Advanced Books

Extensive practical guide to DNA-based biodiversity assessment methods published as a ‘living’ document by DNAqua-Net COST Action

Between 2016 and 2021, over 500 researchers collaborated within the DNAqua-Net international network, funded by the European Union’s European Cooperation in Science and Technology programme (COST), with the goal to develop and advance biodiversity assessment methods based on analysis of DNA obtained from the environment (e.g. river water) or from unsorted collections of organisms.

Such innovative methods are a real game changer when it comes to large-scale assessment of biodiversity and ecological monitoring, as collecting environmental samples that are sent to the lab for analysis is much cheaper, faster and non-invasive, compared with capturing and examining live organisms. However, large-scale adoption has been hindered by a lack of standardisation and official guidance.

Recognising the urgent need to scale up ecological monitoring as we respond to the biodiversity and climate crises, the DNAqua-Net team published a guidance document for the implementation of DNA-based biomonitoring tools.

The guide considers four different types of samples: water, sediments, invertebrate collections and diatoms, and two primary analysis types: single species detection via qPCR and similar targeted methods; and assessment of biological communities via DNA metabarcoding. At each stage of the field and laboratory process the guide sets out the scientific consensus, as well as the choices that need to be made and the trade-offs they entail. In particular, the guide considers how the choices may be influenced by common practical constraints such as logistics, time and budget. Available in an Advanced Book format, the guidelines will be updated as the technology continues to evolve.

Leaders of DNAqua-Net are Prof. Dr. Florian Leese of the University of Duisburg-Essen (Germany) and Dr. Agnès Bouchez of the French National Institute for Agriculture, Food, and Environment (INRAE). The core writing team for the present guide book involves Dr. Micaela Hellström (MIX Research AB, Sweden), Dr. Kat Bruce (NatureMetrics Ltd., UK), Dr. Rosetta Blackman (University of Zurich and EAWAG, Switzerland), Dr. Sarah Bourlat (LIB/Museum Koenig, Germany), and Prof. Kristy Deiner (ETH Zurich and SimplexDNA AG, Switzerland).

“Back in 2016 we realised that all around the globe researchers are testing new eDNA methods, developing individual solutions and products. While this is excellent, we need to reach a consensus and provide this consensus to stakeholders from the applied sectors”,
says Florian Leese.

This video was created as part of EU COST Action DNAqua-Net (CA15219) and shows how environmental DNA (eDNA) can be sampled and analysed from aquatic ecosystems. It shows the whole cycle from the start to final results.
Credit: DNAqua-Net

The guide’s lead author Dr. Kat Bruce adds:

“The urgency of addressing the twin biodiversity and climate crises means that we need to accelerate the adoption of new technologies that can provide data and insights at large scales. In doing so, we walk a tricky line to agree on sufficiently standardised methods that can be usefully applied as soon as they add value, while still continuing to develop them further and innovate within the field. It was a daunting task to seek consensus from several hundred scientists working in a fast-moving field, but we found that our technology is based on a strong foundation of knowledge and there was a high level of agreement on the core principles – even if the details vary and different users make different choices depending on their environmental, financial or logistical constraints.”

Looking back on the last four years that culminated in the publication of a “living” research publication, Prof. Dr. Kristy Deiner says:

“The document took many twists and turns through more than ten versions and passionate discussions across many workshops and late night drinks. All in the days when we could linger at conferences without fear of the pandemic weighing on us. As we worked to find consensus, one thing was clear: we had a lot to say and a standard review paper was not going to cut it. With the knowledge and experience gathered across the DNAqua-Net, it made sense to not limit this flow of information, but rather to try and tackle it head on and use it to address the many questions we’ve all struggled with while developing DNA-based biodiversity survey methods.”

Now that the document – or at least its first version – is publicly available, the researchers are already planning for the next steps and challenges.

“The bottom line is we’ve come a long way in the last ten years. We have a buffet of methods for which many produce accurate, reliable and actionable data to the aid of biodiversity monitoring and conservation. While there is still much work to be done, the many unanswered questions are because the uptake is so broad. With this broad uptake comes novel challenges, but also new insights and a diversity of minds with new ideas to address them. As said this is planned to be a living document and we welcome continued inputs no matter how great or small,” says Deiner.

Dr. Micaela Hellström recalls:

“The book evolved over the four years of COST Action DNAqua-Net which made it possible for the many scientists and stakeholders involved to collaborate and exchange knowledge on an unprecedented scale. Our whole team is well aware of the urgent need to monitor biodiversity loss and to provide accurate species distribution information on large scales, to protect the species that are left. This was a strong driving force for all of us involved in the production of this document. We need consensus on how to coherently collect biodiversity data to fully understand changes in nature.”

“It was a great and intense experience to be a part of the five-person core writing team. In the months prior to submitting the document, we spent countless hours, weekends and late nights researching the field, communicating with researchers and stakeholders, and joining vivid Zoom discussions. As a result, the present book provides solid guidance on multiple eDNA monitoring methods that are – or will soon become – available as the field moves forward.”

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The DNAqua-Net team invites fellow researchers and practitioners to provide their feedback and personal contributions using the contacts below.

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Original source:

Bruce K, Blackman R, Bourlat SJ, Hellström AM, Bakker J, Bista I, Bohmann K, Bouchez A, Brys R, Clark K, Elbrecht V, Fazi S, Fonseca V, Hänfling B, Leese F, Mächler E, Mahon AR, Meissner K, Panksep K, Pawlowski J, Schmidt Yáñez P, Seymour M, Thalinger B, Valentini A, Woodcock P, Traugott M, Vasselon V, Deiner K (2021) A practical guide to DNA-based methods for biodiversity assessment. Advanced Books. https://doi.org/10.3897/ab.e68634

Field research in Turkmenistan’s highest mountain reveals high biological diversity

Camera trap image of male Markhor Capra falconeri at the Koytendag State Nature Reserve
Photo by Koytendag State Nature Reserve

New open-access book presents a comprehensive report on the remarkable ecosystems of the Koytendag nature reserve

Situated in the extreme south-east of Turkmenistan: on the border with Uzbekistan and close to the border with Afghanistan, Koytendag presents one of the most distinct landscapes in Central Asia. Reaching elevations of up to 3,137 m, this is also the highest mountain in Turkmenistan.

Location of Koytendag
Image by Atamyrat Veyisov

Koytendag State Nature Reserve and its three Wildlife Sanctuaries: Hojapil, Garlyk and Hojaburjybelent, were established between 1986 and 1990 to protect and preserve the mountain ecosystem of the Koytendag region and maintain the ecological balance between the environment and increasing economic activities.

Since 2013, a series of scientific expeditions and assessments were coordinated and funded by the Royal Society for the Protection of Birds (RSPB) to pave the way for the protection and preservation of the unique landscape and rare wildlife the site is recognised for.

As a result, the efforts of the conducted field studies of multidisciplinary international research teams are brought together in a comprehensive report, which is now openly available as an Advanced Book from the scientific publisher and technology provider Pensoft, edited by Geoff Welch (RSPB) and Prof. Pavel Stoev (National National Museum of Natural History of Bulgaria and Pensoft). Soon, the book will also be available in Russian.

The book is split into eight sections focused on different areas within the study of biodiversity: Flora, Surface dwelling invertebrates, Cave fauna, Fish, Amphibians, Reptiles, Birds and Mammals. An additional chapter is dedicated to the hydrogeology of the site because of its key role in supporting both the cave fauna and the local communities.

Entrance to the newly discovered record-breaking underground lake at the Koytendag State Nature Reserve
Photo by Mikhail Pereladov

In the summary of the report, the authors make a list of the most significant findings made during the research. These include the discovery of a cave hosting the largest underground lake in the whole North Eurasia (4,400 m2) and a total of 48 species of higher plants that can only be found in Koytendag. In terms of Koytendag’s surface-dwelling fauna, the report lists a number of species new to science: a scorpion (most likely yet unnamed species currently recognised as a species complex) and a spider. Meanwhile, a total of seven previously unknown species were found underground, including the very first exclusively subterranean animal found in the country: the insect-like ‘marvellous’ dipluran named Turkmenocampa mirabilis, and a strongly adapted to the underground waters of a desert sinkhole Gammarus troglomorphus. Additionally, the annual monitoring, conducted since 1995 by the reserve staff, report an encouraging increase in the populations of the rare markhors and mouflons. An intact predator-prey community was also identified as a result of observations of numerous Eurasian lynxes and grey wolves, as well as prey species.

Entrance of the cave Kaptarhana, (Lebap Province, Eastern Turkmenistan), where scientists discovered the first ever exclusively subterranean dweller for the country (find more here).
Photo by Aleksandr Degtyarev

Stephanie Ward, RSPB Central Asia Partner Development Officer, says:

“RSPB has been working in Turkmenistan under a Memorandum of Understanding with the Government since 2004. In that time we have had the privilege of working with a team of talented and dedicated national experts across the diverse and inspiring nature of this fascinating country. Our work in Koytendag has captured the attention and interest of many international scientists who hope that their contemporary biodiversity research will help to deepen the understanding and therefore ensure protection of the unique wonders of this mountain ecosystem. As a potential UNESCO World Heritage Site, we will continue to collaborate with the Turkmen people on the research and promotion of Koytendag State Nature Reserve.

Book editor and member of the research team Prof. Pavel Stoev adds:

“Koytendag Mountain is among the least explored and, simultaneously, one of the most biologically diverse regions in Central Asia. The rapid assessments of its flora and fauna revealed a high number of highly specialised species, all of which have undergone a long evolution to adapt to the harsh environments of the mountain. The establishment of Koytendag State Nature Reserve and the associated wildlife sanctuaries is a step in the right direction for the protection of this unique biota.”

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Cover of the book, available as an open-access Advanced book from: https://doi.org/10.3897/ab.e37858.

Original source:

Welch G, Stoev P (2019) A report of RSPB-supported scientific research at Koytendag State Nature Reserve, East Turkmenistan. Advanced Books. https://doi.org/10.3897/ab.e37858

Additional information:

This work was carried out under the Memorandum of Understanding between the Ministry of Agriculture and Environment Protection of Turkmenistan and the RSPB, within the Project on “Improvement of the status of birds and other biodiversity in Turkmenistan”.

About Koytendag State Nature Reserve:

Koytendag State Nature Reserve was established in 1986 to protect and preserve the mountain ecosystem of the Koytendag region and maintain the ecological balance between the environment and the increasing anthropogenic activities. Of particular importance was the protection of rare species, such as the markhor; important habitats, including pistachio and juniper forests; and the impressive dinosaur trackways at Hojapil.

Advanced Books publishing by Pensoft:

Launched by Pensoft and powered by the scholarly publishing platform ARPHA, the Advanced Books approach aims to issue new books or re-issue books previously only available in print or PDF. In the Advanced Books format, the publications are semantically enhanced and available in HTML and XML as well, in order to accelerate open access, data publication, mining, sharing and reuse. The Advanced books builds on the novel approaches developed by the Pensoft’s journals.

A primer in access and benefit-sharing for DNA barcoders

New open access book provides essential background for molecular biodiversity researchers on international policy regarding use and transfer of genetic materials

Molecular biology approaches, such as DNA barcoding, have become part of the standard toolkit for a growing number of biodiversity researchers and practitioners, with an increasing scope of applications in important areas, such as environmental assessment, food inspection, disease control and public education.

Globalization and the advent of bioinformatics are rapidly changing the landscape of international scientific collaborations, which now often span multiple jurisdictions and increase the volume of international data exchange and transactions of biological materials. At the same time, researchers engaging in such partnerships are often unaware of the complex policy frameworks governing such transactions, which may carry reputational and even legal liabilities.

The United Nations Convention on Biological Diversity (1992) and its supplementary agreement, the Nagoya Protocol (ratified in 2014), are the most prominent international treaties designed to provide a legal framework for ensuring the fair and equitable sharing of the benefits arising from research activities involving genetic resources. Although often challenging and, at times, frustrating, it is important for researchers to understand the ramifications of these international agreements, to ensure that their scientific reputations are not tainted with allegations of unfair or unethical practices.

The recent book by Canadian ABS consultant and advisor to Botanic Gardens Conservation International, Kate Davis, and University of Guelph, Canada, researcher and international development expert, Alex Borisenko, offers a perspective on the ramifications of the Convention and the Nagoya Protocol on molecular biodiversity research.

Titled ‘Introduction to Access and Benefit-Sharing and the Nagoya Protocol: What DNA Barcoding Researchers Need to Know‘, it is openly available from Pensoft as an advanced book or PDF document under Creative Commons License.

This contribution is specifically geared towards researchers and practitioners working in the field of DNA barcoding – an actively developing field of biology that advances molecular tools for fast, reliable identification and discovery of species by analyzing short standardized DNA fragments, known as ‘DNA barcode regions’.

This approach, lying at the interface between genomics and biodiversity science, is creating the global knowledge base needed to assess ecosystem services and detect emerging environmental threats, while addressing the imperative of preserving the world’s biodiversity. Carrying out this mission demands close partnerships between biodiversity researchers worldwide, and also relies on large molecular facilities to provide timely, cost-effective and high-quality analytical services, thereby involving active international transactions of biological materials.

Furthermore, the utility of DNA barcoding depends on active open data sharing in ways similar to those established by the medical community for human genomic information.

The book is prefaced by the Executive Secretary of the Convention on Biological Diversity, Dr. Cristiana Pa?ca Palmer. It provides a brief introduction to the Convention and the Nagoya Protocol, and reviews some of their key legal definitions (e.g., ‘genetic resources’, ‘access’, and ‘utilization’). These definitions are considered within the context of terms more familiar to researchers (e.g., tissue samples, DNA extracts, PCR products, trace files) and their daily activities (e.g., field collecting, molecular analysis, DNA sequence assembly).

The main chapters provide further insights into the structure and function of the access and benefit-sharing mechanism at the international policy level and its possible ramifications in form of national laws and institutional requirements.

The text concludes with a set of practical guidelines for researchers and practitioners on the steps that should be taken to ensure due diligence when working with internationally-sourced biological samples. Adhering to these best practices would help build trust and sustain research collegiality among partners involved in international collaboration.

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Original source:

Davis K, Borisenko A (2017) Introduction to Access and Benefit-Sharing and the Nagoya Protocol: What DNA Barcoding Researchers Need to Know. Advanced Books. https://doi.org/10.3897/ab.e22579

Mapping Ecosystem Services: Collection of theories, methods and practical applications

The new book Mapping Ecosystem Services provides a comprehensive collection of theories, methods and practical applications of ecosystem services (ES) mapping, for the first time bringing together valuable knowledge and techniques from leading international experts in the field. Published by Pensoft, the book is both available in an online open access version via the publisher’s Advanced Books platform, and can be ordered in paperback and hardback format.

Human well-being and economic prosperity are largely dependent on ecosystem conditions and the essential goods and services they provide to mankind, such as fertile soils, multi-functional forests, land and seas, fresh water, clean air, pollination, and climate regulation, to name just a few. Mapping ecosystems and their services is a powerful tool to raise awareness about such areas of ecosystem goods and services supply and demand and to assist environmental education about human dependence on functioning nature.

ES have the potential to become a major tool for policy and decision making on global, national, regional and local scales, with a myriad of possible applications. Sustainable management of natural resources, land use optimisation, environmental protection, nature conservation and restoration, landscape planning, nature-based solutions, climate protection, disaster risk reduction to environmental education and research are just some of the areas where the concept can be applied.

In this context, mapping ecosystem services constitutes a very powerful tool to bring ES into practical application. Being able to efficiently communicate complex spatial information, ES maps are very useful for raising awareness about areas of ecosystem services supply and demand. Furthermore, maps are mandatory instruments for landscape planning, environmental resource management and land use optimisation.

Targeting an audience broader than just the research community, the new Mapping Ecosystem Services book provides in eight chapters insights in ES and mapping theory, ES quantification and mapping methods and tools and related uncertainties, in combination with examples of application in practice.

“Our aim was to present concise chapters in a professional but understandable language in order to facilitate their readability and comprehension. For example footnotes with direct links and suggestions for further reading are provided at the end of each chapter”, explain the editors Prof. Benjamin Burkhard, Leibniz Universität Hannover and Joachim Maes, Joint Research Centre, European Commission. “We hope this book is helpful and supports the appropriate mapping of ES!”.

“There are still big challenges ahead of us such as the improvement of the mapping and assessment of the ecosystem condition and the integration of the assessment of the ecosystem condition with ecosystem services and the construction of the first ecosystem accounts. As highlighted in this book, we are however on a very positive track!”, comments Anne Teller, European Commission, Directorate-General Environment in her preface to the book.

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Original Source:

Burkhard B, Maes J (2017) Mapping Ecosystem Services. Advanced Books. https://doi.org/10.3897/ab.e12837

Order online at: http://books.pensoft.net/book/13161/mapping-ecosystem-services

Additional Information:

The Advanced Books platform is launched by Pensoft to publish new books or re-publish such previously available in paper or PDF only, in an advanced and semantically enhanced HTML and XML formats, to accelerate open access, data publication, mining, sharing and reuse. Advanced Books builds on the novel approaches developed by Pensoft’s journals.