INaturalist accelerates biodiversity research

A comprehensive list of the macrospecies recorded on ten shipwrecks from the Belgian Part of the North Sea is presented. The historical records of these species in the area are also reviewed to address the potential role of shipwrecks in providing habitats for species typically associated with hard substrata. The current pooled species richness for Belgian shipwrecks consists of 224 spp., including 12 fish species. Among these species, 46 are new records to the Belgian fauna. Species on shipwrecks fulfil a gap in the regional distribution of sessile and mobile epibenthos. The records of several species are interrupted in the Southern Bight of the North Sea, simply because their habitats, natural hard substrata, are rare in this area and poorly studied. Another consequence of the presence of hard substrata offered by artificial sources is the increase in the distributional range of several species. Due to the presence of artificial substrata, a total of 12 southern species presented an extension of their known geographical range to the North.

The toolbox of instruments regulating access, transfer and use of biological material is currently re-equipped: the Nagoya Protocol was initiated to provide a legal framework to the third objective of the Convention on Biological Diversity – the fair and equitable sharing of benefits arising from the utilisation of genetic resources and associated traditional knowledge (an aspect not discussed here). In the ongoing implementation of the protocol, potentially harmful and far-reaching effects on biological research become evident. Here, we illustrate how vague definitions, lack of legal clarity and coordination, and often restrictive and complex regulations affect the transfer of biological material and associated data. Instead of promoting basic research in conservation and biodiversity, the current situation potentially jeopardises international collaboration, biodiversity research and its applications in monitoring, biocontrol and food safety. We address these challenges and discuss possible options for its practical implementation in the future.

Planning the future of plant systematics: Report on a special colloquium at the Royal Netherlands Academy of Arts and Sciences.

The global decline in biodiversity, driven by habitat loss, overexploitation, climate change, biological invasions, and illegal trade, poses significant challenges for conservation management. Although many South African ecosystems and species are under threat, effective conservation efforts are hindered by incomplete foundational biodiversity data and assessments, caused by taxonomic gaps and unverified distributions. DNA barcoding has emerged as an invaluable tool for species identification and classification of biodiversity. While substantial barcoding progress has been made, for many taxa, others remain underrepresented in sequence databases. This study evaluates the status and progress of DNA barcoding in South Africa through a gap analysis, comparing verified species checklists with barcoded sequences from the Barcode of Life Database (BOLD) and GenBank to assess taxonomic and geographic representation. A literature review (2003-2023) highlights applications across terrestrial, freshwater, and marine habitats. Of the 931,476 South African species barcode records, 52% were publicly available. Although the insects dominated with the highest number of records and BINs, reptiles had the highest taxonomic representation. Plants and fungi were underrepresented (16.1% and 2.8%, respectively). Regionally, Mpumalanga and Limpopo provinces showed the highest BIN counts, while North-West and Free State provinces had the lowest. The majority of barcode records were for mtDNA genes such as cytochrome c oxidase subunit I (COI) and were contributed by both local and international institutions. Discrepancies between GenBank records and those mined by BOLD indicated that many GenBank sequences for South Africa have poor quality metadata, including geographic sampling locality information. While significant progress has been made across taxa, further efforts are needed to expand species and geographic coverage, enhance sequence quality, improve species metadata, and resolve inconsistencies in BIN assignments, particularly for underrepresented groups such as plants and fungi. These advances would strengthen biodiversity assessments and support conservation efforts in South Africa.

: The U.S. Navy has focused exceptional resources on documenting its impacts to the marine environment by preparing and completing publicly-releasable Environmental Impact Statements (EIS) for operating areas and training ranges. This documentation relies on information from peer-reviewed scientific research and other available data on sound exposure. Two areas where information gaps currently exist in peer-reviewed literature are environmental characterization and acoustic detection opportunities in known habitats of species sensitive to acoustic disturbance (National Research Council, 2003). The purpose of this study is to start filling the knowledge gaps on these topics by publishing existing model results in a series of refereed papers for reference by the scientific and regulatory communities. The goal is to raise public awareness and improve the technical knowledge base for future marine mammal studies.

Biodiversity informatics (BI) plays an important role in helping us know, protect and use biodiversity sustainably. It encompasses activities from data digitization, standardization, sharing and aggregation, to supporting decision and policy making. In a country like Brazil, with a large continental geographic area containing ca. 15% of the planet’s biodiversity, the challenge is even greater: stakeholders are widely distributed over a large country and the amount of data is huge. Brazil has been a part of the international BI community, including Biodiversity Information Standards (TDWG), for around two decades. Initially represented solely by the Centro de Referência em Informação Ambiental (CRIA), gradually other groups from universities, museums and institutions joined the arena. Despite the broader group of stakeholders now involved, the local community is not strong enough. From a human resources point of view, the country has very good universities that train competent professionals both in information technology (IT) and in biology or related fields. Concerning the IT professionals, not surprisingly, other industries and job opportunities are usually more attractive and few people even know about BI. This is probably not unique to Brazil. Biological sciences professionals, for their part, usually have little literacy in computing and are equally unaware of BI as a field. On the institutional level, museums, universities and other biological data owners often lack IT support for biological data management, including digitization, and systems development/maintenance. This may reflect the lack of appreciation of the importance of data and of BI as a foundation for good biodiversity science and management. The same happens when it comes to funding. Biological collections are not adequately funded and lack more than a few episodic programs to support collection and museum maintenance and digitization. This lack of infrastructural funding highlights the tragedies of the fires at the Butantan Museum in 2010 (80,000 snakes, 180,000 spiders) and the Museu Nacional in 2018, (20 million biological specimens and objects of the Brazilian and world history and art were lost). The exception is the São Paulo Research Foundation (FAPESP), which has been supporting projects since 1999 on biodiversity and BI via its successful Biota-FAPESP program, the first to tie biodiversity projects to data digitization and sharing in Brazil. The lack of institutional engagement and support, and funding affects the sustainability of many initiatives and puts at risk the long term data availability. Due to political reasons, Brazil only joined the Global Biodiversity Information Facility (GBIF) in 2012 as an associate (non-contributing financially and non-voting) member with a commitment to become a voting member within five years. Until recently, the Brazilian Biodiversity Information System (SiBBr), Brazil’s GBIF node, was also hindered by politics from having a solid, stable national governance and funding to help “consolidate a solid national infrastructure on biodiversity data”, and to unite the growing Brazilian BI community around it. In the international scenario, while political, cultural and funding reasons may have hindered more equitable collaborations (e.g., tools development and sharing) with countries in the Global South, competing Global North-centric projects have prevailed. Although most remaining biodiversity is in the Global South, where local engagement is crucial, in many cases southern partners still often only act as data providers. Collaborative work is required with genuine co-creation, empowering all parties. Initiatives like the Living Atlases community must be recognized and welcomed as a positive shift. Despite all of these challenges, it can be surprising how much Brazilian biodiversity science has achieved throughout the years, and it gives us hope that in the future, if some of these issues are addressed, a lot more can be done. Education and training, continued funding and institutional support, governance, and international collaboration are essential.

Researchers have become accustomed to online access to data about specimens held in natural history collections. Over several decades, metadata standards have been developed to facilitate the sharing and aggregation of this data, notably Darwin Core and ABCD (Access to Biological Collections Data) developed under the auspices of TDWG but other standards developed in other communities, have also proved useful notably EML (Ecological Metadata Language) and GML (Geography Markup Language). Data aggregators have arisen to both, drive standards development and take advantage of the vast number of records made available through this community effort. Examples include Atlas of Living Australia and spin off Atlas projects, EoL (Encyclopedia of Life), iDigBio, Global Biodiversity Information Facility (GBIF), WFO (World Flora Online). There are still many “dark specimens” that are not visible to the web and efforts continue to digitise metadata on these objects and make them available. The vast majority of the data that has been liberated so far, has therefore been text based and the standards reflect this, although many institutions and projects are also producing large numbers of images and other media. There have been media extensions to some standards to accommodate the sharing of images and other multimedia formats. However, these are restricted to metadata about media objects rather than the exchange of media objects themselves. For example, two extensions to Darwin Core are Audubon Core, which is designed to “determine whether a particular resource or collection will be fit for some particular biodiversity science application before acquiring the media.” and the Simple Multimedia extension, which is a “simple extension for exchanging metadata about multimedia resources”. Therefore image exchange, in particular, has not used open standards. Projects have relied on transferring high resolution versions of images (e.g. submission of type specimen images to JSTOR) or cut down compressed versions (e.g. many herbarium specimens submitted to GBIF or Europeana). The network has not allowed access to high resolution versions of images as curated by the host institutions themselves beyond basic links to web pages. If high resolution images have been published in online catalogues, they have been made available using a hotchpotch of different technologies including the now defunct Java Applets and Adobe Flash player. The network has not supported different views of the same specimen or annotations of those views, or integration of audio and moving images. In an ideal world a researcher should be able to view and annotate images of specimens held across multiple collections in a unified way, and the host institutions should have access to those annotations and statistics on how their specimens are being used. How can we achieve this? The sharing of multimedia representations of objects online is not a problem unique to the biodiversity community. Scholars in museums and archives of all kinds are facing the same issues. In 2011 the British Library, Stanford University, the Bodleian Libraries (Oxford University), the Bibliothèque nationale de France, Nasjonalbiblioteket (National Library of Norway), Los Alamos National Laboratory Research Library, and Cornell University came together to develop an exchange standard called IIIF (International Image Interoperability Framework). This framework now consists of six APIs (Application Programming Interface), four stable and two in beta, to publish and integrate image and other multimedia resources in a uniform manner and has been adopted by many institutions and commercial partners in the digital humanities. Applications based on IIIF enable many of the features desired by biodiversity researchers. The notion of sharing and annotating specimen images is not new to the natural history community. MorphBank, founded in 1998, has grown to allow much of this desirable functionality but at the cost and fragility of being a centralised database. The question we should perhaps be asking is: how can we make the biodiversity data sharing network as a whole more like MorphBank? From 2019 to 2021, part of the EU-funded Synthesys+ programme will support the adoption of IIIF as a unified way to publish images of natural history specimens. We aim to have a set of exemplar institutions publishing IIIF manifests for some millions of specimens by the end of the project and one or more demonstration applications in place. We hope this will act as a catalyst for wider adoption in the natural history community. A key goal is to integrate image data served using IIIF with metadata available via CETAF (Consortium of European Taxonomic Facilities) specimen identifiers. If IIIF were ubiquitous in the natural history community, building tools that implemented this functionality would be feasible. A brief demonstration of a herbarium specimen browser, Herbaria Mundi, will be given. It will illustrate how specimens hosted in different institutions can be manipulated in a single interface. The architecture that supports this behaviour will be explained and its challenges, by implementing the institutions discussed.

Building on the development of Biodiversity Informatics, the Global Biodiversity Information Facility (GBIF) undertook the task of enabling access to the world’s wealth of biodiversity data via the Internet. To date, GBIF has become, in many respects, the most extensive biodiversity information exchange infrastructure in the world, opening up a full range of possibilities for science. Science has benefited from such access to biodiversity data in research areas ranging from the effects of environmental change on biodiversity to the spread of invasive species, among many others. As of this writing, more than 7,000 published items (scientific papers, reviews, conference proceedings) have been indexed in the GBIF Secretariat’s literature tracking programme. On the basis on this database, we will represent trends in GBIF in the users’ behaviour over time regarding openness, social structure, and other features associated to such scientific production: what is the measurable impact of research using GBIF data? How is the GBIF community of users growing? Is the science made with, and enabled by, open data, actually open? Mapping GBIF users’ choices will show how biodiversity research is evolving through time, synthesising past and current priorities of this community in an attempt to forecast whether summer—or winter—is coming.

The initiatives on data mobilization in biodiversity science have been steadily on the rise throughout the past few decades. The Global Biodiversity Information Facility (GBIF) supports this development and enables open access to biodiversity data on an international scale. In Russia, with its immense territory, the initiative is following a unique course; while some regions are well-represented, others are hardly ever mentioned. The operational unit in the GBIF network is a GBIF Participant Node, which coordinates a country or organization to collectively develop an infrastructure for delivering biodiversity information. The Nodes, however, are formally established in countries which become Voting or Associate participants in GBIF, which is not yet the case for Russia. The large size of our country would justify the need to create sub-nodes of the next level. This publication is describing process of establishing a regional initiative in the northern part of West Siberia -within the administrative boundaries of the Khanty-Mansi Autonomous Okrug-Yugra, Yamal-Nenets Autonomous Okrug and Tyumen region. The regional initiative started in 2018, although some biodiversity information initiatives had been developing earlier (since 2012). The work currently covers four main areas of GBIF-nodes responsibilities and services: coordination the landscape of initiatives, support of biodiversity data mobilization, biodiversity data analysis and use, and support of data management and curation. These services are described in more detail in the present paper, and problems in the development of individual services are discussed. By the end of 2020, there are 11 registered publishing organizations and 37 published datasets from the Siberian Northwest. The total number of published records is about 120 000, with 30% published by the Yugra State University; 20% are observations from iNaturalist.org; all organizations in Northwestern Siberia as a whole represent about 50% of the published records.

Biodiversity issues in Brazil have reached a critical point. On one hand, biodiversity science is increasing in quality and quantity, however on the other, habitat destruction in all major biomes still maintain alarmingly high rates. This paradox, from a scientific perspective, has two central tenets that scientists should focus on. First, although science related to biodiversity is of high standard in Brazil as compared to that of peers in the world, it is still not at the leading edge of research. Second, the wealth of information built up by strong research programmes, such as Biota/Fapesp - to which this special issue of Scientia Agricola is dedicated - is beginning to help decision-makers to improve precision and quality of their decisions concerning the environment, but still much is left to be done in this respect. Therefore, I discuss some of the biodiversity issues that remain controversial and demand fast scientific growth. Tackling them Brazil may finally reach the leading edge of biodiversity research. Finally, I discuss how communication between scientists and decision-makers and the general public may be improved, highlighting how a strong education project is urgently needed from kindergarten to graduate programmes in order to solve the two problems above mentioned and definitely crack the paradox biodiversity knowledge vs. biodiversity destruction.

Aim Exotic species may serve as vectors for the introduction of parasites from their native range and may also become infected by parasites already present in invaded areas, but the total number of parasites infecting such exotic species in their invaded areas is typically less than that in their native range. We tested whether the diversity of parasites associated with exotic species in the native and invaded areas is related to the epizootic impact these parasites cause.Location Global.Methods We examined the diversity and epizootic impact of 384 parasite taxa associated with 22 exotic freshwater invertebrate species. The epizootic impact of each parasite was rated based on whether it had been documented to cause a major pathological impact on a large proportion of an infected host population (other than the invader under consideration).Results The total number of parasites associated with an exotic host in its native range was about twice that of all parasites associated with it in its entire invaded range. This was mainly because of the loss in the invaded areas of low impact parasites, whereas the average number of high impact parasites per host in these areas did not differ statistically from that in the native range.Main conclusions Our study suggests similar levels of adverse impact of parasites of exotic species in both their native and invaded areas. In addition to the introduction of highly pathogenic exotic parasites, other mechanisms that may be involved include (1) acquisition by the invaders of new high impact parasites in the invaded ranges, (2) high abundance of the invaders in their new ranges and (3) susceptibility of novel hosts to exotic parasites because of the ‘naive host syndrome’.

This chapter examines the use of quantitative data in general terms, obstacles to generalization, and the extent to which various kinds of data are generalizable. It discusses some limitations that might be associated with the neglect of empirical research by green/conservation criminologists. Quantitative data and methods add to our understanding of things around us, and building an appropriately broad and sound GCC knowledge base cannot happen when quantitative studies are neglected. The fact that quantitative studies are underrepresented in the GCC literature is problematic particularly because the social science fields, as well as conservation sciences, are predominantly quantitative fields. Quantitative data is heavily employed in conservation and biodiversity research outside of criminology. A number of GCC studies add to the arguments by examining specific examples of related offenses and offenders, and sometimes those studies describe those offenses and offenders using empirical data. The chapter also presents an overview of the key concepts discussed in this book.

Aphaniidae killifish represent a group of small-bodied teleosts that inhabit a wide range of transitional and extreme aquatic environments. Their remarkable adaptability, ecological niche, and high levels of endemism make them valuable models for the investigation of biodiversity patterns, evolutionary processes, and conservation strategies in fragmented and vulnerable habitats. Drawing from case studies across the Mediterranean Sea and the Middle East, this research examines how ecological plasticity, reproductive strategies, and molecular tools allow to interpret the resilience patterns of the distribution. Our phylogenetic analyses confirm their complex evolutionary relationships and highlight the role of geological and biogeographical events in shaping their diversification. The potential of Aphaniidae as comprehensive models that connect laboratory insights and ecosystem-level dynamics is highlighted by the integration of genetics, physiology, and field ecology. Encouraging their use in biodiversity research and conservation efforts offers a crucial chance to enhance our capacity to monitor, understand, and mitigate biodiversity loss in rapidly changing aquatic systems. This review synthesizes advances in understanding the evolutionary adaptations, ecological roles, reproductive strategies, and (eco) toxicological applications of killifish. It highlights their potential to bridge the gap between laboratory models and real-world ecological processes, advocating for their broader adoption in scientific research. In this regard, killifish represents an essential resource for addressing global issues of biodiversity conservation, ecosystem management, and environmental resilience. Aphaniidae killifish showcase exceptional adaptability to diverse aquatic habitats. Aphaniidae species excel as bioindicators of habitat changes and pollution impacts. Genetic tools reveal mechanisms of killifish adaptation to extreme environments. Aphanius and phylogenetically related genera offer insights into ecological resilience in stressed habitats. This study underscores the utility of killifish in conservation and ecotoxicology research.

Among tropical areas, Africa is considered to be poor in terms of biodiversity as compared with Amazon or South-East Asia, especially with respect to forest diversity. Despite this lower diversity, some African tropical zones, such as Ghana, harbour a plethora of species, particularly of trees. Unfortunately, as a result of anthropogenic impacts, biological diversity in West Africa dramatically decreased in the last decades, with very limited reference to evaluate the amount of the loss. Due to these growing pressure, a collection of relevant biodiversity information in this region seems to be urgent. We surveyed 127 temporary plots randomly distributed within 3 protected areas in Ghana and we collected data on tree (dbh>10 cm) species richness and their abundances. We also performed α, and β diversity analyses, and estimated the effective number of species, adopting various indices and approaches to provide further information on each assemblage. The main goals of this research were: (i) to provide a wide tree species database (abundance-based data), together with some biodiversity analyses; (ii) to estimate the sampling effort needed for next biodiversity surveys in the same and similar regions; and (iii) to calculate some indices useful to monitor the future of these protected areas both in terms of conservation and biodiversity research.

A discussion session held at a National Science Foundation-sponsored Herbarium Networks Workshop at Michigan State University in September of 2004 resulted in a rallying objective: make all botanical specimen information in United States collections available online by 2020. Rabeler and Macklin 2006 outlined a toolkit for realizing this ambitious goal, which included: a review of relevant and state-of-the-art web resources, data exchange standards and, mechanisms to maximize efficiencies while minimizing costs. a review of relevant and state-of-the-art web resources, data exchange standards and, mechanisms to maximize efficiencies while minimizing costs. Given that we are now in the year 2020, it seems appropriate to examine the progress towards the objective of making all US botanical specimen collections data available online. Our presentation will attempt to answer several questions: How close have we come to meeting the original objective? What fraction of “digitized” specimens are minimally represented by a catalog number, a determination, and/or a photograph? What fraction has been thoroughly transcribed? How close have we come to attaining a seamlessly integrated, comprehensive, and national view of botanical specimen data that guides a stakeholder to appropriate resources regardless of their entry point? What “holes” in this effort still exist and what might be required to fill them? How close have we come to meeting the original objective? What fraction of “digitized” specimens are minimally represented by a catalog number, a determination, and/or a photograph? What fraction has been thoroughly transcribed? How close have we come to attaining a seamlessly integrated, comprehensive, and national view of botanical specimen data that guides a stakeholder to appropriate resources regardless of their entry point? What “holes” in this effort still exist and what might be required to fill them? Given our interest in the success of both the Global Biodiversity Information Facility (GBIF) and the Integrated Digitized Biocollections (iDigBio), as well as the overwhelming likelihood that either one of these initiatives is the usual entry point for someone seeking US-based botanical data, we approached the answers to the above questions by first crafting a repeatable data download and processing workflow in early July 2020. This resulted in 25.6M records of plant, fungi, and Chromista from 216 datasets available through GBIF and 32.8M comparable records available through iDigBio from 525 recordsets. We attempted to align these seemingly discordant sets of records and also chose Darwin Core terms that were best suited to match the four hierarchical levels of digitization defined in the Minimal Information for Digital Specimens (MIDS) (van Egmond et al. 2019). During the analysis/comparison of the datasets, we found several examples where the number of data records from an institution seemed much lower than expected. From a combination of analyzing record content in GBIF/iDigBio and consulting regional/taxonomic portals, it became evident that, besides datasets only being included in either GBIF or iDigBio, there was a significant number of records in regional/taxonomic portals that were not yet made available through either GBIF or iDigBio. Progress on digitization has benefited greatly from the US National Science Foundation's creation of the Advancing Digitization of Biodiversity Collections (ADBC) program, and funding of the 15 Thematic Collection Networks (TCN). The launching of new projects and the ensuing digitization of herbarium collections have led to a multitude of new specimen portals and the enhancement of existing software like Symbiota (Gries et al. 2014). But, it has also led to insufficient data sharing among projects and inadequately aligned data synchronization practices between aggregators. Consistency in terms of data availability and quality between GBIF and iDigBio is low, and the chronic lack of record-level identifiers consistently restricts the flow of enhancements made to records. We conclude that there remains substantial work to be done on the national infrastructure and on international best practices to help facilitate collaboration and to realize the original objective of making all US botanical specimen collections data available online.