Artifacts and Artifictions in Biodiversity Research

2008 ◽  
Vol 43 (3) ◽  
pp. 245-257 ◽  
Author(s):  
Michael W. Palmer ◽  
Daniel J. McGlinn ◽  
Jason D. Fridley
Keyword(s):  
Biodiversity Research

Environmental DNA

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Graduate Students ◽  
Feeding Habits ◽  
Environmental Dna ◽  
Research Field ◽  
Background Information ◽  
Ecological Processes ◽  
Biodiversity Research ◽  
Dna Metabarcoding ◽  
Standard Information

Environmental DNA (eDNA), i.e. DNA released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on the distribution or feeding habits of species. It has therefore great potential for applications in ecology and biodiversity management. However, this research field is fast-moving, involves different areas of expertise and currently lacks standard approaches, which calls for an up-to-date and comprehensive synthesis. Environmental DNA for biodiversity research and monitoring covers current methods based on eDNA, with a particular focus on “eDNA metabarcoding”. Intended for scientists and managers, it provides the background information to allow the design of sound experiments. It revisits all steps necessary to produce high-quality metabarcoding data such as sampling, metabarcode design, optimization of PCR and sequencing protocols, as well as analysis of large sequencing datasets. All these different steps are presented by discussing the potential and current challenges of eDNA-based approaches to infer parameters on biodiversity or ecological processes. The last chapters of this book review how DNA metabarcoding has been used so far to unravel novel patterns of diversity in space and time, to detect particular species, and to answer new ecological questions in various ecosystems and for various organisms. Environmental DNA for biodiversity research and monitoring constitutes an essential reading for all graduate students, researchers and practitioners who do not have a strong background in molecular genetics and who are willing to use eDNA approaches in ecology and biomonitoring.

An infrastructure-oriented approach for supporting biodiversity research

2015 ◽  
Vol 26 ◽  
pp. 162-172 ◽  
Author(s):  
Leonardo Candela ◽  
Donatella Castelli ◽  
Gianpaolo Coro ◽  
Lucio Lelii ◽  
Francesco Mangiacrapa ◽  
...  
Keyword(s):  
Biodiversity Research ◽  
Oriented Approach

Engaging Local Knowledge in Biodiversity Research: Experiences from Large Inter- and Transdisciplinary Projects

2014 ◽  
Vol 39 (4) ◽  
pp. 323-341 ◽  
Author(s):  
Christoph Görg ◽  
Joachim H. Spangenberg ◽  
Vera Tekken ◽  
Benjamin Burkhard ◽  
Dao Thanh Truong ◽  
...  
Keyword(s):  
Local Knowledge ◽  
Research Experiences ◽  
Biodiversity Research

scholarly journals Characterization and comparison of poorly known moth communities through DNA barcoding in two Afrotropical environments in Gabon

Genome ◽  
2019 ◽  
Vol 62 (3) ◽  
pp. 96-107 ◽  
Author(s):  
Sylvain Delabye ◽  
Rodolphe Rougerie ◽  
Sandrine Bayendi ◽  
Myrianne Andeime-Eyene ◽  
Evgeny V. Zakharov ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Insect Communities ◽  
Biodiversity Research ◽  
Local Species Richness ◽  
Biodiversity Knowledge ◽  
Formidable Challenge ◽  
Entire Country ◽  
The Status ◽  
Local Species ◽  
Taxonomic Approach

Biodiversity research in tropical ecosystems—popularized as the most biodiverse habitats on Earth—often neglects invertebrates, yet invertebrates represent the bulk of local species richness. Insect communities in particular remain strongly impeded by both Linnaean and Wallacean shortfalls, and identifying species often remains a formidable challenge inhibiting the use of these organisms as indicators for ecological and conservation studies. Here we use DNA barcoding as an alternative to the traditional taxonomic approach for characterizing and comparing the diversity of moth communities in two different ecosystems in Gabon. Though sampling remains very incomplete, as evidenced by the high proportion (59%) of species represented by singletons, our results reveal an outstanding diversity. With about 3500 specimens sequenced and representing 1385 BINs (Barcode Index Numbers, used as a proxy to species) in 23 families, the diversity of moths in the two sites sampled is higher than the current number of species listed for the entire country, highlighting the huge gap in biodiversity knowledge for this country. Both seasonal and spatial turnovers are strikingly high (18.3% of BINs shared between seasons, and 13.3% between sites) and draw attention to the need to account for these when running regional surveys. Our results also highlight the richness and singularity of savannah environments and emphasize the status of Central African ecosystems as hotspots of biodiversity.

scholarly journals A Global Agenda for Advancing Freshwater Biodiversity Research

2021 ◽  
Author(s):  
Alain Maasri ◽  
Sonja Jähnig ◽  
Mihai Adamescu ◽  
Rita Adrian ◽  
Claudio Baigun ◽  
...  
Keyword(s):  
Sustainable Management ◽  
Freshwater Biodiversity ◽  
Biodiversity Crisis ◽  
Critical Step ◽  
Biodiversity Research ◽  
Coordinated Action ◽  
Global Agenda ◽  
Management And Conservation

Freshwater biodiversity is declining dramatically, and the current biodiversity crisis requires defining bold goals and mobilizing substantial resources to meet the challenges. While the reasons are varied, both research and conservation of freshwater biodiversity lag far behind efforts in the terrestrial and marine realms. We identify fifteen pressing global needs to support informed global freshwater biodiversity stewardship. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated action towards its sustainable management and conservation.

scholarly journals From Raw Biodiversity Data to Indicators, Boosting Products Creation, Integration and Dissemination: French BON FAIR initiatives and related informatics solutions

2019 ◽  
Vol 3 ◽  
Author(s):  
Yvan Le Bras ◽  
Aurélie Delavaud ◽  
Dominique Pelletier ◽  
Jean-Baptiste Mihoub
Keyword(s):  
Environmental Data ◽  
Observation System ◽  
Biodiversity Data ◽  
Digital Products ◽  
Raw Data ◽  
Biodiversity Research ◽  
Ecological Information ◽  
Data Products ◽  
Analytical Tools ◽  
Biodiversity Information

Most biodiversity research aims at understanding the states and dynamics of biodiversity and ecosystems. To do so, biodiversity research increasingly relies on the use of digital products and services such as raw data archiving systems (e.g. structured databases or data repositories), ready-to-use datasets (e.g. cleaned and harmonized files with normalized measurements or computed trends) as well as associated analytical tools (e.g. model scripts in Github). Several world-wide initiatives facilitate the open access to biodiversity data, such as the Global Biodiversity Information Facility (GBIF) or GenBank, Predicts etc. Although these pave the way towards major advances in biodiversity research, they also typically deliver data products that are sometimes poorly informative as they fail to capture the genuine ecological information they intend to grasp. In other words, access to ready-to-use aggregated data products may sacrifice ecological relevance for data harmonization, resulting in over-simplified, ill-advised standard formats. This is singularly true when the main challenge is to match complementary data (large diversity of measured variables, integration of different levels of life organizations etc.) collected with different requirements and scattered in multiple databases. Improving access to raw data, and meaningful detailed metadata and analytical tools associated with standardized workflows is critical to maintain and maximize the generic relevance of ecological data. Consequently, advancing the design of digital products and services is essential for interoperability while also enhancing reproducibility and transparency in biodiversity research. To go further, a minimal common framework organizing biodiversity observation and data organization is needed. In this regard, the Essential Biodiversity Variable (EBV) concept might be a powerful way to boost progress toward this goal as well as to connect research communities worldwide. As a national Biodiversity Observation Network (BON) node, the French BON is currently embodied by a national research e-infrastructure called "Pôle national de données de biodiversité" (PNDB, formerly ECOSCOPE), aimed at simultaneously empowering the quality of scientific activities and promoting networking within the scientific community at a national level. Through the PNDB, the French BON is working on developing biodiversity data workflows oriented toward end services and products, both from and for a research perspective. More precisely, the two pillars of the PNDB are a metadata portal and a workflow-oriented web platform dedicated to the access of biodiversity data and associated analytical tools (Galaxy-E). After four years of experience, we are now going deeper into metadata specification, dataset descriptions and data structuring through the extensive use of Ecological Metadata Language (EML) as a pivot format. Moreover, we evaluate the relevance of existing tools such as Metacat/Morpho and DEIMS-SDR (Dynamic Ecological Information Management System - Site and dataset registry) in order to ensure a link with other initiatives like Environmental Data Initiative, DataOne and Long-Term Ecological Research related observation networks. Regarding data analysis, an open-source Galaxy-E platform was launched in 2017 as part of a project targeting the design of a citizen science observation system in France (“65 Millions d'observateurs”). Here, we propose to showcase ongoing French activities towards global challenges related to biodiversity information and knowledge dissemination. We particularly emphasize our focus on embracing the FAIR (findable, accessible, interoperable and reusable) data principles Wilkinson et al. 2016 across the development of the French BON e-infrastructure and the promising links we anticipate for operationalizing EBVs. Using accessible and transparent analytical tools, we present the first online platform allowing the performance of advanced yet user-friendly analyses of biodiversity data in a reproducible and shareable way using data from various data sources, such as GBIF, Atlas of Living Australia (ALA), eBIRD, iNaturalist and environmental data such as climate data.

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