Core Archive Research Articles

PyDwCA: A Tool for Integrating Biodiversity Data

The Darwin Core Archive (DwC-A) format, based on the Darwin Core standard (Wieczorek et al. 2012), facilitates the exchange, management, and integration of biodiversity data from multiple sources. This ability to collate biodiversity data allows datasets to be aggregated at community-supported infrastructures, merged in different combinations, meta-analyzed and submitted to public repositories (Baker et al. 2014). Thus, the DwC-As serve as unifying archives in concatenated collective efforts, such as biodiversity inventories at different spatial and taxonomic scales. Here we describe PyDwCA*1, 2, a Python library implemented to handle the "star scheme" of DwC-A. This new library reads compressed zip files containing the expected meta.xml and uses it to assign the core component and its extensions. It also provides Python classes to define the core, the extensions, and the metadata file for creating an archive and writing it into a compressed zip file. PyDwCA also implements functionality to select, filter and merge DwC-A files. We present this new tool in the context of the construction of the Chilean National Biodiversity Inventory (Fig. 1), but PyDwCA serves as a versatile technical solution applicable to different contexts in the field of biodiversity informatics (e.g., integration of datasets from biological collection and sampling events). To exemplify how PyDwCA works, we present the step-by-step integration of the Chilean Catalogue of Vascular Plants (Rodriguez et al. 2018) on a matrix provided by the Catalogue of Life (Banki 2024), filtered with the species with occurrences recorded for Chile in the Global Biodiversity Information Facility (GBIF) (GBIF.Org 2023).

Completing the Completeness Measure: the MIDS Specification

The need to rapidly digitise millions of specimens in natural history collections has seen the development of a staged approach for data capture by institutions that have been carrying out mass digitisation projects. The cost and difficulty of transcribing labels associated with specimens has necessitated an approach that prioritises parts of the data based on research and curatorial requirements as well as ease of transcription and methodology available. This approach means that there is currently a wide variation in the completeness of data capture and imaging of specimens within and between collections. The Biodiversity Information Standards (TDWG) Minimum Information about a Digital Specimen (MIDS) specification has been designed to provide a framework for measuring and monitoring the completeness of the data transcribed from the specimen and the presence of an image or other media file. This framework enables a consistent and standardised approach to the calculation of the level of digitisation of specimens within a collection and, by extension/extrapolation, to the collection itself. Four levels of digitisation have been defined in the MIDS specification including a pre-digitisation level. These have been developed to correspond to practical requirements and existing large-scale digitisation programmes. MIDS level 0 (Bare): A bare or skeletal record making the association between an identifier of a physical specimen and its digital representation, allowing for unambiguous attachment of all other information. MIDS level 1 (Basic): A basic record of specimen information enabling basic discoverability as well as how the user is permitted to use the data. MIDS level 2 (Regular): A regular level of information including data that have been agreed over time as essential for most scientific purposes. MIDS level 3 (Extended): An extended level of information about a specimen including identifiers enabling connections to be made to other data present or known about the specimen. The scope of MIDS does not directly include the quality of data entered. Instead, MIDS can be seen as a tool to support the continuing improvement of data access and quality. It provides guidance for prioritising the data to be captured as well as recommendations for data standards and mapping structures. Here we present the progress in the development of the MIDS specification and its implementation. The MIDS elements for each of the four levels have now been defined and a draft version is available here. A machine-readable mapping to Darwin Core and ABCD has been compiled following the Simple Standard for Sharing Ontological Mappings (SSSOM). The differing data relevances and priorities for different disciplines have been recognised and the inclusion of required elements at each level is discipline specific (biology, palaeontology and geology). In addition, MIDS level scores have been increasingly implemented in existing specimen management systems, allowing an evaluation of the levels achieved in various contexts. There are two implementations of MIDS calculators that have been developed and are available to test. One, developed at the Meise Botanic Garden, uses a zipped Global Biodiversity Information Facility (GBIF) annotated archive (a commonly used GBIF download format based on Darwin Core Archive) and is available here. The other, developed at The Natural History Museum London, interacts directly with the GBIF API and is available here. We encourage users to try these and provide feedback to the TDWG MIDS Task Group.

Advancing chronologies for Last Interglacial sequences

ABSTRACTStudies of the Last Interglacial (ca. 129 to 116 ka BP) provide an opportunity to study the impact of high‐latitude warm temperatures on the Earth system. To build an accurate spatio‐temporal picture of climate and environmental variability during the Last Interglacial, building robust chronologies, through which the patchwork of terrestrial, marine, and ice core archives can be correlated, is paramount. In this review, we briefly evaluate the most common approaches used to date climate and environmental archives from the Last Interglacial, as well as the chronostratigraphic tools available for direct correlation between sequences, with a focus on terrestrial archives. We then present a case study on the use of pollen biostratigraphy for correlating sequences in NW Europe, highlighting its strength as a local correlation tool, and the challenges this approach presents in comparing sequences to global records of climate and environmental change. A move towards consistently dated sequences will improve our understanding of environmental responses to Last Interglacial climate variability across different elements of the global climate system and the rates at which different elements of the climate system respond to changes in global temperatures.

The Tropical Andes Biodiversity Hotspot: A Comprehensive Dataset for the Mira-Mataje Binational Basins

We present a flora and fauna dataset for the Mira-Mataje binational basins. This is an area shared between southwestern Colombia and northwestern Ecuador, where both the Chocó and Tropical Andes biodiversity hotspots converge. We systematized data from 120 sources in the Darwin Core Archive (DwC-A) standard and geospatial vector data format for geographic information systems (GIS) (shapefiles). Sources included natural history museums, published literature, and citizen science repositories across 13 countries. The resulting database has 33,460 records from 6,821 species, of which 540 have been recorded as endemic, and 612 as threatened. The diversity represented in the dataset is equivalent to 10% of the total plant species and 26% of the total terrestrial vertebrate species in both hotspots. The dataset can be used to estimate and compare biodiversity patterns with environmental parameters and provide value to ecosystems, ecoregions, and protected areas. The dataset is a baseline for future assessments of biodiversity in the face of environmental degradation, climate change, and accelerated extinction processes.

Biodiversity of testate amoebae in Sphagnum bogs: the dataset from forest-steppe ecotone (Middle Volga Territory, Russia).

Testate amoebae are a polyphyletic group of unicellular eukaryotic organisms that are characterised by a rigid shell and inhabit mostly freshwater and terrestrial ecosystems. They are particularly abundant in peatlands, especially in Sphagnum-dominated biotopes. Peatland hydrology is the most important influence on testate amoebae communities. The good preservation of the shells in peat deposits and their response to hydrological regime changes are the principles for palaeohydrological reconstructions. Any changes in the water balance of mires should be expected to have far-reaching effects on biogeochemical cycles, productivity, carbon dioxide and methane exchange. This paper presents a dataset (Darwin Core Archive - DwC-A) on the distribution of Sphagnum-dwelling testate amoebae in nine mires located in the forest-steppe subzone of the East European Plane. The dataset includes information about 86 taxa belonging to 29 genera and contains 3,123 occurrences of 49,874 individuals. The following environmental variables are provided: microtopography, oxidising and reducing potential, total mineralisation, substrate temperature, acidity, substrate wetness and water table depth. These data might be used for biogeographical and palaeoecological studies, including quantitative reconstructions.

Melting ice core archives

Melting ice core archives

EMDB-the Electron Microscopy Data Bank.

The Electron Microscopy Data Bank (EMDB) is the global public archive of three-dimensional electron microscopy (3DEM) maps of biological specimens derived from transmission electron microscopy experiments. As of 2021, EMDB is managed by the Worldwide Protein Data Bank consortium (wwPDB; wwpdb.org) as a wwPDB Core Archive, and the EMDB team is a core member of the consortium. Today, EMDB houses over 30000 entries with maps containing macromolecules, complexes, viruses, organelles and cells. Herein, we provide an overview of the rapidly growing EMDB archive, including its current holdings, recent updates, and future plans.

Data from Entomological Collections of Aedes (Diptera: Culicidae) in a post-epidemic area of Chikungunya, City of Kinshasa, Democratic Republic of Congo.

Arbovirus epidemics (chikungunya, dengue, West Nile fever, yellow fever and zika) are a growing threat in African areas where Aedes (Stegomyia) aegypti (Linnaeus, 1762) and Aedes albopictus (Skuse, 1895) are present. The lack of comprehensive sampling of these two vectors limits our understanding of their propagation dynamics in areas at risk of arboviruses. Here, we collected 6,943 observations (both larval and human capture) of Ae.aegypti and Ae.albopictus between 2020 and 2022. The study was carried out in the Vallee de la Funa, a post-epidemic zone in the city of Kinshasa, Democratic Republic of Congo. Our results provide important information for future basic and advanced studies on the ecology and phenology of these vectors, as well as on vector dynamics after a post-epidemic period. The data from this study are published in the public domain as the Darwin Core Archive in the Global Biodiversity Information Facility.

Early Holocene ice on the Begguya plateau (Mt. Hunter, Alaska) revealed by ice core 14C age constraints

Abstract. Investigating North Pacific climate variability during warm intervals prior to the Common Era can improve our understanding of the behavior of ocean–atmosphere teleconnections between low latitudes and the Arctic under future warming scenarios. However, most of the existing ice core records from the Alaskan and Yukon region only allow access to climate information covering the last few centuries. Here we present a surface-to-bedrock age scale for a 210 m long ice core recovered in 2013 from the summit plateau of Begguya (Mt. Hunter; Denali National Park, Central Alaska). Combining dating by annual layer counting with absolute dates from micro-radiocarbon dating, a continuous chronology for the entire ice core archive was established using an ice flow model. Calibrated 14C ages from the deepest section (209.1 m, 7.7 to 9.0 ka cal BP) indicate that basal ice on Begguya is at least of early Holocene origin. A series of samples from a shallower depth interval (199.8 to 206.6 m) were dated with near-uniform 14C ages (3 to 5 ka cal BP). Our results suggest this may be related to an increase in annual net snow accumulation rates over this period following the Northern Hemisphere Holocene Climate Optimum (around 8 to 5 kyr BP). With absolute dates constraining the timescale for the last >8 kyr BP, this paleo-archive will allow future investigations of Holocene climate and the regional evolution of spatial and temporal changes in atmospheric circulation and hydroclimate in the North Pacific.

"Publish First": A Rapid, GPT-4 Based Digitisation System for Small Institutes with Minimal Resources

We present a streamlined technical solution ("Publish First") designed to assist smaller, resource-constrained herbaria in rapidly publishing their specimens to the Global Biodiversity Information Facility (GBIF). Specimen data from smaller herbaria, particularly those in biodiversity-rich regions of the world, provide a valuable and often unique contribution to the global pool of biodiversity knowledge (Marsico et al. 2020). However, these institutions often face challenges not applicable to larger herbaria, including a lack of staff with technical skills, limited staff hours for digitization work, inadequate financial resources for specialized scanning equipment, cameras, lights, and imaging stands, limited (or no) access to computers and collection management software, and unreliable internet connections. Data-scarce and biodiversity rich countries are also often linguistically diverse (Gorenflo et al. 2012), and staff may not have English skills, which means pre-existing online data publication resources and guides are of limited use. The "Publish First" method we are trialing, addresses several of these issues: it drastically simplifies the publication process so technical skills are not necessary; it minimizes administrative tasks saving time; it uses simple, cheap and easily available hardware; it does not require any specialized software; and the process is so simple that there is little to no need for any written instructions. "Publish first" requires staff to attach QR code labels containing identifiers to herbarium specimen sheets, scan these sheets using a document scanner costing around €300, then drag and drop these files to an S3 bucket (a cloud container that specialises in storing files). Subsequently, these images are automatically processed through an Optical Character Recognition (OCR) service to extract text, which is then passed on to OpenAI's Generative Pre-Transformer 4 (GPT-4) Application Programming Interface (API), for standardization. The standardized data is integrated into a Darwin Core Archive file that is automatically published through GBIF's Integrated Publishing Toolkit (IPT) (GBIF 2021). The most technically challenging aspect of this project has been the standardization of OCR data to Darwin Core using the GPT-4 API, particularly in crafting precise prompts to address the inherent inconsistency and lack of reliability in these Large Language Models (LLMs). Despite this, GPT-4 outperformed our manual scraping efforts. Our choice of GPT-4 as a model was a naive one: we implemented the workflow on some pre-digitized specimens from previously published Norwegian collections, compared the published data on GBIF with GPT-4's Darwin Core standardized output, and found the results satisfactory. Moving forward, we plan to undertake more rigorous additional research to compare the effectiveness and cost-efficiency of different LLMs as Darwin Core standardization engines. We are also particularly interested in exploring the new "function calling" feature added to the GPT-4 API, as it promises to allow us to retrieve standardized data in a more consistent and structured format. This workflow is currently under trial in Tajikistan, and may possibly be used in Uzbekistan, Armenia and Italy in the near future.

GBIF-Compliant Data Pipeline for the Management and Publication of a Global Taxonomic Reference List of Pests in Natural History Collections

There is a growing demand for monitoring pests in natural history collections (NHCs) and establishing integrated pest management (IPM) solutions (Crossman and Ryde 2022). In this context, up-to-date taxonomic reference lists and controlled vocabularies following standard schemes are crucial and facilitate recording organisms detected in collections. The data pipeline described here results in the publication of a taxon reference list based on information from online resources and standard IPM literature. Most of the over 140 pest taxa on species level and above are insects, the rest belong to other animal groups and fungi. The complete taxon names, synonyms, English and German common names, and the hierarchical classification (parent-child relationships) are organised in a client-server installation of DiversityTaxonNames (DTN) at the Bavarian Natural History Collections (SNSB). DTN is a Microsoft Structured Query Language (MS SQL) database tool of the Diversity Workbench (DWB) framework with a published Entity Relation (ER) diagram (Hagedorn et al. 2019). The management is done using the Global Biodiversity Information Facility (GBIF) backbone taxonomy as external name resource, with linkage to the respective Wikidata Q item ID as a external persistent identifier (PID). Moreover, information on pest occurrence in NHCs is given, distinguishing the Consortium of European Taxonomic Facilities (CETAF) major NHC collection types affected (i.e., heritage sciences, life sciences and earth sciences) and the object categories, e.g., natural objects/specimens damaged. The data management in DTN enables the long-running curation, done by list curators. The generic data pipeline for the management and publication of a Global Taxonomic Reference List of Pests in NHCs is based on the DTN taxon lists concept and architecture and described under About "Taxon list of pest organisms for IPM at natural history collections compiled at the SNSB". It includes four steps (A–D) with significant results for best practices of data processing (Fig. 1). A. The data is managed and processed for publication by list curators in the database DiversityTaxonNames (DTN). As a result, the list can be kept up-to-date and is—without transformation—ready to be used for IPM solutions at any NHC with a DiversityCollection installation and as part of the DWB cloud services. B. The up-to-date data is publicly available via the DTN REST Webservice for Taxon Lists with machine-readable Application Programming Interface (API). As a result, the dynamic list publication service can be used as a reference backbone for establishing IPM solutions for pest monitoring at any NHC. C. The data is provided via the GBIF checklist data publication pipeline of the SNSB through GBIF validation tools and Darwin Core Archive in DwC-A (zip format) for GBIF. As a result, the checklist information becomes part of the GBIF network with GBIF ChecklistBank and GBIF Global Taxonomy. This ensures future compliance of data with the Findability, Accessibility, Interoperability, and Reuse (FAIR) guiding principles. D. The DTN REST Web service for Taxon Lists (currently 60 lists) is registered and accessible through the German Federation for Biological Data (GFBio) Terminology service. As a result, the lists with external PIDs and other information are available as a service (see DTN lists overview). In the upcoming Research Data Commons of the German National Research Data Infrastructure (NFDI) Initiative (Diepenbroek et al. 2021), it will be part of a standardized layer of APIs with an agreed interface scheme for improved accessibility. The provided tools, API and data are part of the upcoming NFDI4Biodiversity service portfolio. Future scenarios include the use of the list items and properties as classes for diagnosis purposes with DiversityNaviKey (Triebel et al. 2021) including the publication of images for identifying pests.

Harmonised Data is Actionable Data: DiSSCo’s solution to data mapping

Predictability is one of the core requirements for creating machine actionable data. The better predictable the data, the more generic the service acting on the data can be. The more generic the service, the easier we can exchange ideas, collaborate on initiatives and leverage machines to do the work. It is essential for implementing the FAIR Principles (Findable, Accessible, Interoperable, Reproducible), as it provides the “I” for Interoperability (Jacobsen et al. 2020). The FAIR principles emphasise machine actionability because the amount of data generated is far too large for humans to handle. While Biodiversity Information Standards (TDWG) standards have massively improved the standardisation of biodiversity data, there is still room for improvement. Within the Distributed System of Scientific Collections (DiSSCo), we aim to harmonise all scientific data derived from European specimen collections, including geological specimens, into a single data specification. We call this data specification the open Digital Specimen (openDS). It is being built on top of existing and developing biodiversity information standards such as Darwin Core (DwC), Minimal Information Digital Specimen (MIDS), Latimer Core, Access to Biological Collection Data (ABCD) Schema, Extension for Geosciences (EFG) and also on the new Global Biodiversity Information Facility (GBIF) Unified Model. In openDS we leverage the existing standards within the TDWG community but combine these with stricter constraints and controlled vocabularies, with the aim to improve the FAIRness of the data. This will not only make the data easier to use, but will also increase its quality and machine actionability. As the first step towards this the harmonisation of terms, we make sure that similar values use the same term in a standard as key. This enables the next step in which we harmonise the values. We can transform free-text values into standardised or controlled vocabularies. For example: instead of using the names J. Doe, John Doe and J. Doe sr. for a collector, we aim to standardise these to J. Doe, with a person identifier that connects this name with more information about the collector. Biodiversity information standards such as DwC were developed to lower the bar for data sharing. The downside of including minimal restraints and flexibility is that they provide room for ambiguity, leading to multiple ways of interpretation. This limits interoperability and hampers machine actionability. In DiSSCo, data will come from different sources that use different biodiversity information standards. To cover this, we need to harmonise terms between these standards. To complicate things further, different serialisation methods are used for data exchange. Darwin Core Archives (DwC-A; GBIF 2021) use Comma-separated values (CSV) files. ABCD(EFG) exposed through Biological Collection Access Service (BioCASe) uses XML. And most custom formats use JavaScript Object Notation (JSON). In this lightning talk, we will dive into DiSSCo’s technical implementation of the harmonisation process. DiSSCo currently supports two biodiversity information standards, DwC and ABCD(EFG), and maps the data to our openDS specification on a record-by-record basis. We will highlight some of the more problematic mappings, but also show how a harmonised model massively simplifies generic actions, such as the calculation of MIDS levels, which provide information about digitisation completeness of a specimen. We will conclude by having a quick look at the next steps and hope to start a discussion about controlled vocabularies. The development of high quality, standardised data based on a strict specification with controlled vocabularies, rooted in community accepted standards, can have a huge impact on biodiversity research and is an essential step towards scaling up research with computational support.

TaxonWorks in its 10th Year: What’s new, what’s next?

TaxonWorks in its 10th Year: What’s new, what’s next?

An Excel Template Generator for Darwin Core

Scientific data is diverse and can be complex, potentially including biotic or abiotic measurements, material samples, DNA derived data and more. Especially for researchers who are new to the Darwin Core standard (Darwin Core Task Group 2009), it is not always obvious what the best practice is for creating a Darwin Core Archive (GBIF 2021) for their data. Which core and extensions should they select? Which Darwin Core terms*1 should they include? We present the 'Learnings from Nansen Legacy template generator' (Marsden and Schneider 2023), a spreadsheet template generator to simplify the creation of Darwin Core Archives. It enables users to create a single Microsoft Excel file that includes one sheet per core or extension using a graphical user interface. The user can select from a complete list Darwin Core terms to use as column headers. There are requirements and recommendations for which terms are selected for each core and extension. Descriptions for all terms are displayed when one hovers over a Darwin Core term, and are stored as notes in the template when one select a relevant cell. The generated template includes cell restrictions to prevent one from inputting data in an incorrect format. A separate configuration is also available to aid researchers in creating CF-NetCDF*2 files for physical data, which are also compliant with the FAIR (Findable, Accessible, Interoperable, Resuable)*3 data management principles. The Learnings from Nansen Legacy template generator is published (Marsden and Schneider 2023) and can be installed for use on your website or computer by following the instructions on the software's GitHub repository*4. The template generator can be tested where it is currently hosted, by SIOS*5 (Svalbard Integrated Arctic Earth Observing System). One can also refer to a YouTube tutorial*6 on how the template generator works.

Building Software for Hierarchical Events in Biodiversity Informatics

In 2019, the Atlas of Living Australia (ALA) ran a national consultation, clarifying a long-held suspicion that while simple occurrence records provide invaluable discoverability and analysis for biodiversity data, the lack of contextual information on data collection methodology and protocols limits its usefulness for species abundance estimation and time-series analysis. The consultation recognised that the ALA has strong leadership in biodiversity standards and development, and that our 12-year history and investment in projects and engagement demonstrates a clear capacity to transition to a repository capable of capturing and aggregating the monitoring and survey data required for conservation efforts (Daly 2019). Around the same time, the larger data landscape was undergoing change in a similar direction, both internationally through the Global Biodiversity Information Facility’s (GBIF) Unified Model engagements, and nationally through the development of the Australian Biodiversity Information Standard (ABIS), an ontology for describing environmental data (Anonymous 2021). We embarked on a project to examine existing data standards and practices, extend our own occurrence model, and build software that could ingest event-based datasets and make them discoverable and interoperable. Initially we focused on well-structured surveys, both marine and terrestrial, to develop the system and user interface (UI). During the project, we restructured and modeled other exemplar datasets, collaborating with GBIF to develop event terms, vocabularies, and user interface components. Seeking interoperability with existing standards, we integrated concepts from both ABIS and the Ocean Biodiversity Information System’s (OBIS) ENV-DATA model (De Pooter et al. 2017) into a standardised yet flexible implementation of Event Core, navigable via a friendly user interface. The initial software release is comprised of an ingestion pipeline for events in parallel to occurrences, an index capable of handling nested data structures, and a user interface. The UI guides the user to explore and filter datasets; includes visualisations for data structures, taxonomic scope, repeat location surveys, extended measurements or facts; and links out to child occurrence records. Users can download filtered original and interpreted datasets with Digital Object Identifiers (DOI), in compressed files that comply simultaneously with Darwin Core Archive and Frictionless Data Package specifications. On release, we will present a range of datasets covering different event-based scenarios. The model has serendipitously provided the flexibility to encapsulate complex seed bank data. During the project, we developed a draft extension, which we used to service a new data portal for the Australian Seed Bank Partnership, a testament to the model’s serviceability for novel use cases. The ALA has taken innovative steps beyond simple collection of complex data types and worked with our local biodiversity informatics community to provide a navigable interface to this data. We intend to continue working with our own data providers and the international community, to realise the benefits of a more complex data model.

The Catalogue of Life Data Package (CoLDP) and the Taxon Concept Standard (TCS): A Comparison

The Catalogue of Life Data Package (CoLDP; Catalogue of Life 2022) is the preferred mechanism for getting data in and out of the ChecklistBank. A CoLDP is a ZIP file containing files with delimiter-separated values, similar to the Darwin Core Archive (DwC-A; Global Biodiversity Information Facility 2023), but does not enforce the DwC-A star schema requiring a single Core file and zero or more Extension files. This makes it preferable for exchanging taxonomic data in tabular format as taxonomic data contains at least three different types of objects—taxa, names and references—that are all interlinked. TCS (currently still Taxon Concept Schema) is the TDWG (Biodiversity Information Standards) standard for dealing with taxonomic data specifically. An effort is currently underway (TCS 2 Task Group 2023) to free TCS from its XML schema and turn it into a TDWG vocabulary standard that is maintainable under the TDWG Vocabulary Maintenance Specification (VMS; Vocabulary Maintenance Specification Task Group 2017). For a domain standard like TCS, it is essential that it supports an important warehouse of taxonomic information like ChecklistBank and an exchange format like CoLDP. Therefore, as part of the Implementation Experience Report that has to accompany a major update to an existing TDWG standard, a comparison has been undertaken between TCS and the data model behind CoLDP. While some of the terms CoLDP uses are different from the ones used by TCS, the two specifications are completely compatible. This presentation will highlight some of the key similarities and differences. It is heartening to see that different groups of people independently chose to make the same departure from the existing specification. As TCS will be maintainable—and, in fact, still has to undergo public review—and CoLDP presumably can evolve as well, there are opportunities for TCS and CoLDP to come even closer together than they already are.

Forest inventory tree core archive reveals changes in boreal wood traits over seven decades

Boreal forests play an important role in the global carbon (C) cycle, and there is great interest in understanding how they respond to environmental change, including nitrogen (N) and water limitation, which could impact future forest growth and C storage. Utilizing tree cores archived by the Swedish National Forest Inventory, we measured stemwood traits, including stable N and C isotope composition which provides valuable information related to N availability and water stress, respectively, as well as N and C content, and C/N ratio over 1950–2017 in two central Swedish counties covering an area of ca. 55,000 sq. km (n = 1038). We tested the hypothesis that wood traits are changing over time, and that temporal patterns would differ depending on alternative dendrochronological reconstruction methods, i.e. the commonly applied “single tree method” (STM) or a conceptually stronger “multiple tree method” (MTM). Averaged across all MTMs, our data showed that all five wood traits for Picea abies and Pinus sylvestris changed over time. Wood δ15N strongly declined, indicating progressive nitrogen limitation. The decline in δ13C tracked the known atmospheric δ13CO2 signal, suggesting no change in water stress occurred. Additionally, wood N significantly increased, while C and C/N ratios declined over time. Furthermore, wood trait patterns sometimes differed between dendrochronological methods. The most notable difference was for δ15N, where the slope was much shallower for the STM compared to MTMs for both species, indicating that mobility of contemporary N is problematic when using the STM, resulting in substantially less sensitivity to detect historical signals. Our study indicates strong temporal changes in boreal wood traits and also indicates that the field of dendroecology should adopt new methods and archiving practices for studying highly mobile element cycles, such as nitrogen, which are critical for understanding environmental change in high latitude ecosystems.

Anopheles sampling collections in the health districts of Korhogo (Côte d'Ivoire) and Diébougou (Burkina Faso) between 2016 and2018.

Characterizing the entomological profile of malaria transmission at fine spatiotemporal scales is essential for developing and implementing effective vector control strategies. Here, we present a fine-grained dataset of Anopheles mosquitoes (Diptera: Culicidae) collected in 55 villages of the rural districts of Korhogo (Northern Côte d'Ivoire) and Diébougou (South-West Burkina Faso) between 2016 and 2018. In the framework of a randomized controlled trial, Anopheles mosquitoes were periodically collected by Human Landing Catches experts inside and outside households, and analyzed individually to identify the genus and, for a subsample, species, insecticide resistance genetic mutations, Plasmodium falciparum infection, and parity status. More than 3,000 collection sessions were carried out, achieving about 45,000h of sampling efforts. Over 60,000 Anopheles were collected (mainly A.gambiae s.s., A.coluzzii, and A.funestus). The dataset is published as a Darwin Core archive in the Global Biodiversity Information Facility, comprising four files: events, occurrences, mosquito characterizations, and environmental data.

Dataset of benthic copepods in the littoral zones of Lake Maggiore

Copepods (Crustacea: Copepoda) are widespread in aquatic ecosystems worldwide and represent an important component of the meiobenthic metazoan assemblages of lake littorals. Yet, little is currently known about the diversity of benthic copepods in lentic habitats. We gathered information on the benthic copepod assemblages of the littoral zone of Lake Maggiore as part of the Interreg Italy-Switzerland 2014-2020 Parchi Verbano Ticino project (ID: 481668), funded by the European Regional Development Fund (ERDF). Lake Maggiore is a large and deep temperate lake in north-western Italy human-managed from mid-March to mid-September. This contributes to substantial changes in water levels in relation to human activities such as hydropower, industrial and agricultural uses. We compiled a dataset listing 234 occurrences of benthic copepod species recorded from three littoral sampling sites situated in three protected areas, two of which are part of the Natura 2000 network in Italy and one is part of the Emerald Network in Switzerland. We collected the specimens during the summer-autumn period in 2019-2021. We identified the copepods at the species level and created a dataset with individual georeferenced occurrence records for each species, organized in a standardized Darwin Core Archive format. We made available, through the Global Biodiversity Information Facility (GBIF), a total of 13 distinct taxonomic entities and 234 unique georeferenced occurrence records related to the benthic copepod assemblages of the littoral zone of Lake Maggiore (Tabilio Di Camillo et al., 2023). The dataset has the potential to support the authorities in charge of managing Lake Maggiore’s water levels in addressing the ecological risk relevant to the littoral zone and in developing shared implementation strategies for sustainable water management.

Seasonal response of coccolithophores and its potential to reconstruct paleomonsoon in the eastern Indonesian seas: an overview

Coccolithophore is a group of marine calcifying phytoplankton and its living distribution is sensitive to ecological change within the photic zone. Their coccoliths contribute majorly to the marine sediments and have become a reliable proxy in paleoceanography and paleoclimatology. The upper hydrology of the eastern Indonesian seas has been strongly influenced by seasonal climate change, the Australian-Indonesian monsoon. We review and discuss the result of previous studies on the response of living coccolithophore to seasonal change and the significance of their coccoliths as a proxy for reconstructing past dynamic of monsoon in the region. Coccolithophores abundance, species assemblages and coccolith malformation change in respond to the shift of photic environment condition modulated by reversing monsoon with particular responds across the region. Coccoliths variations in the marine sediment core archives from off southwest Sumba, eastern Banda Sea and Halmahera Sea show an insignificant control of glacial-interglacial climate variability to paleoproducitivity. Primary productivity based on the relative abundance of Florisphaera profunda has contributed to reconstruction of the past dynamic of Australian-Indonesian monsoon. However, more extensive and continuous observation of coccolithophores and their relationship with the photic environment in the eastern Indonesian seas is necessary for a better understanding of their response to monsoon dynamics in the present, past and future.