Since 2013, following a strict enforcement of provincial wildlife legislation in the less studied regions of Asia, the overall trend of illegal reptile poaching is steadily decreasing. Despite that, the issue is not yet resolved and poached reptiles are largely destined not only for the international pet trade, but also utilised in folk medicines and snake charmer shows, according to a recent study, published in the open-access journal Herpetozoa.
Since 2013, following a strict enforcement of provincial wildlife legislation in the less studied regions of Asia, the overall trend of illegal reptile poaching is steadily decreasing. But it’s too early to claim that the issue is solved. Poached reptiles are largely destined not only for the pet trade, but also folk medicines and snake charmer shows, according to the recent study led by the scientists from the Pakistan Museum of Natural History and the University of Peshawar published in the open-access journal Herpetozoa.
For the first time, the exploitation of reptiles for the pet trade has come to the attention of the public in the late 1960s. In general, illegal poaching is one of the problems we still face a lot all over the world, despite strict restrictions which are coming in force massively over the last decades. The wildlife trade leads not only to biodiversity loss (through capture of protected species), but also threatens with a possible spread of animal-borne diseases, due to interspecies contact at pet and folk medicine markets. The case of the recent COVID-19 pandemic gives a lesson to learn, and in order to stop further occurrences, a focus on law-enforcement activities should be brought to wildlife trade hotspots.
In the particular case of Pakistan, a country with high species diversity of reptiles, still very little is known about the links between illegal wildlife trade and wildlife decline. The illegal poaching and trade in Pakistan are largely undocumented and it’s difficult to bring accurate data since the trade involves many channels and follows informal networks. There is marginal information available about the medicinal use of wild flora and fauna for some parts of Pakistan, but there is no report on the commercialisation, harvest, market dynamics and conservation impact of these activities.
Since 2013, a number of confiscations of different reptile species and their parts from Pakistani nationals have been reported widely from across the country, which resulted in the enforcement of legislations regarding the wildlife trade in Pakistan.
An international team of researchers, led by Dr. Rafaqat Masroor from Pakistan Museum of Natural History investigated the extent of illegal reptile collection in southwestern Balochistan. Scientists tried to determine what impact these activities might have on the wild populations.
A topographic map of southwestern Balochistan showing visit sites in Chagai, Nushki, Panjgur, Kharan and Washuk districts. Credit: Rafaqat Masroor License: CC-BY 4.0
The field trips, conducted in 2013-2017, targeted Chagai, Nushki, Panjgur, Kharan and Washuk districts in Balochistan province. Over those years, scientists interviewed 73 illegal collectors. Most of the collectors worked in groups, consisting of males, aged between 14 to 50 years.
“They were all illiterate and their sole livelihood was based on reptile poaching, trade, and street shows. These collectors were well-organized and had trapping equipment for the collection of reptiles. […] These groups were locally known as “jogeez”, who mainly originated from Sindh Province and included snake charmers, having their roots deep with the local hakeems (herbal medicine practitioners) and wildlife traders, businessmen and exporters based at Karachi city. […] We often observed local people killing lizards and snakes, mostly for fear of venom and part for fun and centuries-old myths”,
share Dr. Masroor.
A total number of illegally poached reptiles, recorded during the investigation, results in 5,369 specimens representing 19 species. All of them had already been declared Protected under Schedule-III of the Balochistan Provincial Wildlife Act.
A view of live reptiles. Lytorhynchus maynardi and Eryx tataricus speciosus, the two rarely encountered snakes inside the locally-made boxes. Credit: Rafaqat Masroor License: CC-BY 4.0
Amongst the reasons for the province of Balochistan to remain unexplored might have been the lack of government environmental and wildlife protection agencies, lack of resources and specialists of high qualification in the provincial wildlife, forest and environment departments, as well as geopolitical position and remoteness of vast tracts of areas.
Number of specimens collected against the number of individuals (illegal collectors). Credit: Rafaqat Masroor License: CC-BY 4.0
Scientists call for the provincial and federal government to take action and elaborate a specific strategy for the conservation of endemic and threatened species as a part of the country’s natural heritage both in southwestern Balochistan and whole Pakistan. The conservation plan needs to be consulted with specialists in the respective fields, in order to avoid incompetence.
Also, the research group suggests to strictly ban illegal poaching of venomous snakes for the purpose of venom extraction.
What is important to remember is that Balochistan represents one of the most important areas of Asia with a high number of endemic reptile species. The illegal capture of these species presents a threat to the poorly documented animals. Even though the current trend for captured reptiles is decreasing, more actions are needed, in order to ensure the safety of the biodiversity of the region.
Contact:
Dr. Rafaqat Masroor Email: rafaqat.masroor78@gmail.com
Original source:
Masroor R, Khisroon M, Jablonski D (2020) A case study on illegal reptile poaching from Balochistan, Pakistan. Herpetozoa 33: 67-75. https://doi.org/10.3897/herpetozoa.33.e51690
Gene drive organisms (GDOs) have been suggested as an approach to solve some of the most pressing environmental and public health issues. Currently, it remains unclear what kind of regulations are to be used to cover the potential risks. In their study, published in the open-access journal BioRisk, scientists evaluate the options for an operational risk assessment of GDOs before their release into environments across the EU.
EU scientists are taking a closer look into the CRISPR/Cas-9-induced population-wide genetic modifications before introducing it into practice
Within the last decades, new genetic engineering tools for manipulating genetic material in plants, animals and microorganisms are getting large attention from the international community, bringing new challenges and possibilities. While genetically modified organisms (GMO) have been known and used for quite a while now, gene drive organisms (GDO) are yet at the consideration and evaluation stage.
The difference between these two technologies, where both are meant to replace certain characters in animals or plants with ones that are more favourable for the human population, is that, even though in GDO there is also foreign “synthetic” DNA being introduced, the inheritance mode differs. In GDO, the genome’s original base arrangements are changed, using CRISPR/Cas-9 genome editing. Once the genome is changed, its alterations are carried down the organism’s offspring and subsequent generations.
In their study, published in the open-access journal Biorisk, an international group of scientists led by Marion Dolezel from the Environment Agency Austria, discuss the potential risks and impacts on the environment.
The research team also points to current regulations addressing invasive alien species and biocontrol agents, and finds that the GMO regulations are, in principle, also a useful starting point for GDO.
There are three main areas suggested to benefit from gene drive systems: public health (e.g. vector control of human pathogens), agriculture (e.g. weed and pest control), environmental protection and nature conservation (e.g. control of harmful non-native species).
In recent years, a range of studies have shown the feasibility of synthetic CRISPR-based gene drives in different organisms, such as yeast, the common fruit fly, mosquitoes and partly in mammals.
Given the results of previous research, the gene drive approach can even be used as prevention for some zoonotic diseases and, hence, possible future pandemics. For example, laboratory tests showed that release of genetically modified mosquitoes can drastically reduce the number of malaria vectors. Nevertheless, potential environment and health implications, related to the release of GDO, remain unclear. Only a few potential applications have so far progressed to the research and development stage.
“The potential of GDOs for unlimited spread throughout wild populations, once released, and the apparently inexhaustible possibilities of multiple and rapid modifications of the genome in a vast variety of organisms, including higher organisms such as vertebrates, pose specific challenges for the application of adequate risk assessment methodologies”,
shares the lead researcher Mrs. Dolezel.
In the sense of genetic engineering being a fastly developing science, every novel feature must be taken into account, while preparing evaluations and guidances, and each of them provides extra challenges.
Today, the scientists present three key differences of gene drives compared to the classical GMO:
1. Introducing novel modifications to wild populations instead of “familiar” crop species, which is a major difference between “classic” GMOs and GDOs.
“The goal of gene drive applications is to introduce a permanent change in the ecosystem, either by introducing a phenotypic change or by drastically reducing or eradicating a local population or a species. This is a fundamental difference to GM crops for which each single generation of hybrid seed is genetically modified, released and removed from the environment after a relatively short period”,
shares Dolezel.
2. Intentional and potentially unlimited spread of synthetic genes in wild populations and natural ecosystems.
Gene flow of synthetic genes to wild organisms can have adverse ecological impact on the genetic diversity of the targeted population. It could change the weediness or invasiveness of certain plants, but also threaten with extinction the species in the wild.
3. Possibility for long-term risks to populations and ecosystems.
Key and unique features of GDOs are the potential long-term changes in populations and large-scale spread across generations.
In summary, the research team points out that, most of all, gene drive organisms must be handled extremely carefully, and that the environmental risks related to their release must be assessed under rigorous scrutiny. The standard requirements before the release of GDOs need to also include close post-release monitoring and risk management measures.
It is still hard to assess with certainty the potential risks and impact of gene drive applications on the environment, human and animal health. That’s why highly important questions need to be addressed, and the key one is whether genetically driven organisms are to be deliberately released into the environment in the European Union. The High Level Group of the European Commission’s Scientific Advice Mechanism highlights that within the current regulatory frameworks those risks may not be covered.
The research group recommends the institutions to evaluate whether the regulatory oversight of GMOs in the EU is accomodate to cover the novel risks and challenges posed by gene drive applications.
“The final decision to release GDOs into the environment will, however, not be a purely scientific question, but will need some form of broader stakeholder engagement and the commitment to specific protection goals for human health and the environment”,
concludes Dolezel.
***
Original source: Dolezel M, Lüthi C, Gaugitsch H (2020) Beyond limits – the pitfalls of global gene drives for environmental risk assessment in the European Union. BioRisk 15: 1-29. https://doi.org/10.3897/biorisk.15.49297
Four native vegetation types in native vegetation in Espinal province (central Argentina), described in the study by Zeballos et al. (2020), openly accessible at https://doi.org/10.1127/VCS/2020/38013. Photos by Sebastián Zeballo
Now, VCS is officially online with the publication of its first six research articles and an exhaustive editorial, written by its four Chief Editors: Prof Dr Florian Jansen, Dr Idoia Biurrun, Prof Dr Jürgen Dengler and Dr Wolfgang Willner. They explain the mission and key features of the new journal. They also address the advantages and challenges of Open Access and share the ways VCS is to handle those.
VCS focuses on vegetation typologies and vegetation classification systems, their methodological foundation, development and application at any organisational and spatial scale. No restrictions are imposed on the methodological approaches used.
Apart from original research papers that develop new vegetation typologies, the journal publishes applied studies that use such typologies, for example, in vegetation mapping, ecosystem modelling, nature conservation, land use management, or monitoring. Particularly encouraged are methodological studies that design and compare tools or algorithms for vegetation classification and mapping, vegetation databases and nomenclatural principles. Papers dealing with conceptual and theoretical bases of vegetation survey and classification are also welcome.
“We are delighted to welcome the latest journal by IAVS to the families of ARPHA and Pensoft. We are eager to support this wonderful Open Science initiative to facilitate access and uptake of research in this emerging field of vegetation science,”
comments Prof Lyubomir Penev, founder and CEO of ARPHA and Pensoft.
Amongst the appealing features of the new journal are its two permanent special collections: Ecoinformatics and Phytosociological Nomenclature. The former invites papers presenting vegetation-plot databases and other ecoinformatics data sources relevant for vegetation classification as well as concepts, methods and tools for using these, while the latter focuses on nomenclature issues of syntaxa.
Another novelty introduced by VCS is the implementation of double-blind peer review meant to reduce potential biases in academia.
***
Proving the international focus of VCS, the first published articles cover research from five continents.
A Chinese study, conducted by the team of Dr Cindy Q. Tang (Yunnan University) analyses the forest structure, regeneration and growth trends of the commercially, culturally and economically important Yunnan pine tree.
The research team of Maged Abutaha (Desert Research Center) provides the first phytosociological classification of the vegetation units of Gebel Elba – an important arid mountain in Egypt – and the environmental factors controlling their distribution.
In their paper, Dr John Hunter (University of New England) and Vanessa Hunter use unsupervised techniques to produce a hierarchical classification of montane mires within the New England Tablelands Bioregion (NETB) of eastern Australia.
A national-scale phytosociological research of freshwater lake vegetation in Greece was conducted by the team of Dimitrios Zervas (Greek Biotope/Wetland Centre).
A Finite Mixture Model is proposed as an additional approach for classifying large datasets of georeferenced vegetation plots from complex vegetation systems by a large research team, led by Dr Fabio Attorre of the Sapienza University of Rome.
A description of the remaining native vegetation of the Espinal province in central Argentina, presented by a research team, led by Dr Sebastián Zeballos (Instituto Multidisciplinario de Biología Vegetal, UNC-CONICET), calls for conservation measures to be taken to preserve the remaining forest patches. They also urge for the establishment of new protected natural areas.
“We would like to see more profound vegetation studies from species-rich regions, from both natural and anthropogenically influenced vegetation types,”
say the editors.
***
Thanks to support from IAVS, VCS will be offering particularly attractive article processing charges (APCs) for submissions during the first two years. Moreover, significant discounts are available for IAVS members, members of the Editorial team and authors from low-income countries or with other financial constraints.
***
Follow Vegetation Classification and Survey (VCS) on Twitter and Facebook.
Check out the official blog of the International Association for Vegetation Science (IAVS), where authors in any of the three IAVS journals are invited to submit blog contributions providing further insights into their work.
Following the recent Coronavirus outbreak, almost three million people have been infected worldwide, whereas the death toll has already passed the 200,000 mark, according to official reports. Meanwhile, a vaccine remains to be found, and classic medications show low efficacy. Under these conditions, it is up to pharmacologists to do their best in the search of novel treatments. However, laboratory studies are limited by the absence of COVID-19 animal models.
To create such a line of mice, researchers have formulated a two-step concept, recently described in the open-access, peer-reviewed scholarly journal Research Results and Pharmacology. Firstly, the mice are to be made biologically safe for routine laboratory practice. Secondly, in order for the mice to be efficient for non-clinical trials, they will need to experience symptoms and pathogenesis as human-like as possible. The scientists believe that they have everything necessary to implement this conception and expect the first results as early as June 2020.
“SARS-CoV-2-inoculated mice will have a human-like pathogenesis and symptoms of the COVID-19. The key difference between a new model and the existing ones will be its biological safety – animals will become sensitive to SARS-CoV-2 only after activation in conditions of a virological laboratory. It makes it possible to nullify the contagion risk for the staff working in nurseries and non-specialised laboratories during a pandemic,”
the team explains.
Already available data shows that there are two key proteins in the human cells, which are involved in the virus entry. First of all, it is the angiotensin-converting enzyme 2 (ACE2), which is the direct and main target of the coronavirus’ “corona”. Three lines of transgenic mice with the human ACE2 variant have been found to be susceptible to the SARS-CoV, a causative agent of the SARS outbreak in 2003. However, it was shown that, in addition to ACE2, a molecular pathway of coronavirus invasion contains another important link: the enzyme transmembrane protease serine 2 (TMPRSS2). The blocking of TMPRSS2 prevents SARS-CoV-2 entry on the cell culture in vitro.
To obtain mice with human-like COVID-19 symptoms and pathology, the researchers will introduce human ACE2 and TMPRSS2 genes into the murine genome under the mice’s own Tmprss2 promoter. Another key decision on the way of creating the new model is to ensure that SARS-CoV-2 sensitivity is inducible only after the introduction of LoxP sites in front of the human ACE2 and TMPRSS2 genes. As a result, human genes in a murine genome will turn on once a crossbreeding with mice expressing Cre-recombinase occurs.
“The main trick here is that this crossbreed will only happen in specialised virological laboratories, which will prevent the novel line of mice from becoming an infection ‘reservoir’ in ordinary laboratories,”
say the researchers.
Original source:
Soldatov VO, Kubekina MV, Silaeva YuYu, Bruter AV, Deykin AV (2020) On the way from SARS-CoV-sensitive mice to murine COVID-19 model. Research Results in Pharmacology 6(2): 1-7. https://doi.org/10.3897/rrpharmacology.6.53633
The ICZN Commissioners (Singapore, 2019) Photo by ICZN
The International Commission on Zoological Nomenclature (ICZN) proposes amendments to its Constitution – the legal basis determining how the Commission is to be governed – to solicit feedback from the zoological community, who will have one year, starting 30 April 2020, to submit constructive comments before the Commissioners cast their votes. To prompt useful debate on the revision of the foundational rules and principles at the ICZN, these comments will be openly published in the Bulletin of Zoological Nomenclature and the ICZN website.
In compliance with the ICZN Constitution, the proposed amendments are now available in the Bulletin of Zoological Nomenclature (BZN) and three other suitable journals, including the peer-reviewed open-access journal ZooKeys. Given there is a sufficient consensus on the proposed amendments, the final version of the Constitution will be presented to the International Union of Biological Sciences for provisional ratification. Afterwards, the decision and date of effective ratification will also be published in BZN.
Established in 1895, the ICZN is an organisation, whose task is to act as the adviser and arbiter for the zoological community by generating and disseminating information on the correct formation and use of the scientific names of animals. The ICZN is responsible for producing the International Code of Zoological Nomenclature, which is a set of rules for the naming of animals and the resolution of nomenclatural problems.
Key proposed amendments address the terms of service and eligibility of members of the Commission; the inclusion of the ICZN website as a primary venue for information dissemination; reducing the standard voting period from three months to two, in recognition of the faster transmission speed of electronic mail compared to postal mail; and adding the maintenance of ZooBank – the Official Register of Zoological Nomenclature – to the list of responsibilities of the Commission.
“Along with recent amendments to its Bylaws, the proposed amendments to the ICZN Constitution will help the Commission to fulfil its aim of promoting stability and universality in the nomenclature of animals,”
comment from the ICZN.
Original source:
ICZN (2020) Proposed Amendments to the Constitution of the International Commission on Zoological Nomenclature. ZooKeys 931: 1–9. https://doi.org/10.3897/zookeys.931.51583
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.
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.
The 1st overview of current #conservation statuses of #myriapods from around the world?️ reveals a missing overlap between species in the global @IUCNRedList and regional ones
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.
Neighbouring populations of two Tasmanian species of flat-backed #millipedes seem to have come to their own terms to keep distance between each other in a remarkable case of #parapatry
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.
David Lama (1990 – 2019), a legendary alpinist, recognised by the study’s author also for his commitment to conservation. Photo by MoserB / Copyrighted free use
The discovery of new, still unnamed animal species in a well-researched European region like the Alps is always a small sensation. All the more surprising is the description of a total of three new to science species previously misidentified as long-known alpine moths.
During a genetic project of the Tyrolean State Museums in Innsbruck (Austria), Austrian entomologist and head of the Natural Science Collections Peter Huemer used an integrative research approach that relies on molecular methods to study four European moths. Despite having been known for decades, those species remained quite controversial, because of many unknowns around their biology.
At the end, however, it turned out that the scientist was not dealing with four, but seven species. The three that were not adding up were indeed previously unknown species. Therefore, Huemer described the moths in a paper in the open-access, peer-reviewed journal Alpine Entomology. Curiously, all three species were given the names of legendary alpinists: Reinhold Messner, Peter Habeler and David Lama.
Habitat of Caryocolum lamai (Lama’s Curved-horn moth), Italy, Alpi Cozie, Colle Valcavera. Photo by Peter Huemer
Tribute to three legends in alpinism
“The idea to name the new species in honour of three world-renowned climbers was absolutely no coincidence,”
explains Huemer.
One of the newly described species, Caryocolum messneri, or Messner’s Curved-horn moth, is dedicated to Reinhold Messner. Messner is a famous alpinist who was the first to reach Mount Everest without additional oxygen, but also the first climber to ascend all fourteen peaks over 8,000 metres. For decades, he has been inspiring followers through lectures and books. His is also the Messner Mountain Museum project, which comprises six museums located at six different locations in South Tyrol, northern Italy, where each has the task to educate visitors on “man’s encounter with mountains” by showcasing the science of mountains and glaciers, the history of mountaineering and rock climbing, the history of mythical mountains, and the history of mountain-dwelling people.
“So what could have been a better fit for a name for the species that flutters on the doorstep of his residence, the Juval Castle in South Tyrol?”
says Huemer.
The second new species, Caryocolum habeleri, or Habeler’s Curved-horn moth, honours another extraordinary mountaineer: Peter Habeler. Having joined Messner on his expedition to Mount Everest, he also climbed this mountain without additional oxygen in a first for history. Another achievement is his climbing the famous Eiger North Face in mere 10 hours. Additionally, together with the study’s author, he sits on the advisory board of the nature conservation foundation “Blühendes Österreich“. However, the species’ name is also a nod to Peter Habeler’s cousin: Heinz Habeler, recognised as “the master of butterfly and moth research in Styria”. His collection is now housed in the Tyrolean State Museums.
The third alpinist, whose name is immortalised in a species name, is David Lama, specially recognised by Huemer for his commitment to conservation. Once, in order to protect endangered butterflies along the steep railway embankments in Innsbruck, Lama took care to secure volunteers in a remarkable action. Nevertheless, Lama earned his fame for his spectacular climbing achievements. His was the first free ascent of the Compressor route on the south-eastern flank of Cerro Torre.
“Unfortunately, David lost his life far too soon in a tragic avalanche accident on 16 April 2019 in Banff National Park, Canada. Now, Caryocolum lamai (Lama’s Curved-horn moth) is supposed to make him ‘immortal’ also in the natural sciences,”
says Huemer.
Many unresolved questions
The newly described moth species are closely related and belong to the genus Caryocolum of the so-called Curved-horn moths (family Gelechiidae).
A Curved-horn moth of the genus Caryocolum feeding on a carnation plant. This genus feeds exclusively on plants in the carnation family (Caryophyllaceae). Photo by P. Buchner / Tiroler Landesmuseen
As caterpillars, the species of this genus live exclusively on carnation plants. Even though the biology of the new moths is still unknown, because of their collection localities, it could be deduced that plants such as the stone carnation are likely their hosts. All species are restricted to dry and sunny habitats and sometimes inhabit altitudes of up to 2,500 m. So far, they have only been observed with artificial light at night.
While Messner’s Curved-horn moth occurs from northern Italy to Greece, the area of Habeler’s Curved-horn Moth is limited to the regions between southern France, northern Switzerland and southeastern Germany. On the other hand, Caryocolum lamai, only inhabits a small area in the western Alps of Italy and France.
Research on alpine butterflies and moths has been an important scientific focus at the Tyrolean state museums for decades. In 30 years, Peter Huemer discovered and named over 100 previously unknown to science species of lepidopterans. All these new discoveries have repeatedly shown the gaps in the study of biodiversity, even in Central Europe.
“How could we possibly protect a species that we don’t even have a name for is one of the key questions for science that derives from these studies,”
says Huemer in conclusion.
###
Original source:
Huemer P (2020) Integrative revision of the Caryocolum schleichi species group – a striking example of a temporally changing species concept (Lepidoptera, Gelechiidae). Alpine Entomology 4: 39-63. https://doi.org/10.3897/alpento.4.50703
At this alarming time, when the COVID-19 pandemic is on everyone’s mind, a new special issue in the open-access peer-reviewed journal Population and Economics provides a platform for discussion on the impact of the pandemic on the population and economics, both in Russia and worldwide. Economists, demographers and sociologists are invited to submit research on the impact of the pandemic to the special issue, which is open for submissions until the end of June 2020.
At this alarming time, when the COVID-19 pandemic is on everyone’s mind, a new special issue in the open-access peer-reviewed journal Population and Economics by Lomonosov Moscow State University (Faculty of Economics) provides a platform for discussion on the impact of the pandemic on the population and economics, both in Russia and worldwide by opening a special issue. An introductory overview of the issue is provided by its Editor-in-Chief, Irina E. Kalabikhina of the Faculty of Economics at Lomonosov Moscow University.
Today is still too early to draw any final conclusions, with too many things yet to happen. Nevertheless, the time is right to start a discussion on how to soften the possible consequences of the pandemic.
In the first published papers, brought together in the special issue, various teams of economists assess the uneasy dilemma – saving lives now or saving the economy to preserve lives in the future; demographers draw parallels with previous pandemics and its impact on demographic development; and sociologists analyse the state of various strata throughout the crisis.
The coronavirus pandemic came to Russia in mid-March – two months after China, two weeks after Spain, Italy, France, and about the same time as the United States.
As of 24th April, according to the data available at the Center for System Science and Engineering at John Hopkins University, Russia is amongst the top 10 countries by number of recorded cases. International comparability of national data on COVID-19 is a separate issue; it will be addressed in one of the special issue articles.
“Now I just want to state that Russia is affected by the pandemic, and it disturbs population and society. Moreover, a number of anti-epidemic measures taken in the country can bite the economy. In this context, the search for specific Russian consequences of the pandemic initiated by our authors along with the global consequences are particularly interesting”,
shares Editor-in-Chief of Population and Economics, Prof. Irina E. Kalabikhina.
All economists, demographers and sociologists are invited to consider the impact of the pandemic and its attendant recession on the population and economy in Russia and the global world. Research papers are welcome to the special issue, which will remain open for submissions until the end of June 2020.
Different aspects of the current pandemic are considered in a series of research: cost of the pandemic to globalisation,proposals of tax system revision and reforms, future technological shift and a change in the direction and volumes of trade flows.
The current COVID-19 pandemic is “a global social drama”, after which income and wealth inequalities are expected to increase, and it’s still a good question how reliable are the data on the virus we are receiving and what could be theperception of the mass public and voters. While citizens are getting used to the existing rules, both the population and the state are in uncertainty, and lacking the flexible informal rules, which normally determine human behaviour.
Many countries face the issues of unemployment, caused by the virus outburst, and in many countries young people and those of low education level, as well as migrants and refugees are the most vulnerable groups.
Russian families face new issues in the conditions of self-isolation, while “dachas” (countryside family houses) play an important role during the pandemic.
On one hand, the current reduction in production makes a positive impact on the environment, but in the upcoming years it can get replaced by the negative effect – as weakened attention to environmental issues and redirection of cash flows to maintain or prevent a significant drop in the material standard of living.
Scientists try to consider the lessons of the previous pandemics, based on the cases of the Spanish flu of 1918 and the latest Ebola outbreak in Sierra Leone.
These and many other topics are considered by researchers in the COVID-19 issue, and it is already quite obvious that even though the pandemic may have touched every side of our lives, life doesn’t stop. These early research works are meant to help humanity to overcome the following crisis, find the way out and adjust to the life after the pandemic.
“We are going through difficult times, and it is hardly possible to overestimate the role of science in the quickest passing through the crisis with the least human and economic losses. We hope that our Journal will contribute to the crucially important discussion on the impact of the pandemic on the economy and population”,
concludes Editor-in-Chief of Population and Economics, Irina E. Kalabikhina.
Additional information
About Population and Economics
Population and Economics is a peer-reviewed, open access journal, published by Lomonosov Moscow State University (Faculty of Economics). The journal covers basic and applied aspects of the relationship between population and economics in a broad sense.
The journal is running on the innovative scholarly publishing platform ARPHA, developed by scholarly publisher and technology provider Pensoft.
Original sources:
Kalabikhina IE (2020) What after? Essays on the expected consequences of the COVID-19 pandemics on the global and Russian economics and population. Population and Economics 4(2): 1-3. https://doi.org/10.3897/popecon.4.e53337
Kartseva MA, Kuznetsova PO (2020) The economic consequences of the coronavirus pandemic: which groups will suffer more in terms of loss of employment and income? Population and Economics 4(2): 26-33. https://doi.org/10.3897/popecon.4.e53194
Ivakhnyuk I (2020) Coronavirus pandemic challenges migrants worldwide and in Russia. Population and Economics 4(2): 49-55. https://doi.org/10.3897/popecon.4.e53201
Bobylev SN (2020) Environmental consequences of COVID-19 on the global and Russian economics. Population and Economics 4(2): 43-48. https://doi.org/10.3897/popecon.4.e53279
Contact:
Prof. Irina E. Kalabikhina Editor-in-Chief of the “Population and Economics” Email: niec@econ.msu.ru
Pensoft’s journals introduce a standard appendix template for primary biodiversity data to provide direct harvesting and conversion to interlinked FAIR data
by Lyubomir Penev, Mariya Dimitrova, Iva Kostadinova, Teodor Georgiev, Donat Agosti, Jorrit Poelen
Linking open data is far from being a “new” or “innovative” concept ever since Tim Berners-Lee published his “5-Star Rating of Linked Open Data (LOD)” in 2006. The real question is how to implement it in practice, especially when most data are still waiting to be liberated from the narratives of more than 2.5 million scholarly articles published annually? We are still far from the dream world of linked and re-usable open data, not least because the inertia in academic publishing practices appears much stronger than the necessary cultural changes.
Already, there are many exciting tools and projects that harvest data from large corpora of published literature, including historical papers, such as PubMedCentral in biomedicine or Biodiversity Heritage Library in biodiversity science. Yet, finding data elements within the text of these corpora and linking data to external resources, even with the help of AI tools, is still in its infancy and is presently only half way there.
Data should not only be extracted, they should be semantically enriched and linked to both their original resources (e.g. accession numbers for sequences need to be linked to GenBank), but also between each other, as well as with data from other domains. Only then, the data can be made FAIR: Findable, Accessible, Interoperable and Re-usable. There are already research infrastructures, which provide extraction, liberation and semantic enrichment of data from the published narratives, for example, the Biodiversity Literature Repository, established at Zenodo by the digitisation company Plazi and the science publisher and technology provider Pensoft.
Quick access to high-quality Linked Open Data can become vitally important in cases like the current COVID-19 pandemic, when scientists need re-usable data from different research fields to come up with healthcare solutions. To complete the puzzle, they need data related to the taxonomy and biology of viruses, but also data taken from their potential hosts and vectors in the animal world, like bats or pangolins. Therefore, what could publishers do to facilitate the re-usability and interoperability of data they publish?
In a recently published paper by Patterson et al. (2020) on the phylogenetics of Old World Leaf-nosed bats in the journal ZooKeys, the authors and the publisher worked together to present the data on the studied voucher specimens of bats in an Appendix table, where each row represents a set of valuable links between the different data related to a specimen (see Fig. 1).
Fig. 1. Screenshot of the Appendix table with data on 324 specimens of bats (Patterson et al. 2020).
Specimens in natural history collections, for instance, have their so-called human-readable Specimen codes, for example, FMNH 221308 translates to a specimen with Catalogue No 221308, which is preserved in the collection of the Field Museum of Natural History Chicago (FMNH). When added to a collection, such voucher specimens are also assigned Globally Unique Identifiers (GUIDs). For example, the GUID of the above-mentioned specimen looks like this:
25634cae-5a0c-490b-b380-9cabe456316a
and is available from the Global Biodiversity Information Facilities (GBIF) under Original Occurrence ID (Fig. 2), from where computer algorithms can locate various types of data associated with the GUID of a particular specimen, regardless of where these data are stored. Examples for data types and relevant repositories, besides the occurrence record of the specimen available from the GBIF, are specimen data stored at the US-based natural history collection network iDigBio, specimen’s genetic sequences at GenBank, images or sound recordings stored in other third-party databases (e.g. MorphoSource, BioAcustica) and others.
The complex digital environment of various information linked to the globally unique identifier of a physical specimen in a collection together constitutes its “openDS digital specimen” representation, recently formulated within the EU project ICEDIG. Nevertheless, this complex linking could occur more easily and at a modest cost if only the GUIDs were always submitted to the respective data repositories together with the data about that particular specimen. Unfortunately, this is too rarely the case, hence we have to look for other ways to link these fragmented data.
Fig. 2. The representation of the specimen FMNH 221308 on GBIF. The Global Unique Identifier (GUID) of the specimen is shown in the Original Occurrence ID field.
Next to the Specimen code in the table (Fig. 1), there are one or more columns containing accession numbers of different gene sequences from that specimen, linked to their entries in GenBank. There is also a column for the species names associated with the specimens, linked through the Pensoft Taxon Profile (PTP) tool to several trusted international resources, in whose data holdings it appears, such as GBIF, GenBank, Biodiversity Heritage Library, PubMedCentral and many more (see example for the bat species Hipposideros ater). The next column contains the country where the specimen has been collected. The last columns contain the geo-coordinated locations of the collecting spot.
The structure of such a specimen-based table is not fixed and can also have several other data elements, for example, resolvable persistent identifiers for the deposition of MicroCt or other images of the specimen at a repository (e.g. MorphoSource) or of a tissue sample from where a virus has been isolated (see the sample table template below).
So far, so good, but what would the true value of those interlinked data be, besides that a reader could easily click on to a linked data item and see immediately more information about that particular element? What other missinglinks can we include to bring extra value to the data, so that these can be put together and re-used by the research community? Moreover, from where do we take these missing links?
The missing links are present in the table rows!
Firstly, if we open the GBIF record for the specimen in question (FMNH 221308), we see a lot of additional information there (Fig.2), which can be read by humans and retrieved by computers through GBIF’s Application Programming Interface (API). However, the links to the GenBank accession numbers KT583829 of the cyt-b gene sequenced from that specimen are missing, probably because, at the time of deposition of this specimen data in GBIF, its sequences had not yet been submitted to GenBank.
Now, we would probably wish to determine the specimen from which a particular gene has been sequenced and deposited in GenBank and where this specimen is preserved? We can easily click on any accession number in the table but, again, while we find a lot of useful information about the gene, for example, about the methods of sequencing, its taxon name etc., the voucher specimen’s GUID is actually missing (see KT583829 accession number of the specimen FMNH 221308, Fig. 3). How could we then locate the GUID of that specimen and the additional information linked to it? By publishing all this information in the Appendix in the way described here, we can easily locate this missing link between the specimen’s GUID and its sequence, either “by hand” or through API call requests provided by computers.
Fig. 3. GenBank record for the accession number KT583829 of the voucher specimen FMNH 221308. The GUID for the voucher specimen is not present in the record.
While biodiversity researchers are used to working with taxon names, these names are far from being stable entities. Names can either change over time or several different names could be associated with the same “thing” (synonyms) or identical names (homonyms) may be used for different “things”. The biodiversity community needs to resolve this problem by agreeing in the future Catalogue of Life on taxon names that are unambiguously identified with GUIDs through their taxon concepts (the content behind each name, according to a particular author who has already used that name in a publication, for example, Hipposideros vittatus (Peters, 1852) is used in the work of Patterson et al. (2020). Here comes another missing link that the table could provide – the link between the specimen, the taxon name to which it belongs and the taxon concept of that name, according to the article in which this name has been used and published.
Now, once we have listed all available linked information about several specimens belonging to a number of different species in a table, we can continue by adding some other important data, such as the biotic interactions between specimens or species. For example, we can name the table we have already constructed “Source specimens/species” and add to it some more columns under the heading “Target specimens/species”. The linking between the two groups of specimens or species in the extended biotic interaction table can be modelled using the OBO Relations Ontology, especially its list of terms, in a drop-down menu provided in the table template. Observed biotic interactions between specimens or species of the type “pathogen of”, “preys on”, “has vector” etc. can then be easily harvested and recorded in the Global Biotic Interactions database GloBI (see example on interactions between specimens).
As a result, we could have a table like the one below, where column names and data elements linked in the rows follow simple but strict rules:
Appendix A. Specimen data table. Legend: 1 – Two groupings of specimen/species data (Source and Target); 2 – Data type groups – not changeable, linked to the appropriate ontology terms, whenever possible; 3- Column names – not changeable, linked to the appropriate ontology terms, whenever possible; 4- Linked to; 5 – Linked by.
As one can imagine, some columns or cells provided in the table could be empty, as the full completion of this kind of data is rarely possible. For the purposes of a publication, the author can remove all empty columns or add additional columns, for example, for listing more genes or other types of data repository records containing data about a particular specimen. What should not be changed, though, are the column names, because they give the semantic meaning of the data in the table, which allows computers to transform them into machine-readable formats.
At the end of the publishing process, this table is published, not only for humans, but also in a code language, called Extensive Markup Language (XML), which makes the data in the table “understandable” for computers. At the moment of publication, tables published in XML contain not only data, but also information about what these data mean (semantics) and how they could be identified. Thanks to these two features, an algorithm can automatically convert the data into another machine-readable language: Resource Description Framework (RDF), which, in turn, makes the data compatible (interoperable) with other data that can be linked together, using any of the identifiers of the data elements in the table. Such converted data are represented as simple statements, called “RDF triples” and stored in special triple stores, such as OpenBiodiv or Ozymandias, from where knowledge graphs can be created and used further. As an example, one can search and access data associated with a particular specimen, but deposited at various data repositories, for example, other research groups might be interested in having together all pathogens that have been extracted from particular tissues from specimens belonging to a particular host species within a specific geographical location and so on.
Finding and preserving links between the different data elements, for example, between a Specimen, Tissue, Sequence, Taxon name and Location, is by itself a task deserving special attention and investments. How could such bi- and multilateral linking work? Having the table above in place alongside all relevant tools and competences, one can run, for example, the following operations via scripts and APIs:
Locate the GUID for Specimen Code at GBIF (= OccurrenceID)
Lookup sequence data associated with that GUID at GenBank
Represent the link between the GUID and Sequence accession numbers in a series of RDF triples
Link and express in RDF the presentation of the specimen on GBIF with the article where it has been published.
Automatically inform institutions/collections for published materials containing data on their holdings (specimens, authors, publications, links to other research infrastructures, etc.).
Semantic representation of data found in such an Appendix Specimen Data Table allows the utilisation of the Linked Open Data model to map and link several data elements to each other, including the provenance record, that is the original source (article) from where these links have been extracted (Fig. 4).
Fig. 4. Example of a semantic representation between some of the data elements from the Appendix Specimen Data Table. The proposed schema for mapping these elements uses mostly Darwin Core terms to maintain interoperability across different platforms. The link between the specimen GUID, GBIF occurrence, GenBank sequence and scientific name is marked in red.
At the very end, we will be able to construct a new “virtual super-table“ of semantic links between the data elements associated with a specimen, which, in the ideal case, would provide the fully-linked information on data and metadata along and across the lines:
Species A: Specimen <> Tissue sample <> Sequence <> Location <> Taxon name <> Habitat <> Publication source
↑↓
Species B: Specimen <> Tissue sample <> Sequence <> Location <> Taxon name <> Habitat <> Publication source
Retrieving such additional information, for example, about an occurrence from GBIF or sequence information from GenBank through APIs and linking these pieces of information together in one dataset opens new possibilities for data discovery and re-use, as well as to the reproducibility of the research results.
An example for how data from different resources could be put and represented together is the visualisation of the host-parasite interactions between species, such as those between bats and coronaviruses, indexed by the Global Biotic Interactions (GloBI) (Fig. 5). Various other interactions, such as pollination, feeding, co-existence and others, are stored in GloBI’s database which is also available in the form of a Linked Open Dataset, openly accessible through files or through a SPARQL endpoint.
Fig. 5. Visualisation resulting from querying biotic interactions existing between a bat species from order Chiroptera (Plecotus auritus) and bat coronavirus.
The technology of Linked Open Data is already widely used across many fields, so data scientists will not be tremendously impressed by the fact that all of the above is possible. The problem is how to get there. One of the most obvious ways seems to be for publishers to start publishing data in a standard, community-agreed format so that these can easily be handled by machines with little or no human intervention. Will they do that? Some will, but until it becomes routine practice, most of the published data, i.e. high-quality, peer-reviewed data vetted by the act of publishing, will remain hardly accessible, hence unusable.
This pilot was elaborated as a use case published as the first article in a free-to-publish special issue on the biology of bats and pangolins as potential vectors for Coronaviruses in the journal ZooKeys. An additional benefit from the use case is the digitisation and data liberation from many articles on bats contained in the bibliography of the Patterson et al. article by Plazi. The use case is also a contribution to the recently opened COVID-19 Joint Task Force of the Consortium of European Taxonomic Facilities (CETAF), the Distributed System for Scientific Collections (DiSSCo) and the Integrated Digitized Biocollections (iDigBio).
To facilitate the quick adoption of the improved data table standards, Pensoft invites all who would like to test and see how their data are distributed and re-used after publication to submit manuscripts containing specimen data and biotic interaction tables, following the standard described above. The authors would be provided with a template table for completion of all fields relevant to their study while conforming to the standard used by Pensoft.
This initiative was supported in part by the IGNITE project.
Information:
Pensoft Publishers
Field Museum of Natural History Chicago
References:
Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240
Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and analyze species-interaction datasets. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2014.08.005.
Hardisty A, Ma K, Nelson G, Fortes J (2019) ‘openDS’ – A New Standard for Digital Specimens and Other Natural Science Digital Object Types. Biodiversity Information Science and Standards 3: e37033. https://doi.org/10.3897/biss.3.37033
The Kem Kem beds in Morocco are famous for the spectacular fossils found there, including at least four large-bodied non-avian theropods, several large-bodied pterosaurs and crocodilians. In their study, published in the open-access journal Zookeys, an international group of scientists, led by Dr. Nizar Ibrahim and Prof. Paul Sereno, evaluate the geological and paleontological significance of the study area.
The Kem Kem beds in Morocco are famous for the spectacular fossils found there, including at least four large-bodied non-avian theropods, several large-bodied pterosaurs and crocodilians.
The aim of the new research is to provide the international community with an in-depth review of the rocks and fossils of the region. It reviews the geology and paleontology of this famous but surprisingly understudied area, describing and formally naming the strata and summarizing all of the preserved life forms, from fragile plants and insects to massive dinosaurs. The monograph also paints a picture of life as it once was some 95 million years ago by describing the paleoenvironments of the region, and the unusual predator-dominated fauna.
In 1996 Prof. Sereno and colleagues introduced the informal term “Kem Kem beds” for this fossil-rich escarpment. In this monograph, the authors review the original tri-level proposal for the region by French geologist Choubert (his informal “trilogie mésocretacée”) and propose the Kem Kem Group for the entire package of rock with two new names for the dinosaur-bearing layers based on the richest fossil sites, the Gara Sbaa and Douira formations.
The region is famous for the prodigious fossils found in all of these units, many derived from commercial fossil collecting, which obscures the precise location and level of the specimens. The monograph is the first work to pinpoint where many of the most important finds were made. Over the last 25 years in particular, paleontologists have brought to light a diverse array of new vertebrate fossils including at least four large-bodied non-avian theropods, several large-bodied pterosaurs, crocodilians, turtles and an array of sharks and bony fish.
One of the key features of the Kem Kem assemblage is the presence of several large-bodied theropods, a group of dinosaurs that includes all of the meat-eaters. Most famous among these from the Kem Kem include the sail-backed Spinosaurus and the sabre-toothed Carcharodontosaurus.
Most fossils in the Kem Kem region are discovered as isolated fragmentary pieces weathered from sandstones. Only four partial dinosaur skeletons or skulls have been recovered, which include the long-necked sauropod Rebbachisaurus garasbae and the theropods Deltadromeus agilis, Carcharodontosaurus saharicus and Spinosaurus aegyptiacus. These Kem Kem theropods are among the largest known dinosaurian predators on record reaching adult body lengths in excess of 12 meters.
“Given the continued input of new specimens and the continuing expansion of paleontological research, we predict that diversity in the Kem Kem Group will increase substantially in the coming decades. Based on our review of existing collections, this increase will include scores of taxa from the pond locality Oum Tkout including nonvertebrates, such as plants, insects, and ostracods, as well as an array of actinopterygian fish. We also anticipate a continuing trickle of new terrestrial vertebrates that will be named on better preserved specimens that are diagnostic at present only at the familial level, including turtles and various kinds of archosaurs. As nearly half of the reptilian families listed are indeterminate, better preserved specimens will offer future opportunities to recognize new reptilian genera” ,
share the authors.
Predators abound on land, in the air and in water some 95 million years on the shores of northern Africa —as shown by the abundant fossils in the Kem Kem region. Large herbivores, such as the long-necked sauropod Rebbachisaurus, could have been hunted or scavenged by several large predators. Credit: Artwork by Davide Bonadonna License: CC-BY 4.0
“In summary, the Kem Kem assemblage of non-vertebrates and vertebrates is likely to continue to show dramatic increase in diversity in the coming decades. Nonetheless, the array of taxa currently known, which extends from plants across a range of aquatic and terrestrial vertebrates, is sufficiently mature to allow a summary of the vertebrate assemblage and a discussion of its paleoecological contex”,
The most famous of Kem Kem dinosaurs, the semi-aquatic giant Spinosaurus, and the most common of Kem Kem fossils, the giant sawfish Onchopristis, tangle in the shallow coastal waters on a warm Late Cretaceous day. Credit: Artwork by Davide Bonadonna License: CC-BY 4.0 The wealth of aquatic life, including shrimp, bony fish, lungfish and giant lobe-finned coelacanths, supported a remarkable array of predators, including the fish-eating sail-backed Spinosaurus and toothless pterosaur Alanqa soaring overhead. Credit: Artwork by Davide Bonadonna License: CC-BY 4.0
Original source:
Ibrahim N, Sereno PC, Varricchio DJ, Martill DM, Dutheil DB, Unwin DM, Baidder L, Larsson HCE, Zouhri S, Kaoukaya A (2020) Geology and paleontology of the Upper Cretaceous Kem Kem Group of eastern Morocco. ZooKeys 928: 1-216. https://doi.org/10.3897/zookeys.928.47517
