Research applications of primary biodiversity databases in the digital age

Data mobilisation in the LWS Herbarium: success and prospects

Background

Digitisation of hosted specimens is a crucial task for all herbaria worldwide and is one of the main streams for today. By digitising their collections and publishing the datasets, the herbaria grant access to essential data to a wide research audience and, as a result, involve their collections in scientific work more actively. Digitisation also allows virtual preservation of the collections, which is especially important in conditions of hostilities, when the entire collection can be destroyed or damaged in one moment. This paper describes two datasets recently published in GBIF in the framework of the LWS herbarium digitisation initiative. It also contains some considerations about further digitisation priorities and plans in the LWS Herbarium in the context of complicated war conditions and limited facilities.

New information

In total, 2,419 occurrence records from Ukraine mobilised from LWS Herbarium were published. These datasets are planned to be dynamic with the addition of new records along with progress of digitisation work at LWS. At least 6,000 more records are planned to be published through these datasets in 2024.

Enhancing biodiversity conservation and monitoring in protected areas through efficient data management

A scientifically informed approach to decision-making is key to ensuring the sustainable management of ecosystems, especially in the light of increasing human pressure on habitats and species. Protected areas, with their long-term institutional mandate for biodiversity conservation, play an important role as data providers, for example, through the long-term monitoring of natural resources. However, poor data management often limits the use and reuse of this wealth of information. In this paper, we share lessons learned in managing long-term data from the Italian Alpine national parks. Our analysis and examples focus on specific issues faced by managers of protected areas, which partially differ from those faced by academic researchers, predominantly owing to different mission, governance, and temporal perspectives. Rigorous data quality control, the use of appropriate data management tools, and acquisition of the necessary skills remain the main obstacles. Common protocols for data collection offer great opportunities for the future, and complete recovery and documentation of time series is an urgent priority. Notably, before data can be shared, protected areas should improve their data management systems, a task that can be achieved only with adequate resources and a long-term vision. We suggest strategies that protected areas, funding agencies, and the scientific community can embrace to address these problems. The added value of our work lies in promoting engagement with managers of protected areas and in reporting and analysing their concrete requirements and problems, thereby contributing to the ongoing discussion on data management and sharing through a bottom-up approach.

Fisheries data management systems in the NW Mediterranean: from data collection to web visualization

The European Union Data Collection Framework (DCF) states that scientific data-driven assessments are essential to achieve sustainable fisheries. To respond to the DCF call, this study introduces the information systems developed and used by Institut Català de Recerca per a la Governança del Mar (ICATMAR), the Catalan Institute of Research for the Governance of the Seas. The information systems include data from a biological monitoring, curation, processing, analysis, publication and web visualization for bottom trawl fisheries. Over the 4 years of collected data (2019-2022), the sampling program developed a dataset of over 1.1 million sampled individuals accounting for 24.6 tons of catch. The sampling data are ingested into a database through a data input website ensuring data management control and quality. The standardized metrics are automatically calculated and the data are published in the web visualizer, combined with fishing landings and Vessel Monitoring System (VMS) records. As the combination of remote sensing data with fisheries monitoring offers new approaches for ecosystem assessment, the collected fisheries data are also visualized in combination with georeferenced seabed habitats from the European Marine Observation and Data Network (EMODnet), climate and sea conditions from Copernicus Monitoring Environment Marine Service (CMEMS) on the web browser. Three public web-based products have been developed in the visualizer: geolocated bottom trawl samplings, biomass distribution per port or season and length-frequency charts per species. These information systems aim to fulfil the gaps in the scientific community, administration and civil society to access high-quality data for fisheries management, following the Findable, Accessible, Interoperable, Reusable (FAIR) principles, enabling scientific knowledge transfer. Database URL  https://icatmar.github.io/VISAP/(www.icatmar.cat).

Species catalogue of Drymaeus (Mesembrinus) Alberts, 1850 (Gastropoda: Bulimulidae) from Brazil and new data on morphology and distribution of Drymaeus (Mesembrinus) interpunctus (Martens, 1887)

Background

Herein, we attempted to obtain detailed data on the distribution of the species of Drymaeus (Mesembrinus) in Brazil, using biodiversity databases, malacological collections and literature as sources of occurrence records. We provided a catalogue of species, along with distribution maps. We also estimated the suitable distribution of Drymaeus (Mesembrinus) interpunctus using the maximum entropy approach. A detailed description of the anatomy of the soft parts of this species was provided, with new data on the pallial system.

Materials and Methods

For each species we provided information on the compiled data associated with museum collections and the literature. Distribution maps including geographic boundaries, Brazilian biomes and altitude were made with QGIS software 3.16.10 Hannover. For niche modelling, nineteen bioclimatic variables and a topographic variable were used as predictors. The models were performed with MaxEnt version 3.3.3k.

Results

Most of the species are represented by scarce material in malacological collections; for some species, these records correspond to type material, indicating that they have not been recollected. Most of the species were represented by shells making anatomical comparison and DNA analysis difficult, limiting our ability to provide new criteria for species delimitation. Our results allowed us to expand the known distribution area for three species, Drymaeus dutaillyi, D. gereti and D. oreades, with new occurrence records in Brazil. The MaxEnt model showed a thin area of high suitability to D. (M.) interpunctus in the Southeastern Brazil, corresponding to the Atlantic Forest. Minimum temperature of the coldest month and mean temperature of coldest quarter were the variables that most influenced the development of the model.

Discussion

Drymaeus interpunctus was described based on specimens collected in Brazil without mention to the exact localities. Herein the new records from databases allowed to expand the known geographic distribution for this species and to infer its potential distribution. Although the type locality of D. interpunctus is in Brazil, the anatomy of the soft parts of specimens from this country was not previously described. The anatomy of the reproductive system of the specimens analyzed herein mostly corresponds to a previous description for specimens from Paraguay, except for the absence of penial sheath and the relative length of the bursa copulatrix duct. The results of niche modeling showed a thin area of high suitability for D. interpunctus and a vast area of moderate suitability, indicating that this species present a niche breadth that favors its occurrence in a range of different biomes, including less suitable areas.

Conclusion

The small number of records obtained for most of the species and their restricted ranges associated with habitat destruction may indicate that they are of conservation concern.

Marine macroinvertebrate ecosystem services under changing conditions of seagrasses and mangroves

This study aimed to investigate the impact of changing environmental conditions on MMI ES in seagrasses and mangroves. We used data from satellite and biodiversity platforms combined with field data to explore the links between ecosystem pressures (habitat conversion, overexploitation, climate change), conditions (environmental quality, ecosystem attributes), and MMI ES (provisioning, regulation, cultural). Both seagrass and mangrove extents increased significantly since 2016. While sea surface temperature showed no significant annual variation, sea surface partial pressure CO2, height above sea level and pH presented significant changes. Among the environmental quality variables only silicate, PO4 and phytoplankton showed significant annual varying trends. The MMI food provisioning increased significantly, indicating overexploitation that needs urgent attention. MMI regulation and cultural ES did not show significant trends overtime. Our results show that MMI ES are affected by multiple factors and their interactions can be complex and non-linear. We identified key research gaps and suggested future directions for research. We also provided relevant data that can support future ES assessments.

The Afrotropical breeding grounds of the Palearctic-African migratory painted lady butterflies (Vanessa cardui)

Migratory insects are key players in ecosystem functioning and services, but their spatiotemporal distributions are typically poorly known. Ecological niche modeling (ENM) may be used to predict species seasonal distributions, but the resulting hypotheses should eventually be validated by field data. The painted lady butterfly (Vanessa cardui) performs multigenerational migrations between Europe and Africa and has become a model species for insect movement ecology. While the annual migration cycle of this species is well understood for Europe and northernmost Africa, it is still unknown where most individuals spend the winter. Through ENM, we previously predicted suitable breeding grounds in the subhumid regions near the tropics between November and February. In this work, we assess the suitability of these predictions through i) extensive field surveys and ii) two-year monitoring in six countries: a large-scale monitoring scheme to study butterfly migration in Africa. We document new breeding locations, year-round phenological information, and hostplant use. Field observations were nearly always predicted with high probability by the previous ENM, and monitoring demonstrated the influence of the precipitation seasonality regime on migratory phenology. Using the updated dataset, we built a refined ENM for the Palearctic-African range of V. cardui. We confirm the relevance of the Afrotropical region and document the missing natural history pieces of the longest migratory cycle described in butterflies.

Collating biodiversity occurrence data for conservation

Plant and animal checklists, with conservation status information, are fundamental for conservation management. Historical field data, more recent data of digital origin and data-sharing platforms provide useful sources for collating species locality data. However, different biodiversity datasets have different formats and inconsistent naming systems. Additionally, most digital data sources do not provide an easy option for download by protected area. Further, data-entry-ready software is not readily available for conservation organization staff with limited technical skills to collate these heterogeneous data and create distribution maps and checklists for protected areas. The insights presented here are the outcome of conceptualizing a biodiversity information system for South African National Parks. We recognize that a fundamental requirement for achieving better standardization, sharing and use of biodiversity data for conservation is capacity building, internet connectivity, national institutional data management support and collaboration. We focus on some of the issues that need to be considered for capacity building, data standardization and data support. We outline the need for using taxonomic backbones and standardizing biodiversity data and the utility of data from the Global Biodiversity Information Facility and other available sources in this process. Additionally, we make recommendations for the fields needed in relational databases for collating species data that can be used to inform conservation decisions and outline steps that can be taken to enable easier collation of biodiversity data, using South Africa as a case study.

Phototank setup and focus stack imaging method for reptile and amphibian specimens (Amphibia, Reptilia)

Fluid-preserved reptile and amphibian specimens are challenging to photograph with traditional methods due to their complex three-dimensional forms and reflective surfaces when removed from solution. An effective approach to counteract these issues involves combining focus stack photography with the use of a photo immersion tank. Imaging specimens beneath a layer of preservative fluid eliminates glare and risk of specimen desiccation, while focus stacking produces sharp detail through merging multiple photographs taken at successive focal steps to create a composite image with an extended depth of field. This paper describes the wet imaging components and focus stack photography workflow developed while conducting a large-scale digitization project for targeted reptile and amphibian specimens housed in the University of Colorado Museum of Natural History Herpetology Collection. This methodology can be implemented in other collections settings and adapted for use with fluid-preserved specimen types across the Tree of Life to generate high-quality, taxonomically informative images for use in documenting biodiversity, remote examination of fine traits, inclusion in publications, and educational applications.

Role of digitalization in environment, social and governance, and sustainability: Review-based study for implications

Digitalization gives people access to a vast network of untapped data, which has the potential to help society and the environment. Smart systems connected to the internet can systematically provide a unique opportunity to solve difficulties related to long-term sustainability. The goals are to create an egalitarian, ecologically sustainable, and healthy society. Technological resources are envisioned as game-changing instruments. Three key concerns integration benefits are highlighted here: (i) sustainable development goals, (ii) socio-economic development, and (iii) the role of digital technology in environmental sustainability. This viewpoint describes the potential that digitization can create a future sustainable society. The technological network would unite the urban and rural worlds under a shared banner of sustainable development, keeping all social elements in the loop. Nations that take a comprehensive strategy will be able to provide equitable growth and an efficient, sustainable, and digital existence for their citizens. As a result, digitization provides better living conditions, active public involvement, clean governance, and transparency in public welfare programs and processes. People who are well-informed, self-aware, and digitally equipped will be better learners, thinkers, reformers, participators, and change and growth agents, marching forward on sustainable progress. The advantages of digitization in hastening the transition to sustainable industrial processes and improving people's health and happiness are explored. Finally, the perspective encapsulates the advantages of digitization by offering a holistic vision of how technology could aid in addressing major challenges such as endangered world biodiversity and climate change.

Mining rare Earth elements: Identifying the plant species most threatened by ore extraction in an insular hotspot

Conservation efforts in global biodiversity hotspots often face a common predicament: an urgent need for conservation action hampered by a significant lack of knowledge about that biodiversity. In recent decades, the computerisation of primary biodiversity data worldwide has provided the scientific community with raw material to increase our understanding of the shared natural heritage. These datasets, however, suffer from a lot of geographical and taxonomic inaccuracies. Automated tools developed to enhance their reliability have shown that detailed expert examination remains the best way to achieve robust and exhaustive datasets. In New Caledonia, one of the most important biodiversity hotspots worldwide, the plant diversity inventory is still underway, and most taxa awaiting formal description are narrow endemics, hence by definition hard to discern in the datasets. In the meantime, anthropogenic pressures, such as nickel-ore mining, are threatening the unique ultramafic ecosystems at an increasing rate. The conservation challenge is therefore a race against time, as the rarest species must be identified and protected before they vanish. In this study, based on all available datasets and resources, we applied a workflow capable of highlighting the lesser known taxa. The main challenges addressed were to aggregate all data available worldwide, and tackle the geographical and taxonomic biases, avoiding the data loss resulting from automated filtering. Every doubtful specimen went through a careful taxonomic analysis by a local and international taxonomist panel. Geolocation of the whole dataset was achieved through dataset cross-checking, local botanists’ field knowledge, and historical material examination. Field studies were also conducted to clarify the most unresolved taxa. With the help of this method and by analysing over 85,000 data, we were able to double the number of known narrow endemic taxa, elucidate 68 putative new species, and update our knowledge of the rarest species’ distributions so as to promote conservation measures.

Maps of area of habitat for Italian amphibians and reptiles

Planning conservation actions requires detailed information on species’ geographic distribution. Species distribution data are most needed in areas hosting unique or endangered biodiversity. Italy is one of the European countries with the highest levels of herpetological diversity and endemism and is home to several threatened species of amphibians and reptiles. Information on the distribution of species’ habitats can help identify sites where the species is most likely to thrive, as viable populations depend on it. Area of Habitat (AOH) maps reveal the distribution of the habitat available to the species within their geographic range. We produced high resolution, freely accessible global area of habitat maps for 60 species of reptiles and amphibians distributed in Italy, which represent 60% of all Italian amphibian and reptile species. We validated a total of 44 AOH maps through a presence-only based evaluation method, with 86% of these maps showing a performance better than expected by chance. AOH maps can be used as a reference for conservation planning, as well as to investigate macroecological patterns of Italian herpetofauna. Furthermore, AOH maps can help monitoring habitat loss, which is known to be a major threat to many reptile and amphibian species in Europe.

ROBITT: A tool for assessing the risk-of-bias in studies of temporal trends in ecology

Aggregated species occurrence and abundance data from disparate sources are increasingly accessible to ecologists for the analysis of temporal trends in biodiversity. However, sampling biases relevant to any given research question are often poorly explored and infrequently reported; this can undermine statistical inference. In other disciplines, it is common for researchers to complete 'risk-of-bias' assessments to expose and document the potential for biases to undermine conclusions. The huge growth in available data, and recent controversies surrounding their use to infer temporal trends, indicate that similar assessments are urgently needed in ecology.We introduce ROBITT, a structured tool for assessing the 'Risk-Of-Bias In studies of Temporal Trends in ecology'. ROBITT has a similar format to its counterparts in other disciplines: it comprises signalling questions designed to elicit information on the potential for bias in key study domains. In answering these, users will define study inferential goal(s) and relevant statistical target populations. This information is used to assess potential sampling biases across domains relevant to the research question (e.g. geography, taxonomy, environment), and how these vary through time. If assessments indicate biases, then users must clearly describe them and/or explain what mitigating action will be taken.Everything that users need to complete a ROBITT assessment is provided: the tool, a guidance document and a worked example. Following other disciplines, the tool and guidance document were developed through a consensus-forming process across experts working in relevant areas of ecology and evidence synthesis.We propose that researchers should be strongly encouraged to include a ROBITT assessment when publishing studies of biodiversity trends, especially when using aggregated data. This will help researchers to structure their thinking, clearly acknowledge potential sampling issues, highlight where expert consultation is required and provide an opportunity to describe data checks that might go unreported. ROBITT will also enable reviewers, editors and readers to establish how well research conclusions are supported given a dataset combined with some analytical approach. In turn, it should strengthen evidence-based policy and practice, reduce differing interpretations of data and provide a clearer picture of the uncertainties associated with our understanding of reality.

State of biodiversity documentation in the Philippines: Metadata gaps, taxonomic biases, and spatial biases in the DNA barcode data of animal and plant taxa in the context of species occurrence data

Anthropogenic changes in the natural environment have led to alarming rates of biodiversity loss, resulting in a more urgent need for conservation. Although there is an increasing cognizance of the importance of incorporating biodiversity data into conservation, the accuracy of the inferences generated from these records can be highly impacted by gaps and biases in the data. Because of the Philippines' status as a biodiversity hotspot, the assessment of potential gaps and biases in biodiversity documentation in the country can be a critical step in the identification of priority research areas for conservation applications. In this study, we systematically assessed biodiversity data on animal and plant taxa found in the Philippines by examining the extent of metadata gaps, taxonomic biases, and spatial biases in DNA barcode data while using species occurrence data as a backdrop of the 'Philippines' biodiversity. These barcode and species occurrence datasets were obtained from public databases, namely: GenBank, Barcode of Life Data System and Global Biodiversity Information Facility. We found that much of the barcode data had missing information on either records and publishing, geolocation, or taxonomic metadata, which consequently, can limit the usability of barcode data for further analyses. We also observed that the amount of barcode data can be directly associated with the amount of species occurrence data available for a particular taxonomic group and location-highlighting the potential sampling biases in the barcode data. While the majority of barcode data came from foreign institutions, there has been an increase in local efforts in recent decades. However, much of the contribution to biodiversity documentation only come from institutions based in Luzon.

Toward an atlas of Salish Sea biodiversity: the flora and fauna of Galiano Island, British Columbia, Canada. Part I. Marine zoology

Background

Based on records dating from 1859 to 2021, we provide an overview of the marine animal diversity reported for Galiano Island, British Columbia, Canada. More than 650 taxa are represented by 20,000 species occurrence records in this curated dataset, which includes dive records documented through the Pacific Marine Life Surveys, museum voucher specimens, ecological data and crowd-sourced observations from the BC Cetacean Sightings Network and iNaturalist.

New information

We describe Galiano Island's marine animal diversity in relation to the Salish Sea's overall biodiversity and quantify the proportional contributions of different types of sampling effort to our current local knowledge. Overviews are provided for each taxonomic group in a format intended to be accessible to amateur naturalists interested in furthering research into the region's marine biodiversity. In summary, we find that the Pacific Marine Life Surveys, a regional community science diving initiative, account for 60% of novel records reported for Galiano Island. Voucher specimens account for 19% and crowd-sourced biodiversity data 18% of novel records, respectively, with the remaining 3% of reports coming from other sources. These findings shed light on the complementarity of different types of sampling effort and demonstrate the potential for community science to contribute to the global biodiversity research community. We present a biodiversity informatics framework that is designed to enable these practices by supporting collaboration among researchers and communities in the collection, curation and dissemination of biodiversity data.

speciesLink: rich data and novel tools for digital assessments of biodiversity

Abstract speciesLink is a large-scale biodiversity information portal that exists thanks to a broad collaborative network of people and institutions. CRIA’s involvement with the scientific community of Brazil and other countries is responsible for the significant results achieved, currently reaching more than 15 million primary biodiversity data records, 95% of which are associated with preserved specimens and about 25% with high-quality digital images. The network provides data on over 200,000 species, of which over 110,000 occur in Brazil. This article describes thematic networks within speciesLink, as well as some of the most useful tools developed. The importance and contributions of speciesLink are outlined, as are concerns about securing stable budgetary support for such biodiversity data e-infrastructures. Here we review the value of speciesLink as a major source of biodiversity information for research, education, informed decision-making, policy development, and bioeconomy.

A global agenda for advancing freshwater biodiversity research

Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.

Open Data Practices among Users of Primary Biodiversity Data

Presence-only biodiversity data are increasingly relied on in biodiversity, ecology, and conservation research, driven by growing digital infrastructures that support open data sharing and reuse. Recent reviews of open biodiversity data have clearly documented the value of data sharing, but the extent to which the biodiversity research community has adopted open data practices remains unclear. We address this question by reviewing applications of presence-only primary biodiversity data, drawn from a variety of sources beyond open databases, in the indexed literature. We characterize how frequently researchers access open data relative to data from other sources, how often they share newly generated or collated data, and trends in metadata documentation and data citation. Our results indicate that biodiversity research commonly relies on presence-only data that are not openly available and neglects to make such data available. Improved data sharing and documentation will increase the value, reusability, and reproducibility of biodiversity research.

occAssess: An R package for assessing potential biases in species occurrence data

Species occurrence records from a variety of sources are increasingly aggregated into heterogeneous databases and made available to ecologists for immediate analytical use. However, these data are typically biased, i.e. they are not a probability sample of the target population of interest, meaning that the information they provide may not be an accurate reflection of reality. It is therefore crucial that species occurrence data are properly scrutinised before they are used for research. In this article, we introduce occAssess, an R package that enables straightforward screening of species occurrence data for potential biases. The package contains a number of discrete functions, each of which returns a measure of the potential for bias in one or more of the taxonomic, temporal, spatial, and environmental dimensions. Users can opt to provide a set of time periods into which the data will be split; in this case separate outputs will be provided for each period, making the package particularly useful for assessing the suitability of a dataset for estimating temporal trends in species' distributions. The outputs are provided visually (as ggplot2 objects) and do not include a formal recommendation as to whether data are of sufficient quality for any given inferential use. Instead, they should be used as ancillary information and viewed in the context of the question that is being asked, and the methods that are being used to answer it. We demonstrate the utility of occAssess by applying it to data on two key pollinator taxa in South America: leaf-nosed bats (Phyllostomidae) and hoverflies (Syrphidae). In this worked example, we briefly assess the degree to which various aspects of data coverage appear to have changed over time. We then discuss additional applications of the package, highlight its limitations, and point to future development opportunities.

Collections Education: The Extended Specimen and Data Acumen

Biodiversity scientists must be fluent across disciplines; they must possess the quantitative, computational, and data skills necessary for working with large, complex data sets, and they must have foundational skills and content knowledge from ecology, evolution, taxonomy, and systematics. To effectively train the emerging workforce, we must teach science as we conduct science and embrace emerging concepts of data acumen alongside the knowledge, tools, and techniques foundational to organismal biology. We present an open education resource that updates the traditional plant collection exercise to incorporate best practices in twenty-first century collecting and to contextualize the activities that build data acumen. Students exposed to this resource gained skills and content knowledge in plant taxonomy and systematics, as well as a nuanced understanding of collections-based data resources. We discuss the importance of the extended specimen in fostering scientific discovery and reinforcing foundational concepts in biodiversity science, taxonomy, and systematics.

Integrating Literature, Biodiversity Databases, and Citizen-Science to Reconstruct the Checklist of Chondrichthyans in Cyprus (Eastern Mediterranean Sea)

Chondrichthyans are apex predators influencing the trophic web through a top-down process thus their depletion will affect the remaining biota. Notwithstanding that, research on chondrichthyans is sparse or data-limited in several biogeographic areas worldwide, including the Levantine Sea. We revise and update the knowledge of chondrichthyans in Cyprus based on a bibliographic review that gains information retrieved from peer-reviewed and grey literature, Global Biodiversity Information Facility (135 records of at least 18 species) and the Ocean Biodiversity Information System (65 records of at least14 species), and the citizen science project Mediterranean Elasmobranchs Citizen Observations (117 records per 23 species). Our updated checklist reports 60 species that account for about 70% of the Mediterranean chondrichthyan biota. The list includes 15 more species than the previous checklist and our study reports three new species for Cyprus waters, namely the blackmouth catshark Dalatias licha, the round fantail stingray Taeniurops grabatus, and the sawback angelshark Squatina aculeata. Our research highlights the need for conservation measures and more studies regarding the highly threatened blackchin guitarfish Glaucostegus cemiculus and the devil ray Mobula mobular, and stresses the importance for training a new generation of observers to strengthen the knowledge and conservation of elasmobranchs in the region.

Citizen Science Contributions to Address Biodiversity Loss and Conservation Planning in a Rapidly Developing Region

Biodiversity data support conservation research and inform conservation decisions addressing the wicked problem of biodiversity loss. However, these data often need processing and compilation before use, which exceed the time availability of professional scientists. Nevertheless, scientists can recruit, train, and support a network of citizen scientists to prepare these data using online platforms. Here, we describe three citizen science projects sponsored by the Arkansas Natural Heritage Commission to transcribe and georeference historic herbarium specimens and document current biodiversity through iNaturalist for two highly biodiverse and rapidly developing counties in Northwest Arkansas, USA. Citizen science-generated data will be used in a county natural heritage inventory (CNHI) report, including a comprehensive list of taxa tied to voucher specimens and records for rare plant populations. Since the CNHI project started in 2018, citizen scientists have transcribed 8855 and georeferenced 2636 specimen records. From iNaturalist observations, 125 rare plant populations of 39 taxa have been documented. This CNHI report will determine the most critical taxa, habitats, and sites for conservation action in the region and will inform conservation stakeholders at the local, state, and federal levels as they engage in land acquisition, ecological restoration, natural resource management, planning of growth and development, and environmental review/regulation.

Data integration enables global biodiversity synthesis

The accessibility of global biodiversity information has surged in the past two decades, notably through widespread funding initiatives for museum specimen digitization and emergence of large-scale public participation in community science. Effective use of these data requires the integration of disconnected datasets, but the scientific impacts of consolidated biodiversity data networks have not yet been quantified. To determine whether data integration enables novel research, we carried out a quantitative text analysis and bibliographic synthesis of >4,000 studies published from 2003 to 2019 that use data mediated by the world's largest biodiversity data network, the Global Biodiversity Information Facility (GBIF). Data available through GBIF increased 12-fold since 2007, a trend matched by global data use with roughly two publications using GBIF-mediated data per day in 2019. Data-use patterns were diverse by authorship, geographic extent, taxonomic group, and dataset type. Despite facilitating global authorship, legacies of colonial science remain. Studies involving species distribution modeling were most prevalent (31% of literature surveyed) but recently shifted in focus from theory to application. Topic prevalence was stable across the 17-y period for some research areas (e.g., macroecology), yet other topics proportionately declined (e.g., taxonomy) or increased (e.g., species interactions, disease). Although centered on biological subfields, GBIF-enabled research extends surprisingly across all major scientific disciplines. Biodiversity data mobilization through global data aggregation has enabled basic and applied research use at temporal, spatial, and taxonomic scales otherwise not possible, launching biodiversity sciences into a new era.

STOREFISH 2.0: a database on the reproductive strategies of teleost fishes

Teleost fishes show the most outstanding reproductive diversity of all vertebrates. Yet to date, no one has been able to decisively explain this striking variability nor to perform large-scale phylogenetic analyses of reproductive modes. Here, we describe STrategies Of REproduction in FISH (STOREFISH) 2.0, an online database easing the sharing of an original data set on reproduction published in 2007, enriched with automated data extraction and presentation to display the knowledge acquired on temperate freshwater fish species. STOREFISH 2.0 contains the information for 80 freshwater fish species and 50 traits from the analysis of 1219 references. It is anticipated that this new database could be useful for freshwater biodiversity research, conservation, assessment and management. Database URL: www.storefish.org.

Small herbaria contribute unique biogeographic records to county, locality, and temporal scales

PREMISE

With digitization and data sharing initiatives underway over the last 15 years, an important need has been prioritizing specimens to digitize. Because duplicate specimens are shared among herbaria in exchange and gift programs, we investigated the extent to which unique biogeographic data are held in small herbaria vs. these data being redundant with those held by larger institutions. We evaluated the unique specimen contributions that small herbaria make to biogeographic understanding at county, locality, and temporal scales.

METHODS

We sampled herbarium specimens of 40 plant taxa from each of eight states of the United States of America in four broad status categories: extremely rare, very rare, common native, and introduced. We gathered geographic information from specimens held by large (≥100,000 specimens) and small (<100,000 specimens) herbaria. We built generalized linear mixed models to assess which features of the collections may best predict unique contributions of herbaria and used an Akaike information criterion-based information-theoretic approach for our model selection to choose the best model for each scale.

RESULTS

Small herbaria contributed unique specimens at all scales in proportion with their contribution of specimens to our data set. The best models for all scales were the full models that included the factors of species status and herbarium size when accounting for state as a random variable.

CONCLUSIONS

We demonstrated that small herbaria contribute unique information for research. It is clear that unique contributions cannot be predicted based on herbarium size alone. We must prioritize digitization and data sharing from herbaria of all sizes.

Taxonomic bias in occurrence information of angiosperm species in China

Taxonomic bias is a well-known shortcoming of species occurrence databases. Understanding the causes of taxonomic bias facilitates future biological surveys and addresses current knowledge gaps. Here, we investigate the main drivers of taxonomic bias in occurrence data of angiosperm species in China. We used a database including 5,936,768 records for 28,968 angiosperm species derived from herbarium specimens and literature sources. Generalized additive models (GAMs) were applied to investigate explanatory powers of 17 variables on the variation in record numbers of species. Five explanatory variables were selected for a multi-predictor GAM that explained 69% of the variation in record numbers: plant height, range size, elevational range, numbers of scientific publications and web pages. Range size was the most important predictor in the model and positively correlated with number of records. Morphological and phenological traits and social-economic factors including economic values and conservation status had weak explanatory powers on record numbers of plant species, which differs from the findings in animals, suggesting that causes of taxonomic bias in occurrence databases may vary between taxonomic groups. Our results suggest that future floristic surveys in China should more focus on range-restricted and socially or scientifically less "interesting" species.

Spotlight on the invasion of a carabid beetle on an oceanic island over a 105-year period

The flightless beetle Merizodus soledadinus, native to the Falkland Islands and southern South America, was introduced to the sub-Antarctic Kerguelen Islands in the early Twentieth Century. Using available literature data, in addition to collecting more than 2000 new survey (presence/absence) records of M. soledadinus over the 1991-2018 period, we confirmed the best estimate of the introduction date of M. soledadinus to the archipelago, and tracked subsequent changes in its abundance and geographical distribution. The range expansion of this flightless insect was initially slow, but has accelerated over the past 2 decades, in parallel with increased local abundance. Human activities may have facilitated further local colonization by M. soledadinus, which is now widespread in the eastern part of the archipelago. This predatory insect is a major threat to the native invertebrate fauna, in particular to the endemic wingless flies Anatalanta aptera and Calycopteryx moseleyi which can be locally eliminated by the beetle. Our distribution data also suggest an accelerating role of climate change in the range expansion of M. soledadinus, with populations now thriving in low altitude habitats. Considering that no control measures, let alone eradication, are practicable, it is essential to limit any further local range expansion of this aggressively invasive insect through human assistance. This study confirms the crucial importance of long term biosurveillance for the detection and monitoring of non-native species and the timely implementation of control measures.

Towards Global Volunteer Monitoring of Odonate Abundance

Insects are reportedly experiencing widespread declines, but we generally have sparse data on their abundance. Correcting this shortfall will take more effort than professional entomologists alone can manage. Volunteer nature enthusiasts can greatly help to monitor the abundance of dragonflies and damselflies (Odonata), iconic freshwater sentinels and one of the few nonpollinator insect groups appreciated by the public and amenable to citizen science. Although counting individual odonates is common in some locations, current data will not enable a global perspective on odonate abundance patterns and trends. Borrowing insight from butterfly monitoring efforts, we outline basic plans for a global volunteer network to count odonates, including organizational structure, advertising and recruiting, and data collection, submission, and synthesis. We hope our proposal serves as a catalyst for richer coordinated efforts to understand population trends of odonates and other insects in the Anthropocene.

Use of web-based species occurrence information systems by academics and government professionals

Web-based information systems designed to increase access to species occurrence data for use in research and natural resource decision-making have become more prevalent over the past few decades. The effectiveness of these systems depends on their usability and extent of use by their intended audiences. We conducted an online survey of academics and government professionals in the United States to compare their species occurrence data needs and their perceptions and use of web-based species occurrence information systems. Our results indicate that although views and perceptions held by academics and government professionals about the importance, usefulness, and ease of use of these information systems tend to be similar, there were differences in their use of species occurrence data and web-based species occurrence information systems. The baseline information obtained in this study will help inform future directions for improvements in species occurrence information systems.

An expert study on hierarchy comparison methods applied to biological taxonomies curation

Comparison of hierarchies aims at identifying differences and similarities between two or more hierarchical structures. In the biological taxonomy domain, comparison is indispensable for the reconciliation of alternative versions of a taxonomic classification. Biological taxonomies are knowledge structures that may include large amounts of nodes (taxa), which are typically maintained manually. We present the results of a user study with taxonomy experts that evaluates four well-known methods for the comparison of two hierarchies, namely, edge drawing, matrix representation, animation and agglomeration. Each of these methods is evaluated with respect to seven typical biological taxonomy curation tasks. To this end, we designed an interactive software environment through which expert taxonomists performed exercises representative of the considered tasks. We evaluated participants' effectiveness and level of satisfaction from both quantitative and qualitative perspectives. Overall quantitative results evidence that participants were less effective with agglomeration whereas they were more satisfied with edge drawing. Qualitative findings reveal a greater preference among participants for the edge drawing method. In addition, from the qualitative analysis, we obtained insights that contribute to explain the differences between the methods and provide directions for future research.

The Odonata of Quebec: Specimen data from seven collections

Background

The Odonata, dragonflies and damselflies, constitute one of the more charismatic and better-studied orders of insects. The approximately 6,000 extant species on Earth can be variously found on all continents, except Antarctica. A relatively stable taxonomy, a relative ease of species identification and an aquatic immature stage has made the Odonata a taxon of interest in documenting the symptoms of global environmental change, especially at higher latitudes. The Odonata fauna of the north-temperate Canadian province of Quebec includes 150 species, many of which are at the northern limits of their geographic distribution.

New information

Quebec hosts multiple entomological specimen depositories, including seven publicly-accessible research collections. One of these, the University of Montreal's Ouellet-Robert Entomological Collection, houses an exceptionally large collection of Odonata. An initial specimen data capture project for this collection gathered 31,595 Quebec Odonata occurrence records, but several Quebec species were missing and geographic coverage was biased towards the Montreal region. To complement this dataset, we undertook to digitise the Odonata records of six other public research collections. They are, in order of Quebec Odonata collection size, the Laval University Entomological Collection, McGill University's Lyman Entomological Museum, the Insectarium of Montreal Research Collection, the Quebec Government's Insect Collection, Bishop's University's Insect Collection and the Laurentian Forestry Centre's René-Martineau Insectarium. Of the 40,447 total specimen occurrence records, 36,951 are identified to the species level, including 137 of the 150 species officially-recorded in Quebec and 2 non-nominotypical subspecies. We here summarise the data and highlight the strengths and weaknesses of the datasets. The complete dataset is available with this publication (Suppl. material 1), whereas the specimen data associated with each collection are available as Darwin Core archives at Canadensys.net and will be updated as appropriate.

Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research

Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a "vast hidden treasure trove" of biodiversity -95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation's decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number of specimens in collections has increased by approximately 1% per year over the past 30 years. We propose that this rate of increase is insufficient to provide enough data to address biodiversity research needs, and that arthropod collections should aim to triple their rate of new specimen acquisition. (4) The collections we surveyed in the United States vary broadly in a number of indicators. Collectively, there is depth and breadth, with smaller collections providing regional depth and larger collections providing greater global coverage. (5) Increased coordination across museums is needed for digitization efforts to target taxa for research and conservation goals and address long-term data needs. Two key recommendations emerge: collections should significantly increase both their specimen holdings and their digitization efforts to empower continental and global biodiversity data pipelines, and stimulate downstream research.