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Journal articleArino S, Sgueglia G, Leone L, et al., 2025,
Deep-Learning Driven Identification of Novel Antimicrobial Peptides
, CHEMISTRY-A EUROPEAN JOURNAL, Vol: 31, ISSN: 0947-6539 -
Journal articleNgoh A, Clark M, Greenaway R, et al., 2025,
Clinical and Molecular Genetic Characterization of Landau Kleffner Syndrome: An Observational Cohort and Experimental Study
, ANNALS OF NEUROLOGY, ISSN: 0364-5134 -
Journal articleSmith DJ, Maretvadakethope S, Wilson LG, et al., 2025,
Emerging directions for biologically active fluids
, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol: 383, ISSN: 1364-503X -
Journal articleMountain K, MacIntyre D, Lee Y, et al., 2025,
ABO blood group antigens influence host-microbe interactions and risk of early spontaneous preterm birth
, npj Biofilms and Microbiomes, Vol: 11, ISSN: 2055-5008The mechanisms by which vaginal microbiota shape spontaneous preterm birth (sPTB) risk remain poorly defined. Using electronic clinical records data from 74,913 maternities in conjunction with metaxanomic (n=596) and immune profiling (n=314) data, we show that the B blood group phenotype associates with increased risk of sPTB and adverse vaginal microbiota composition. The O blood group associates with sPTB in women who have a combination of a previous history of sPTB, an adverse vaginal microbial composition and pro-inflammatory cervicovaginal milieu. In contrast, women of blood group A have a higher prevalence of vaginal Lactobacillus crispatus, a lower risk of sPTB, with sPTB cases showing no association with vaginal microbiota composition or inflammation. We found that cervicovaginal fluid contains ABH(O) glycans, and show variable binding to key vaginal bacteria. This indicates that cervicovaginal ABH(O) glycans influence microbiota-host interactions implicated in sPTB risk, suggesting a novel target for sPTB prediction and prevention.
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Journal articlePenadés JR, Gottweis J, He L, et al., 2025,
AI mirrors experimental science to uncover a mechanism of gene transfer crucial to bacterial evolution
, Cell, ISSN: 0092-8674Artificial intelligence (AI) models have been proposed for hypothesis generation, but testing their ability to drive high-impact research is challenging since an AI-generated hypothesis can take decades to validate. Here, we challenge the ability of a recently developed large language model (LLM)-based platform, AI co-scientist, to generate high-level hypotheses by posing a question that took years to resolve experimentally but remained unpublished: how could capsid-forming phage-inducible chromosomal islands (cf-PICIs) spread across bacterial species? Remarkably, the AI co-scientist’s top-ranked hypothesis matched our experimentally confirmed mechanism: cf-PICIs hijack diverse phage tails to expand their host range. We critically assess its five highest-ranked hypotheses, showing that some opened new research avenues in our laboratories. We benchmark its performance against other LLMs and outline best practices for integrating AI into scientific discovery. Our findings suggest that AI can act not just as a tool but as a creative engine, accelerating discovery and reshaping how we generate and test scientific hypotheses.
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Journal articleHe L, Patkowski JB, Wang J, et al., 2025,
Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization
, Cell, ISSN: 0092-8674Some mobile genetic elements spread among unrelated bacterial species through unknown mechanisms. Recently, we discovered that identical capsid-forming phage-inducible chromosomal islands (cf-PICIs), a new family of phage satellites, are present across multiple species and genera, raising questions about their widespread dissemination. Here, we have identified and characterized a new biological entity enabling this transfer. Unlike other satellites, cf-PICIs produce their own capsids and package their DNA, relying solely on phage tails for transfer. cf-PICIs release non-infective, tailless capsids containing their DNA into the environment. These subcellular entities then interact with phage tails from various species, forming chimeric particles that inject DNA into different bacterial species depending on the tail present. Additionally, we elucidated the structure of the tailless cf-PICIs and the mechanism behind their unique capsid formation. Our findings illuminate the mechanisms used by satellites to spread in nature, contributing to bacterial evolution and the emergence of new pathogens.
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Journal articleBarker-Clarke RJ, Gray JM, Leither S, et al., 2025,
The balance between intrinsic and ecological fitness reveals hidden regimes in eco-evolutionary population dynamics.
, Res SqUnderstanding how populations evolve requires accounting for both intrinsic fitness, defined by genotype and environment, and ecological interactions that emerge in mixed communities. While evolutionary experiments typically assess fitness in isolation, such monoculture measures may misrepresent dynamics in realistic, interacting populations. Here, we present a game-theoretic framework that explicitly separates intrinsic and ecological contributions to fitness, allowing us to map how ecological interactions can mask, mirror, maintain, or mimic selection driven by genetic differences. We derive analytical conditions for these regimes using deterministic replicator dynamics and validate them in stochastic Wright-Fisher models with mutation and drift. Applying our model to published microbial and cancer co-culture data, we show that real systems span both intrinsic-dominant and ecology-dominant regimes, with ecological effects sometimes reversing or neutralizing intrinsic fitness advantages. These results expose a critical blind spot in experimental design and interpretation, emphasizing the need to account for ecological interactions when inferring evolutionary dynamics and designing therapeutic strategies.
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Journal articleMichael DR, John DA, Coates N, et al., 2025,
The impact of three distinct probiotic supplements on the gut microbiota and its metabolites in healthy adults
, Beneficial Microbes, ISSN: 1876-2883The effects of probiotics on the gut microbiota and microbial metabolites in healthy individuals are not well understood. Faecal and serum samples were collected at the start and end of a 3-month, double-blind, placebo-controlled, randomised study with three different probiotic formulations in free-living healthy adults. The composition of the faecal microbiota and levels of faecal and/or serum short-chain fatty acids (SCFA) and bile acids (BA) were measured and the probiotic formulations were found to impart differing effects including shifts in the composition and structure of the faecal microbiota, enhanced levels of circulating short chain fatty acids such as butyrate and propionate and elevated levels of sulphated bile acids infaeces. This was in contrast to the outcomes with the placebo population where very little change occurred over the study. These findings demonstrate that probiotic supplementation elicits formulation specific effects and that there are potential benefits for healthy individuals.
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Journal articleOjiogu AD, Patkowski JB, Kuang X, et al., 2025,
Capsid redirection mechanism of the Staphylococcus aureus pathogenicity island SaPIpT1028
, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol: 380, ISSN: 0962-8436Staphylococcus aureus pathogenicity islands (SaPIs) are prototypical members of the phage-inducible chromosomal islands (PICI) family. These elements redirect helper phage capsid assembly to produce smaller capsids, accommodating the satellite genome while excluding the phage genome. This study identifies how SaPIpT1028 mediates capsid redirection through a unique gene, rcm (redirecting capsid morphogenesis). While rcm has no sequence similarity to known capsid assembly regulators, our results demonstrate that its expression is necessary and sufficient for redirecting capsid morphogenesis in S. aureus phages, such as φ7206. We show that, to do this, Rcm interacts with the φ7206 major capsid protein. Comparative evolutionary and structural analyses reveal functional parallels between Rcm and CpmB, a regulator used by other SaPIs. However, Rcm has evolved a multi-helical topology to match the multi-helical topology of the scaffold protein of φ7206. Sequence homology and AlphaFold predictions suggest that Rcm competitively interacts with the φ7206 scaffold protein, altering capsid size through a mechanism akin to CpmB. This work highlights SaPI adaptation, exemplified by Rcm's ability to exploit phages resistant to other remodellers, while inhibiting their reproduction. These findings underscore the dynamic co-evolution of phages and SaPIs, with Rcm playing a pivotal role in capsid size regulation and phage interference.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.
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Journal articleBermúdez-Puga S, Mendes B, Ramos-Galarza JP, et al., 2025,
Revolutionizing agroindustry: towards the industrial application of antimicrobial peptides against pathogens and pests
, Biotechnology Advances, Vol: 82, ISSN: 0734-9750Antibiotics are essential chemicals for medicine and agritech. However, all antibiotics are small molecules that pathogens evolve antimicrobial resistance (AMR). Alternatively, antimicrobial peptides (AMPs) offer potential to overcome or evade AMR. AMPs provide broad-spectrum activity, favourable biosafety profiles, and a rapid and efficient mechanism of action with low resistance incidence. These properties have driven innovative applications, positioning AMPs as promising contributors to advancements in various industrial sectors. This review evaluates the multifaceted nature of AMPs and their biotechnological applications in underexplored sectors. In the food industry, the application of AMPs helps to suppress the growth of microorganisms, thereby decreasing foodborne illnesses, minimizing food waste, and prolonging the shelf life of products. In animal husbandry and aquaculture, incorporating AMPs into the diet reduces the load of pathogenic microorganisms and enhances growth performance and survival rates. In agriculture, AMPs provide an alternative to decrease the use of chemical pesticides and antibiotics. We also review current methods for obtaining AMPs, including chemical synthesis, recombinant DNA technology, cell-free protein synthesis, and molecular farming, are also reviewed. Finally, we look to the peptide market to assess its status, progress, and transition from the discovery stage to benefits for society and high-quality products. Overall, our review exemplifies the other side of the coin of AMPs and how these molecules provide similar benefits to conventional antibiotics and pesticides in the agritech sector.
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Journal articleBeaghton PJ, Burt A, 2025,
Natural selection of synthetic gene drives for population suppression can favor an intermediate strength of drive
, The American Naturalist, Vol: 206, Pages: 206-217, ISSN: 0003-0147Synthetic gene drives are being investigated as tools to suppress pest populations, and it is important to understand how natural selection will act on variant drivers that may either arise by de novo mutation or are intentionally released. In this study we extend previous spatially implicit stochastic models to examine the evolutionary dynamics of synthetic driving Y chromosomes in patchy environments when population size is responding dynamically to the spread of the driver, and derive conditions for the existence of an evolutionarily stable strategy (ESS) for drive strength. Under broad conditions an intermediate drive strengthemerges as the ESS, capable of outcompeting both stronger and weaker variants. Additionally, we show how the intentional release of two drivers straddling the ESS can help stabilize population dynamics. Finally, inbreeding depression has the effect of expanding the range ofconditions under which no intermediate ESS exists, with ever stronger drive being selected until the population is eliminated. These results provide insights into the expected evolutionary trajectories of gene drive systems, with important implications for the design and release of gene drives for pest and vector control.
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Journal articleCalderon-Morales E, Werden LK, Smith-Martin CM, et al., 2025,
Physiological and Growth Responses of Tropical Dry Forest Tree Seedlings to Water and Nutrient Additions: Comparisons Between Nitrogen Fixers and Non-Fixers
, BIOTROPICA, Vol: 57, ISSN: 0006-3606 -
Journal articleAlkemade JA, Hawkins NJ, Baraldi E, et al., 2025,
Learning from fungicide resistance: Evolutionary insights to guide RNAi-based control of fungal crop pathogens
, FUNGAL BIOLOGY REVIEWS, Vol: 53, ISSN: 1749-4613- Cite
- Citations: 1
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Journal articleYordanova M, Zhang X, Torres CB, et al., 2025,
Friend or foe? Concentration of a commensal microbe induces distinct responses in developing honey bees exposed to field-realistic pesticide concentrations
, FEMS MICROBIOLOGY ECOLOGY, Vol: 101, ISSN: 0168-6496 -
Journal articleYuen ELH, Savage Z, Prazak V, et al., 2025,
Membrane contact sites between chloroplasts and the pathogen interface underpin plant focal immune responses
, PLANT CELL, Vol: 37, ISSN: 1040-4651- Cite
- Citations: 2
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Journal articleDaniel O, Heon SP, Donnelly CA, et al., 2025,
Rapid spread of African Swine Fever across Borneo
, Animals, Vol: 15, ISSN: 2076-2615African Swine Fever (ASF) reached the island of Borneo at the end of 2020. The first mortalities were recorded in wild bearded pigs (Sus barbatus) in Sabah, north-east Borneo. The virus then began to spread across the island but due to COVID-19 lockdowns the spread was difficult to monitor on the ground. With the urgent need to track this epidemic, and in the absence of traditional monitoring, the Babi Hutan Project was launched in April 2021 to gather data on pig sightings using citizen science. Any sightings of bearded pigs were requested via the website, social media and a WhatsApp hotline. Here we bring together the data from this project and other online sources to show how the virus spread across almost the entire island within a one-year period. The speed of spread appeared to increase with time following an exponential model: we estimate an average speed of spread of 0.89 km/day after 100 days since the first observation and at 4.28 km/day after 400 days. Our key recommendations are: that existing hunting bans on bearded pigs remain in place; that urgent biosecurity measures should be put in place if outbreaks occur in areas with backyard (domestic) pigs; that surviving pigs are tested for resistance; that the disease dynamics are modelled and that the International Union for Conservation of Nature (IUCN) urgently re-evaluates the bearded pig’s status.
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Journal articleOno M, 2025,
TockyLocus: quantitative analysis of flow cytometric fluorescent timer data in Nr4a3-Tocky and Foxp3-Tocky mice
, Biology Methods & Protocols, ISSN: 2396-8923Fluorescent Timer proteins undergo a time-dependent shift from blue to red fluorescence after translation, providing a temporal record of transcriptional activity in Timer reporter systems. While Timer proteins are well suited for studying dynamic cellular processes such as T cell activation using the Timer of-Cell-Kinetics-and-Activity (Tocky) framework, quantitative analysis of Timer-based flow cytometry data has yet to be fully standardised.In this study, we optimise quantitative analysis methods for the key parameter within the Tocky framework, Timer Angle, and introduce TockyLocus, an open-source R package that implements a five category scheme based on biologically grounded angular intervals (designated as Tocky Loci). This approach is validated using both simulated and experimental datasets and enables downstream statistical testing and visualisation of transcriptional dynamics in flow cytometry data.Using computational modelling of Timer protein kinetics, we define transcriptional dynamics in relation to key anchoring points in Timer Angle values at 0◦, 45◦, and 90◦. Comprehensive simulations with synthetic spike-in datasets further demonstrate the robustness of the five-locus approach, which capturesthe three key points and the intermediate regions between these points. Building on the TockyPrep pre processing framework, we systematically evaluated categorisation schemes ranging from three to sevenloci on real-world datasets from Nr4a3-Tocky and Foxp3-Tocky mice. The five-locus model emerged asoptimal, showing significant advantages in balancing biological interpretability and statistical robustness.Optimised algorithms implemented in the TockyLocus package now standardise quantitative analysisof Timer Angle data, enabling reproducible interpretation without reliance on arbitrary gating or complexassumptions. In summary, the five-locus categorisation of Timer Angle data effectively links underlyingbiological dynamics to the percentage of cells in each Tocky
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Journal articleBarker-Clarke RJ, Gray JM, Leither S, et al., 2025,
The balance between intrinsic and ecological fitness reveals hidden regimes in eco-evolutionary population dynamics.
, bioRxivUnderstanding how populations evolve requires accounting for both intrinsic fitness, defined by genotype and environment, and ecological interactions that emerge in mixed communities. While evolutionary experiments typically assess fitness in isolation, such monoculture measures may misrepresent dynamics in realistic, interacting populations. Here, we present a game-theoretic framework that explicitly separates intrinsic and ecological contributions to fitness, allowing us to map how ecological interactions can mask, mirror, maintain, or mimic selection driven by genetic differences. We derive analytical conditions for these regimes using deterministic replicator dynamics and validate them in stochastic Wright-Fisher models with mutation and drift. Applying our model to published microbial and cancer co-culture data, we show that real systems span both intrinsic-dominant and ecology-dominant regimes, with ecological effects sometimes reversing or neutralizing intrinsic fitness advantages. These results expose a critical blind spot in experimental design and interpretation, emphasizing the need to account for ecological interactions when inferring evolutionary dynamics and designing therapeutic strategies.
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Journal articleAlzate A, Rozzi R, Velasco JA, et al., 2025,
Evolutionary age correlates with range size across plants and animals
, NATURE COMMUNICATIONS, Vol: 16 -
Journal articleYoun T, Ehsan M, Hariharan P, et al., 2025,
Tailoring butane-1,2,3,4-tetraol-based maltosides (BTMs) via group-swapping and detergent unsymmetry: new detergent design strategies for membrane protein studies
, Journal of Materials Chemistry B, Vol: 13, Pages: 12569-12578, ISSN: 2050-750XMembrane proteins are essential bio-macromolecules involved in numerous critical biological processes and serve as therapeutic targets for a wide range of modern pharmaceuticals. Small amphipathic molecules, called detergents or surfactants, are widely used for the isolation and structural characterization of these proteins. A key requirement for such studies is their ability to maintain membrane protein stability in aqueous solution, a task where conventional detergents often fall short. While many new detergents have been developed based on novel molecular scaffolds, comparatively little effort has been made to enhance detergent performance through rational modification of existing structures, largely due to the limited availability of guiding design principles and strategies. In this study, we refined previously developed butane-1,2,3,4-tetraol based maltosides (BTMs), using two structural modification strategies, head/tail group-swapping and the introduction of hydrophobic unsymmetry. The resulting group-swapped (GS)-BTMs exhibited distinctive physical properties compared to the original BTM, including differences in water-solubility (∼7 to >10 wt%), critical aggregation concentration (5 to 15 μM), and self-assembly size (7.6 to 34.2 nm). When evaluated using model membrane proteins, including the human adrenergic receptor (β2AR), symmetric GS-BTMs (e.g., GS-BTM-C11 and GS-BTM-C12) showed superior performance relative to the original BTM-C11 and benchmark detergents (DDM and LMNG). The unsymmetric variants, such as GS-BTM-C14,10 and GS-BTM-C15,9, further improved protein stability. These findings highlight group-swapping and hydrophobic unsymmetry as effective strategies for enhancing detergent performance. This work demonstrates how minimal structural modifications can impact detergent properties and efficacy, providing valuable insights for the development of improved detergents from existing molecular frameworks.
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Journal articleHazime KS, Sheppard S, Niembro-Vivanco O, et al., 2025,
Nanoscale re-structuring of the immune synapse with an engager enhances NK cell function
, Proceedings of the National Academy of Sciences of USA, ISSN: 0027-8424 -
Journal articleCambron TW, Fisher JB, Hungate B, et al., 2025,
Plant nutrient acquisition under elevated CO2 and implications for the land carbon sink
, Nature Climate Change, ISSN: 1758-678XTerrestrial ecosystems currently sequester around a third of anthropogenic carbon emitted each year, slowing the pace of climate change. However, the future of this sink under rising atmospheric CO2 concentrations remains uncertain, in part due to the impact that nutrient limitation may have on plant biomass. Here, we review plant nutrient acquisition strategies and evidence of the enhanced utilization of these strategies under experimental and real-world elevated CO2 (eCO2). Many of the strategies that are key to nutrient limitation alleviation under eCO2 are not yet well represented in Earth System Models (ESMs). A simple, data-driven analysis implies that ESMs without nutrient acquisition strategies could underestimate the land sink.
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Journal articleClaramunt S, Sheard C, Brown JW, et al., 2025,
A new time tree of birds reveals the interplay between dispersal, geographic range size, and diversification
, Current Biology, Vol: 35, Pages: 3883-3895.e4, ISSN: 0960-9822The spatial and temporal dynamics of biodiversity are shaped by complex interactions among species characteristics and geographic processes. A key example is the effect of dispersal on geographical range expansion and gene flow, both of which may determine speciation rates. In this study, we constructed a time-calibrated phylogeny of over 9,000 bird species and leveraged extensive data on avian traits and spatial occurrence to explore the connections between dispersal, biogeography, and speciation. Phylogenetic path analyses and trait-dependent diversification models reveal that geographic range size is strongly associated with the hand-wing index, a proxy for wing aspect ratio related to flight efficiency and dispersal ability. By contrast, we found mixed evidence for the effect of dispersal on diversification rates: dispersive lineages show either slightly higher speciation rates or higher extinction rates. Our results therefore suggest that high dispersal ability increases range expansion and turnover, perhaps because dispersive lineages expand into islands or other geographically restricted environments and have lower population sizes. Our results highlight the nuanced and interconnected roles of dispersal and range size in shaping global patterns of avian diversification and biogeography and provide a richly sampled phylogenetic template for exploring a wide array of research questions in macroecology and macroevolution.
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Journal articleVarga T, Woods R, Pitsillides F, et al., 2025,
Whole genome sequencing of historical specimens from the world's largest fungal collection yields high-quality assemblies
, NEW PHYTOLOGIST, ISSN: 0028-646X -
Journal articleDonini R, Blundell P, Pleass RJ, et al., 2025,
Genetic Divergence and Antibody Expression Influence the N-Glycomes of CHO-K1 and CHO-S Cells
, BIOTECHNOLOGY AND BIOENGINEERING, ISSN: 0006-3592 -
Journal articleVerma A, Khadke L, Budakoti S, 2025,
Understanding the dynamics of 2024 extreme heat event in India: spatial variability, hydrometeorological impacts, and model evaluation
, Atmospheric Research, Vol: 322, ISSN: 0169-8095Heatwaves are becoming more intense, frequent, and prolonged due to global warming, posing significant risks to ecosystems and human societies. Despite their profound impact, detailed regional assessments of extreme heat events remain limited, particularly in India. This study addresses the gap by systematically investigating the 2024 extreme heat event in India. We evaluated the performance of various land surface schemes in simulating heat extremes using the Weather Research and Forecasting model and also assessed the accuracy of Global Forecast System (GFS) forecasts. Our analysis reveals a strong co-occurrence of drought and heat stress during the extreme heat event. This combination results in increased fire risk and negative impacts on vegetation productivity in regions affected by both drought and heat stress highlighting the severe consequences of this compound event. We compare different land surface models (RUC, Noah, Noah-MP, Noah-MP with dynamic vegetation, CLM) against India Meteorological Department (IMD) observations. We observe that Noah is optimal for reducing bias and RMSE, while Noah-MP with dynamic vegetation is most accurate for simulating extreme heat, with the highest hit rate and threat score for the 90th percentile threshold. Additionally, GFS maximum temperature forecasts for 1–3 day lead times perform well at short lead times, especially in Southern India but overestimate temperatures in heatwave-prone regions like the Indo-Gangetic Plains. Our findings highlight the importance of enhancing land surface models and forecasting systems to better predict extreme heat events, which is crucial for localized hazard and risk assessments and improving disaster management efficiency.
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Journal articleMadsen CD, Barbensi A, Zhang SY, et al., 2025,
The topological properties of the protein universe
, NATURE COMMUNICATIONS, Vol: 16 -
Journal articleMadge Pimentel I, Albini D, Beermann AJ, et al., 2025,
Hypothesis-Driven Research on Multiple Stressors: An Analytical Framework for Stressor Interactions
, ECOLOGY AND EVOLUTION, Vol: 15, ISSN: 2045-7758 -
Journal articleKontopoulos D-G, Patmanidis I, Barraclough TG, et al., 2025,
Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases
, EVOLUTION LETTERS -
Journal articleTobias JA, Bullock JM, Dicks LV, et al., 2025,
Biodiversity conservation requires integration of species-centric and process-based strategies
, Proceedings of the National Academy of Sciences, Vol: 122, ISSN: 0027-8424Conservation science and policy are geared primarily toward the preservation of species and habitats, with priority often given to the rarest, most vulnerable or most charismatic forms. This pattern-based approach has broad appeal and offers a pragmatic short-cut for targeting conservation action. However, the long-term efficacy of species and landscape conservation programs remains highly uncertain, amid growing evidence that sustainable conservation action requires an increased emphasis on preserving ecological and evolutionary processes. This reframing of conservation goals was first proposed 50 y ago, but the concept has struggled to gain traction, particularly in terms of translation into policy. Nonetheless, recent events have shifted the narrative, with multiple interlinked global challenges—including biological invasions, food security, disease, and climate change—putting ecological processes firmly back on the agenda. Concurrently, conservation finance is changing rapidly, driven in part by the 2022 Kunming-Montreal Global Biodiversity Framework, which prioritized actions to enhance and restore ecosystem stability, connectivity, and resilience. These ecosystem properties are fundamentally process-driven and appear to create an operational gulf between current conservation practice and the targets of international agreements. We describe how new approaches can be used to close this gap by redirecting conservation attention toward processes at the heart of ecosystem function, including adaptation, gene flow, dispersal, and trophic interactions. Wider adoption of these approaches is urgently needed to forge a deeper connection between conservation practice and policy targets, thereby ensuring that ongoing investment in biodiversity conservation goes beyond damage limitation and instead leaves a lasting legacy of resilient ecosystems.
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