New York Botanical Garden

Taxonomic uncertainty is prevalent across many biological groups. Yet, it remains overlooked in ecology, evolution, and conservation, leading to potential misinterpretations of biodiversity patterns. Here, we argue that this uncertainty emerges from the interaction between biological processes shaping natural lineages and human efforts to name and classify them. Based on this, we propose a set of metrics to quantify confidence in species boundaries and to track the history of taxonomic change and stability. We show how these metrics can be embedded into biodiversity analyses, from mapping uncertainty across taxa and geographic regions to assigning weights to species and deriving more realistic error ranges in ecological models. Making taxonomic uncertainty explicit advances biodiversity science and strengthens conservation decisions.

Societal Impact Statement Collections of dried plant specimens (herbaria) provide an invaluable resource for the study of many areas of scientific interest and conservation globally. Digitisation increases access to specimens and metadata, enabling efficient use across a broad spectrum of research. The value of physical specimens is enhanced by digitisation, but these specimens remain fundamental for the study of traits not yet captured digitally. We investigate the requirements for physical access and the curation and facilities needed to maximise specimen use and value. We present recommendations to ensure that specimens and data are both fully accessible to support research into global challenges. Summary Herbarium management has traditionally focused on providing direct access to the physical specimens, but this scope must now expand to also embrace digital collections. Advances in technologies such as artificial intelligence and high‐throughput genomics are increasing the amount of information that can be extracted from specimens, and it is becoming commonplace to provide digital access to specimen images and collection metadata. These developments are facilitating the use of herbarium collections to inform conservation planning and in studies plant and fungal taxonomy, distribution and evolution. This paper examines how herbaria are transitioning from physical specimen‐centric collection management practices to increasingly digitised curation, and the effects that digital availability of data are having on demands for physical access. We provide a set of recommendations to institutions holding herbarium collections. We emphasise the critical importance of further digitising herbaria of all sizes; the need to ensure that historical inequalities in deposition of specimens are not perpetuated; and that the capacity to utilise new technologies must be further developed, especially in biodiverse regions from which most herbarium collections are derived. To improve access to collection data, herbarium managers need to more rigorously adopt community‐agreed data standards, and more strongly support open access platforms such as the Global Biodiversity Information Facility either directly or through regional coalitions. As digitisation and open data access increase, herbaria will need to offer users with seamless hybrid access to physical and digital records while continuing to develop their collections to advance research and conservation.

Abstract The rapid expansion of biodiversity data presents new opportunities to understand and forecast biosphere dynamics. However, disparate and dispersed data, taxonomic and geographic inconsistencies, pervasive quality issues, and a lack of reproducable workflows hinder synthesis, introduce biases and limit accurate assessment of biodiversity trends. The Botanical Information and Ecology Network (BIEN) addresses these challenges through two core contributions: (1) an ecosystem of modular, open‐source BIEN tools for collecting, harmonizing, validating, integrating, visualizing and analysing biodiversity data, and (2) a standardized, augmented and integrated global database (BIEN db) of plant occurrences, traits and geographic ranges. BIEN tools—including the Taxonomic Name Resolution Service (TNRS), Geographic Name Resolution Service (GNRS), Geocoordinate Validation Service (GVS) and Native Species Resolver (NSR)—enable the construction of analysis‐ready data sets. Using this framework, we integrated over 284 million botanical observation records. BIEN db (current version 4.2) is so far the most extensive compilation of standardized observation records and plant traits (25,932,454 unique trait observation records) for land plants, drawn from herbaria, ecological plots, citizen science and trait databases and integrated into a unified geospatial platform. Here, we present the BIEN workflow, the database and several use cases. The BIEN workflow and database support reproducible biodiversity science at scale. BIEN provides improved and unprecedented trait coverage, new estimates of total plant species richness, geographic ranges for over 250,000 species and global maps of plant biodiversity. These tools enable researchers to integrate disparate biodiversity observation records, generate tailored data sets, resolve taxonomic and geographic ambiguities, and estimate species richness across spatial and temporal scales for conservation and forecasting applications. BIEN provides a scalable, open and reproducible informatics platform that integrates global plant biodiversity data. By linking data infrastructure with accessible tools, BIEN democratizes biodiversity science. It enhances transparency, reproducibility and analytical capacity across the research community, enabling more scientists to address a wider range of questions in ecology, evolution and biodiversity science and engage in global change biology and biodiversity forecasting. BIEN offers a robust Open Science platform to understand and respond to the biodiversity crisis.

Bacterial vaginosis (BV) is caused by vaginal microbiome dysbiosis, when beneficial Lactobacillus species are no longer dominant and are replaced by harmful anaerobic bacteria such as Gardnerella vaginalis. In Caribbean cultures, women use plants topically, such as Argemone mexicana, to treat several vaginal infections, including BV. There has been little research into how traditional botanical extracts affect the vaginal microbiota, especially as these extracts are often prepared in different ways for the same condition. This study aims to evaluate the effect of botanical preparations using an in vitro co-culture assay with beneficial Lactobacillus species and BV-causing Gardnerella vaginalis. This is an application of an in vitro co-culture assay to assess the effect of botanical preparations on the vaginal microbiota. We hypothesized that variations in the chemical composition of these preparations would affect the composition of vaginal microbiota. Argemone mexicana extractions were tested using an in vitro co-culture method with Gardnerella vaginalis and one of three vaginal Lactobacillus species and evaluated by UPLC-qToF-MS for metabolomic chemical analysis. Aqueous extractions that did not have significant antibacterial effect compared to the control in monoculture suppressed the growth of Gardnerella vaginalis in co-culture with Lactobacillus, supporting the traditional Dominican use of this plant. These results are likely related to the presence of berberine and polysaccharides in the aqueous extractions.

Amazon rainforests face intensifying water stress due to increases in vapour pressure deficit and changing hydrological regimes. Embolism resistance (Ψ50) is a critical metric of tree survival under drought conditions, it is defined as a plant's capacity to resist disruption of xylem water flow due to air bubble formation from water stress. However, measurements of Ψ50 are only available for a limited number of Amazon locations and species. Conversely, data on forest taxonomic composition are abundant across Amazonia, and if Ψ50 is conserved phylogenetically, these data could provide a way to scale-up drought resistance patterns. Here we evaluate Ψ50 measurements across non-flooded Amazonian tree taxa and reveal a moderate phylogenetic signal, with phylogenetic conservatism evident at the family-level. Notably, Fabaceae is amongst the most embolism-resistant tree families in Amazonia. Leveraging the phylogenetic signal we use species composition and tree size data from 448 forest plots across Amazonia to produce a macroecological assessment of Amazonian vulnerability to embolism. The resulting estimate spatial pattern reveals that forests in the Brazilian and Guiana Shield regions, where Fabaceae abundance is high, show strong resistance to embolism. In contrast, tree communities in Western Amazonia appear more vulnerable to embolism, suggesting a reduced capacity to withstand future drought conditions.