Contributions to the biodiversity of Vietnam – Results of VIETBIO inventory work and field training in Cuc Phuong National Park

VIETBIO [Innovative approaches to biodiversity discovery and characterisation in Vietnam] is a bilateral German-Vietnamese research and capacity building project focusing on the development and transfer of new methods and technology towards an integrated biodiversity discovery and monitoring system for Vietnam. Dedicated field training and testing of innovative methodologies were undertaken in Cuc Phuong National Park as part and with support of the project, which led to the new biodiversity data and records made available in this article collection. VIETBIO is a collaboration between the Museum für Naturkunde Berlin – Leibniz Institute for Evolution and Biodiversity Science (MfN), the Botanic Garden and Botanical Museum, Freie Universität Berlin (BGBM) and the Vietnam National Museum of Nature (VNMN), the Institute of Ecology and Biological Resources (IEBR), the Southern Institute of Ecology (SIE), as well as the Institute of Tropical Biology (ITB); all Vietnamese institutions belong to the Vietnam Academy of Science and Technology (VAST). The article collection "VIETBIO" (https://doi.org/10.3897/bdj.coll.63) reports original results of recent biodiversity recording and survey work undertaken in Cuc Phuong National Park, northern Vietnam, under the framework of the VIETBIO project. The collection consist of this “main” cover paper – characterising the study area, the general project approaches and activities, while also giving an extensive overview on previous studies from this area – followed by individual papers for higher taxa as studied during the project. The main purpose is to make primary biodiversity records openly available, including several new and interesting findings for this biodiversity-rich conservation area. All individual data papers with their respective primary records are expected to provide useful baselines for further taxonomic, phylogenetic, ecological and conservation-related studies on the respective taxa and, thus, will be maintained as separate datasets, including separate GUIDs also for further updating.

Experience Distributed in the Biodiversity Science-Base

Critics of biodiversity science and environmental governance point to exclusion and absence of diverse experience from science-based governance, sometimes effectively dividing domains of science and experience/values. This paper, following an alternate line of thought drawn from John Dewey’s Nature and Experience, analyses a series of scientific publications on biodiversity from 1989-2020. It argues that experience abundantly populates the biodiversity science-base, although in highly distributed forms. Dewey’s account suggests that knowledge of biodiversity derives from an unanalyzed continuum of experience. Reading the publications as traces of occurrences of encounters preceding, accompanying, and sometimes deriving from knowledge, the paper locates and characterises differentiated, sometimes impersonal gradients of experience, developing a figurative model of distributed biodiversity experience. It concludes that experiential diversity occurs widely in the science-base, but communication of and participation in this experience is frequently marginalised by the primacy of knowing.

CURRENT PERSPECTIVES OF DNA BARCODING IN BOSNIA AND HERZEGOVINA THROUGH BOLD DATABASE

UDK: 577.212:574]:007.5(497.6) DNA barcoding is a method designed to provide rapid and precise species identifications by using one or more of short gene sequences called barcodes. In most plant and fungi studies, the standard barcodes of choice are three plastid (rbcL, matK and trnH-psbA) and one nuclear (ITS) gene regions. The relatively high, but comparatively conserved rate of sequence evolution of mtDNA has made COI the marker of choice in animals. BOLD is a freely available cloud-based data storage and analysis platform developed with the aim to advance biodiversity science through DNA barcoding species identification. To date, over 6 million barcodes have been deposited in BOLD with 196,000 animal species, 68,000 plant species and 22,000 species of fungi and other organism entries. In this database, there are currently 447 entries for organisms from Bosnia and Herzegovina, which makes 0.0067% of the total number of BOLD entries. According to BOLD statistics, only 1.11% of all organism entries from B&H were submitted by B&H institutions. Despite the fact that Bosnia and Herzegovina has valuable natural resources with a high percentage of endemic and autochthonous species, BOLD statistics elucidated the lack of coordinated and systematic DNA barcoding research so far. It is necessary to establish continuous progress of molecular-genetic characterization of these resources in the future. It is up to B&H institutions to decide if they want to continue the practice of submitting the data sporadically or if they will animate the research community to actively participate in this global project.

An overview of plant collecting in Angola from 1690 to 2000

Angola is a large south-tropical African country with a rich plant diversity of over 7000 species. The vast majority of the plants collected in the country for deposition in preserved collections was obtained while Angola was under Portuguese rule. An historical analysis is presented of plant collecting in the country from the earliest times until the end of the 20th century. We also reflect on connections between biodiversity science and slavery; only recently have these links been acknowledged and receiving attention. The social environment prevalent in Angola at the time of its historical botanical exploration is discussed to enable an improved understanding of connections between scientific endeavour, colonialism, and slavery in the country. Gender- and ethnic group-based aspects are analysed and discussed.

Grand challenges in biodiversity–ecosystem functioning research in the era of science–policy platforms require explicit consideration of feedbacks

Feedbacks are an essential feature of resilient socio-economic systems, yet the feedbacks between biodiversity, ecosystem services and human wellbeing are not fully accounted for in global policy efforts that consider future scenarios for human activities and their consequences for nature. Failure to integrate feedbacks in our knowledge frameworks exacerbates uncertainty in future projections and potentially prevents us from realizing the full benefits of actions we can take to enhance sustainability. We identify six scientific research challenges that, if addressed, could allow future policy, conservation and monitoring efforts to quantitatively account for ecosystem and societal consequences of biodiversity change. Placing feedbacks prominently in our frameworks would lead to (i) coordinated observation of biodiversity change, ecosystem functions and human actions, (ii) joint experiment and observation programmes, (iii) more effective use of emerging technologies in biodiversity science and policy, and (iv) a more inclusive and integrated global community of biodiversity observers. To meet these challenges, we outline a five-point action plan for collaboration and connection among scientists and policymakers that emphasizes diversity, inclusion and open access. Efforts to protect biodiversity require the best possible scientific understanding of human activities, biodiversity trends, ecosystem functions and—critically—the feedbacks among them.

bddashboard: An infrastructure for biodiversity dashboards in R

The bdverse is a collection of packages that form a general framework for facilitating biodiversity science in R (programming language). Exploratory and diagnostic visualization can unveil hidden patterns and anomalies in data and allow quick and efficient exploration of massive datasets. The development of an interactive yet flexible dashboard that can be easily deployed locally or remotely is a highly valuable biodiversity informatics tool. To this end, we have developed 'bddashboard', which serves as an agile framework for biodiversity dashboard development. This project is built in R, using the Shiny package (RStudio, Inc 2021) that helps build interactive web apps in R. The following key components were developed: Core Interactive Components The basic building blocks of every dashboard are interactive plots, maps, and tables. We have explored all major visualization libraries in R and have concluded that 'plotly' (Sievert 2020) is the most mature and showcases the best value for effort. Additionally, we have concluded that 'leaflet' (Graul 2016) shows the most diverse and high-quality mapping features, and DT (DataTables library) (Xie et al. 2021) is best for rendering tabular data. Each component was modularized to better adjust it for biodiversity data and to enhance its flexibility. Field Selector The field selector is a unique module that makes each interactive component much more versatile. Users have different data and needs; thus, every combination or selection of fields can tell a different story. The field selector allows users to change the X and Y axis on plots, to choose the columns that are visible on a table, and to easily control map settings. All that in real-time, without reloading the page or disturbing the reactivity. The field selector automatically detects how many columns a plot needs and what type of columns can be passed to the X-axis or Y-axis. The field selector also displays the completeness of each field. Plot Navigation We developed the plot navigation module to prevent unwanted extreme cases. Technically, drawing 1,000 bars on a single bar plot is possible, but this visualization is not human-friendly. Navigation allows users to decide how many values they want to see on a single plot. This technique allows for fast drawing of extensive datasets without affecting page reactivity, dramatically improving performance and functioning as a fail-safe mechanism. Reactivity Reactivity creates the connection between different components. The changes in input values automatically flow to the plots, text, maps, and tables that use the input, and cause them to update. Reactivity facilitates drilling down functionality, which enhances the user’s ability to explore and investigate the data. We developed a novel and robust reactivity technique that allows us to add a new component and effectively connect it with all existing components within a dashboard tab, using only one line of code. Generic Biodiversity Tabs We developed five useful dashboard tabs (Fig. 1): (i) the Data Summary tab to give a quick overview of a dataset; (ii) the Data Completeness tab helps users get valuable information about missing records and missing Darwin Core fields; (iii) the Spatial tab is dedicated to spatial visualizations; (iv) the Taxonomic tab is designed to visualize taxonomy; and (v) the Temporal tab is designed to visualize time-related aspects. Performance and Agility To make a dashboard work smoothly and react quickly, hundreds of small and large modules, functions, and techniques must work together. Our goal was to minimize dashboard latency and maximize its data capacity. We used asynchronous modules to write non-blocking code, clusters in map components, and preprocessing and filtering data before passing it to plots to reduce the load. The 'bddashboard' package modularized architecture allows us to develop completely different interactive and reactive dashboards within mere minutes.

Big Data in Biodiversity Science: A Framework for Engagement

Despite best efforts, the loss of biodiversity has continued at a pace that constitutes a major threat to the efficient functioning of ecosystems. Curbing the loss of biodiversity and assessing its local and global trends requires a vast amount of datasets from a variety of sources. Although the means for generating, aggregating and analyzing big datasets to inform policies are now within the reach of the scientific community, the data-driven nature of a complex multidisciplinary field such as biodiversity science necessitates an overarching framework for engagement. In this review, we propose such a schematic based on the life cycle of data to interrogate the science. The framework considers data generation and collection, storage and curation, access and analysis and, finally, communication as distinct yet interdependent themes for engaging biodiversity science for the purpose of making evidenced-based decisions. We summarize historical developments in each theme, including the challenges and prospects, and offer some recommendations based on best practices.

How Do Young Community and Citizen Science Volunteers Support Scientific Research on Biodiversity? The Case of iNaturalist

Online community and citizen science (CCS) projects have broadened access to scientific research and enabled different forms of participation in biodiversity research; however, little is known about whether and how such opportunities are taken up by young people (aged 5–19). Furthermore, when they do participate, there is little research on whether their online activity makes a tangible contribution to scientific research. We addressed these knowledge gaps using quantitative analytical approaches and visualisations to investigate 249 youths’ contributions to CCS on the iNaturalist platform, and the potential for the scientific use of their contributions. We found that nearly all the young volunteers’ observations were ‘verifiable’ (included a photo, location, and date/time) and therefore potentially useful to biodiversity research. Furthermore, more than half were designated as ‘Research Grade’, with a community agreed-upon identification, making them more valuable and accessible to biodiversity science researchers. Our findings show that young volunteers with lasting participation on the platform and those aged 16–19 years are more likely to have a higher proportion of Research Grade observations than younger, or more ephemeral participants. This study enhances our understanding of young volunteers’ contributions to biodiversity research, as well as the important role professional scientists and data users can play in helping verify youths’ contributions to make them more accessible for biodiversity research.

Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation

Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerable development that builds on microbial metabarcoding methods to develop appropriate and efficient sampling and laboratory protocols for whole organism metazoan communities. However, considerably less attention has focused on ensuring bioinformatic methods are adapted and applied comprehensively in wocDNA metabarcoding. In this study we examined over 600 papers and identified 111 studies that performed COI metabarcoding of wocDNA. We then systematically reviewed the bioinformatic methods employed by these papers to identify the state-of-the-art. Our results show that the increasing use of wocDNA COI metabarcoding for metazoan diversity is characterised by a clear absence of bioinformatic harmonisation, and the temporal trends show little change in this situation. The reviewed literature showed (i) high heterogeneity across pipelines, tasks and tools used, (ii) limited or no adaptation of bioinformatic procedures to the nature of the COI fragment, and (iii) a worrying underreporting of tasks, software and parameters. Based upon these findings we propose a set of recommendations that we think the wocDNA metabarcoding community should consider to ensure that bioinformatic methods are appropriate, comprehensive and comparable. We believe that adhering to these recommendations will improve the long-term integrative potential of wocDNA COI metabarcoding for biodiversity science.