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.

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.

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.

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.

Understanding the patterns and processes of cophylogeny and coevolution has long been of high importance in evolutionary ecology despite theoretical and methodological challenges. As widespread hybridization and histories of introgression become increasingly clear across the tree of life, biologists must contend with the methodological and theoretical implications. Nowhere is the challenge clearer than in the field of cophylogeny, where current approaches are fundamentally dependent on bifurcating trees, and evolutionary thinking often has neglected network perspectives. From plant-pollinator mutualisms to host-parasite antagonisms, contemporary hybridization, introgression, and reticulation (“network evolution”) are present in cophylogenetic and coevolutionary systems, yet much research assumes these processes are absent or negligible. We argue here that network evolutionary processes in cophylogenetic and coevolutionary systems are not just nuisances, but may be regulators of relationships, causing acceleration, disruption, or prevention of potential coevolutionary dynamics. In the face of continued recognition that network evolution is a significant force across the tree of life, specific theories, methodologies, and hypotheses on the result of interactions between network evolution and cophylogeny or coevolution must be developed, three of which are advanced here. First, we hypothesize that hybrid host individuals may act as phylogenetic “bridges,” facilitating symbiont transfer between otherwise reproductively isolated lineages. Second, we hypothesize that coevolutionary dynamics and network evolution may form feedback loops, wherein coevolutionary trajectories elevate introgression rates, and introgression in turn alters the coevolutionary landscape. Third, we hypothesize that introgression may act as an accelerator of coevolution, analogous to known effects of horizontal gene transfer and population mixing. We explore these questions in two relatively well-studied coevolutionary systems that involve extensive histories of introgression and contemporary hybrid lineages. We also suggest additional hypotheses in systems where hybridization in symbiotic lineages and cophylogenetic or coevolutionary dynamics may influence one another. Finally, we discuss the methodological and theoretical challenges of incorporating network evolutionary thinking into the fields of cophylogenetics and coevolution.