The first 2020 issue of the journal by the Academy’s Forest Research Institute is already online on a brand new and user-friendly website
The scholarly publisher and technology provider Pensoft welcomes the open-access, peer-reviewed international journal in forest science concerning the Balkan Peninsula, Central and Southern Europe Silva Balcanica to its self-developed publishing platform ARPHA. Having become the latest addition to the lengthy portfolio of scholarly outlets dedicated to the fields of ecology and biology for Pensoft and ARPHA, Silva Balcanica is now offering a wide range of benefits and services to its readers, authors, reviewers and editors alike.
Having already acquired its own glossy and user-friendly website provided by ARPHA, Silva Balcanica also takes advantage of the platform’s signature fast-track, end-to-end publishing system. In addition, the published content enjoys automated export of data to aggregators, as well as web-service integrations with major global indexing and archiving databases.
Ever since its inception in 2001, the journal by the Forest Research Institute at the Bulgarian Academy of Sciences (FRI-BAS), has been providing open access to the latest research in all aspects of forest ecosystems and landscapes of the Balkan Peninsula, and also Central and Southern Europe.
Silva Balcanica invites scientific analysis of practical results, as well as investigations, in the forest sciences, including forest ecology; forest soil science; forest genetics, tree breeding and plantation forestry; biometry and sylviculture; forest economy and management; forest entomology and pathology; ecology and management of game fauna, urban forestry and green infrastructure. Constructive critique addressing scientific publications or events in the field of forestry and forest science are also accepted.
In the first 2020 issue of Silva Balcanica, we can find a total of eight research papers, dealing with a range of various topics, including studies on local plant diversity, genetics, application of experimental designs for forestry research, ecosystem services, population dynamics, invasive pathogens and previously unknown populations of forest-dwelling insects. It brings together single-authored research contributions as well as international collaborative projects, with input from authors from Bulgaria, Greece, Northern Macedonia and Italy.
CEO and founder of both Pensoft and ARPHA Platform Prof. Lyubomir Penev comments:
“Silva Balcanica is an important scholarly outlet and also a remarkable example of international cooperation, inspired and maintained by curiosity, care and responsibility towards the unique, but fragile ecosystems this part of Europe hosts. This is why we take pride in having this particular journal joining our portfolio,”
Silva Balcanica’s Editorial Board says:
“The Scientific Council of the Forest Research Institute at the Bulgarian Academy of Sciences decided to begin publishing Silva Balcanica as an international series in 2001 and since 2014, Silva Balcanica has been published as an international journal.
We are honored to have as members of our Editorial Advisory Board eminent European professors and researchers in forestry and related sciences that join our efforts in pursuit of high quality scientific publishing.
We are confident that Silva Balcanica will unite the research of scientists and specialists in forestry from Southeastern, Central and Eastern Europe and beyond, and will help them in the processes of their European integration.”
Metabarcoding allows scientists to extract DNA from the environment, in order to rapidly detect species inhabiting a particular habitat. While the method is a great tool that facilitates conservation activities, few studies have looked into its applicability in monitoring species’ populations and their genetic diversity, which could actually be critical to assess negative trends early on. The potential of the method is confirmed in a new study, published in the peer-reviewed scholarly journal Metabarcoding & Metagenomics.
In a new study, German scientists confirm that responses below species level can be inferred with DNA metabarcoding
Metabarcoding allows scientists to extract DNA from the environment (known as environmental DNA or eDNA), for example, river water or, as in the case of the study by the team from the University of Duisburg-Essen (Essen, Germany) within the German Barcode of Life project (GBOL II): Vera Zizka, Dr Martina Weiss and Prof Florian Leese, from individuals in bulk samples. Thus, they are able to detect what species inhabit a particular habitat.
However, while the method has already been known to be of great use in getting an approximate picture of local fauna, hence facilitating conservation prioritisation, few studies have looked into its applicability to infer responses below species level. That is, how the populations of a particular species fare in the environment of interest, also referred to as intraspecific diversity. Meanwhile, the latter could actually be a lot more efficient in ecosystem monitoring and, consequently, biodiversity loss mitigation.
The potential of the method is confirmed in a new study, published in the peer-reviewed scholarly journal Metabarcoding & Metagenomics. To do so, the researchers surveyed the populations of macroinvertebrate species (macrozoobenthos) in three German rivers: Emscher, Ennepe and Sieg, where each is subject to a different level of ecological disturbance. They were looking specifically at species reported at all of the survey sites by studying the number of different haplotypes (a set of DNA variations usually inherited together from the maternal parent) in each sample. The researchers point out that macrozoobenthos play a key role in freshwater ecosystem functionality and include a wide range of taxonomic groups with often narrow and specific demands with respect to habitat conditions.
“As the most basal level of biodiversity, genetic diversity within species is typically the first to decrease, and the last to regenerate, after stressor’s impact. It consequently provides a proxy for environmental impacts on communities long before, or even if never visible on species diversity level,”
explain the scientists.
Emscher is an urban stream in the Ruhr Metropolitan Area that has been used as an open sewage channel for the past hundred years, and is considered to be a very disturbed environment. Ennepe – regarded as moderately stressed – runs through both rural and urban sites, including ones with sewage treatment plant inflow. Meanwhile, Sieg is considered as a stable, near-natural river system with a good ecological and chemical status.
As a result, despite their original assumption that Sieg would support the most prominent diversity within populations of species sensitive to organic pollution, such as mayflies, stoneflies and caddisflies, the scientists reported no significant difference to the medium stressed river Ennepe. This was also true for overall biodiversity. On the other hand, the team discovered higher intraspecific diversity for species resilient to ecological disturbance like small worms and specialised crustaceans in the heavily disturbed Emscher. The latter phenomenon may be explained with low competition pressure for these species, their ability to use organic compounds as resources and, consequently, increased population growth.
“[T]his pioneer study shows that the extraction of intraspecific genetic variation, so-called ‘haplotypes’ from DNA metabarcoding datasets is a promising source of information to assess intraspecific diversity changes in response to environmental impacts for a whole metacommunity simultaneously,”
conclude the scientists.
However, the researchers also note limitations of their study, including the exclusion of specialist species that only occured at single sites. They prompt future studies to also carefully control for the individual number of specimens per species to quantify genetic diversity change specifically.
###
Original source:
Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
by Mariya Dimitrova, Jorrit Poelen, Georgi Zhelezov, Teodor Georgiev, Lyubomir Penev
Fig. 1. Pensoft-GloBI workflow for indexing biotic interactions from scholarly literature
Tables published in scholarly literature are a rich source of primary biodiversity data. They are often used for communicating species occurrence data, morphological characteristics of specimens, links of species or specimens to particular genes, ecology data and biotic interactions between species, etc. Tables provide a structured format for sharing numerous facts about biodiversity in a concise and clear way.
Inspired by the potential use of semantically-enhanced tables for text and data mining, Pensoft and Global Biotic Interactions (GloBI) developed a workflow for extracting and indexing biotic interactions from tables published in scholarly literature. GloBI is an open infrastructure enabling the discovery and sharing of species interaction data. GloBI ingests and accumulates individual datasets containing biotic interactions and standardises them by mapping them to community-accepted ontologies, vocabularies and taxonomies. Data integrated by GloBI is accessible through an application programming interface (API) and as archives in different formats (e.g. n-quads). GloBI has indexed millions of species interactions from hundreds of existing datasets spanning over a hundred thousand taxa.
The workflow
First, all tables extracted from Pensoft publications and stored in the OpenBiodiv triple store were automatically retrieved (Step 1 in Fig. 1). There were 6993 tables from 21 different journals. To identify only the tables containing biotic interactions, we used an ontology annotator, currently developed by Pensoft using terms from the OBO Relation Ontology (RO). The Pensoft Annotator analyses free text and finds words and phrases matching ontology term labels.
We used the RO to create a custom ontology, or list of terms, describing different biotic interactions (e.g. ‘host of’, ‘parasite of’, ‘pollinates’) (Step 2 in Fig. 1).. We used all subproperties of the RO term labeled ‘biotically interacts with’ and expanded the list of terms with additional word spellings and variations (e.g. ‘hostof’, ‘host’) which were added to the custom ontology as synonyms of already existing terms using the property oboInOwl:hasExactSynonym.
This custom ontology was used to perform annotation of all tables via the Pensoft Annotator (Step 3 in Fig. 1). Tables were split into rows and columns and accompanying table metadata (captions). Each of these elements was then processed through the Pensoft Annotator and if a match from the custom ontology was found, the resulting annotation was written to a MongoDB database, together with the article metadata. The original table in XML format, containing marked-up taxa, was also stored in the records.
Thus, we detected 233 tables which contain biotic interactions, constituting about 3.4% of all examined tables. The scripts used for parsing the tables and annotating them, together with the custom ontology, are open source and available on GitHub. The database records were exported as json to a GitHub repository, from where they could be accessed by GloBI.
GloBI processed the tables further, involving the generation of a table citation from the article metadata and the extraction of interactions between species from the table rows (Step 4 in Fig. 1). Table citations were generated by querying the OpenBiodiv database with the DOI of the article containing each table to obtain the author list, article title, journal name and publication year. The extraction of table contents was not a straightforward process because tables do not follow a single schema and can contain both merged rows and columns (signified using the ‘rowspan’ and ‘colspan’ attributes in the XML). GloBI were able to index such tables by duplicating rows and columns where needed to be able to extract the biotic interactions within them. Taxonomic name markup allowed GloBI to identify the taxonomic names of species participating in the interactions. However, the underlying interaction could not be established for each table without introducing false positives due to the complicated table structures which do not specify the directionality of the interaction. Hence, for now, interactions are only of the type ‘biotically interacts with’ (Fig. 2) because it is a bi-directional one (e.g. ‘Species A interacts with Species B’ is equivalent to ‘Species B interacts with Species A’).
Fig. 2. Example of a biotic interaction indexed by GloBI.
Examples of species interactions provided by OpenBiodiv and indexed by GloBI are available on GloBI’s website.
In the future we plan to expand the capacity of the workflow to recognise interaction types in more detail. This could be implemented by applying part of speech tagging to establish the subject and object of an interaction.
In addition to being accessible via an API and as archives, biotic interactions indexed by GloBI are available as Linked Open Data and can be accessed via a SPARQL endpoint. Hence, we plan on creating a user-friendly service for federated querying of GloBI and OpenBiodiv biodiversity data.
This collaborative project is an example of the benefits of open and FAIR data, enabling the enhancement of biodiversity data through the integration between Pensoft and GloBI. Transformation of knowledge contained in existing scholarly works into giant, searchable knowledge graphs increases the visibility and attributed re-use of scientific publications.
Tables published in scholarly literature are a rich source of primary biodiversity data. They are often used for communicating species occurrence data, morphological characteristics of specimens, links of species or specimens to particular genes, ecology data and biotic interactions between species etc. Tables provide a structured format for sharing numerous facts about biodiversity in a concise and clear way.
Inspired by the potential use of semantically-enhanced tables for text and data mining, Pensoft and Global Biotic Interactions (GloBI) developed a workflow for extracting and indexing biotic interactions from tables published in scholarly literature. GloBI is an open infrastructure enabling the discovery and sharing of species interaction data. GloBI ingests and accumulates individual datasets containing biotic interactions and standardises them by mapping them to community-accepted ontologies, vocabularies and taxonomies. Data integrated by GloBI is accessible through an application programming interface (API) and as archives in different formats (e.g. n-quads). GloBI has indexed millions of species interactions from hundreds of existing datasets spanning over a hundred thousand taxa.
The workflow
First, all tables extracted from Pensoft publications and stored in the OpenBiodiv triple store were automatically retrieved (Step 1 in Fig. 1). There were 6,993 tables from 21 different journals. To identify only the tables containing biotic interactions, we used an ontology annotator, currently developed by Pensoft using terms from the OBO Relation Ontology (RO). The Pensoft Annotator analyses free text and finds words and phrases matching ontology term labels.
We used the RO to create a custom ontology, or list of terms, describing different biotic interactions (e.g. ‘host of’, ‘parasite of’, ‘pollinates’) (Step 1 in Fig. 1). We used all subproperties of the RO term labeled ‘biotically interacts with’ and expanded the list of terms with additional word spellings and variations (e.g. ‘hostof’, ‘host’) which were added to the custom ontology as synonyms of already existing terms using the property oboInOwl:hasExactSynonym.
This custom ontology was used to perform annotation of all tables via the Pensoft Annotator (Step 3 in Fig. 1). Tables were split into rows and columns and accompanying table metadata (captions). Each of these elements was then processed through the Pensoft Annotator and if a match from the custom ontology was found, the resulting annotation was written to a MongoDB database, together with the article metadata. The original table in XML format, containing marked-up taxa, was also stored in the records.
Thus, we detected 233 tables which contain biotic interactions, constituting about 3.4% of all examined tables. The scripts used for parsing the tables and annotating them, together with the custom ontology, are open source and available on GitHub. The database records were exported as JSON to a GitHub repository, from where they could be accessed by GloBI.
GloBI processed the tables further, involving the generation of a table citation from the article metadata and the extraction of interactions between species from the table rows (Step 4 in Fig. 1). Table citations were generated by querying the OpenBiodiv database with the DOI of the article containing each table to obtain the author list, article title, journal name and publication year. The extraction of table contents was not a straightforward process because tables do not follow a single schema and can contain both merged rows and columns (signified using the ‘rowspan’ and ‘colspan’ attributes in the XML). GloBI were able to index such tables by duplicating rows and columns where needed to be able to extract the biotic interactions within them. Taxonomic name markup allowed GloBI to identify the taxonomic names of species participating in the interactions. However, the underlying interaction could not be established for each table without introducing false positives due to the complicated table structures which do not specify the directionality of the interaction. Hence, for now, interactions are only of the type ‘biotically interacts with’ because it is a bi-directional one (e.g. ‘Species A interacts with Species B’ is equivalent to ‘Species B interacts with Species A’).
In the future, we plan to expand the capacity of the workflow to recognise interaction types in more detail. This could be implemented by applying part of speech tagging to establish the subject and object of an interaction.
In addition to being accessible via an API and as archives, biotic interactions indexed by GloBI are available as Linked Open Data and can be accessed via a SPARQL endpoint. Hence, we plan on creating a user-friendly service for federated querying of GloBI and OpenBiodiv biodiversity data.
This collaborative project is an example of the benefits of open and FAIR data, enabling the enhancement of biodiversity data through the integration between Pensoft and GloBI. Transformation of knowledge contained in existing scholarly works into giant, searchable knowledge graphs increases the visibility and attributed re-use of scientific publications.
References
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.
Additional Information
The work has been partially supported by the International Training Network (ITN) IGNITE funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 764840.
Large Cabbage trees (Pisonia grandis) dominate the landscape of a small island in the Pacific Ocean Photo by Jean-Yves Meyer (Délégation à la Recherche de Polynésie Française, Tahiti, French Polynesia)
Guest blog post by Marcos Caraballo
The birdcatcher trees – genus Pisonia – are infamous for trapping birds with their super-sticky seed pods that would frequently entangle the body of the ‘victim’. Left flightless, the poor feathered creatures eventually die either from starvation or fatigue, or predators. Similarly notorious are the birdcatcher trees for botanists, who have been baffled by their complicated classification for the last three centuries.
Here’s why myself and graduate student Elson Felipe Rossetto of the Universidade Estadual de Londrina (Brazil) decided to take up the untangling of this issue with our recent taxonomic studies. You can find our research paper published in the open-access scholarly journal PhytoKeys.
Ripe fruits (anthocarps) of the Birdlime tree (Ceodes umbellifera) Photo by Ching-I Peng [deceased]
We reestablished two genera: Ceodes and Rockia, where both had been previously merged under the name of Pisonia. Now, as a result, there are three distinct lineages of birdcatcher trees from the islands of the Pacific and Indian Oceans: Ceodes, Pisonia, and Rockia.
“Previous molecular studies on Pisonia species from around the world showed that species were clustered into three major groups, and here we assign names for each of them. With this new classification, a large number of the species known as Pisonia will be henceforth named Ceodes. This includes the Parapara (Ceodes brunoniana) and the Birdlime (Ceodes umbellifera) trees, both native to many islands, including Hawaii and New Zealand. They are commonly planted in gardens for their lush and sometimes variegated foliage, as well as their fragrant white flowers. However, the Cabbage tree (Pisonia grandis) will still be technically known as Pisonia.”
adds the study’s lead author Felipe Rossetto.
Male (staminate) showy flowers of the Birdlime tree (Ceodes umbellifera) Photo by Joel Bradshaw (Far Outliers, Honolulu, Hawaii)
Birdcatcher trees have generated much controversy in the popular media because of their seed pods (technically called “anthocarps”) secreting a sticky substance that glues them to the feathers of seabirds or other animals for dispersal. Sometimes, though, too many seed pods can harm or kill birds, especially small ones, by weighing them down and rendering them flightless. This macabre practice has led to many controversies and local campaigns aiming to remove the trees, even illegally.
Brown noddy (Anous stolidus) covered with the sticky fruits (anthocarps) of the Cabbage tree (Pisonia grandis) Photo by Jean-Yves Meyer (Délégation à la Recherche de Polynésie Française, Tahiti, French Polynesia)
In spite of their forbidding reputation, however, we would like to stress that birdcatcher trees have positive effects on ecosystems and are important components of vegetation, especially for small islands. Sadly, there are many endemic and already endangered species of birdcatcher trees that only exist on a few small islands, where they are effectively placed at the mercy of local people.
Many species of birdcatcher trees are large and, thereby, tolerate harsh environments like seafronts and rocky cliffs, making them prime nesting spots for seabirds. Birdcatcher trees are also ecologically curious and could be regarded as keystone species in small islands, because their soft branches can sustain many types of invertebrates; their flowers are an important food source for bees and ants; their dense leaf litter nourishes the soil; and their roots have intimate interaction with native underground fungi (mycorrhiza).
All in all, clarifying the taxonomy of the birdcatcher trees is the first step to understanding how many species exist and how they relate to each other.
Although most people relate birdcatcher trees with beaches and coastal habitats, there are species that are only found in mountains or rainforests. For example, the species now allocated to the genus Rockia is endemic to the Hawaiian archipelago. These are small trees able to grow in dry to mesic mountain forests. Using our new classification, future studies can explore in detail the hidden diversity of these enigmatic plants, and find out how trees with high dispersal capabilities evolve into species endemic to small island ecosystems.
Cabbage trees (Pisonia grandis) are important components of the vegetation in small islands due to their massive size Photo by Jean-Yves Meyer (Délégation à la Recherche de Polynésie Française, Tahiti, French Polynesia)
About the author:
Marcos A. Caraballo-Ortiz is a research associate at the Smithsonian Institution (Washington, D.C., United States). His research interests include plant systematics and ecology, with a focus on flora of the Caribbean Islands. Dr. Caraballo-Ortiz has experience studying the taxonomy of several groups of tropical plants, with a particular interest in neotropical Mistletoes (Loranthaceae, Santalaceae, Viscaceae) and the Four O’Clock family (Nyctaginaceae).
In a new editorial, Plant Sociology’s Editor-in-Chief Daniela Gigante and Co-editors Gianni Bacchetta, Simonetta Bagella and Daniele Viciani reflect on the current position and outlook of the official journal of the Italian Society of Vegetation Science (Società Italiana di Scienza della Vegetazione or SISV), now that it has completed its first issue since transitioning to the scientific publisher and technology provider Pensoft and ARPHA Platform earlier this year.
The Editorial board briefly analyses the issues around the inaccessibility to scholarly research and suitable scholarly outlets still persisting in our days that impede both readers and authors across branches of science. Naturally, they go on to focus on the situation in vegetation science, where, unfortunately, there are rather few outlets open to original research related to any aspect within vegetation science.
By telling their own experience, but also citing the stories of other similarly positioned society journals, including other journals that have moved to Pensoft’s self-developed ARPHA Platform over the past several years (e.g. Journal of Hymenoptera Research, European Science Editing, Italian Botanist, Vegetation Classification and Survey, Nota Lepidopterologica), the editors present an example how to address the challenges of securing the long-term sustainability and quality for a journal used to being run by a small editorial staff in what they refer to as a “home made” method.
Other society journals that have moved to Pensoft’s self-developed ARPHA Platform over the past several years
In this process, the SISV supported its official scholarly outlet to be published as a “gold open access” journal and ensured that the APCs are kept to a reasonable low in line with its non-profit international business model. Further discounts are available for the members of the Society.
Then, the journal management also reorganised its Editorial Board and welcomed a dedicated Social media team responsible for the increased outreach of published research in the public domain through the channels of Twitter and Facebook.
Besides making the publications publicly available as soon as they see the light of day, the journal strongly supports other good open science practices, such as open data dissemination. In Plant Sociology, authors are urged to store their vegetation data in the Global Index of Vegetation-Plot Databases (GIVD). Additionally, the journal is integrated with the Dryad Digital Repository to make it easier for authors to publish, share and, hence, have their data re-used and cited.
The team behind Plant Sociology is perfectly aware of the fact that it is only through easy to find and access knowledge about life on Earth that the right information can reach the right decision-makers, before making the right steps towards mitigating and preventing future environmental catastrophes.
“A journal focusing on all aspects of natural, semi-natural and anthropic plant systems, from basic investigation to their modelisation, assessment, mapping, management, conservation and monitoring, is certainly a precious tool to detect environmental unbalances, understand processes and outline predictive scenarios that support decision makers. In this sense, we believe that more and more OA journals focused on biodiversity should find space in the academic editorial world, because only through deep knowledge of processes and functions of a complex planet, humankind can find a way to survive healthy,”
elaborate the editors.
To take the burden of technical journal management off the shoulders of Plant Sociology’s own editorial team, the journal has entrusted Pensoft to provide a user-friendly and advanced submission system, in addition to the production, online publishing and archiving of the accepted manuscripts. Thus, the editorial team is able to focus entirely on the scientific quality of the journal’s content.
“The renewal of Plant Sociology is a challenge that we have undertaken with conviction, aware of the difficulties and pitfalls that characterize the life of a scientific journal today. Entrusting the technical management of the journal to a professional company aims to improve its dissemination and attractiveness, but also to focus our efforts only on scientific content,”
explain the editors.
***
About Plant Sociology:
Plant Sociology publishes articles dealing with all aspects of vegetation, from plant community to landscape level, including dynamic processes and community ecology. It favours papers focusing on plant sociology and vegetation survey for developing ecological models, vegetation interpretation, classification and mapping, environmental quality assessment, plant biodiversity management and conservation, EU Annex I habitats interpretation and monitoring, on the ground of rigorous and quantitative measures of physical and biological components. The journal is open to territorial studies at different geographic scale and accepts contributes dealing with applied research, provided they offer new methodological perspectives and a robust, updated vegetation analysis.
Pensoft creates a specialised data paper article type for the omics community within Biodiversity Data Journal to reflect the specific nature of omics data. The scholarly publisher and technology provider established a manuscript template to help standardise the description of such datasets and their most important features.
By Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Lyubomir Penev
Data papers are scientific papers which describe a dataset rather than present and discuss research results. The concept was introduced to the biodiversity community by Chavan and Penev in 2011 as the result of a joint project of GBIF and Pensoft.
Since then, Pensoft has implemented the data paper in several of its journals (Fig. 1). The recognition gained through data papers is an important incentive for researchers and data managers to author better quality metadata and to make it Findable, Accessible, Interoperable and Re-usable (FAIR). High quality and FAIRness of (meta)data are promoted through providing peer review, data audit, permanent scientific record and citation credit as for any other scholarly publication. One can read more on the different types of data papers and how they help to achieve these goals in the Strategies and guidelines for scholarly publishing of biodiversity data (https://doi.org/10.3897/rio.3.e12431).
Fig. 1 Number of data papers published in Pensoft’s journals since 2011.
The data paper concept was initially based on the standard metadata descriptions, using the Ecological Metadata Language (EML). Apart from distinguishing a specialised place for dataset descriptions by creating a data paper article type, Pensoft has developed multiple workflows for streamlined import of metadata from various repositories and their conversion into data paper a manuscripts in Pensoft’s ARPHA Writing Tool (AWT). You can read more about the EML workflow in this blog post.
Similarly, we decided to create a specialised data paper article type for the omics community within Pensoft’s Biodiversity Data Journal to reflect the specific nature of omics data. We established a manuscript template to help standardise the description of such datasets and their most important features. This initiative was supported in part by the IGNITE project.
How can authors publish omics data papers?
There are two ways to do publish omics data papers – (1) to write a data paper manuscript following the respective template in the ARPHA Writing Tool (AWT) or (2) to convert metadata describing a project or study deposited in EMBL-EBI’s European Nucleotide Archive (ENA) into a manuscript within the AWT.
The first method is straightforward but the second one deserves more attention. We focused on metadata published in ENA, which is part of the International Nucleotide Sequence Database Collaboration (INSDC) and synchronises its records with these of the other two members (DDBJ and NCBI). ENA is linked to the ArrayExpress and BioSamples databases, which describe sequencing experiments and samples, and follow the community-accepted metadata standards MINSEQE and MIxS. To auto populate a manuscript with a click of a button, authors can provide the accession number of the relevant ENA Study of Project and our workflow will automatically retrieve all metadata from ENA, as well as any available ArrayExpress or BioSamples records linked to it (Fig. 2). After that, authors can edit any of the article sections in the manuscript by filling in the relevant template fields or creating new sections, adding text, figures, citations and so on.
An important component of the OMICS data paper manuscript is a supplementary table containing MIxS-compliant metadata imported from BioSamples. When available, BioSamples metadata is automatically converted to a long table format and attached to the manuscript. The authors are not permitted to edit or delete it inside the ARPHA Writing Tool. Instead, if desired, they should correct the associated records in the sourced BioSamples database. We have implemented a feature allowing the automatic re-import of corrected BioSamples records inside the supplementary table. In this way, we ensure data integrity and provide a reliable and trusted source for accessing these metadata.
Fig. 2 Automated generation of omics data paper manuscripts through import and conversion of metadata associated with the Project ID or Study ID at ENA
Here is a step-by-step guide for conversion of ENA metadata into a data paper manuscript:
The author has published a dataset to any of the INSDC databases. They copy its ENA Study or Project accession number.
The author goes to the Biodiversity Data Journal (BDJ) webpage, clicks the “Start a manuscript” buttоn and selects OMICS Data Paper template in the ARPHA Writing Tool (AWT). Alternatively, the author can also start from the AWT website, click “Create a manuscript”, and select “OMICS Data Paper” as the article type, the Biodiversity Data Journal will be automatically marked by the system. The author clicks the “Import a manuscript” button at the bottom of the webpage.
The author pastes the ENA Study or Project accession number inside the relevant text box (“Import an European Nucleotide Archive (ENA) Study ID or Project ID”) and clicks “Import”.
The Project or Study metadata is converted into an OMICS data paper manuscript along with the metadata from ArrayExpress and BioSamples if available. The author can start making changes to the manuscript, invite co-authors and then submit it for technical evaluation, peer review and publication.
Our innovative workflow makes authoring omics data papers much easier and saves authors time and efforts when inserting metadata into the manuscript. It takes advantage of existing links between data repositories to unify biodiversity and omics knowledge into a single narrative. This workflow demonstrates the importance of standardisation and interoperability to integrate data and metadata from different scientific fields.
We have established a special collection for OMICS data papers in the Biodiversity Data Journal. Authors are invited to describe their omics datasets by using the novel streamlined workflow for creating a manuscript at a click of a button from metadata deposited in ENA or by following the template to create their manuscript via the non-automated route.
To stimulate omics data paper publishing, the first 10 papers will be published free of charge. Upon submission of an omics data paper manuscript, do not forget to assign it to the collection Next-generation publishing of omics data.
Despite the active ongoing taxonomic progress on the Madagascar frogs, the amphibian inventory of this hyper-diverse island is still very far from being complete. More new species are constantly being discovered, often within already well-studied areas. So, in one of the relatively well-studied parks in northern Madagascar, a new species of diamond frog, Rhombophryne ellae, was found in 2017. Now, the discovery is published in the open-access journal Zoosystematics and Evolution.
Despite the active ongoing taxonomic progress on Madagascar’s frogs, the amphibian inventory of this hyper-diverse island is still very far from being complete. The known diversity of the diamond frog genus Rhombophryne in Madagascar has increased significantly (more than doubled!) over the last 10 years, but still there are several undescribed candidate species awaiting description. New species are constantly being discovered in Madagascar, often even within already well-studied areas. One such place is the Montagne d’Ambre National Park in northern Madagascar.
Montagne d’Ambre National Park is widely known for its endemic flora and fauna, waterfalls and crater lakes, and considered to be a relatively well-studied area. Yet, only two studies have been published so far on the reptiles and amphibians of the Park.
Rhombophryne ellae was captured just as Cyclone Ava began to make itself felt across Madagascar with high winds and heavy rain. The camp where Dr. Scherz and his team were based became flooded, with rivers running through the kitchen and sleeping area. Miserable weather for humans, but a time of increased activity for some of the more elusive amphibians of the forest. Credit: Mark D. Scherz License: CC-BY 4.0
Rhomobphryne ellae Credit: Mark D. Scherz License: CC-BY 4.0
“As soon as I saw this frog, I knew it was a new species. The orange flash-markings on the legs and the large black spots on the hip made it immediately obvious to me. During my Master’s and PhD research, I studied this genus and described several species, and there are no described species with such orange legs, and only few species have these black markings on the hip. It’s rare that we find a frog and are immediately able to recognise that it is a new species without having to wait for the DNA sequence results to come back, so this was elating”,
shares Dr. Scherz.
The new species is most closely related to a poorly-known and still undescribed species from Tsaratanana in northern Madagascar, but is otherwise quite different from all other diamond frogs. With the orange colouration on its legs, Rhombophryne ellae joins the growing list of frogs that have red to orange flash-markings. The function of this striking colouration remains unknown, despite having evolved repeatedly in frogs, including numerous times in Madagascar’s narrow-mouthed frogs alone.
The new species, Rhombophryne ellae, is well camouflaged among the rainforest leaflitter Credit: Mark D. Scherz License: CC-BY 4.0
“The discovery of such a distinctive species within a comparatively well-studied park points towards the gaps in our knowledge of the amphibians of the tropics. It also highlights the role that bad weather, especially cyclones, can play in bringing otherwise hidden frogs out of hiding—Rhombophryne ellae was caught just as Cyclone Ava was moving in on Madagascar, and several other species my colleagues and I have recently described were also caught under similar cyclonic conditions”,
says Dr. Scherz.
Rhombophryne ellae is a small, probably semi-fossorial (sub-terranean-dwelling) species of diamond frog, at home amongst the leaf litter of Montagne d’Ambre National Park, north Madagascar Credit: Mark D. Scherz License: CC-BY 4.0
The species is known so far only from a single specimen, making it difficult to estimate its conservation status. Yet, based on the status of other, related frogs from the same area, it will probably be Red-listed as Near Threatened due to its presumably small range and micro-endemicity.
Original source:
Scherz MD (2020) Diamond frogs forever: a new species of Rhombophryne Boettger, 1880 (Microhylidae, Cophylinae) from Montagne d’Ambre National Park, northern Madagascar. Zoosystematics and Evolution 96(2): 313-323. https://doi.org/10.3897/zse.96.51372
For the first time, a complete time-calibrated phylogeny for a large group of invertebrates is published for an entire continent. A German-Swedish team of scientists provide a diagrammatic hypothesis of the relationships and evolutionary history for all 496 European species of butterflies currently in existence. Their study provides an important tool for evolutionary and ecological research, meant for the use of insect and ecosystem conservation.
For the first time, a complete time-calibrated phylogeny for a large group of invertebrates is published for an entire continent.
The figure shows the relationships of the 496 extant European butterfly species in the course of their evolution during the last 100 million years. Image by Dr Martin Wiemers
In a recent research paper in the open-access, peer-reviewed academic journal ZooKeys, a German-Swedish team of scientists provide a diagrammatic hypothesis of the relationships and evolutionary history for all 496 European species of butterflies currently in existence. Their study provides an important tool for evolutionary and ecological research, meant for the use of insect and ecosystem conservation.
In order to analyse the ancestral relationships and history of evolutionary divergence of all European butterflies currently inhabiting the Old continent, the team led by Martin Wiemers – affiliated with both the Senckenberg German Entomological Institute and the Helmholtz Centre for Environmental Research – UFZ, mainly used molecular data from already published sources available from NCBI GenBank, but also contributed many new sequences, some from very local endemics for which no molecular data had previously been available.
The phylogenetic tree also includes butterfly species that have only recently been discovered using molecular methods. An example is this Blue (Polyommatus celina), which looks similar to the Common Blue. It used to be mistaken for the Common Blue in the Canary Islands and the southwestern part of the Mediterranean Region. Photo by Dr Martin Wiemers
Butterflies, the spectacular members of the superfamily Papilionoidea, are seen as an important proponent for nature conservation, as they present an excellent indicator group of species, meaning they are capable of inferring the environmental conditions of a particular habitat. All in all, if the local populations of butterflies are thriving, so is their habitat.
Furthermore, butterflies are pollinating insects, which are of particular importance for the survival of humans. There is no doubt they have every right to be recognised as a flagship invertebrate group for conservation.
While many European butterflies are seriously threatened, this one: Madeiran Large White (Pieris wollastoni) is already extinct. The study includes the first sequence of this Madeiran endemic which was recorded in 1986 for the last time. The tree demonstrates that it was closely related to the Canary Island Large White (Pieris cheiranthi), another threatened endemic butterfly, which survives only on Tenerife and La Palma, but is already extinct on La Gomera. Photo by Dr Martin Wiemers
In recent times, there has been a steady increase in the molecular data available for research, however, those would have been only used for studies restricted either to a selected subset of species, or to small geographic areas. Even though a complete phylogeny of European butterflies was published in 2019, also co-authored by Wiemers, it was not based on a global backbone phylogeny and, therefore, was also not time-calibrated.
In their paper, Wiemers and his team point out that phylogenies are increasingly used across diverse areas of macroecological research, such as studies on large-scale diversity patterns, disentangling historical and contemporary processes, latitudinal diversity gradients or improving species-area relationships. Therefore, this new phylogeny is supposed to help advance further similar ecological research.
The study includes molecular data from 18 localised endemics with no public DNA sequences previously available, such as the Canary Grayling (Hipparchia wyssii), which is only found on the island of Tenerife (Spain). Photo by Dr Martin Wiemers
Original source:
Wiemers M, Chazot N, Wheat CW, Schweiger O, Wahlberg N (2020) A complete time-calibrated multi-gene phylogeny of the European butterflies. ZooKeys 938: 97-124. https://doi.org/10.3897/zookeys.938.50878
A new endemic deep-water dogfish shark: Squalus shiraii, was discovered in the tropical waters of Southern Japan by an international team of scientists led by Dr. Sarah Viana from South African Institute for Aquatic Biodiversity. The finding brings the amount of spurdogs shark species inhabiting Japanese waters to six. The discovery is published in the open-access journal Zoosystematics and Evolution.
Newly discovered creatures can often be as impressive and exciting as the ones from the Japanese movies and shows. Many of those fictional characters, including inhabitants of the famous Pokémon universe, might have their analogues among the real animals native to Japan. Maybe, a new species of the dogfish shark published in the open-access journal Zoosystematics and Evolution is also “a real Pokémon” to be?
A new deep-water dogfish shark: Squalus shiraii, was discovered in the tropical waters of Southern Japan by an international team of scientists, led by Dr. Sarah Viana from South African Institute for Aquatic Biodiversity.
Map of the North-western Pacific Ocean, showing the geographical distribution of Squalus shiraii Credit: Sarah Viana License: CC-BY 4.0
The new shark has the body length of 59-77 cm and some unique characteristics such as tall first dorsal fin and caudal fin with broad white margins. Currently, the species is known exclusively as a Japanese endemic, occurring in the tropical shallow waters of Southern Japan in the North-western Pacific.
Squalus shiraii lateral view Credit: Sarah Viana License: CC-BY 4.0
Spurdogs represent commercially important for the world fish trade taxa. They are caught for a range of purposes: consumption of meat, fins and liver oil. Despite their high occurrence, the accurate identification data of species is scarce, population threats and trends remain unknown.
Japan currently represents one of the world’s leading shark fish trade countries, though, during the last decades the amount of shark catches is decreasing and over 78 elasmobranch species traded in Japanese shark fin markets are now evaluated as threatened.
The new species Squalus shiraii previously used to be massively misidentified with shortspine spurdog, due to the resembling shape of body, fins and snout length. However, there are some differences, defining the specificity of the new species.
“Squalus shiraii has body brown in colour, postventral and preventral caudal margins whitish, dorsal and ventral caudal tips broadly white and black upper caudal blotch evident in adults. S. mitsukurii has body conspicuously black to dark grey and caudal fins black throughout with post-ventral caudal margin fairly whitish and black upper caudal blotch not evident in adults”, shares lead author Dr. Viana.
Scientists propose the name for the newly described species as Shirai’s spurdog in honour to Dr. Shigeru Shirai, the former Japanese expert of the group.
Original source: Viana STFL, Carvalho MR (2020) Squalus shiraii sp. nov. (Squaliformes, Squalidae), a new species of dogfish shark from Japan with regional nominal species revisited. Zoosystematics and Evolution 96(2): 275-311. https://doi.org/10.3897/zse.96.51962
aitik Patel and Dr Abhijit Das of the Wildlife Institute of India came up with one of the very first non-invasive approaches to identify individual frogs using photos from their natural habitats, which are then processed with the animal recognition software HotSpotter. Their unique method is described in the open-access, peer-reviewed scientific journal Herpetozoa.
A Beautiful stream frog (Amolops formosus) in a Himalayan torrent stream Photo by Naitik Patel
Globally, 41% amphibian species are regarded as threatened with extinction. However, when it comes to the case of India, the majority of the species falls in the Data Deficient group, according to the criteria of the International Union for Conservation of Nature‘s (IUCN) Red List of Threatened Species.
This means that we hardly have any population data for Indian amphibians, which leads to a serious conservation bottleneck, especially when you are dealing with elusive herpiles. Therefore, there is the pressing priority to obtain demographic trends to prompt and support conservation actions for endemic and habitat-dependent species.
While demographics of natural populations is best estimated with the mark-recapture technique, used in animals, where individuals have distinct body markings, such as the stripes in a tiger, the dots in a whale shark and the fingerprints in a human. In the meantime, while frogs are well known for their individual-specific markings and colour patterns, this kind of technique has never been used in amphibians, even though they have long been recognised as some of the most vulnerable animals on Earth.
On the other hand, it is hardly possible to capture and mark individual frogs in the wild. So, Naitik Patel and Dr Abhijit Das of the Wildlife Institute of India came up with one of the very first non-invasive approaches to identify individual frogs using photos from their natural habitats, which are then processed with the animal recognition software HotSpotter. Their unique method is described in the open-access, peer-reviewed scientific journal Herpetozoa.
“Capturing each frog is not possible in the field, so to address this problem, we conducted a short study on Beautiful stream frogs (Amolops formosus), a species that, just like many other amphibians, has variable body markings amongst individuals. As this species inhabits the Himalayan torrent stream, which is difficult to access, we tried our best to photograph each frog from a distance to avoid any kind of physical contact,”
A Beautiful stream frog (Amolops formosus) Photo by Abhijit Das
Having concluded their study with a success rate of 94.3%, the research team is hopeful that their protocol could be effectively implemented in rapid population estimation for many endangered species of frogs.
“We conducted photographic documentation to capture the unique markings of each frog, and then compared them, using computer-assisted individual identification. With this method, the number of individuals can be counted to estimate the population structure. This study is exceptional, owing to the minimal disturbance it causes to the frogs. Such a technique has rarely been tried on amphibians and is a promising method to estimate their numbers. It can also be used in citizen science projects,”
Patel NG, Das A (2020) Shot the spots: A reliable field method for individual identification of Amolops formosus (Anura, Ranidae). Herpetozoa 33: 7-15. https://doi.org/10.3897/herpetozoa.33.e47279
