Turning biodiversity data into evidence: the role of protocols in the epistemology of evidence-based conservation

BackgroundSouth America hosts some of the world’s most prominent biodiversity hotspots. Yet, Uruguay – a country where multiple major ecosystems converge – ranks amongst the countries with the lowest levels of available digital biodiversity data in the continent. Such prevalent data scarcity has significantly undermined our ability to progress towards evidence-based conservation actions – a critical limitation for a country with a strong focus on agricultural industries and only 1.3% of the land surface guarded by protected areas. Under today’s rapid biodiversity loss and environmental changes, the need for open-access biodiversity data is more pressing than ever before. To address this national issue, Biodiversidata – Uruguay’s first Consortium of Biodiversity Data – has recently emerged with the aim of assembling a constantly growing database for the biodiversity of this country. While the first phase of the project targeted vertebrate biodiversity, the second phase presented in this paper spans the biodiversity of plants.New informationAs part of the second phase of the Biodiversidata initiative, we present the first comprehensive open-access species-level database of the vascular plant diversity recorded in Uruguay to date (i.e. all species for which data are currently available and species presence has been confirmed). It contains 12,470 occurrence records from across 1,648 species and 160 families, which roughly represents 60% of the total recorded flora of Uruguay. The primary biodiversity data include extant native and introduced species from the lycophytes, ferns, gymnosperms and angiosperms groups. Records were collated from multiple sources, including data available in peer-reviewed scientific literature, institutional scientific collections and datasets contributed by members of the Biodiversidata initiative. The complete database can be accessed at the Zenodo repository: doi.org/10.5281/zenodo.3954406

From LSA to LLM: Evolution and limitations of topic modelling methods for biodiversity conservation

Biodiversity loss poses significant threats to forest ecosystem services (FES) and human well-being. Despite their critical importance, understanding FES dynamics in developing countries like Ethiopia remains limited due to a lack of comprehensive data on biodiversity, vegetation structure, and their relationships with FES. This study aimed to address these gaps by investigating the diversity, structure, regeneration status, and FES provision of woody plant species in Menagesha Suba Forest, one of Ethiopia’s oldest dry Afromontane forests. A vegetation inventory conducted across 94 systematically sampled plots (20 × 20 m) identified 71 woody species, comprising 42.3% trees, 46.5% shrubs, and 11.3% woody climbers, belonging to 56 genera and 43 families. Dominant species included Juniperus procera (IVI = 86.5%) and Olea europaea (IVI = 28.2%). Diversity indices indicated high species richness (H’ = 3.06), moderate evenness (0.72), and high biodiversity (D = 0.93). Household surveys (n = 145) revealed that 43 woody species were utilized for nine key uses. Fuelwood was the most common use (26 species), followed by fences (22 species), farming tools (21 species), house construction (17 species), and household utilities (16 species). Apart native woody species, exotic species, including Eucalyptus globulus, Cupressus lusitanica, and Grevillea robusta, were among the most utilized. Despite disturbances such as illegal fuelwood collection and grazing, the forest remains a critical biodiversity hotspot and an essential provider of ecosystem services. Strengthening landscape multifunctionality through assisted regeneration, targeted reforestation, and afforestation is imperative to balance biodiversity conservation with FES provision. Future research should integrate biodiversity and ecosystem service data to guide evidence-based conservation strategies, fostering socioecological resilience in Ethiopia and similar regions.

Demanding but not sharing: barriers and counteracting strategies for compilation of biodiversity data from researchers and practitioners

Biodiversity portals are emerging as some of the most powerful tools for scientific research and management based on scientific collections. We discuss the importance of web portals in biodiversity research and highlight the commendable progress made by two digitisation projects in Chile: herbariodigital.cl and the Atlas of Chilean Biodiversity. The aim of herbariodigital.cl and ALA-Chile is to take advantage of technological advances to improve the digitisation of biodiversity data. Using cutting-edge methods, herbariodigital.cl has successfully digitised an extensive collection of plant specimens and associated data from Chilean herbaria (>25,000 specimens), promoting a more accessible and inclusive platform for researchers, educators and decision-makers. Recognising that the complex nature of biodiversity information requires a careful approach to data storage and organisation to ensure efficient exchange across different platforms, we discuss our experience of using the Darwin Core standard (Darwin Core Task Group 2009), a widely accepted data standard in the field of biodiversity informatics. In turn, we discuss the incongruence that arises from adopting different global taxonomic checklists, such as the GBIF taxonomic backbone (GBIF Secretariat 2022) and World Flora Online (WFO 2023), in addition to a localised community catalogue. Using these different taxonomic frameworks is a significant challenge, as discrepancies and inconsistencies can arise, leading to potential under- or over-estimation of biodiversity indicators. By addressing these challenges, we believe that both herbariodigital.cl and ALA-Chile will prove to be invaluable assets for scientific research, educational initiatives, and environmental monitoring and assessment. The comprehensive digitisation of biodiversity information will make it easier for researchers to conduct interdisciplinary studies and formulate evidence-based conservation strategies. In addition, educators will be able to use these web portals to develop interactive teaching materials, fostering a deeper connection between students and the natural world. Stakeholders in both the public and private sectors can also make informed decisions about biodiversity offsetting. In conclusion, we highlight the transformative impact of web portals in the field of biodiversity research. The remarkable progress made by herbariodigital.cl and ALA-Chile in digitising Chile's biodiversity information is opening up unprecedented opportunities for scientific research, education and environmental management. By overcoming the challenges of data standardisation and taxonomic harmonisation, these projects are paving the way for a more comprehensive and collaborative approach to understanding and conserving Chile's biodiversity.

Conservation efforts must be evidence-based, so rapid and economically feasible methods should be used to quantify diversity and distribution patterns. We have attempted to overcome current impediments to the gathering of biodiversity data by using integrative phylogenomic and three mtDNA fragment analyses. As a model, we sequenced the Metriorrhynchini beetle fauna, sampled from ~700 localities in three continents. The species-rich dataset included ~6500 terminals, ~ 1850 putative species delimited at 5% uncorrected pairwise threshold, possibly ~1000 of them unknown to science. Neither type of data could alone answer our questions on biodiversity and phylogeny. The phylogenomic backbone enabled the integrative delimitation of robustly defined natural genus-group units that will inform future research. Using constrained mtDNA analysis, we identified the spatial structure of species diversity, very high species-level endemism, and a biodiversity hotspot in New Guinea. We suggest that focused field research and subsequent laboratory and bioinformatic workflow steps would substantially accelerate the inventorying of any hyperdiverse tropical group with several thousand species. The outcome would be a scaffold for the incorporation of further data from environmental sequencing and ecological studies. The database of sequences could set a benchmark for the spatiotemporal evaluation of biodiversity, would support evidence-based conservation planning, and would provide a robust framework for systematic, biogeographic, and evolutionary studies.

Conservation efforts must be evidence-based, so rapid and economically feasible methods should be used to quantify diversity and distribution patterns. We have attempted to overcome current impediments to the gathering of biodiversity data by using integrative phylogenomic and three mtDNA fragment analyses. As a model, we sequenced the Metriorrhynchini beetle fauna, sampled from ~700 localities in three continents. The species-rich dataset included ~6500 terminals, ~ 1850 putative species delimited at 5% uncorrected pairwise threshold, possibly ~1000 of them unknown to science. Neither type of data could alone answer our questions on biodiversity and phylogeny. The phylogenomic backbone enabled the integrative delimitation of robustly defined natural genus-group units that will inform future research. Using constrained mtDNA analysis, we identified the spatial structure of species diversity, very high species-level endemism, and a biodiversity hotspot in New Guinea. We suggest that focused field research and subsequent laboratory and bioinformatic workflow steps would substantially accelerate the inventorying of any hyperdiverse tropical group with several thousand species. The outcome would be a scaffold for the incorporation of further data from environmental sequencing and ecological studies. The database of sequences could set a benchmark for the spatiotemporal evaluation of biodiversity, would support evidence-based conservation planning, and would provide a robust framework for systematic, biogeographic, and evolutionary studies.

• Practical, interpretable method supports EU Habitats Directive Article 17 reporting. • Structured framework standardizes monitoring and strengthens biodiversity data. • AI, ML, satellites, and field data enable large-scale Annex I habitat mapping. • HDTM identifies suitable areas, supporting habitat detection and prioritization. • Validated field data underpin standardized national Habitats Directive databases. Habitat monitoring and conservation assessment have gained importance in the EU, especially since the adoption of the Habitats Directive and the creation of the Natura 2000 network. Accurate reporting on habitat conservation status depends on detailed knowledge of habitat distribution. Advances in open-access biodiversity databases, remote sensing, and machine learning algorithms have improved ecosystem mapping, while field surveys remain essential for understanding habitat dynamics. This study proposes a standardized framework for habitat mapping and monitoring, applied to the Annex I habitat types of the Habitats Directive in the Latium region - Central Italy. A large dataset of georeferenced vegetation plots was collected through systematic fieldwork and classified using expert systems and clustering analysis. These labeled plots were then used to train Habitat Distribution Models based on Random Forest algorithms, generating high-resolution habitat maps. The maps were refined through probability thresholding and validated using the Article 17 reporting dataset, primarily based on expert judgment. The methodology successfully identified 41 habitat types, including coastal, dune, grassland, rocky, and forest ecosystems. Beyond mapping known habitats, the proposed modeling framework also serves as a tool for identifying knowledge gaps and uncovering conservation opportunities, providing ecologically meaningful signals that can reveal overlooked biodiversity hotspots and uncover previously undocumented vegetation history events. This reproducible and scalable workflow delivers robust spatial data on habitat distribution, extent, and condition, supporting both regional and national conservation reporting. It offers a valuable tool for practitioners and researchers, enhancing long-term monitoring, informing restoration actions, and improving evidence-based conservation planning.