEncyclopedia of Life and the IUCN Red List, to collate the names of all species on the planet set in the context of a taxonomic hierarchy and their distribution.

Recently, the scholarly publisher and technological provider Pensoft has implemented a new integration with CoL, so that it joins in the effort to encourage authors publishing global taxonomic review in any of the publisher’s journals to upload their taxonomic contributions to the database.

Whenever authors submit a manuscript containing a world revision or checklist of a taxon to a Pensoft journal, they are offered the possibility to upload their datasets in CoL-compliant format, so that they can contribute to CoL, gain more visibility and credit for their work, and support future research and conservation initiatives.

Once the authors upload the dataset, Pensoft will automatically notify CoL about the new contribution, so that the organisation can further process the knowledge and contact the authors, if necessary.

In addition, CoL will also consider for indexing global taxonomic checklists, which have already been published by Pensoft.

It is noteworthy to mention that unlike an automated search engine, CoL does not simply gather the uploaded data and store them. All databases in CoL are thoroughly reviewed by experts in the relevant field and comply with a set of explicit instructions.

“Needless to say that the Species 2000 / Catalogue of Life community is very happy with this collaboration,” says Dr. Peter Schalk, Executive Secretary.

“It is essential that all kinds of data and information sharing initiatives in the realm of taxonomy and biodiversity science get connected, in order to provide integrated quality services to the users in and outside of our community. The players in this field carry responsibility to forge partnerships and collaborations that create added value for science and society and are mutually reinforcing for the participants. Our collaboration is a fine example how this can be achieved,” he adds.

“With our extensive experience in biodiversity research, at Pensoft we have already taken various steps to encourage and support data sharing practices,” says Prof. Lyubomir Penev, Pensoft’s founder and CEO. To better serve this purpose, last year, we even published a set of guidelines and strategies for scholarly publishing of biodiversity data as recommended by our own experience. Furthermore, at our Biodiversity Data Journal, we have not only made the publication of open data mandatory, but we were also the first to implement integrated narrative and data publication within a single paper.”

“It only makes sense to collaborate with organisations, such as Catalogue of Life, to make sure that all these global indexers are up-to-date and serve the world’s good in preserving our wonderful biodiversity,” he concludes.