Extensive surveys on wildlife markets and households in the Khammouane Province of Laos showed overlaps between the most traded species at wildlife markets and those of highest conservation importance.
It’s not a surprise to anyone that numerous vertebrate species are being sold at different wildlife markets, but at the moment there is still no comprehensive understanding of how much people are involved in those actions in Laos (Lao PDR), nor what the impact on local wildlife populations really is.
East Asian bullfrogs with broken legs at a market in Laos Photo by Dr Thomas Ziegler
The majority of Laotians live in rural areas and their income largely depends on wildlife. Since wildlife products are used as one of the major food sources, numerous species of terrestrial vertebrates are currently being offered at local markets.
Across the tropical regions, mammals and birds have been vanishing, with recent models estimating up to 83% decline by 2050. Furthermore, wild-caught reptiles have been reported from Southeast Asian wildlife markets for over 20 years, with Laos occupying the position of a very popular source.
Due to the large number of native endemic species, Lao PDR should assume the responsibility to introduce conservation measures to keep control over the predicted population declines. At the moment, the regulations on wildlife use and trade in Laos are mostly based on the Lao Wildlife and Aquatic Law, which, however, largely disregards international statuses of the species and other biological factors.
Slow loris (left), bats (top right) and squirrels (bottom right) offered at a food market in Laos Photo by C.L. Ebert
Stricter and reinforced legislation is needed in the fields related to wildlife trade and consumption, since such practices are not only causing biodiversity loss, but also suggested to pose a great threat of wildlife-associated emergence of zoonotic parasites and pathogens to humans. As an immediate example, the outbreak of the Coronavirus (COVID-19) is primarily considered to be a consequence of human consumption of wild animals.
An international group of students and scientists, led by Professor Dr. Thomas Ziegler at the University of Cologne and the Cologne Zoo (Germany), has conducted a number of extensive surveys on wildlife markets (66 observational surveys at 15 trade hubs) and households (63 households at 14 sites) in the Khammouane Province of Laos. The key question of the survey was: “Which species are traded and to what extent?” The results of the study are published in the open-access journal Nature Conservation.
The surveys showed overlaps between the most traded species at wildlife markets and those of highest conservation importance.
As for the households, approximately 90% of the surveyed respondents confirmed the use of wildlife. For the majority of the population, wildlife harvesting was found to be important for their livelihood and trapping activities were mostly aimed at self-consumption / subsistence. The reason for this could be explained by the prices of domesticated meat, which can be three times as higher as those of wildlife products.
A Buffy fish owl and a Chinese water dragon offered at a food market in Laos Photos by K. Kasper and T. Ziegler
The demand for the species on the wildlife market remained the same over time, according to the opinions of 84,1% of respondents, while the availability of wild meats was reported to have decreased, due to increasing price.
“We recommend local authorities to assess the markets within the province capital Thakhek in particular, as they showed the highest quantity of wild meats. The markets at Namdik and Ban Kok turned out to be very active trade hubs for wildlife as well, regardless of the vertebrate group. The loss of certain species may cause a cascade of unforeseeable effects in the ecosystems. Therefore, the biodiversity of tropical Southeast Asian countries like Lao PDR must be protected,”
shares Dr. Thomas Ziegler.
To help the local population to avoid the crisis related to the change of activity and growing unemployment, scientists propose to introduce new activities in the region.
“Eco-tourism presents a great opportunity to combine conservation efforts and an alternative source of income. Former hunters with excellent knowledge of the forest and wildlife habitats can serve as professional wildlife tour guides or their involvement in the Village Forest Protection Group could help to protect natural resources in Laos”,
suggests Dr. Thomas Ziegler.
###
Original source:
Kasper K, Schweikhard J, Lehmann M, Ebert CL, Erbe P, Wayakone S, Nguyen TQ, Le MD, Ziegler T (2020) The extent of the illegal trade with terrestrial vertebrates in markets and households in Khammouane Province, Lao PDR. Nature Conservation 41: 25-45. https://doi.org/10.3897/natureconservation.41.51888
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.
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
In recognition of the love and devotion that Terry expressed for the study of the World’s biodiversity, ZooKeys invites contributions to this memorial issue, covering all subjects falling within the area of systematic zoology. Titled “Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020)”.
In tribute to our beloved friend and founding Editor-in-Chief, Dr Terry
Erwin, who passed away on 11th May 2020, we are planning a special
memorial volume to be published on 11 May 2021, the date Terry left us. Terry
will be remembered by all who knew him for his radiant spirit, charming
enthusiasm for carabid beetles and never-ceasing exploration of the world of
biodiversity!
In recognition of the love and devotion that Terry expressed for study of the World’s biodiversity, ZooKeys invites contributions to this memorial issue, titled “Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020)”, to all subjects falling within the area of systematic zoology. Of special interest are papers recognising Terry’s dedication to collection based research, massive biodiversity surveys and origin of biodiversity hot spot areas. The Special will be edited by John Spence, Achille Casale, Thorsten Assmann, James Liebherr and Lyubomir Penev.
Article processing charges (APCs) will be waived for: (1) Contributions
to systematic biology and diversity of carabid beetles, (2) Contributions from
Terry’s students and (3) Contributions from his colleagues from the Smithsonian
Institution. The APC for articles which do not fall in the above categories
will be discounted at 30%.
The submission deadline is 31st December 2020.
Contributors are also invited to send memories and photos which shall be
published in a special addendum to the volume.
The memorial volume will also include a joint project of Plazi, Pensoft and the Biodiversity Literature Repository aimed at extracting of taxonomic data from Terry Erwin’s publications and making it easily accessible to the scientific community.
In recent years, the concept of Ecosystem Services (ES): the benefits people obtain from ecosystems, such as pollination provided by bees for crop growing, timber provided by forests or recreation enabled by appealing landscapes, has been greatly popularised, especially in the context of impeding ecological crises and constantly degrading natural environments.
Hence, there has been an increasing need for robust and practical methodologies to assess ES, in order to provide key stakeholders and decision-makers with crucial information. One such method to map and assess ES: the ES Matrix approach, has been increasingly used in the last decade.
The ES Matrix approach is based on the use of a lookup table consisting of geospatial units (e.g. types of ecosystems, habitats, land uses) and sets of ES, meant to be assessed for a specific study area, which means that the selection of a particular study area is the starting point in the assessment. Only then, suitable indicators and methods for ES quantification can be defined. Based on this information, a score for each of the ES considered is generated, referring to ES potential, ES supply, ES flow/use or demand for ES.
Ten years later, a research led by Dr C. Sylvie Campagne (Leibniz University Hannover, Germany), Dr Philip Roche (INRAE, France), Prof Dr Felix Muller (University of Kiel, Germany) and Prof Dr Benjamin Burkhard conducted a review of 109 published studies applying the ES matrix approach to find out how the ES matrix approach was applied and whether this was done in an oversimplified way or not.
In their recent paper, published in the open-access, peer-reviewed journal One Ecosystem, the review confirms the method’s flexibility, appropriateness and utility for decision-making, as well as its ability to increase awareness of ES. Nevertheless, the ES matrix approach has often been used in a “quick and dirty” way that urges more transparency and integration of variability analyses, they conclude.
“We analysed the diversity of application contexts, highlighted trends of uses and proposed future recommendations for improved applications of the ES matrix. Amongst the main patterns observed, the ES matrix approach allows for the assessment of a higher number of ES than other ES assessment methods. ES can be jointly assessed with indicators for ecosystem condition and biodiversity in the ES matrix,”
explains Campagne.
“Although the ES matrix allows us to consider many data sources to achieve the assessment scores for the individual ES, these were mainly used together with expert-based scoring (73%) and/or ES scores that were based on an already-published ES matrix or deduced by information found in related scientific publications (51%),”
she elaborates.
In 29% of the studies, an already existing matrix was used as an initial matrix for the assessment and in 16% no other data were used for the matrix scores or no adaptation of the existing matrix used was made.
“Nevertheless, we recommend to use only scores assessed for a specific study or, if one wishes to use pre-existing scores from another study, to revise them in depth, taking into account the local context of the new assessment,”
she points out.
The researchers also acknowledge the fact that 27% of the reviewed studies did not clearly explain their methodology, which underlines the lack of method elucidation on how the data had been used and where the scores came from. Although some studies addressed the need to consider variabilities and uncertainties in ES assessments, only a minority of studies (15%) did so. Thus, the team also recommends to systematically report and consider variabilities and uncertainties in each ES assessment.
“We emphasise the need for all scientific studies to describe clearly and extensively the whole methodology used to score or evaluate ES, in order to be able to rate the quality of the scores obtained. The increasing number of studies that use the ES matrix approach confirms its success, appropriateness, flexibility and utility to generate information for decision-making, as well as its ability to increase awareness of ES, but the application of the ES matrix has to become more transparent and integrate more variability analyses,”
concludes the research team.
Original source: Campagne CS, Roche P, Müller F, Burkhard B (2020) Ten years of ecosystem services matrix: Review of a (r)evolution. One Ecosystem 5: e51103. https://doi.org/10.3897/oneeco.5.e51103
