Tag: biodiversity loss

Scientists conceptualize a species ‘stock market’ to put a price tag on actions posing risks to biodiversity

“…the most realistic and tangible way out of the looming biodiversity crisis is to put a price tag on species and thereby a cost to actions that compromise them.”

So far, science has described more than 2 million species, and millions more await discovery. While species have value in themselves, many also deliver important ecosystem services to humanity, such as insects that pollinate our crops. 

Meanwhile, as we lack a standardized system to quantify the value of different species, it is too easy to jump to the conclusion that they are practically worthless. As a result, humanity has been quick to justify actions that diminish populations and even imperil biodiversity at large.

In a study, published in the scholarly open-science journal Research Ideas and Outcomes, a team of Estonian and Swedish scientists propose to formalize the value of all species through a conceptual species ‘stock market’ (SSM). Much like the regular stock market, the SSM is to act as a unified basis for instantaneous valuation of all items in its holdings.

However, other aspects of the SSM would be starkly different from the regular stock market. Ownership, transactions, and trading will take new forms. Indeed, species have no owners, and ‘trade’ would not be about transfer of ownership rights among shareholders. Instead, the concept of ‘selling’ would comprise processes that erase species from some specific area – such as war, deforestation, or pollution.

“The SSM would be able to put a price tag on such transactions, and the price could be thought of as an invoice that the seller needs to settle in some way that benefits global biodiversity,”

explains the study’s lead author Prof. Urmas Kõljalg (University of Tartu, Estonia).

Conversely, taking some action that benefits biodiversity – as estimated through individuals of species – would be akin to buying on the species stock market. Buying, too, has a price tag on it, but this price should probably be thought of in goodwill terms. Here, ‘money’ represents an investment towards increased biodiversity. 

“By rooting such actions in a unified valuation system it is hoped that goodwill actions will become increasingly difficult to dodge and dismiss,”

adds Kõljalg.

Interestingly, the SSM revolves around the notion of digital species. These are representations of described and undescribed species concluded to exist based on DNA sequences and elaborated by including all we know about their habitat, ecology, distribution, interactions with other species, and functional traits. 

For the SSM to function as described, those DNA sequences and metadata need to be sourced from global scientific and societal resources, including natural history collections, sequence databases, and life science data portals. Digital species might be managed further by incorporating data records of non-sequenced individuals, notably observations, older material in collections, and data from publications.

The study proposes that the SSM is orchestrated by the international associations of taxonomists and economists. 

“Non-trivial complications are foreseen when implementing the SSM in practice, but we argue that the most realistic and tangible way out of the looming biodiversity crisis is to put a price tag on species and thereby a cost to actions that compromise them,”

says Kõljalg.

“No human being will make direct monetary profit out of the SSM, and yet it’s all Earth’s inhabitants – including humans – that could benefit from its pointers.”

Original source

Kõljalg U, Nilsson RH, Jansson AT, Zirk A, Abarenkov K (2022) A price tag on species. Research Ideas and Outcomes 8: e86741. https://doi.org/10.3897/rio.8.e86741

***

Follow RIO Journal on Twitter and Facebook.

Pets or threats? Goldfish might be harmful for biodiversity

Goldfish pose a triple threat: not only are they readily available, but they combine insatiable appetites with bold behaviour

Invasive species are one of the leading causes of global biodiversity loss, and the pet trade is responsible for a third of all aquatic invasive species. Pet owners releasing unwanted pets into the wild is a major problem. Whilst many believe this is a humane option, a new research suggests that attempting to ‘save’ the life of a goldfish could in fact lead to catastrophic outcomes for native biodiversity.

To better understand the ecological risks posed by species within the pet trade, the researchers focused on the two most commonly traded fish species in Northern Ireland: goldfish and the white cloud mountain minnow.

Photo by Jeff-o-matic under a CC BY-NC 2.0 license

The globally popular goldfish was first domesticated over a thousand years ago and has since established non-native populations around the world. The white cloud mountain minnow on the other hand is a species with a limited invasion history to date.

This study, published in NeoBiota, developed a new method for assessing the ecological impacts and risks of potential pet trade invaders, based on availability, feeding rates and behaviour. The research showed goldfish to be voracious, consuming much more than the white cloud mountain minnow or native species. In terms of behaviour patterns, goldfish were also found to be much braver, a trait linked with invasive spread.

Dr James Dickey.

Lead author, Dr James Dickey from Queen’s University Belfast, explains: “Our research suggests that goldfish pose a triple threat. Not only are they readily available, but they combine insatiable appetites with bold behaviour. While northern European climates are often a barrier to non-native species surviving in the wild, goldfish are known to be tolerant to such conditions, and could pose a real threat to native biodiversity in rivers and lakes, eating up the resources that other species depend on.

“Our research highlights that goldfish are high risk, but we hope that the methods developed here can be used to assess others in the pet trade across Ireland and further afield. Readily available species are most likely to be released, so limiting the availability of potentially impactful ones, alongside better education of pet owners, is a solution to preventing damaging invaders establishing in the future.”

The research led by Queen’s University Belfast was funded by the Alexander von Humboldt Foundation, Inland Fisheries Ireland and the Department of Agriculture, Environment and Rural Affairs (DAERA) NI. The study was presented at the International Conference on Aquatic Invasive Species in Oostende, Belgium along with a range of other leading research from Queen’s on alien species.

Research article:

Dickey JWE, Arnott G, McGlade CLO, Moore A, Riddell GE, Dick JTA (2022) Threats at home? Assessing the potential ecological impacts and risks of commonly traded pet fishes. NeoBiota 73: 109–136. https://doi.org/10.3897/neobiota.73.80542

Simplified method to survey amphibians will aid conservation

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

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

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

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

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

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

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

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

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

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

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

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

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

Research Background

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

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

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

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

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

***

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

***

Research article: 

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

One water bucket to find them all: Detecting fish, mammals, and birds from a single sample

Revolutionary environmental DNA analysis holds great potential for the future of biodiversity monitoring, concludes a new study.

Revolutionary environmental DNA analysis holds great potential for the future of biodiversity monitoring, concludes a new study

Collection of water samples for eDNA metabarcoding bioassessment.
Photo by Till-Hendrik Macher.

In times of exacerbating biodiversity loss, reliable data on species occurrence are essential, in order for prompt and adequate conservation actions to be initiated. This is especially true for freshwater ecosystems, which are particularly vulnerable and threatened by anthropogenic impacts. Their ecological status has already been highlighted as a top priority by multiple national and international directives, such as the European Water Framework Directive.

However, traditional monitoring methods, such as electrofishing, trapping methods, or observation-based assessments, which are the current status-quo in fish monitoring, are often time- and cost-consuming. As a result, over the last decade, scientists progressively agree that we need a more comprehensive and holistic method to assess freshwater biodiversity.

Meanwhile, recent studies have continuously been demonstrating that eDNA metabarcoding analyses, where DNA traces found in the water are used to identify what organisms live there, is an efficient method to capture aquatic biodiversity in a fast, reliable, non-invasive and relatively low-cost manner. In such metabarcoding studies, scientists sample, collect and sequence DNA, so that they can compare it with existing databases and identify the source organisms.

Furthermore, as eDNA metabarcoding assessments use samples from water, often streams, located at the lowest point, one such sample usually contains not only traces of specimens that come into direct contact with water, for example, by swimming or drinking, but also collects traces of terrestrial species indirectly via rainfalls, snowmelt, groundwaters etc. 

In standard fish eDNA metabarcoding assessments, these ‘bycatch data’ are typically left aside. Yet, from a viewpoint of a more holistic biodiversity monitoring, they hold immense potential to also detect the presence of terrestrial and semi-terrestrial species in the catchment.

In their new study, reported in the open-access scholarly journal Metabarcoding and Metagenomics, German researchers from the University of Duisburg-Essen and the German Environment Agency successfully detected an astonishing quantity of the local mammals and birds native to the Saxony-Anhalt state by collecting as much as 18 litres of water from across a two-kilometre stretch along the river Mulde.

After water filtration the eDNA filter is preserved in ethanol until further processing in the lab.
Photo by Till-Hendrik Macher.

In fact, it took only one day for the team, led by Till-Hendrik Macher, PhD student in the German Federal Environmental Agency-funded GeDNA project, to collect the samples. Using metabarcoding to analyse the DNA from the samples, the researchers identified as much as 50% of the fishes, 22% of the mammal species, and 7.4% of the breeding bird species in the region. 

However, the team also concluded that while it would normally take only 10 litres of water to assess the aquatic and semi-terrestrial fauna, terrestrial species required significantly more sampling.

Unlocking data from the increasingly available fish eDNA metabarcoding information enables synergies among terrestrial and aquatic biodiversity monitoring programs, adding further important information on species diversity in space and time. 

“We thus encourage to exploit fish eDNA metabarcoding biodiversity monitoring data to inform other conservation programs,”

says lead author Till-Hendrik Macher. 

“For that purpose, however, it is essential that eDNA data is jointly stored and accessible for different biodiversity monitoring and biodiversity assessment campaigns, either at state, federal, or international level,”

concludes Florian Leese, who coordinates the project.

Original source:

Macher T-H, Schütz R, Arle J, Beermann AJ, Koschorreck J, Leese F (2021) Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species. Metabarcoding and Metagenomics 5: e66557. https://doi.org/10.3897/mbmg.5.66557

The first Red List of Taxonomists in Europe is calling for the support of insect specialists

The Red List of Taxonomists portal, where taxonomy experts in the field of entomology can register to help map and assess expertise across Europe, in order to provide action points necessary to overcome the risks, preserve and support this important scientific community, will remain open until 31st October 2021.

About 1,000 insect taxonomists – both professional and citizen scientists – from across the European region have already signed up on the Red List of Taxonomists, a recently launched European Commission-funded initiative by the Consortium of European Taxonomic Facilities (CETAF), the International Union for Conservation of Nature (IUCN) and the scholarly publisher best-known for its biodiversity-themed journals and high-tech innovations in biodiversity data publishing Pensoft.

Insect taxonomists, both professional and citizen scientists, are welcome to register on the Red List of Taxonomists portal at: red-list-taxonomists.eu and further disseminate the registration portal to fellow taxonomists until 31st October 2021.

Within the one-year project, the partners are to build a database of European taxonomy experts in the field of entomology and analyse the collected data to shed light on the trends in available expertise, including best or least studied insect taxa and geographic distribution of the scientists who are working on those groups. Then, they will present them to policy makers at the European Commission.

By recruiting as many as possible insect taxonomists from across Europe, the Red List of Taxonomists initiative will not only be able to identify taxa and countries, where the “extinction” of insect taxonomists has reached a critical point, but also create a robust knowledge base on taxonomic expertise across the European region to prompt further support and funding for taxonomy in the Old Continent.

On behalf of the project partners, we would like to express our immense gratitude to everyone who has self-declared as an insect taxonomist on the Red List of Taxonomists registration portal. Please feel welcome to share our call for participation with colleagues and social networks to achieve maximum engagement from everyone concerned about the future of taxonomy!

***

Read more about the rationale of the Red List of Taxonomists project.

***

Follow and join the conversation on Twitter using the #RedListTaxonomists hashtag. 

Recruiting participants to the first European Red list of insect taxonomists

Latest results of myriapod research from the 18th International Congress of Myriapodology

Last year, the 18th International Congress of Myriapodology brought together 92 of the world’s top experts on the curious, yet still largely unknown multi-legged centipedes, millipedes, pauropods, symphylans (collectively referred to as myriapods) and velvet worms (onychophorans).

Held between 25th and 31st August 2019 at the Hungarian Natural History Museum in Budapest and co-organised by the Hungarian Biological Society, the biennial event saw the announcement of the latest findings related to the diversity, distribution and biology of these creatures. Now, the public gets the chance to learn about a good part of the research presented there on the pages of the open-access scholarly journal ZooKeys.


Find all articles published in ZooKeys here
?

The special issue in ZooKeys, “Proceedings of the 18th International Congress of Myriapodology (25-31 August 2019, Budapest, Hungary)“, features a total of 11 research articles reporting on species new to science, updates on the distribution and conservation of already known myriapods and discoveries about the biology, ecology and evolution of individual species. Together, the publications reveal new insights into the myriapod life on four continents: Europe, Asia, Africa and Australia.

Amongst the published research outputs worth mentioning is the comparison between regional and global Red Listings of Threatened Species that worryingly identifies a missing overlap between the myriapod species included in the global IUCN Red List and the regional ones. This first-of-its-kind overview of the current conservation statuses of myriapods from around the world highlights the lack of dedicated funding for the conservation of hundreds of threatened myriapods. As a result, the scientists behind the study urge for the establishment of a Myriapoda Specialist Group in the Species Survival Commission of the IUCN.

Meanwhile, to give us a hint about how many millipedes are out there unbeknownst to the world and any conservation authorities, at the congress, three research teams revealed a total of seven new to science species: three giant pill-millipedes from Vietnam, another three from the biodiversity hotspot Madagascar and a spirostreptid millipede inhabiting Sao Tome and Principe.

Amongst the rest of the papers is the curious discovery of two Tasmanian species of flat-backed millipedes of the genus Tasmaniosoma whose neighbouring populations have seemingly come to their own terms to keep distance between each other, save for a little stretch of land, for no obvious reason. Not a single site where both species occur together was found by Dr Bob Mesibov, the millipede expert behind the study. How is the parapatric boundary maintained? How, when and where did the parapatry originate? These are the big mysteries that the already retired Australian scientist leaves for his successors to resolve.

###

All articles published in the “Proceedings of the 18th International Congress of Myriapodology (25-31 August 2019, Budapest, Hungary” special issue, edited by Dr. Zoltan Korsos (now University of Veterinary Medicine Budapest) and Dr. Laszlo Danyi (Hungarian Natural History Museum), are publicly available in the online, open-access, peer-reviewed scholarly journal ZooKeys.

###

Follow ZooKeys journal on Twitter and Facebook. Use #Myriapoda2019 to learn more about the studies published in the special issue.

Fifteen years & 20 million insects later: Sweden’s impressive effort to document its insect fauna in a changing world

The Swedish Malaise Trap Project (SMTP) was launched in 2003 with the aim of making a complete list of the insect diversity of Sweden. Over the past fifteen years, an estimated total of 20 million insects, collected during the project, have been processed for scientific study. Recently, the team behind this effort published the resulting inventory in the open-access journal Biodiversity Data Journal. In their paper, they also document the project all the way from its inception to its current status by reporting on its background, organisation, methodology and logistics.

The SMTP deployed a total of 73 Malaise traps – a Swedish invention designed to capture flying insects – and placed them across the country, where they remained from 2003 to 2006. Subsequently, the samples were sorted by a dedicated team of staff, students and volunteers into over 300 groups of insects ready for further study by expert entomologists. At the present time, this material can be considered as a unique timestamp of the Swedish insect fauna and an invaluable source of baseline data, which is especially relevant as reports of terrifying insect declines keep on making the headlines across the world.

The first author and Project Manager of the SMTP, Dave Karlsson started his academic paper on the project’s results years ago by compiling various tips, tricks, lessons and stories that he had accumulated over his years as SMTP’s Project Manager. Some fun examples include the time when one of the Malaise traps was destroyed by a moose bull rubbing his antlers against it, or when another trap was attacked and eaten by a group of 20 reindeer. The project even had a trap taken out by Sweden’s military! Karlsson’s intention was that, by sharing the details of the project, he would inspire and encourage similar efforts around the globe.

Animals were not as kind to our traps as humans,” recall the scientists behind the project. One of the Malaise traps, located in the Brännbergets Nature Reserve in Västerbotten, was destroyed by a bull moose rubbing his antlers against it.
Photo by Anna Wenngren

Karlsson has worked with and trained dozens of workers in the SMTP lab over the past decade and a half. Some were paid staff, some were enthusiastic volunteers and a good number were researchers and students using SMTP material for projects and theses. Thus, he witnessed first-hand how much excitement and enthusiasm the work on insect samples under a microscope can generate, even in those who had been hesitant about “bugs” at first.

Stressing the benefits of traditional morphological approaches to inventory work, he says: “Appreciation for nature is something you miss when you go ‘hi-tech’ with inventory work. We have created a unique resource for specialists in our sorted material while fostering a passion for natural history.”

Sorted SMTP material is now available to specialists. Hundreds of thousands of specimens have already been handed over to experts, resulting in over 1,300 species newly added to the Swedish fauna. A total of 87 species have been recognised as new to science from the project thus far, while hundreds more await description.

The SMTP is part of the Swedish Taxonomy Initiative, from where it also receives its funding. In its turn, the latter is a project by the Swedish Species Information Center, a ground-breaking initiative funded by the Swedish Parliament since 2002 with the aim of documenting all multicellular life in Sweden.

The SMTP is based at Station Linné, a field station named after the famous Swedish naturalist and father of taxonomy, Carl Linneaus. Situated on the Baltic island of Öland, the station is managed by Dave Karlsson. Co-authors Emily Hartop and Mathias Jaschhof are also based at the station, while Mattias Forshage and Fredrik Ronquist (SMTP Project Co-Founder) are based at the Swedish Museum of Natural History.

###

Original source:

Karlsson D, Hartop E, Forshage M, Jaschhof M, Ronquist F (2020) The Swedish Malaise Trap Project: A 15 Year Retrospective on a Countrywide Insect Inventory. Biodiversity Data Journal 8: e47255. https://doi.org/10.3897/BDJ.8.e47255

Illegal hunting and bushmeat trade threatens biodiversity and wildlife of Angola

Hunting and bushmeat trade negatively impact wildlife worldwide with serious implications for biodiversity conservation. The current situation in Angola shows a concerning increase in bushmeat trade along main roads. In a recent publication in the open-access journal Nature Conservation, an international group of scientists presented data gathered on a roundtrip around five main Angolan cities. It turned out that the influence of those activities on wildlife population is very unsettling.

Hunting wild animals has been practised by humans for millions of years; however, the extraction of wildlife for subsistence and commercialisation has become a major biodiversity threat in recent decades. Meanwhile, over-exploitation is reported to be the second most important driver of change and biodiversity loss globally. 

To assess the state of affairs, an international group of scientists, led by Dr. Francisco M. P. Gonçalves of the University of Hamburg in Germany, went on a roundtrip along the roads between five main Angolan cities. Their observations made it possible to conclude that, despite the existing legislation, as well as government efforts to handle poaching and bushmeat trade, currently there is no effective law enforcement mechanism to help dealing with the situation.

Map of Africa showing the location of Angola (left) and the provinces covered by the study along the main road from Lubango (Huíla province) to Uíge (right).
Credit: Francisco Maiato P. Gonçalves

In their study, the team also states that Angola is one of the richest and most biodiverse countries in Africa with an estimated 6,850 native and 226 non-native plant species, 940 bird species (including many endemic species), 117 amphibians species, 278 reptile species, 358 freshwater fishes (22% of them endemic) and 275 species of mammals.

The long-lasting civil war in Angola has contributed to the dramatic loss of wildlife and led to the near extinction of many species, as a result of the increase in illegal poaching. A variety of fresh, smoked or dried bushmeat, as well as live animals, are being sold along the roads, mostly to urban dwellers travelling between the main cities of Angola.

Despite the recent outbreaks of diseases (i.e. Ebola in the neighbouring Democratic Republic of Congo), animals still appear to be obtained directly from hunters and slaughtered with no sanitary measures, while the consumption of wildlife in Africa is frequently associated with an increased risk of acquiring zoonotic diseases.

The major trade road runs between the provinces of Bengo and Uíge, where the animals sold include many species of antelopes, monkeys, snakes and a globally protected species of pangolin (Manis tricuspis). Multiple species of wading birds and parrots are often sold in pet shops, as well as along the streets. At fairs and entry points to the main cities, these can be found offered by young boys.


Wild animals and smoked bushmeat on sale along the roadside of the Sequele village, between Bengo and Uíge provinces: Blue duikers, Talapoin and Vervet (green) monkey in the cage on the ground on the left,  Northern Rock Python on the right top and Tree pangolin (bottom right).
Photo by Francisco Maiato P. Gonçalves

Although there is no evidence of cross-border trade, there might, however, be cases of bushmeat trade in the informal markets at the principal border posts. Commercial activities between the countries are not regulated and stay intense, note the scientists.

“We witnessed a Chinese customer looking for pangolins in one of the villages; pangolin scales, when soaked, are trusted for having medicinal properties for a large variety of human illnesses mostly in Asia. It is currently estimated there are 0.4–0.7 million pangolins hunted annually, representing an increase of around 150% only for medicinal purposes over the past four decades,” share the researches.

Wild animals and smoked bushmeat on sale along the roadside of the Sequele village, between Bengo and Uíge provinces: Blue duikers, Talapoin and Vervet (green) monkey in the cage on the ground on the left, Northern Rock Python on the right top and Tree pangolin (bottom right).
Photo by Francisco Maiato P. Gonçalves

Trying to find a solution, the Angolan government has undertaken a number of measures, including: a list of species prohibited for hunting and trade (five of those species were found on the markets during the survey); banning hunting of certain species outside the hunting season; introducing compensation fees.

However, despite the legal basis, local authorities (i.e. police checkpoints close to the road markets) do not take the necessary measures to discourage hunting and bushmeat trade practices in the region. Due to lack of clear definition and responsibility arrangements, the hunting and trade of wild animals remain uncontrolled.

All these recent observations bring us to the necessity for a re-assessment of the wildlife in Angola and the need to produce appropriate legislation to be efficiently enforced across the whole territory of the country.  This can be achieved through better-educated police officials and alternative sources of meat supply in rural areas. These actions should bring down the demand for bushmeat and reduce the overharvesting of wildlife, suggest the scientists.

###

Original source:

Gonçalves FMP, Luís JC, Tchamba JJ, Cachissapa MJ, Chisingui AV (2019) A rapid assessment of hunting and bushmeat trade along the roadside between five Angolan major towns. Nature Conservation 37: 151-160. https://doi.org/10.3897/natureconservation.37.37590 


Data mining applied to scholarly publications to finally reveal Earth’s biodiversity

At a time when a million species are at risk of extinction, according to a recent UN report, ironically, we don’t know how many species there are on Earth, nor have we noted down all those that we have come to know on a single list. In fact, we don’t even know how many species we would have put on such a list.

The combined research including over 2,000 natural history institutions worldwide, produced an estimated ~500 million pages of scholarly publications and tens of millions of illustrations and species descriptions, comprising all we currently know about the diversity of life. However, most of it isn’t digitally accessible. Even if it were digital, our current publishing systems wouldn’t be able to keep up, given that there are about 50 species described as new to science every day, with all of these published in plain text and PDF format, where the data cannot be mined by machines, thereby requiring a human to extract them. Furthermore, those publications would often appear in subscription (closed access) journals.

The Biodiversity Literature Repository (BLR), a joint project ofPlazi, Pensoft and Zenodo at CERN, takes on the challenge to open up the access to the data trapped in scientific publications, and find out how many species we know so far, what are their most important characteristics (also referred to as descriptions or taxonomic treatments), and how they look on various images. To do so, BLR uses highly standardised formats and terminology, typical for scientific publications, to discover and extract data from text written primarily for human consumption.

By relying on state-of-the-art data mining algorithms, BLR allows for the detection, extraction and enrichment of data, including DNA sequences, specimen collecting data or related descriptions, as well as providing implicit links to their sources: collections, repositories etc. As a result, BLR is the world’s largest public domain database of taxonomic treatments, images and associated original publications.

Once the data are available, they are immediately distributed to global biodiversity platforms, such as GBIF–the Global Biodiversity Information Facility. As of now, there are about 42,000 species, whose original scientific descriptions are only accessible because of BLR.

The very basic principle in science to cite previous information allows us to trace back the history of a particular species, to understand how the knowledge about it grew over time, and even whether and how its name has changed through the years. As a result, this service is one avenue to uncover the catalogue of life by means of simple lookups.

So far, the lessons learned have led to the development of TaxPub, an extension of the United States National Library of Medicine Journal Tag Suite and its application in a new class of 26 scientific journals. As a result, the data associated with articles in these journals are machine-accessible from the beginning of the publishing process. Thus, as soon as the paper comes out, the data are automatically added to GBIF.

While BLR is expected to open up millions of scientific illustrations and descriptions, the system is unique in that it makes all the extracted data findable, accessible, interoperable and reusable (FAIR), as well as open to anybody, anywhere, at any time. Most of all, its purpose is to create a novel way to access scientific literature.

To date, BLR has extracted ~350,000 taxonomic treatments and ~200,000 figures from over 38,000 publications. This includes the descriptions of 55,800 new species, 3,744 new genera, and 28 new families. BLR has contributed to the discovery of over 30% of the ~17,000 species described annually.

Prof. Lyubomir Penev, founder and CEO of Pensoft says,

“It is such a great satisfaction to see how the development process of the TaxPub standard, started by Plazi some 15 years ago and implemented as a routine publishing workflow at Pensoft’s journals in 2010, has now resulted in an entire infrastructure that allows automated extraction and distribution of biodiversity data from various journals across the globe. With the recent announcement from the Consortium of European Taxonomic Facilities (CETAF) that their European Journal of Taxonomy is joining the TaxPub club, we are even more confident that we are paving the right way to fully grasping the dimensions of the world’s biodiversity.”

Dr Donat Agosti, co-founder and president of Plazi, adds:

“Finally, information technology allows us to create a comprehensive, extended catalogue of life and bring to light this huge corpus of cultural and scientific heritage – the description of life on Earth – for everybody. The nature of taxonomic treatments as a network of citations and syntheses of what scientists have discovered about a species allows us to link distinct fields such as genomics and taxonomy to specimens in natural history museums.”

Dr Tim Smith, Head of Collaboration, Devices and Applications Group at CERN, comments:

“Moving the focus away from the papers, where concepts are communicated, to the concepts themselves is a hugely significant step. It enables BLR to offer a unique new interconnected view of the species of our world, where the taxonomic treatments, their provenance, histories and their illustrations are all linked, accessible and findable. This is inspirational for the digital liberation of other fields of study!”

###

Additional information:

BLR is a joint project led by Plazi in partnership with Pensoft and Zenodo at CERN.

Currently, BLR is supported by a grant from Arcadia, a charitable fund of Lisbet Rausing and Peter Baldwin.

‘Insectageddon’ is ‘alarmist by bad design’: Scientists point out the study’s major flaws

Many insects species require pristine environments, including old-growth forests. Photo by Atte Komonen.

Earlier this year, a research article triggered a media frenzy by predicting that as a result of an ongoing rapid decline, nearly half of the world’s insects will be no more pretty soon

Amidst worldwide publicity and talks about ‘Insectageddon’: the extinction of 40% of the world’s insects, as estimated in a recent scientific review, a critical response was published in the open-access journal Rethinking Ecology.

Query- and geographically-biased summaries; mismatch between objectives and cited literature; and misuse of existing conservation data have all been identified in the alarming study, according to Drs Atte Komonen, Panu Halme and Janne Kotiaho of the University of Jyväskylä (Finland). Despite the claims of the review paper’s authors that their work serves as a wake-up call for the wider community, the Finnish team explain that it could rather compromise the credibility of conservation science.

The first problem about the paper, titled “Worldwide decline of the entomofauna: A review of its drivers” and published in the journal Biological Conservation, is that its authors have queried the Web of Science database specifically using the keywords “insect”, “decline” and “survey”.

“If you search for declines, you will find declines. We are not questioning the conclusion that insects are declining,” Komonen and his team point out, “but we do question the rate and extent of declines.”

Many butterflies have declined globally. Scolitantides orion, for example, is an endangered species in Finland. Photo by Atte Komonen.

The Finnish research team also note that there are mismatches between methods and literature, and misuse of IUCN Red List categories. The review is criticised for grouping together species, whose conservation status according to the International Union for Conservation of Nature (IUCN) is Data Deficient with those deemed Vulnerable. By definition, there are no data for Data Deficient species to assess their declines.

In addition, the review paper is seen to use “unusually forceful terms for a peer-reviewed scientific paper,” as the Finnish researchers quote a recent news story published in The Guardian. Having given the words dramatic, compelling, extensive, shocking, drastic, dreadful, devastating as examples, they add that that such strong intensifiers “should not be acceptable” in research articles.

“As actively popularising conservation scientists, we are concerned that such development is eroding the importance of the biodiversity crisis, making the work of conservationists harder, and undermining the credibility of conservation science,” the researchers explain the motivation behind their response.

###

Original source:

Komonen A, Halme P, Kotiaho JS (2019) Alarmist by bad design: Strongly popularized unsubstantiated claims undermine credibility of conservation science. Rethinking Ecology 4: 17-19. https://doi.org/10.3897/rethinkingecology.4.34440