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Introduction: Historic museum collections hold a wealth of biodiversity data that are essential to our understanding of the rapidly changing natural world. Novel curatorial practices are needed to extract and digitise these data, especially for the innumerable pinned insects whose collecting information is held on small labels. Methods: We piloted semi-automated specimen imaging and digitisation of specimen labels for a collection of ~29,000 pinned insects of ground beetles (Carabidae: Lebiinae) held at the Natural History Museum, London. Raw transcription data were curated against literature sources and non-digital collection records. The primary data were subjected to statistical analyses to infer trends in collection activities and descriptive taxonomy over the past two centuries. Results: This work produced research-ready digitised records for 2,546 species (40% of known species of Lebiinae). Label information was available on geography in 91% of identified specimens, and the time of collection in 39.8% of specimens and could be approximated for nearly all specimens. Label data revealed the great age of this collection (average age 91.4 years) and the peak period of specimen acquisition between 1880 and 1930, with little differences among continents. Specimen acquisition declined greatly after about 1950. Early detected species generally were present in numerous specimens but were missing records from recent decades, while more recently acquired species (after 1950) were represented mostly by singleton specimens only. The slowing collection growth was mirrored by the decreasing rate of species description, which was affected by huge time lags of several decades to formal description after the initial specimen acquisition. Discussion: Historic label information provides a unique resource for assessing the state of biodiversity backwards to pre-industrial times. Many species held in historical collections especially from tropical super-diverse areas may not be discovered ever again, and if they do, their recognition requires access to digital resources and more complete levels of species description. A final challenge is to link the historical specimens to contemporary collections that are mostly conducted with mechanical trapping of specimens and DNA-based species recognition. [ABSTRACT FROM AUTHOR]

Climate warming has triggered shifts in plant distributions, resulting in changes within communities, characterized by an increase in warm‐demanding species and a decrease in cold‐adapted species – referred to as thermophilization. Researchers conventionally rely on co‐occurrence data from vegetation assemblages to examine these community dynamics. Despite the increasing availability of presence‐only data in recent decades, their potential has largely remained unexplored due to concerns about their reliability. Our study aimed to determine whether climate‐induced changes in community dynamics, as inferred from presence‐only data from the Global Biodiversity Information Facility (GBIF), corresponded with those derived from co‐occurrence plot data. To assess the differences between these datasets, we computed a community temperature index (CTI) using a transfer function, weighted‐averaging partial least squares regression (WA‐PLS). We calibrated the transfect function model based on the species–temperature relationship using data before recent climate warming. Then we assessed the differences in CTI and examined the temporal trend in thermophilization. In a preliminary analysis, we assessed the performance of this calibration using three datasets: 1) Norwegian co‐occurrence data, 2) presence‐only data from a broader European region organized into pseudo‐plots (potentially capturing a larger part of the species niches), and 3) a combined dataset merging 1) and 2). The transfer function including the combined dataset performed best. Subsequently, we compared the CTI for the co‐occurrence plots paired up spatially and temporally with presence‐only pseudo‐plots. The results demonstrated that presence‐only data can effectively evaluate species assemblage responses to climate warming, with consistent CTI and thermophilization values to what was found for the co‐occurrence data. Employing presence‐only data for evaluating community responses opens up better spatial and temporal resolution and much more detailed analyses of such responses. Our results therefore outline how a large amount of presence‐only data can be used to enhance our understanding of community dynamics in a warmer world. [ABSTRACT FROM AUTHOR]

The ever‐increasing and expanding globalisation of trade and transport underpins the escalating global problem of biological invasions. Developing biosecurity infrastructures is crucial to anticipate and prevent the transport and introduction of invasive alien species. Still, robust and defensible forecasts of potential invaders are rare, especially for species without known invasion history. Here, we aim to support decision‐making by developing a quantitative invasion risk assessment tool based on invasion syndromes (i.e., generalising typical attributes of invasive alien species). We implemented a workflow based on 'Multiple Imputation with Chain Equation' to estimate invasion syndromes from imputed datasets of species' life‐history and ecological traits and macroecological patterns. Importantly, our models disentangle the factors explaining (i) transport and introduction and (ii) establishment. We showcase our tool by modelling the invasion syndromes of 466 amphibians and reptile species with invasion history. Then, we project these models to amphibians and reptiles worldwide (16,236 species [c.76% global coverage]) to identify species with a risk of being unintentionally transported and introduced, and risk of establishing alien populations. Our invasion syndrome models showed high predictive accuracy with a good balance between specificity and generality. Unintentionally transported and introduced species tend to be common and thrive well in human‐disturbed habitats. In contrast, those with established alien populations tend to be large‐sized, are habitat generalists, thrive well in human‐disturbed habitats, and have large native geographic ranges. We forecast that 160 amphibians and reptiles without known invasion history could be unintentionally transported and introduced in the future. Among them, 57 species have a high risk of establishing alien populations. Our reliable, reproducible, transferable, statistically robust and scientifically defensible quantitative invasion risk assessment tool is a significant new addition to the suite of decision‐support tools needed for developing a future‐proof preventative biosecurity globally. [ABSTRACT FROM AUTHOR]

Two Southeast Asian spider collections: that of Frances and John Murphy, now in the Manchester University Museum and the Deeleman collection, now at the Naturalis Biodiversity Center in Leiden constituted the basis of this analysis of Chrysilla Thorell, 1887 and related genera. The latter collection also includes many thousands of spiders obtained by canopy fogging for an ecological project in Borneo by A. Floren. Some incongruences within the genera of the tribe Chrysillini are disentangled. The transfer of C. jesudasi Caleb & Mathai, 2014 from Chrysilla as type species of Phintelloides Kanesharatnam & Benjamin, 2019, based on analysis of molecular data is validated by morphology. An interesting new species known only from the forest canopy in Borneo, Phintelloides scandens sp. nov, is described based on both male and female specimens. Distinguishing chrysilline genera is mostly based on traditional somatic characters, e.g., habitus, carapace and abdomen patterns, mouthparts, and genital organs. The utility of two character systems for distinguishing chrysilline genera is highlighted: 1) the presence of a flexible, articulating embolic tegular branch (etb) in combination with the conformation of the characteristic construction of the epigyne in Chrysilla and Phintelloides; 2) presence of red colour on carapace and abdomen of live males and females, in combination with abundant blue/violet/white iridescent scales such as in Chrysilla and Siler. The red colour usually gets lost in alcohol, hampering species identification of alcohol material. The genera Chrysilla and Phintelloides are redefined. Specimens of the heretofore unknown female of Chrysilla deelemani Prószyński & Deeleman-Reinhold, 2010 are described. The male and female of Chrysilla lauta and male of C. volupe are redescribed. The genus Chrysilla is diagnosed and discriminated from Phintella Bösenberg & Strand, 1906, Siler Simon, 1889, Phintelloides Kanesharatnam & Benjamin, 2019 and Proszynskia Kanesharatnam & Benjamin, 2019. The structure of the female genital organ of Phintelloides flavumi Kanesharatnam & Benjamin, 2019 is scrutinized and the generic placement of Phintelloides is discussed. Males and females of one of the most variable species, Phintelloides versicolor (C. L. Koch, 1846) are redescribed. Phintelloides munita (Bösenberg & Strand, 1906) is removed from synonymy with P. versicolor. Phintella leucaspis Simon 1903 (male, Sumatra) is synonymized with P. versicolor.Biodiversity data are increasingly reliant on digital infrastructure. By linking physical specimens to digital representations of their associated data, we can lower barriers to information flow. Here we demonstrate a workflow whereby persistent identifiers (PIDs) in the form of DOIs issued by DataCite are assigned to specimens. Recognized taxa are identified by their catalog of life identifier, or by registration in ZooBank where no catalog of life identifier is available. We demonstrate the use of nanopublications, creating a series of machine readable, scientifically meaningful assertions regarding the provenance and identification of cited specimens. All human agents associated with the specimen data are linked to a persistent identifier issued by either ORCiD or Wikidata.

Abstract Ecology increasingly relies on a massive volume of biodiversity occurrence records to draw insights into large‐scale biogeographical, ecological and evolutionary phenomena. This often involves defining a set of criteria that guides the collection, filtering and standardising of available records. These curation processes are often neither described in detail nor well documented. This hampers the comparability and reproducibility of studies and thus undermines the robustness of any ecological result. Yet, to date, there is no guide providing a friendly way to reason and document a complete data curation process. We reviewed the available literature on data curation, including tools such as R packages and workflows. From this assessment, we created a complete guide organised into five modules that allows users to consciously select and validate occurrence records based on these curation criteria. This is presented in the user‐friendly Shiny R OCCUR application, available at https://ecoinformatic.shinyapps.io/OCCUR/. OCCUR application provides a guide for researchers to deal with the trade‐off between data certainty and coverage generated in each data curation step. An interactive graph of these changes is provided within each module. OCCUR also produces a custom‐made final report including all steps used for data filtering. This report helps to streamline the writing of the methods section of manuscripts and technical reports, thus promoting the reproducibility of data curation processes. This Shiny application provides an interactive overview of the data curation methods and their use for handling occurrence records from public repositories. It brings together the taxonomic, temporal and spatial dimensions of data and also the identification of duplicates of the records. OCCUR can be applied for multiple purposes, such as teaching R to ecologists or enhancing reproducibility of macroecology and biogeography.

Here we present 'APCalign', an R package and accompanying browser-sourced application to align and update scientific names for Australian vascular plants to the most likely currently accepted name in the Australian Plant Census (APC) or a name in the Australian Plant Names Index (APNI). Scientific names are the label assigned to unique taxon concepts by the scientific community, but this common terminology is most useful if a taxon concept is consistently referred to by the same name. These links can be broken because of either spelling mistakes or taxonomic changes. Automated tools are required to resolve taxon lists, aligning and updating long lists of possibly erroneous scientific names to the most likely currently accepted names. It is essential that tools specific to the APC/APNI be developed, because these lists specify an endorsed national-level nomenclature used in government legislation and include the uniquely Australian concept of phrase names, absent in global taxonomic datasets. To align input names to names within the APC or APNI, 'APCalign' works progressively through a sequence of checks that combine different permutations of the input name, exact versus fuzzy matches, matches that consider the entire name input versus a subset of words, and character strings that indicate a name can be resolved only to a genus or family. The aligned names are then, when possible, updated to a currently accepted taxon concept within the APC. This package should facilitate all research outputs that require diverse scientific name lists to be merged or outdated lists to be updated. To facilitate communication, research projects, biodiversity assessments and nurseries across Australia should use the scientific names accepted by the Australian Plant Census (APC), Australia's national taxonomic standard for vascular plants. Here we present 'APCalign', an R package and browser-sourced application to efficiently align and update lists of scientific names for Australian vascular plants to the most likely currently accepted name. This package will be useful for all research outputs that require diverse scientific name lists to be updated. Image by Elizabeth Wenk. [ABSTRACT FROM AUTHOR]

Ecology increasingly relies on a massive volume of biodiversity occurrence records to draw insights into large‐scale biogeographical, ecological and evolutionary phenomena. This often involves defining a set of criteria that guides the collection, filtering and standardising of available records. These curation processes are often neither described in detail nor well documented. This hampers the comparability and reproducibility of studies and thus undermines the robustness of any ecological result. Yet, to date, there is no guide providing a friendly way to reason and document a complete data curation process.We reviewed the available literature on data curation, including tools such as R packages and workflows. From this assessment, we created a complete guide organised into five modules that allows users to consciously select and validate occurrence records based on these curation criteria. This is presented in the user‐friendly Shiny R OCCUR application, available at https://ecoinformatic.shinyapps.io/OCCUR/.OCCUR application provides a guide for researchers to deal with the trade‐off between data certainty and coverage generated in each data curation step. An interactive graph of these changes is provided within each module. OCCUR also produces a custom‐made final report including all steps used for data filtering. This report helps to streamline the writing of the methods section of manuscripts and technical reports, thus promoting the reproducibility of data curation processes.This Shiny application provides an interactive overview of the data curation methods and their use for handling occurrence records from public repositories. It brings together the taxonomic, temporal and spatial dimensions of data and also the identification of duplicates of the records. OCCUR can be applied for multiple purposes, such as teaching R to ecologists or enhancing reproducibility of macroecology and biogeography. [ABSTRACT FROM AUTHOR]

IntroductionHistoric museum collections hold a wealth of biodiversity data that are essential to our understanding of the rapidly changing natural world. Novel curatorial practices are needed to extract and digitise these data, especially for the innumerable pinned insects whose collecting information is held on small labels.MethodsWe piloted semi-automated specimen imaging and digitisation of specimen labels for a collection of ~29,000 pinned insects of ground beetles (Carabidae: Lebiinae) held at the Natural History Museum, London. Raw transcription data were curated against literature sources and non-digital collection records. The primary data were subjected to statistical analyses to infer trends in collection activities and descriptive taxonomy over the past two centuries.ResultsThis work produced research-ready digitised records for 2,546 species (40% of known species of Lebiinae). Label information was available on geography in 91% of identified specimens, and the time of collection in 39.8% of specimens and could be approximated for nearly all specimens. Label data revealed the great age of this collection (average age 91.4 years) and the peak period of specimen acquisition between 1880 and 1930, with little differences among continents. Specimen acquisition declined greatly after about 1950. Early detected species generally were present in numerous specimens but were missing records from recent decades, while more recently acquired species (after 1950) were represented mostly by singleton specimens only. The slowing collection growth was mirrored by the decreasing rate of species description, which was affected by huge time lags of several decades to formal description after the initial specimen acquisition.DiscussionHistoric label information provides a unique resource for assessing the state of biodiversity backwards to pre-industrial times. Many species held in historical collections especially from tropical super-diverse areas may not be discovered ever again, and if they do, their recognition requires access to digital resources and more complete levels of species description. A final challenge is to link the historical specimens to contemporary collections that are mostly conducted with mechanical trapping of specimens and DNA-based species recognition.

Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth’s biosphere and human health and well-being. ELIXIR can help address the technical challenges of biodiversity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate biodiversity preservation and restoration. This white paper, prepared by the ELIXIR Biodiversity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the biodiversity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Biodiversity Community in ELIXIR and is an appeal to identify and involve new stakeholders.

The digitization and open availability of life history traits measured directly from individuals provide a key means of linking organismal function to environmental and ecological contexts at fine resolution. These linkages play a critical role in understanding trait‐mediated response to global change, with particular need to resolve them for taxa that are secretive and hard to monitor, like most mammals. In this study, we use digitized museum specimen and census data to document how climate and body size each shape a key life history trait – litter size – in 39 small mammals across North America. We employ mixed models to test associations between litter size, climate and body size, with a focus on joint estimation of inter‐ and intraspecific trends. Among species, no single climate predictor explained a large amount of litter size variation. Instead, interactions between temperature‐related (continentality, solar irradiation) and moisture‐related (annual precipitation, relative humidity) indices, along with body size, exert a stronger influence on litter size. We observed maximal litter sizes for species inhabiting seasonal or xeric regions under conditions of increased moisture availability, or conversely, mesic or aseasonal regions under conditions of reduced moisture availability. These patterns are consistent with primary productivity as a mechanistic driver of litter size. At the intraspecific level, litter size responds to continentality and temperature‐related indices experienced by populations, but is most strongly shaped by body size of individual females. We also find evidence of phylogenetic covariation in these intraspecific trends. Our study demonstrates how life history traits assembled from individual‐level biodiversity records improve precision and granularity of ecological studies, help to parse among‐ and within‐species trends, and foster improved understanding of tradeoffs between energetic supply and demand (e.g. reproduction) in wild mammals. [ABSTRACT FROM AUTHOR]

Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth’s biosphere and human health and well-being. ELIXIR can help address the technical challenges of biodiversity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate biodiversity preservation and restoration. This white paper, prepared by the ELIXIR Biodiversity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the biodiversity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Biodiversity Community in ELIXIR and is an appeal to identify and involve new stakeholders.

Here, we introduce SPARSE (acronym for "SPecies AcRoss ScalEs"), a simple and portable template for databases that can store data on species composition derived from ecological inventories, surveys and checklists, with emphasis on metadata describing sampling effort and methods. SPARSE can accommodate resurveys and time series and data from different spatial scales, as well as complex sampling designs. SPARSE focuses on inventories that report multiple species for a given site, together with sampling methods and effort, which can be used in statistical models of true probability of occurrence of species. SPARSE is spatially explicit and can accommodate nested spatial structures from multiple spatial scales, including sampling designs where multiple sites within a larger area have been surveyed and the larger area can again be nested in an even larger region. Each site in SPARSE is represented either by a point, line (for transects) or polygon, stored in an ESRI shapefile. SPARSE implements a new combination of our own field definitions with Darwin Core biodiversity data standard and its Humboldt core extension. The use of Humboldt core also makes SPARSE suitable for biodiversity data with temporal replication.We provide an example use of the SPARSE framework by digitising data on birds from the Czech Republic, from 348 sites and 524 sampling events, with 15,969 unique species-per-event observations of presence, abundance or population density. To facilitate use without the need for a high-level database expertise, the Czech bird example is implemented as MS Access .accdb file, but can be ported to other database engines. The example of Czech birds complements other bird datasets from the Czech Republic, specifically the four gridded national atlases and the breeding bird survey which cover a similar temporal extent, but different locations and spatial scales.

Linking records for the same taxa between different databases is an essential step when working with biodiversity data. However, name-matching alone is error-prone, because of issues such as homonyms (unrelated taxa with the same name) and synonyms (same taxon under different names). Therefore, most projects will require some curation to ensure that taxon identifiers are correctly linked. Unfortunately, formal guidance on such curation is uncommon and these steps are often ad hoc and poorly documented, which hinders transparency and reproducibility, yet the task requires specialist knowledge and cannot be easily automated without careful validation. Here, we present a case study on linking identifiers between the GBIF and NCBI taxonomies for a species checklist. This represents a common scenario: finding published sequence data (from NCBI) for species chosen by occurrence or geographical distribution (from GBIF). Wikidata, a publicly editable knowledge base of structured data, can serve as an additional information source for identifier linking. We suggest a software toolkit for taxon name-matching and data-cleaning, describe common issues encountered during curation and propose concrete steps to address them. For example, about 2.8% of the taxa in our dataset had wrong identifiers linked on Wikidata because of errors in name-matching caused by homonyms. By correcting such errors during data-cleaning, either directly (through editing Wikidata) or indirectly (by reporting errors in GBIF or NCBI), we crowdsource the curation and contribute to community resources, thereby improving the quality of downstream analyses.

Linking records for the same taxa between different databases is an essential step when working with biodiversity data. However, name-matching alone is error-prone, because of issues such as homonyms (unrelated taxa with the same name) and synonyms (same taxon under different names). Therefore, most projects will require some curation to ensure that taxon identifiers are correctly linked. Unfortunately, formal guidance on such curation is uncommon and these steps are often ad hoc and poorly documented, which hinders transparency and reproducibility, yet the task requires specialist knowledge and cannot be easily automated without careful validation. Here, we present a case study on linking identifiers between the GBIF and NCBI taxonomies for a species checklist. This represents a common scenario: finding published sequence data (from NCBI) for species chosen by occurrence or geographical distribution (from GBIF). Wikidata, a publicly editable knowledge base of structured data, can serve as an additional information source for identifier linking. We suggest a software toolkit for taxon name-matching and datacleaning, describe common issues encountered during curation and propose concrete steps to address them. For example, about 2.8% of the taxa in our dataset had wrong identifiers linked on Wikidata because of errors in name-matching caused by homonyms. By correcting such errors during data-cleaning, either directly (through editing Wikidata) or indirectly (by reporting errors in GBIF or NCBI), we crowdsource the curation and contribute to community resources, thereby improving the quality of downstream analyses. [ABSTRACT FROM AUTHOR]

Here, we introduce SPARSE (acronym for "SPecies AcRoss ScalEs"), a simple and portable template for databases that can store data on species composition derived from ecological inventories, surveys and checklists, with emphasis on metadata describing sampling effort and methods. SPARSE can accommodate resurveys and time series and data from different spatial scales, as well as complex sampling designs. SPARSE focuses on inventories that report multiple species for a given site, together with sampling methods and effort, which can be used in statistical models of true probability of occurrence of species. SPARSE is spatially explicit and can accommodate nested spatial structures from multiple spatial scales, including sampling designs where multiple sites within a larger area have been surveyed and the larger area can again be nested in an even larger region. Each site in SPARSE is represented either by a point, line (for transects) or polygon, stored in an ESRI shapefile. SPARSE implements a new combination of our own field definitions with Darwin Core biodiversity data standard and its Humboldt core extension. The use of Humboldt core also makes SPARSE suitable for biodiversity data with temporal replication. We provide an example use of the SPARSE framework by digitising data on birds from the Czech Republic, from 348 sites and 524 sampling events, with 15,969 unique species-perevent observations of presence, abundance or population density. To facilitate use without the need for a high-level database expertise, the Czech bird example is implemented as MS Access .accdb file, but can be ported to other database engines. The example of Czech birds complements other bird datasets from the Czech Republic, specifically the four gridded national atlases and the breeding bird survey which cover a similar temporal extent, but different locations and spatial scales. [ABSTRACT FROM AUTHOR]

Biological scientists have established 'Biodiversity Informatics' to map the global diversity of biological organisms by using cutting-edge bioinformatics tools. This review depicts an overview of microbial diversity's status worldwide and discusses microbial biodiversity in the marine and terrestrial ecosystems. The study shows how the 'Biodiversity Informatics' could help scientists to map the variety of microbial species recorded in terrestrial and marine habitats. The status of microbial biodiversity globally is also discussed. Besides, it also illustrates how biologists could utilize databases to explore not only microbial biodiversity but also various species of fauna and flora. We have represented microbial biodiversity informatics and its growth, tools and technologies, data management, digital taxonomy for biodiversity informatics to categorize microbial species. Moreover, molecular biodiversity informatics and current progress of biodiversity informatics have also been discussed. Finally, we have also depicted the policy and managerial implications and research gaps in this direction. Our article will lead to the novel path, which will show the interdisciplinary approaches of biodiversity informatics with the support of metagenomics and genomics. [ABSTRACT FROM AUTHOR]

Ellenberg indicator values (EIV) are widely used in vegetation ecology, but the values for many species in Southeastern Europe are not available due to incomplete knowledge of their ecology: it is therefore of paramount importance to estimate missing values in existing databases. The entire EIV set for a single species can be missing or a single EIV can be missing for species for which other indicator values are available. Our aim here is to provide a simple method to impute missing values for species who have missing data in a single or multiple EIV. For this purpose, we adopt a multiple imputation procedure and compare a number of imputation methods on the basis of two datasets: i) “indices”, the set of 9 Ellenberg indicators taken from literature, available for 10,824 species and ii) “vegetation”, a set describing the physical and climatic characteristics (Light, Temperature, Continentality, Soil moisture, Nitrogen, Soil pH, Hemeroby index, Humidity, Organic_matter) of 29,935 relevés from Southeastern Europe where at least one tree species is present. The imputation methods we considered are: k-Nearest Neighbour, multiple linear regression (with or without collinearity correction), Reprediction Algorithm, Weighted Averaging (WA) and Weighted Averaging Partial Least Squares (WAPLS) regression. The different methods of imputation were compared by looking at the output produced and its deviation from the “true” observed values for a set of species with known EIVs. We have considered a set of species with known EIVs and proceeded to multiple imputation using the methods above; as a measure of performance we adopted the mean squared error (MSE) estimate, and expert judgement of ecological consistency. Models based on Regression and k-Nearest Neighbour seem to outperform the others. On the contrary, Reprediction algorithm in its different forms: produced less satisfactory results.Imputation of missing values is generally based on expert knowledge or on some variant of weighted averaging (also known as Hill’s method). Here we show that other methods may be more effective and should be appropriately considered by vegetation scientists, since those may allow the application of EIVs in other biogeographic regions.

With the rapid development of biodiversity informatics, more and more open biological data can be used by researchers. Taking an open data platform as an example, analyzing the research hotspots and development trends in the field of biodiversity in China will help biodiversity researchers and policy-makers keep abreast of the current status and trends of biological research, and provide decision support for the construction of biodiversity in China. We searched the full text of the literature in CNKI and Google Scholar from 2013 to 2023 with the relevant search terms of “National Specimen Information Infrastructure (NSII)”, and retrieved a total of 1 070 supported by NSII literature, including journal articles (822), dissertations (233), popular science articles (5), conference articles (6) and reports (4). Through the means and methods of bibliometrics, the 822 journal articles supported by NSII are explored from the aspects of publication status, research topics and hot spots, research institutions, etc., to explore the current status, hot spots and trends of biodiversity research supported by NSII. According to the results obtained from the keyword co-occurrence network map, the research hotspots of biodiversity focus on the analysis and modeling of species distribution, climate change, taxonomy, biodiversity research, and research platform construction. Biodiversity informatics is developing rapidly in China, in the future, it is still necessary to improve data source construction, resource integration, sharing capability, professional competence and international cooperation, etc. to promote the development of biodiversity scientific research continuously.

The Biodiversity Knowledge Hub (BKH) is a web platform acting as an integration point and broker of an open, FAIR (Findable, Accessible, Interoperable, Reusable) and interlinked corpora of biodiversity data, services and knowledge. It serves the entire biodiversity research cycle, from specimens and observations to sequences, taxon names and finally to scientific publications. The strategic aim of the BKH is to support a functional and integrated biodiversity knowledge graph and an emerging new community of users. The BKH is aimed at biodiversity researchers in the widest sense, research infrastructures and publishers (Fig. 1). The BKH is the key product of the EU-funded Biodiversity Community Integrated Knowledge Library (BiCIKL) project (Penev et al. 2022). The four goals of BiCIKL and the BKH are: 1. Improved access to open and FAIR biodiversity data; 2. Establishing of bi-directional data linkages between infrastructures; 3. Development of new methods and workflows for semantic publishing, harvesting, liberating, linking, accessing and re-using of data in literature (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables); 4. Testing and implementation of services through use cases and open call projects for researchers outside the project. The BKH consists of several modules, such as the Home page that presents the main user groups and the benefits that the BKH provides to them. It has guidelines and protocols, such as various documents on the policies, functions, and recommendations for the users. And it has relevant projects, that use linked FAIR biodiversity data. In the core of the BKH is the FAIR Data Place (FDP), which presents novel services and tools developed over the course of BiCIKL. In the future, the FDP will also accept services for linked data provided by new contributors. The FDP consists of three sub-modules: • Infrastructures and organisations: Lists the contributing organisations and research infrastructures with short descriptions and links to their data, tools and services. Research infrastructures are sorted by the main type of biodiversity data they aggregate and serve: specimens, sequences, taxon names and literature. • Linked data services: A catalogue of novel services that deliver FAIR data linked between the participating research infrastructures. Examples of such services are: ChecklistBank, LifeBlock, OpenBiodiv, TreatmentBank, SIBiLS "BiodiversityPMC", eBioDiv, SynoSpecies, PlutoF Curation Tool and others. • Become a contributor application form: A formal questionnaire which serves as a basis to check the suitability of an organisation or research infrastructure to join the BKH. Part of the application form is a FAIR data checklist. The BKH serves as a navigation system in a universe of interconnected biodiversity research infrastructures and is open to new contributors and collaborators in accessing open data and knowledge by anybody, anywhere, at any time. [ABSTRACT FROM AUTHOR]

With the rapid development of biodiversity informatics, more and more open biological data can be used by researchers. Taking an open data platform as an example, analyzing the research hotspots and development trends in the field of biodiversity in China will help biodiversity researchers and policy-makers keep abreast of the current status and trends of biological research, and provide decision support for the construction of biodiversity in China. We searched the full text of the literature in CNKI and Google Scholar from 2013 to 2023 with the relevant search terms of “National Specimen Information Infrastructure (NSII) ”, and retrieved a total of 1 070 supported by NSII literature, including journal articles (822), dissertations (233), popular science articles (5), conference articles (6) and reports (4). Through the means and methods of bibliometrics, the 822 journal articles supported by NSII are explored from the aspects of publication status, research topics and hot spots, research institutions, etc., to explore the current status, hot spots and trends of biodiversity research supported by NSII. According to the results obtained from the keyword co-occurrence network map, the research hotspots of biodiversity focus on the analysis and modeling of species distribution, climate change, taxonomy, biodiversity research, and research platform construction. Biodiversity informatics is developing rapidly in China, in the future, it is still necessary to improve data source construction, resource integration, sharing capability, professional competence and international cooperation, etc. to promote the development of biodiversity scientific research continuously. [ABSTRACT FROM AUTHOR]

The scientific names of organisms are key identifiers of plants and animals. Correctly treating scientific names is a prerequisite for biodiversity research and documentation. Here, we present an R package, ‘U.Taxonstand’, which can standardize and harmonize scientific names in plant and animal species lists at a fast speed and at a high rate of matching success. Unlike most of other similar R packages each of which works with only one taxonomic database, U.Taxonstand can work with all taxonomic databases, as long as they are properly formatted. Multiple databases for plants and animals that can be directly used by U.Taxonstand, which include bryophytes, vascular plants, amphibians, birds, fishes, mammals, and reptiles, are available online. U.Taxonstand can be a very useful tool for botanists, zoologists, ecologists and biogeographers to standardize and harmonize scientific names of organisms.

Abstract Background The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas. Results The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure. Conclusion The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.

In South Africa, as in other parts of the world, Biodiversity Informatics (BDI) has been identified as a young field of science that lies at the nexus of several disciplines, including informatics, biology and mathematics/statistics. Being such a new and dynamic field, there are challenges in the recruitment, training and retention of personnel that can support inter alia the mobilisation, management, coordination, and utilisation of biodiversity information for key conservation and biodiversity outcomes. The lack of human capital also place at risk the implementation of (e.g.) the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), and hinders attainment of the Convention on Biological Diversity post-2020 framework targets. There is a clear demand for broad efforts to build human capital in the field. Using our experiences in South Africa, we provide a framework for establishing BDI as a field of science in developing countries and look at the potential building blocks towards this broad objective, including the need and requirements for the establishment of a Centre for BDI. We explore this concept against a backdrop of the South African government’s 2019 White Paper on Science, Technology and Innovation, and the associated Decadal Plan, both developed under the auspices of the Department of Science and Innovation. We also reflect on efforts in the broader landscape to look at the establishment of BDI curricula.

Biodiversity informatics produces global biodiversity knowledge through the collection and analysis of biodiversity data using informatics techniques. To do so, biodiversity informatics relies upon data accrual, standardization, transferability, openness, and "invisible" infrastructure. What biodiversity informatics mean to society, however, cannot be adequately understood without recognizing what organizes biodiversity data. Using insights from science and technology studies, we story the organizing "visions" behind the growth of biodiversity informatics infrastructures in Sweden—an early adopter of digital technologies and significant contributor to global biodiversity data—through interviews, scientific literature, governmental reports and popular publications. This case story discloses the organizational formation of Swedish biodiversity informatics infrastructures from the 1970s to the present day, illustrating how situated perspectives or "visions" shaped the philosophies, directions and infrastructures of its biodiversity informatics communities. Specifically, visions related to scientific progress and species loss, their institutionalization, and the need to negotiate external interests from governmental organizations led to unequal development across multiple infrastructures that contribute differently to biodiversity knowledge. We argue that such difference highlights that the social and organizational hurdles for combining biodiversity data are just as significant as the technological challenges and that the seemingly inconsequential organizational aspects of its infrastructure shape what biodiversity data can be brought together, modelled and visualised. [ABSTRACT FROM AUTHOR]

The BiCIKL project is born from a vision that biodiversity data are most useful if they are presented as a network of data that can be integrated and viewed from different starting points. BiCIKL’s goal is to realise that vision by linking biodiversity data infrastructures, particularly for literature, molecular sequences, specimens, nomenclature and analytics. To make those links we need to better understand the existing infrastructures, their limitations, the nature of the data they hold, the services they provide and particularly how they can interoperate. In light of those aims, in the autumn of 2021, 74 people from the biodiversity data community engaged in a total of twelve hackathon topics with the aim to assess the current state of interoperability between infrastructures holding biodiversity data. These topics examined interoperability from several angles. Some were research subjects that required interoperability to get results, some examined modalities of access and the use and implementation of standards, while others tested technologies and workflows to improve linkage of different data types.These topics and the issues in regard to interoperability uncovered by the hackathon participants inspired the formulation of the following recommendations for infrastructures related to (1) the use of data brokers, (2) building communities and trust, (3) cloud computing as a collaborative tool, (4) standards and (5) multiple modalities of access:If direct linking cannot be supported between infrastructures, explore using data brokers to store linksCooperate with open linkage brokers to provide a simple way to allow two-way links between infrastructures, without having to co-organize between many different organisationsFacilitate and encourage the external reporting of issues related to their infrastructure and its interoperability.Facilitate and encourage requests for new features related to their infrastructure and its interoperability.Provide development roadmaps openlyProvide a mechanism for anyone to ask for helpDiscuss issues in an open forumProvide cloud-based environments to allow external participants to contribute and test changes to featuresConsider the opportunities that cloud computing brings as a means to enable shared management of the infrastructure.Promote the sharing of knowledge around big data technologies amongst partners, using cloud computing as a training environmentInvest in standards compliance and work with standards organisations to develop new, and extend existing standardsReport on and review standards compliance within an infrastructure with metrics that give credit for work on standard compliance and developmentProvide as many different modalities of access as possibleAvoid requiring personal contacts to download dataProvide a full description of an API and the data it servesFinally, the hackathons were an ideal meeting opportunity to build, diversify and extend the BiCIKL community further, and to ensure the alignment of the community with a common vision on how best to link data from specimens, samples, sequences, taxonomic names and taxonomic literature.

Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth’s biosphere and human health and well-being. ELIXIR can help address the technical challenges of biodiversity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate biodiversity preservation and restoration. This white paper, prepared by the ELIXIR Biodiversity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the biodiversity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Biodiversity Community in ELIXIR and is an appeal to identify and involve new stakeholders.

The beetle fauna of the California Channel Islands is here enumerated for the first time in over 120 years. We provide an annotated checklist documenting species-byisland diversity from an exhaustive literature review and analysis of a compiled dataset of 26,609 digitized specimen records to which were added over 3,000 individual specimen determinations. We report 825 unique species from 514 genera and 71 families (including 17 new family records) comprising 1,829 species-by-island records. Species totals for each island are as follows: Anacapa (74); San Clemente (197); San Miguel (138); San Nicolas (146); Santa Barbara (64); Santa Catalina (370); Santa Cruz (503); and Santa Rosa (337). This represents the largest list of species published to date for any taxonomic group of animals on the Channel Islands; despite this, we consider the checklist to be preliminary. We present evidence that both inventory and taxonomic efforts on Channel Islands beetles are far from complete. Rarefaction estimates indicate there are at least several hundred more species of beetles yet to be recorded from the islands. Despite the incomplete nature of existing records, we found that species diversity is highly correlated with island area. We report 56 species which are putatively geographically restricted (endemic) to the Channel Islands, with two additional species of questionable endemic status. We also report 52 species from the islands which do not natively occur in the southern California region. [ABSTRACT FROM AUTHOR]

Mozambique biodiversity richness plays a pivotal role to achieve the sustainable development of the country. However, Mozambique's flora and fauna diversity still remains broadly unknown and poorly documented. To properly address this issue, one of the strategic needs expressed by the Mozambican institutions was the development of a national biodiversity data repository to aggregate, manage and make data available online. Thus, a sustainable infrastructure for the standardisation, aggregation, organisation and sharing of primary biodiversity data was developed. Named the "Biodiversity Network of Mozambique" (BioNoMo), such a tool serves as a national repository of biodiversity data and aggregates occurrence records of plants and animals in the country obtained from floristic and faunistic observations and from specimens of biological collections. In this paper, the authors present the structure and data of BioNoMO, including software details, the process of data gathering and aggregation, the taxonomic coverage and the WebGIS development. Currently, aggregating a total of 273,172 records, including 85,092 occurrence records of plants and 188,080 occurrence records of animals (41.2% terrestrial, 58,8% aquatic), BioNoMo represents the largest aggregator of primary biodiversity data in Mozambique and it is planned to grow further by aggregating new datasets. [ABSTRACT FROM AUTHOR]

Background: The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas. Results: The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure. Conclusion: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform. [ABSTRACT FROM AUTHOR]

The beetle fauna of the California Channel Islands is here enumerated for the first time in over 120 years. We provide an annotated checklist documenting species-by-island diversity from an exhaustive literature review and analysis of a compiled dataset of 26,609 digitized specimen records to which were added over 3,000 individual specimen determinations. We report 825 unique species from 514 genera and 71 families (including 17 new family records) comprising 1,829 species-by-island records. Species totals for each island are as follows: Anacapa (74); San Clemente (197); San Miguel (138); San Nicolas (146); Santa Barbara (64); Santa Catalina (370); Santa Cruz (503); and Santa Rosa (337). This represents the largest list of species published to date for any taxonomic group of animals on the Channel Islands; despite this, we consider the checklist to be preliminary. We present evidence that both inventory and taxonomic efforts on Channel Islands beetles are far from complete. Rarefaction estimates indicate there are at least several hundred more species of beetles yet to be recorded from the islands. Despite the incomplete nature of existing records, we found that species diversity is highly correlated with island area. We report 56 species which are putatively geographically restricted (endemic) to the Channel Islands, with two additional species of questionable endemic status. We also report 52 species from the islands which do not natively occur in the southern California region.

IntroductionEfforts to collect ecological data have intensified over the last decade. This is especially true for freshwater habitats, which are among the most impacted by human activity and yet lagging behind in terms of data availability. Now, to support conservation programmes and management decisions, these data need to be analyzed and interpreted; a process that can be complex and time consuming. The South African Biodiversity Data Pipeline for Wetlands and Waterbirds (BIRDIE) aims to help fast and efficient information uptake, bridging the gap between raw ecological datasets and the information final users need.MethodsBIRDIE is a full data pipeline that takes up raw data, and estimates indicators related to waterbird populations, while keeping track of their associated uncertainty. At present, we focus on the assessment of species abundance and distribution in South Africa using two citizen-science bird monitoring datasets, namely: the African Bird Atlas Project and the Coordinated Waterbird Counts. These data are analyzed with occupancy and state-space models, respectively. In addition, a suite of environmental layers help contextualize waterbird population indicators, and link these to the ecological condition of the supporting wetlands. Both data and estimated indicators are accessible to end users through an online portal and web services.Results and discussionWe have designed a modular system that includes tasks, such as: data cleaning, statistical analysis, diagnostics, and computation of indicators. Envisioned users of BIRDIE include government officials, conservation managers, researchers and the general public, all of whom have been engaged throughout the project. Acknowledging that conservation programmes run at multiple spatial and temporal scales, we have developed a granular framework in which indicators are estimated at small scales, and then these are aggregated to compute similar indicators at broader scales. Thus, the online portal is designed to provide spatial and temporal visualization of the indicators using maps, time series and pre-compiled reports for species, sites and conservation programmes. In the future, we aim to expand the geographical coverage of the pipeline to other African countries, and develop more indicators specific to the ecological structure and function of wetlands.

Background: The 8th version of the "World Checklist of Vascular Plants" (WCVP) was recently published under the coordination of the Royal Botanic Gardens, Kew. It consists of a list of taxonomic names of species, genera, and families of vascular plants representing the most comprehensive and integrated list available today. Questions: How many accepted species does the WCVP include? Is the quality of the included information acceptable? How has the publication of worldwide species names evolved over time? Does the checklist include the species recorded for Mexico? Studied species: Worldwide species of vascular plants included in the WCVP. Study site: Worldwide and Mexico. Methods: A database was created based on the WCVP to answer the research questions. The number of genera and species by taxonomic status (accepted and synonyms) was quantified, some information quality tests were carried out, and the potential number of undiscovered species in the world was estimated using non-parametric techniques. Results: The WCVP contains 1,233,172 names, of which 418,737 are accepted. It is estimated that around 25 % more unknown species remain to be discovered in the world. The quality of the information contained in the WCVP is quite reliable and complete; only 3 % of Mexican species are not included in the WCVP. Conclusions: The WCVP synthesizes current taxonomic knowledge in an integrated manner and is useful for systematic and automated analyses. At the country level, at least for Mexico, it stands as an important reference source when attempting to understand and evaluate floristic knowledge.

Effects of global climate change on population persistence are often mediated by life‐history traits of individuals, especially the timing of somatic growth, reproductive development, and reproduction itself. These traits can vary among age groups and between the sexes, a result of differential life‐history tactics and levels of lifetime reproductive investment. Unfortunately, the trait data necessary for revealing sex‐specific breeding behaviors and use of breeding cues over reasonably large geographic areas remain sparse for most taxa. In this study, we assembled and analyzed a new reproductive trait base for the North American deer mouse (Peromyscus maniculatus) from digitized natural history specimens and field censuses. We used the data to reconstruct sex‐specific breeding phenologies and their drivers within and among North American ecoregions. Male and female phenologies varied across the geographic range of this species, with discordance in timing and intensity being highest in regions of lower seasonality (and longer breeding seasons). Reliance on environmental variables as breeding cues also appeared to vary in a sex‐specific manner, being most similar for photoperiod and least similar for temperature (positive male response and negative female response); in addition, model validation indicated that phenological models generalized better for males than for females. Finally, our individual‐level trait data also show that male reproductive investment (quantified as relative testis size) varies across the vastly different abiotic and social (i.e., female breeding) contexts studied here. By harmonizing across a broad set of digital data resources, we demonstrate the potential to uncover drivers of phenological variation within species and inform global change predictions at multiple scales of biological organization. [ABSTRACT FROM AUTHOR]

Patterns of genetic diversity within species contain information the history of that species, including how they have responded to historical climate change and how easily the organism is able to disperse across its habitat. More than 40,000 phylogeographic and population genetic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite these millions of data points, meta‐analyses are challenging because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time‐consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. To facilitate data repurposing, we created a database (phylogatR) that aggregates data from different sources and conducts automated multiple sequence alignments and data curation to provide users with nearly ready‐to‐analyse sets of data for thousands of species. Two types of scientific research will be made easier by phylogatR: large meta‐analyses of thousands of species that can address classic questions in evolutionary biology and ecology, and student‐ or citizen‐ science based investigations that will introduce a broad range of people to the analysis of genetic data. phylogatR enhances the value of existing data via the creation of software and web‐based tools that enable these data to be recycled and reanalysed and increase accessibility to big data for research laboratories and classroom instructors with limited computational expertise and resources. [ABSTRACT FROM AUTHOR]

The BiCIKL project is born from a vision that biodiversity data are most useful if they are presented as a network of data that can be integrated and viewed from different starting points. BiCIKL's goal is to realise that vision by linking biodiversity data infrastructures, particularly for literature, molecular sequences, specimens, nomenclature and analytics. To make those links we need to better understand the existing infrastructures, their limitations, the nature of the data they hold, the services they provide and particularly how they can interoperate. In light of those aims, in the autumn of 2021, 74 people from the biodiversity data community engaged in a total of twelve hackathon topics with the aim to assess the current state of interoperability between infrastructures holding biodiversity data. These topics examined interoperability from several angles. Some were research subjects that required interoperability to get results, some examined modalities of access and the use and implementation of standards, while others tested technologies and workflows to improve linkage of different data types. These topics and the issues in regard to interoperability uncovered by the hackathon participants inspired the formulation of the following recommendations for infrastructures related to (1) the use of data brokers, (2) building communities and trust, (3) cloud computing as a collaborative tool, (4) standards and (5) multiple modalities of access: • If direct linking cannot be supported between infrastructures, explore using data brokers to store links • Cooperate with open linkage brokers to provide a simple way to allow two-way links between infrastructures, without having to co-organize between many different organisations • Facilitate and encourage the external reporting of issues related to their infrastructure and its interoperability. • Facilitate and encourage requests for new features related to their infrastructure and its interoperability. • Provide development roadmaps openly • Provide a mechanism for anyone to ask for help • Discuss issues in an open forum • Provide cloud-based environments to allow external participants to contribute and test changes to features • Consider the opportunities that cloud computing brings as a means to enable shared management of the infrastructure. • Promote the sharing of knowledge around big data technologies amongst partners, using cloud computing as a training environment • Invest in standards compliance and work with standards organisations to develop new, and extend existing standards • Report on and review standards compliance within an infrastructure with metrics that give credit for work on standard compliance and development • Provide as many different modalities of access as possible • Avoid requiring personal contacts to download data • Provide a full description of an API and the data it serves. Finally, the hackathons were an ideal meeting opportunity to build, diversify and extend the BiCIKL community further, and to ensure the alignment of the community with a common vision on how best to link data from specimens, samples, sequences, taxonomic names and taxonomic literature. [ABSTRACT FROM AUTHOR]

Biodiversity informatics is a new and evolving field, requiring efforts to develop capacity and a curriculum for this field of science. The main objective was to summarise the level of activity and the efforts towards developing biodiversity informatics curricula, for work-based training and/or academic teaching at universities, taking place within the Global Biodiversity Information Facility (GBIF) countries and its associated network. A survey approach was used to identify existing capacities and resources within the network. Most of GBIF Nodes survey respondents (80%) are engaged in onsite training activities, with a focus on work-based professionals, mostly researchers, policy-makers and students. Training topics include data mobilisation, digitisation, management, publishing, analysis and use, to enable the accessibility of analogue and digital biological data that currently reside as scattered datasets. An initial assessment of academic teaching activities highlighted that countries in most regions, to varying degrees, were already engaged in the conceptualisation, development and/or implementation of formal academic programmes in biodiversity informatics, including programmes in Benin, Colombia, Costa Rica, Finland, France, India, Norway, South Africa, Sweden, Taiwan and Togo. Digital e-learning platforms were an important tool to help build capacity in many countries. In terms of the potential in the Nodes network, 60% expressed willingness to be recruited or commissioned for capacity enhancement purposes. Contributions and activities of various country nodes across the network have been highlighted and a working curriculum framework has been defined.

Abstract Effects of global climate change on population persistence are often mediated by life‐history traits of individuals, especially the timing of somatic growth, reproductive development, and reproduction itself. These traits can vary among age groups and between the sexes, a result of differential life‐history tactics and levels of lifetime reproductive investment. Unfortunately, the trait data necessary for revealing sex‐specific breeding behaviors and use of breeding cues over reasonably large geographic areas remain sparse for most taxa. In this study, we assembled and analyzed a new reproductive trait base for the North American deer mouse (Peromyscus maniculatus) from digitized natural history specimens and field censuses. We used the data to reconstruct sex‐specific breeding phenologies and their drivers within and among North American ecoregions. Male and female phenologies varied across the geographic range of this species, with discordance in timing and intensity being highest in regions of lower seasonality (and longer breeding seasons). Reliance on environmental variables as breeding cues also appeared to vary in a sex‐specific manner, being most similar for photoperiod and least similar for temperature (positive male response and negative female response); in addition, model validation indicated that phenological models generalized better for males than for females. Finally, our individual‐level trait data also show that male reproductive investment (quantified as relative testis size) varies across the vastly different abiotic and social (i.e., female breeding) contexts studied here. By harmonizing across a broad set of digital data resources, we demonstrate the potential to uncover drivers of phenological variation within species and inform global change predictions at multiple scales of biological organization.

Background The landscape of biodiversity data infrastructures and organisations is complex and fragmented. Many occupy specialised niches representing narrow segments of the multidimensional biodiversity informatics space, while others operate across a broad front, but differ from others by data type(s) handled, their geographic scope and the life cycle phase(s) of the data they support. In an effort to characterise the various dimensions of the biodiversity informatics landscape, we developed a framework and dataset to survey these dimensions for ten organisations (DiSSCo, GBIF, iBOL, Catalogue of Life, iNaturalist, Biodi versity Heritage Library, GeoCASe, LifeWatch, eLTER ELIXIR), relative to both their current activities and long-term strategic ambitions. New information The survey assessed the contact between the infrastructure organisations by capturing the breadth of activities for each infrastructure across five categories (data, standards, software, hardware and policy), for nine types of data (specimens, collection descriptions, opportunistic observations, systematic observations, taxonomies, traits, geological data, molecular data and literature) and for seven phases of activity (creation, aggregation, access, annotation, interlinkage, analysis and synthesis). This generated a dataset of 6,300 verified observations, which have been scored and validated by leading members of each infrastructure organisation. The resulting data allow high-level questions about the overall biodiversity informatics landscape to be addressed, including the greatest gaps and contact between organisations. [ABSTRACT FROM AUTHOR]

Aim: Addressing global environmental challenges requires access to biodiversity data across wide spatial, temporal and taxonomic scales. Availability of such data has increased exponentially recently with the proliferation of biodiversity databases. However, heterogeneous coverage, protocols, and standards have hampered integration among these databases. To stimulate the next stage of data integration, here we present a synthesis of major databases, and investigate (a) how the coverage of databases varies across taxonomy, space, and record type; (b) what degree of integration is present among databases; (c) how integration of databases can increase biodiversity knowledge; and (d) the barriers to database integration. Location: Global. Time period: Contemporary. Major taxa studied: Plants and vertebrates. Methods: We reviewed 12 established biodiversity databases that mainly focus on geographic distributions and functional traits at global scale. We synthesized information from these databases to assess the status of their integration and major knowledge gaps and barriers to full integration. We estimated how improved integration can increase the data coverage for terrestrial plants and vertebrates. Results: Every database reviewed had a unique focus of data coverage. Exchanges of biodiversity information were common among databases, although not always clearly documented. Functional trait databases were more isolated than those pertaining to species distributions. Variation and potential incompatibility of taxonomic systems used by different databases posed a major barrier to data integration. We found that integration of distribution databases could lead to increased taxonomic coverage that corresponds to 23 years' advancement in data accumulation, and improvement in taxonomic coverage could be as high as 22.4% for trait databases. Main conclusions: Rapid increases in biodiversity knowledge can be achieved through the integration of databases, providing the data necessary to address critical environmental challenges. Full integration across databases will require tackling the major impediments to data integration: taxonomic incompatibility, lags in data exchange, barriers to effective data synchronization, and isolation of individual initiatives. [ABSTRACT FROM AUTHOR]

Background: Two Southeast Asian spider collections: that of Frances and John Murphy, now in the Manchester University Museum and the Deeleman collection, now at the Naturalis Biodiversity Center in Leiden constituted the basis of this analysis of Chrysilla Thorell, 1887 and related genera. The latter collection also includes many thousands of spiders obtained by canopy fogging for an ecological project in Borneo by A. Floren., New Information: Some incongruences within the genera of the tribe Chrysillini are disentangled. The transfer of C.jesudasi Caleb & Mathai, 2014 from Chrysilla as type species of Phintelloides Kanesharatnam & Benjamin, 2019, based on analysis of molecular data is validated by morphology. An interesting new species known only from the forest canopy in Borneo, Phintelloidesscandens sp. nov, is described based on both male and female specimens. Distinguishing chrysilline genera is mostly based on traditional somatic characters, e.g., habitus, carapace and abdomen patterns, mouthparts, and genital organs. The utility of two character systems for distinguishing chrysilline genera is highlighted: 1) the presence of a flexible, articulating embolic tegular branch (etb) in combination with the conformation of the characteristic construction of the epigyne in Chrysilla and Phintelloides ; 2) presence of red colour on carapace and abdomen of live males and females, in combination with abundant blue/violet/white iridescent scales such as in Chrysilla and Siler . The red colour usually gets lost in alcohol, hampering species identification of alcohol material. The genera Chrysilla and Phintelloides are redefined. Specimens of the heretofore unknown female of Chrysilla deelemani Prószyński & Deeleman-Reinhold, 2010 are described. The male and female of Chrysillalauta and male of C.volupe are redescribed. The genus Chrysilla is diagnosed and discriminated from Phintella Bösenberg & Strand, 1906, Siler Simon, 1889 , Phintelloides Kanesharatnam & Benjamin, 2019 and Proszynskia Kanesharatnam & Benjamin, 2019 . The structure of the female genital organ of Phintelloidesflavumi Kanesharatnam & Benjamin, 2019 is scrutinized and the generic placement of Phintelloides is discussed. Males and females of one of the most variable species , Phintelloidesversicolor (C. L. Koch, 1846) are redescribed. Phintelloidesmunita (Bösenberg & Strand, 1906) is removed from synonymy with P.versicolor. Phintellaleucaspis Simon 1903 (male, Sumatra) is synonymized with P.versicolor .Biodiversity data are increasingly reliant on digital infrastructure. By linking physical specimens to digital representations of their associated data, we can lower barriers to information flow. Here we demonstrate a workflow whereby persistent identifiers (PIDs) in the form of DOIs issued by DataCite are assigned to specimens. Recognized taxa are identified by their catalog of life identifier, or by registration in ZooBank where no catalog of life identifier is available. We demonstrate the use of nanopublications, creating a series of machine readable, scientifically meaningful assertions regarding the provenance and identification of cited specimens. All human agents associated with the specimen data are linked to a persistent identifier issued by either ORCiD or Wikidata., (Christa L. Deeleman-Reinhold, Wouter Addink, Jeremy A. Miller.)

Worldwide, herbaria maintain collections of reference specimens representing global plant diversity. These collections are a valuable resource for fundamental botanical research and applied scientific research across various disciplines, and play a significant role in addressing major societal challenges such as biodiversity conservation. The digitisation of herbarium specimens and their online dissemination is one of the most important recent developments in the curation of these collections. Digitisation significantly enhances access to the collections for the research community and facilitates large-scale analysis of biodiversity data. Digitisation also provides a means for preserving the physical specimens, as it reduces the need for handling and transportation. Rapid technological developments have greatly accelerated the rate of databasing and digital imaging of collections. Meise Botanic Garden recently completed a six-year project to mass digitise its herbarium collections of about 3 million specimens mounted on sheets and through this process we have learned valuable lessons. We have captured our experience in 10 recommendations for other collection-holding institutions to take inspiration from as they start planning their own digitisation efforts. We also present case studies where we delve deeper into certain topics as examples., Competing Interests: The authors have declared that no competing interests exist., (Sofie De Smedt, Ann Bogaerts, Niko De Meeter, Mathias Dillen, Henry Engledow, Paul Van Wambeke, Frederik Leliaert, Quentin Groom.)

We introduce a new method of estimating accepted species diversity by adapting mark-recapture methods to comparisons of taxonomic databases. A taxonomic database should become more complete over time, so the error bar on an estimate of its completeness and the known diversity of the taxon it treats will decrease. Independent databases can be correlated, so we use the time course of estimates comparing them to understand the effect of correlation. If a later estimate is significantly larger than an earlier one, the databases are positively correlated, if it is significantly smaller, they are negatively correlated, and if the estimate remains roughly constant, then the correlations have averaged out. We tested this method by estimating how complete MolluscaBase is for accepted names of terrestrial gastropods. Using random samples of names from an independent database, we determined whether each name led to a name accepted in MolluscaBase. A sample tested in August 2020 found that 16.7% of tested names were missing; one in July 2021 found 5.3% missing. MolluscaBase grew by almost 3,000 accepted species during this period, reaching 27,050 species. The estimates ranged from 28,409 ± 365 in 2021 to 29,063 ± 771 in 2020. All estimates had overlapping 95% confidence intervals, indicating that correlations between the databases did not cause significant problems. Uncertainty beyond sampling error added 475 ± 430 species, so our estimate for accepted terrestrial gastropods species at the end of 2021 is 28,895 ± 630 species. This estimate is more than 4,000 species higher than previous ones. The estimate does not account for ongoing flux of species into and out of synonymy, new discoveries, or changing taxonomic methods and concepts. The species naming curve for terrestrial gastropods is still far from reaching an asymptote, and combined with the additional uncertainties, this means that predicting how many more species might ultimately be recognized is presently not feasible. Our methods can be applied to estimate the total number of names of Recent mollusks (as opposed to names currently accepted), the known diversity of fossil mollusks, and known diversity in other phyla. [ABSTRACT FROM AUTHOR]

Egyptian flower mantis Blepharopsis mendica (Order: Mantodea) is a widespread mantis species throughout the southwest Palearctic region. The ecological and geographical distribution of such interesting species is rarely known. So, through this work, habitat suitability models for its distribution through Egyptian territory were created using MaxEnt software from 90 occurrence records. One topographic (altitude) and eleven bioclimatic variables influencing the species distribution were selected to generate the models. The predicted distribution in Egypt was focused on the Delta, South Sinai, the north-eastern part of the country, and some areas in the west including Siwa Oasis. Temporal analysis between the two periods (1900–1961) and (1961–2017) show current reduction of this species distribution through Delta and its surrounding areas, may be due to urbanization. On the other hand, it increases in newly protected areas of South Sinai. Under the future climate change scenario, the MaxEnt model predicted the habitat gains for B. mendica in RCP 2.6 for 2070 and loss of habitat in RCP 8.5 for the same year. Our results can be used as a basis for conserving this species not only in Egypt, but also throughout the whole of its range, also, it show how the using of geo-information could help in studying animal ecology.

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. [ABSTRACT FROM AUTHOR]

Background Animal pollination is an important ecosystem function and service, ensuring both the integrity of natural systems and human well-being. Although many knowledge shortfalls remain, some high-quality data sets on biological interactions are now available. The development and adoption of standards for biodiversity data and metadata has promoted great advances in biological data sharing and aggregation, supporting large-scale studies and science-based public policies. However, these standards are currently not suitable to fully support interaction data sharing. Results Here we present a vocabulary of terms and a data model for sharing plant–pollinator interactions data based on the Darwin Core standard. The vocabulary introduces 48 new terms targeting several aspects of plant–pollinator interactions and can be used to capture information from different approaches and scales. Additionally, we provide solutions for data serialization using RDF, XML, and DwC-Archives and recommendations of existing controlled vocabularies for some of the terms. Our contribution supports open access to standardized data on plant–pollinator interactions. Conclusions The adoption of the vocabulary would facilitate data sharing to support studies ranging from the spatial and temporal distribution of interactions to the taxonomic, phenological, functional, and phylogenetic aspects of plant–pollinator interactions. We expect to fill data and knowledge gaps, thus further enabling scientific research on the ecology and evolution of plant–pollinator communities, biodiversity conservation, ecosystem services, and the development of public policies. The proposed data model is flexible and can be adapted for sharing other types of interactions data by developing discipline-specific vocabularies of terms. [ABSTRACT FROM AUTHOR]