Clade size distributions under the coalescent diversification model.

Identify detailed dynamic processes and driving forces of forest fragmentation based on explainable AI: Taking a global biodiversity priority area as a case

Bats are important reservoir hosts for zoonotic viruses owing to their unusual ability to avoid development of clinical disease and pathological lesions upon viral infection. Research efforts to understand the unique responses of bats to viral infection have been limited by the vast number of bat species and the lack of accessible experimental model systems. Over the past 5years, organoid models, which are long-term cultures of primary cells, have been developed from gastrointestinal, respiratory and kidney tissues of multiple fruit-eating and insectivorous bats. Compared with human organoids, bat organoids showed increased expression of type I and type III interferon genes, other antiviral genes and complement genes at baseline and in response to viral stimulation. Bat organoids generally showed strong upregulation of interferon genes and interferon-stimulated genes in response to viruses. Conversely, the ability of bat organoids to support viral replication was dependent on the virus, tissue type and bat species. Overall, the recent progress in the field demonstrates the potential of organoids to serve as relevant models for exploring species- and tissue-specific responses to viruses in bats.

Filling data gaps in soil environmental risk assessment (ERA): Species sensitivity distribution (SSD) and regulatory challenges for in-soil invertebrates exposed to chlorothalonil and chlorpyrifos.

Fleas represent a neglected group of ectoparasites of significant public health importance, due to their active role in transmitting various infectious agents associated with emerging and re-emerging diseases. In Mexico, flea borne-rickettsioses represent a growing public health concern, driven by the widespread presence of arthropod vectors and a vulnerable population, compounded by limited knowledge of pathogen-vector-host interactions. This study aimed to identify flea species parasitising dogs and cats in the state of Nuevo Leon, Mexico and to detect and characterise Rickettsia species present through molecular sequencing. Flea samples were collected from dogs and cats in veterinary clinics and private residences during the period of October-May 2022-2023, across nine municipalities in the state of Nuevo Leon. Samples were identified morphologically and the gltA gene for Rickettsia was amplified and sequenced. Three flea species were identified from dogs and cats: Ctenocephalides felis felis (Bouché, 1835), Pulex simulans (Baker, 1895) and Echidnophaga gallinacea (Westwood, 1875). Rickettsia DNA was detected in 29.47% of the total flea pools through amplification of the citrate synthase (gltA) gene. Sequence analysis revealed the presence of Candidatus Rickettsia senegalensis in C. felis felis collected from dogs in Nuevo León, representing the first record in Mexico. Simultaneously, an unexpected finding of Rickettsia rickettsii, the causative agent of Rocky Mountain spotted fever (RMSF), was also identified in the same flea species, marking the first report of this pathogen in fleas worldwide. Our findings provide for the first time in Mexico, the molecular detection of Ca. R. senegalensis in Ct. felis felis, increases the number of Rickettsia species recorded in the country to 19. Additionally, R. rickettsii DNA was detected in Ct. felis felis. These findings highlight the need for further studies on clarify the epidemiological relevance of fleas-associated Rickettsia and to better understand their role within rickettsial systems.

In clinical settings, the intensive use of antibiotics, particularly in intensive care settings, leads to a significant increase in the number of bacterial species that are resistant to treatments. In this context, biofilm is a crucial virulence factor that enable bacteria to persist within the host, often resulting in the need for extensive antibiotic treatment. Staphylococcus epidermidis, a notable nosocomial pathogen, poses a risk to vulnerable patients due to its ability to form biofilms on indwelling medical devices and its high resistance to antibiotic therapy. For this purpose, investigating alternative strategies that target the virulence of pathogens could offer a promising alternative strategy. In this study, we analyzed innovative polymeric materials, such as polysaccharide-based nanohydrogels, for their potential application contrasting S. epidermidis monospecies biofilm on the surfaces of materials most employed in medical devices. These nanohydrogels were found to be effective in eradicating the biofilm matrix and preventing bacterial adhesion. Additionally, the treatment with hyaluronan-based nanohydrogels altered the surface protein profile of S. epidermidis, leading to the disappearance of AtlE, the primary autolysin involved in biofilm formation, suggesting a potential mechanism of action for these nanogels. Data are available via ProteomeXchange with identifier PXD074516.

As the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to accurately understand the current state of natural habitats and their constituent species. We assess the feasibility of a single assay: long-read shotgun metagenomic sequencing of environmental DNA (eDNA), to monitor species from across the tree of life, from viruses to complex multicellular organisms, across a representative Irish river system (Avoca River, Co. Wicklow). We conducted aquatic eDNA sampling and long-read shotgun metagenomic sequencing from a mountain tributary through to the sea. This approach could detect and quantify organismal DNA present in environmental samples, from microbes (including DNA viruses) to mammals. Rather than the traditional siloing of microbial and multicellular studies of DNA recovered from environmental samples, simultaneously considering viruses, microbes, and eukaryotes (animals, plants, and fungi) can provide deeper insights. This single assay can simultaneously quantify differences in DNA abundance for a broad range of species and pathogens across sites and sample types, enabling wide-ranging biodiversity assessments. This included human, wildlife, plant, and microbial pathogens and parasites with health, agricultural, and economic importance. The environmental genomic data enabled animal phylogeny and transmissible cancer analysis (blue mussel, Mytilus edulis) even from natural complex community settings. Oxford Nanopore sequencing provides a quantitative approach for river biodiversity, pollution, and environmental health monitoring. Long-read shotgun metagenomic sequencing of environmental samples offers the means to assess whole ecosystems and the ecological, trophic, and host-pathogen interactions occurring within them.

Reef fish assemblages are dynamic and heterogeneous across both temporal and spatial scales. Understanding these patterns is essential for effective management strategies that aim to protect marine communities. We investigated whether previously described cross and longshore patterns in reef fish assemblages persisted after a decade of high ocean temperature variability driven by the El Niño-Southern oscillation and a significant marine heatwave in 2011. Two nearshore marine parks near Perth, Western Australia, located 70 km apart, were sampled in 2012 and 2023 using Baited Remote Underwater stereo-Video systems. At each location, distinct inshore, midshore, and offshore reef lines were targeted across a depth gradient of 3-23 m. Inshore-to-offshore assemblage patterns described in 2012 remained temporally consistent in 2023, with each reef line representing distinct compositions at both locations. The mean relative number of species, the mean relative abundance of fish per deployment, and the mean relative abundances of most individual feeding guilds, were also similar between years. Although assemblage and feeding guild compositions differed at a few locations between years, these changes were likely driven by the localised variation in the distribution of some focal species across reef lines. Planktivores were the only feeding guild to significantly increase in abundance over time. As cumulative anthropogenic and climate pressures increase, it is likely assemblage modification will occur more often. To protect the full range of fish assemblages, it would be appropriate for future spatial management to include fully protected sanctuary zones across inshore, midshore, and offshore reef lines at both locations. • Cross-shore assemblage patterns of increasing species richness and fish abundance was consistent in 2012 and 2023 • Reef fish assemblage compositions had minor differences between 2012 and 2023 • Planktivores were the only feeding guild to increase in abundance • For future management, including no-take sanctuary zones across all three reef lines would be most appropriate

High-fidelity combustion simulations require detailed chemical kinetics to accurately capture reactive flow behaviour, but their computational cost remains prohibitive due to the large number of species and stiff chemistry. To address this challenge, this study introduces a novel integration of Principal Component Analysis (PCA) with the Cell Agglomeration (CA) framework through a Dynamic Multi-Zone (DMZ) clustering algorithm. Previous work by Stock et al. (2024) used PCA to construct a compact thermochemical space, relying on a prescribed clustering grid, which however fixes cluster boundaries a priori and limits adaptability to evolving flow conditions. In contrast, the present work removes this reliance on static, pre-defined grids by embedding PCA directly inside the dynamic agglomeration loop, allowing cluster boundaries to emerge and evolve naturally from the instantaneous thermochemical state. The proposed PCA-DMZ framework identifies thermochemical similarities in a reduced-dimensional principal component space and dynamically constructs clusters that minimise chemistry evaluations while preserving predictive fidelity. The methodology is evaluated for two benchmark configurations of the Adelaide Jet in Hot Coflow (AJHC) burner: (i) unsteady Reynolds-Averaged Navier–Stokes (uRANS) simulations of an n -heptane flame with a reduced mechanism (106 species, 1738 reactions), and (ii) Large Eddy Simulations (LES) of a methane-hydrogen flame using GRI3.0 chemistry. Compared with the standard CA approach, the PCA-DMZ formulation yields more compact and effective cluster structures, achieving approximately 20%–30% fewer ODE system integrations at similar accuracy levels, leading to higher overall speed-up primarily due to improved clustering efficiency. It also significantly reduces the need for manual tuning of the CA tolerances, with a ∼ 10% cluster-to-cell ratio repeatedly emerging as the optimal operating point across both uRANS and LES cases. The proposed PCA-DMZ coupling achieves an overall computational speed-up of approximately 7 × and a chemical integration speed-up of about 10 × , while maintaining high accuracy in temperature and major species predictions. • Fully adaptive and largely case-independent clustering achieved via PCA-based CA-DMZ. • Accuracy preserved while solving 20%–30% fewer ODEs through PC-driven clustering. • PC-based clustering yields higher speed-up than standard clustering at similar fidelity. • Robust, self-adjusting clustering delivered by PCA-DMZ with minimal case dependence.

Like many oceanic regions in the world, the Southwestern Indian Ocean (SWIO) is facing challenges to sustain economic growth, livelihoods and food security, while preserving essential habitats to safeguarding the marine ecosystems. Reaching the Global Biodiversity Framework targets and implementing the Blue Economy roadmaps developed in the SWIO region require reliable data and science-based strategies to manage the marine space as well as knowledge-based governance schemes at both national and regional levels. Monaco Explorations, as a platform committed to foster knowledge, sustainable management and protection of the ocean, organised a multidisciplinary expedition in 2022, in partnership with Mauritius and Seychelles, to advance the state of knowledge of unique sites in the SWIO and contribute to setting harmonised ocean governance in the region. This paper sets the general framework of the Monaco Explorations-Indian Ocean (ME-IO) Expedition and its grand objectives. It provides an outline of the projects developed during the expedition and summarizes the main results for an integrated understanding of the biophysical processes and ecological features in the Mascarene Basin, its underwater plateaus and the waters surrounding the islands.

Bridging the gaps from core to core: Modeling shared ecological networks for waterbirds across the urban-nature reserve interface

Tracking important site safeguard through different approaches to measuring the indicator of protected area coverage of Key Biodiversity Areas

Late Quaternary loess-paleosol sequences in the Armenian highlands represent key terrestrial archives for reconstructing past climate variability. Related proxy data are essential both for understanding the environmental and cultural history of the Caucasus area - a global biodiversity hotspot and archaeological key region - and for benchmarking Earth system models. However, robust quantitative paleoclimate records remain scarce for this climatically and topographically complex area. Here, we present a combined approach integrating (1) stable isotope analysis (δ 18 O, δ 13 C) of land snail shells with transfer functions build on modern calibration datasets and (2) probabilistic climatic niche modeling. For the latter, assemblage-weighted climatic optima are derived from species-specific response curves based on modern species distribution data. Our results reveal predominantly xerophilous faunas associated with colder glacial phases, and mesophilous high-grass to forest-steppe assemblages during interstadial and interglacial intervals. δ 18 O shell was used to reconstruct δ 18 O precipitation signals, which in this study area strongly correlate with temperature. Growing season temperature estimates, based on modern empirical relationships, suggest a mean difference of ∼4.9 °C between glacial minima and interglacial maxima, while precipitation reconstructions from climatic niche modeling suggest a shift from ∼511 mm to ∼770 mm. This study provides the first mollusk-based quantitative reconstructions of Late Quaternary temperature and precipitation in the Caucasus area, demonstrating the potential of integrated mollusk proxies as powerful tools for resolving glacial-interglacial climate dynamics. • Land snail shell isotopes and climatic niche modeling provides new insights into Late Quaternary climatic conditions. • First mollusk-based quantitative reconstructions of temperature and precipitation for the Southern Caucasus. • Palaeoclimate reconstructions indicate glacial-interglacial growing season temperature contrasts of up to ∼5 °C. • PDF-based climatic niche modeling indicates a shift from ∼511 mm during glacial minima to ∼770 mm during interglacial maxima.

An expert-curated dataset of glass sponges (Porifera, Hexactinellida) distribution across the Atlantic and Arctic Oceans.

Host ecology shapes chigger mite parasitism on wild, captive, and domestic birds across Malaysia and Thailand

Anthropogenic climate change poses a substantial threat to global biodiversity, expediting the rate of decline and elevating the risk of extinction for species across the world. Understanding the climate vulnerability and genomic diversity across landscapes undergoing rapid climate change, is therefore crucial for preserving biodiversity and informing conservation interventions. In this study, we attempted to characterize the patterns of genetic variation, and evaluate the range dynamics and genomic offset to anticipated climate change for Tetraena mongolica , an endangered species endemic to China based on 1,113 genomic-wide single nucleotide polymorphisms (SNPs) derived from reduced-representation genome sequencing in 48 individuals. We further dissected the key environmental variables associated with genetic variation and predicted its range dynamics and genomic offset to future climate scenarios. Our results indicated that this species showed limited genetic divergence and weak population structure. Temperature- and solar radiation-related variables were pivotal in shaping the genomic variation of T. mongolica across its range. Moreover, the species' current range is likely to be at high risk of maladaptation to forthcoming climate changes. Our findings have implications for understanding the evolutionary trajectories of endangered species with limited ranges, and the strong signals of genomic offset presented to projected climate change could guide proactive managements and conservative decision-makings for this endangered species.

ConspectusHypervalent halogens (I(III) and Br(III) derivatives) represent a versatile and effective class of reagents that are widely used in synthetic organic chemistry. Many of these compounds, however, are unstable and pose risks during handling, which limits their practical application, especially on a larger scale. In this context, the electrochemical in situ generation of hypervalent halogen species represents an interesting alternative to conventional methods. Inspired by these ideas, we launched a collaborative "trans-Baltic" research program 10 years ago that is still ongoing. Our efforts focus on developing electrochemical methods for synthesis of these reactive species, their synthetic application and mechanistic elucidation. After initial studies on the electrochemical generation of dialkoxy-λ3-iodanes, our activities have expanded to include analogous hypervalent bromine compounds as well as diaryliodonium and bromonium salts. Our work has resulted in a large number of new species, most of which exhibit interesting, useful, and versatile reactivity. Their synthesis, electrochemical properties, and reactivity are the focus of this article.Our review starts with the discussion of fluorinated dialkoxy-λ3-iodanes, which are readily formed via anodic oxidation of iodoarenes in fluorinated alcohols such as HFIP or TFE, the latter acting both as solvent and stabilizing ligands. To date, no nonelectrochemical access to such species has been reported, likely due to their sensitivity toward nucleophiles. Although the λ3-iodanes derived from iodoarene conversion in HFIP cannot be isolated, they are effective in various oxidative coupling reactions when generated in situ. Incorporating ionic tags enables dual functionality as mediator and supporting electrolyte and allows facile recovery after electrolysis. In contrast, analogous dialkoxy-λ3-bromanes could not be synthesized electrochemically. However, singly and doubly chelation-stabilized bromanes can be prepared by anodic oxidation in HFIP. The doubly chelated species is significantly more stable and isolable. The less stable singly chelated form can be converted into a stable [Br-O-Br] dimer, which is suitable both as a precursor for other hypervalent bromine compounds and as a reagent for synthetic applications. The intrinsic Br(III) reactivity of the doubly chelated bromane is moderate but can be activated either thermally or with TfOH, enabling both ionic and single-electron transfer (SET) reactions. In contrast, the [Br-O-Br] dimer undergoes homolytic cleavage upon heating or near-UV irradiation, enabling radical coupling.When using noncoordinating solvents such as acetonitrile, anodic oxidation of iodoarenes yields iodonium salts. An acid-free, anion-flexible method was developed, allowing counterion variation via the supporting electrolyte and enabling aryl transfer reactions. Compared to the iodonium species, the bromonium analogues are much more difficult to access and are limited to cyclic species formed from 2,2'-dibromobiphenyls. Together with other newly identified hypervalent species, these compounds offer promising starting points for future research.

While colorectal cancer (CRC) has been linked to the gut microbiome, it remains unclear whether specific microbial signatures are detectable in precursor lesions such as adenomatous polyps, serrated lesions or sessile serrated lesions. To assess gut microbiome taxonomic and functional associations with colorectal neoplasia presence, severity (non-advanced, advanced and CRC) and subtype and evaluate predictive potential in high-risk neoplasia. Analysed cross-sectional stool metagenomes (pre-colonoscopy) from 1762 participants (97% White British) undergoing colonoscopy in the multicentre COLO-COHORT study. Neoplasia was classified per British Society of Gastroenterology surveillance guidelines. Linear mixed-effects models and random forest classifiers assessed taxonomic and functional associations, adjusting for dietary, clinical and lifestyle covariates. Gut microbiome composition differences between individuals with and without neoplasia were statistically significant but minimal (R2=0.0008, p=0.03). A small number of species, including Mediterraneibacter faecis and Pseudoruminococcus massiliensis, and microbial pathways, including amino acid biosynthesis and β-lactam resistance, were modestly linked to neoplasia, particularly early lesions (q value <0.05). Associations were generally weak and attenuated after covariate adjustment. Predictive models combining the microbiome with clinical/demographic features modestly improved high-risk neoplasia classification (area under the curve=0.64 vs 0.58 for clinical/demographic features alone). This large prospective cross-sectional study found weak and inconsistent associations between the gut microbiome and premalignant colorectal neoplasia, with no robust microbial signatures. Findings suggest that previously reported microbial shifts may emerge later in disease progression, potentially as a consequence rather than a cause of CRC. Longitudinal, multiomic studies disentangling temporal and causal pathways between the gut microbiome and neoplasia are required.

Biodiversity loss is accelerating at an unprecedented rate, threatening ecosystem function, animal health, and public well-being. As advocates for animal and environmental health, veterinary professionals play a critical role in addressing this crisis, yet biodiversity remains largely absent from core veterinary curricula. Aligned with the action-oriented goals of the Kunming-Montreal Global Biodiversity Framework, this paper proposes a veterinary-specific framework for developing biodiversity education in veterinary training. Developed with input from subject matter experts in veterinary and ecological sciences, the framework includes three primary actions: Prevent, Protect, and Restore, using Stewardship as the mechanism of action. This framework adapts Global Biodiversity Framework targets to veterinary-relevant content and competencies, and provides examples to illustrate relevance. By recognizing biodiversity as a health issue, veterinary educators can help students understand its relevance to clinical practice, public health, and policy. Ultimately, this training could enable students to incorporate actions to sustain and restore biodiversity into their own professional practices, as well as enhance veterinary contributions to addressing this global crisis.

Some women have persistent incontinence or pain after tension-free vaginal tape (TVT) surgery. Our objective was to study any association between culture-detected bacteriuria and incontinence, complications and satisfaction 10-20 years after TVT. Cross-sectional study in 2022 of 127 women operated with TVT between 2001-2012 at Trondheim University Hospital, Norway. Validated questionnaires assessed stress urinary incontinence (SUI), urgency urinary incontinence (UUI), pelvic pain and satisfaction. Urine collected by sterile catheterization was cultivated for two (chromogenic and blood agar) and five days (blood, fastidious and chocolate agar). Symptoms and demographics were compared between women with and without significant bacterial growth, defined as ≥ 1.000 CFU/ml for this study, using chi-square test, Fishers exact test, t-test and logistic regression. Number of species detected after five days culture was tested in association to demographics and symptoms using Mann Whitney-U-test. 50/111 women (45.0%) had SUI, 54/122 (44.3%) had UUI, 95/116 (81.9%) were satisfied and 7/123 (5.7%) stated persistent pain. 16 (12.4%) had significant bacterial growth after two days of whom seven (44%) had a positive dipstick screening test (leukocytes or nitrite). After five days culture, 28 (22%) had significant bacterial growth. We found non-significantly higher odds for SUI (aOR 4.2, 95% CI 0.5-36.1) and UUI (aOR 2.1, 95% CI 0.3-13.7) in women with bacterial growth after two days. Bacterial growth after five days was associated with non-significantly increased risk of SUI (aOR 2.3, 95% CI 0.6-8.9) and UUI (aOR 3.4, 95% CI 0.9-13.6). Age was significantly associated with bacterial growth after two (aOR 1.2, 95% CI 1.02-1.3) and five days (aOR 1.1, 95% CI 1.04-1.2). The number of bacterial species after five days culture was higher in women with UUI, BMI > 75 percentile, in those dissatisfied or with persistent pain, than in women without these conditions (p < 0.01). Significant bacteriuria and larger variety of bacterial species were associated with incontinence, pain and dissatisfaction 10-20 years after TVT. The dipstick screening test had a sensitivity of only 44%. Extended urinary culture may be of value in optimizing treatment of urinary tract symptoms after TVT. ClinicalTrials.gov (NCT04912830).