PeerJ

Abstract 1. Biomes are continental-scale vegetation units widely used in ecological and evolutionary research, often together with large-scale species-distribution data. Many conceptually distinct biome schemes exist, differing in the underlying definition, delineation methodology and spatial resolution, yet most studies using biomes default to a few readily available schemes rather than choosing the one best suited to the research question. 2. We present biomes, an R package distributing spatially explicit raster layers of 31 published global biome schemes in a harmonised format at a 10 x 10 km resolution, together with metadata and a concise description. To facilitate their use, biomes provides a user-friendly classification workflow to classify occurrence records into specific biomes and a data-driven ranking algorithm to help researchers to choose the most suitable biome scheme for their data and research question in a transparent, reproducible way. 3. The biomes workflow can be applied to any dataset of georeferenced terrestrial occurrences. It (1) accepts either user-provided occurrence records or records downloaded by the package, (2) ranks the schemes according to their fit to the occurrence data, (3) assigns the records to specific biomes, and (4) summarises the resulting taxon-biome patterns. We demonstrate this workflow using 17,030 occurrence records of 185 species of Bombacoideae (Malvaceae). The analysis identified the vegetation-based biome scheme of Ramankutty and Foley (1999) as the best fit and recovered the forest and savanna biome signal known in the group from the literature, with tropical evergreen woodland being the biome with the largest share of records (46.1%) and highest number of species (162 of 185 species; 87.6%). 4. biomes provides user-friendly access to technically standardised and spatially explicit layers of 31 biome schemes, and thereby enables the transparent, data-driven choice of biome schemes tailored to a specific research data and questions, improving the reproducibility and the specificity of biome use across ecological and evolutionary research.

Rubber vines (Cryptostegia madagascariensis and C. grandiflora) are highly invasive weeds in the semi-arid landscapes of many tropical regions. The rust fungus Maravalia cryptostegiae has provided a spetatular and sustainable control of invasive C. grandiflora populations in Australia, after its scientific and quarantine-authorized release in the context of a classical biological control program. The Caatinga biome of Northeastern Brazil is under a devastating invasion by C. madagascariensis. This species is also susceptible to M. cryptostegia but its epidemic potential towards C. madagascariensis in Brazil remains unknown. We developed a weather-driven epidemiological model integrating experimentally derived relationships for infection as a function of temperature and wetness duration and for temperature-dependent latent development. Three infection-response models were fitted to 20 experimental temperature x wetness combinations from the literature and compared using information criteria, grouped cross-validation and a parametric bootstrap. The selected model, in which thermal breadth increases with wetness duration, was best supported (R2 = 0.931; {Delta}AICc [≥] 3.3 relative to the alternatives), and prolonged wetness significantly broadened the thermal range favorable for infection ({gamma} = 0.30 oC h-1; bootstrap P = 0.002). The infection and latent-development models were coupled with 25 years (2001-2025) of hourly NASA POWER data for 65 grid cells representing rubber-vine-infested locations in Northeastern Brazil, with wetness defined as hours with relative humidity equal or greater than 90%. Infection potential was concentrated in March-June (73% of the annual total, peaking in April), coinciding with the regional rainy season, and was highest in the interior of northern and central Ceara. Predicted potential varied more than a hundredfold among grid cells and was lowest along parts of the Ceara coast and the lower Jaguaribe valley, which include some of the largest infestations; the magnitude of these contrasts depended on the humidity threshold used to define wetness. Applied with identical rules to 13 historical release sites in Queensland, Australia, the model reproduced the documented wet-season timing of rust activity, and predicted potential was on average higher at sites with reported high rust impact, although the difference was not statistically significant. These results indicate strong seasonal and geographic structuring of weather-driven epidemic potential and provide testable hypotheses for selecting release periods and locations for M. cryptostegiae in Brazil.

Translocations are commonly used to reduce the risk of extinction of threatened species, and often to reintroduce animals to their former habitats. If extirpation occurred a long time ago, individuals may be placed into novel environments outside of conditions they have previously experienced, which can affect translocation success. To measure success of translocations, particularly those to novel habitats, it is important to monitor post-release spatial behaviour. In 2023, ten critically endangered k[a]k[a]p[o] (Strigops habroptilus) were released to form a new population at the fenced mainland island of Sanctuary Mountain Maungatautari (hereafter Maungatautari) in the North Island of New Zealand, an area from which they were extirpated approximately a century earlier. The spatial behaviour and habitat selection of these k[a]k[a]p[o] was analysed using dynamic space use and step selection functions with temporally dynamic responses applied to GPS logger data recorded over a seven month period. These showed three unexpected results: k[a]k[a]p[o] were highly mobile and used larger areas compared to other sites; there was synchronicity of movement, with most individuals simultaneously moving toward the perimeter fence in spring; and when near the fence k[a]k[a]p[o] selected for areas of pasture and exotic vegetation more than anticipated. While direct comparisons are difficult due to varying data availability, this unexpected spatial behaviour and habitat selection suggests that k[a]k[a]p[o] behavioural responses were different at Maungatautari compared to other sites. This may indicate that k[a]k[a]p[o] released at Maungatautari had a longer exploratory stage than elsewhere; that there were behavioural effects influenced by conspecific density or the availability of novel and exotic vegetation; or that there were specific breeding habitat requirements not met at the site during the study period. These results highlight the importance of high-resolution spatial monitoring to evaluate the success of translocations, particularly those to novel environments.

Ecdysozoans is one of the most abundant and diverse groups of metazoans and grow through moulting the rigid exoskeleton that provided protection. But the moulting process is often dangerous, resulting in malformations or death. Injuries have been well documented in the calcitic exoskeleton of trilobites, some of which have been attributed to moulting complications when long spines are deformed. Injuries in trilobites are often found in the trunk rather than the cephalon, and abnormal genal spines are rarely documented. Here we examine injuries in eleven specimens of Olenoides serratus from the Burgess Shale (Cambrian, Wuluian) and demonstrate an increased frequency of genal spine malformations compared to other trilobites. The unusual pattern of malformations may be attributed to moulting injuries of the long and delicate genal spines in O. serratus. To moult, trilobites curved ventrally to press the anterior margin of their cephalon into the substrate and open the facial sutures. This process exerted force on the librigenae. To exit the exuvia, the genal spines were forced to bend as the old librigenae dipped ventrally along the anterior edge, resulting in the injured genal spines in O. serratus. A similar process of moulting resulting in injuries may be seen in other early Euarthropods.

Motivation: High-throughput sequencing technologies have driven rapid growth of biological sequence databases. Public repositories must therefore rely on automated computational heuristics to screen submitted sequences for errors and low quality. For example, SILVA SSU Ref, which exploits the conserved nature of 16S and 18S rRNA sequences, applies strict algorithmic quality controls yet still accepts sequences with up to 30% of their nucleotides deviating from any previously accepted sequence. This permissiveness creates opportunities for the admission of modified sequences, such as biologically plausible sequences generated by DNA foundation models. The vulnerability of public sequence databases to becoming polluted or poisoned with modified sequences necessitates the development of methods to detect such sequences. Results: We present the first investigation, to our knowledge, of the detectability of modified sequences. We consider simple computationally-modified 16S rRNA sequences that pass the quality control inclusion criteria of the SILVA database, which we generate via random substitutions. We present classifiers that can distinguish such modified sequences from natural 16S rRNA using conserved motifs. Our best classifier achieves over 90% sensitivity and specificity on our testing set when using a 5% artificial mutation rate. One feature used in our classifiers, gapped k-mers constructed from universally conserved nucleotides, was conserved across all three domains of life despite relying on exact matches to patterns found in E. coli, advancing our understanding of conserved grammatical structure in small subunit rRNA sequences. Availability and Implementation: Our source code is available at https://github.com/rainhaworth/16S-Mutation-Classifiers.

Infection following high-energy open fractures remains a major challenge. Open fractures are exposed to environmental and skin pathogens, which, along with traumatized tissue and implanted hardware, create a favorable environment for infection. 24-83% of open fractures yield positive culture results. Despite culture-positive wounds being at higher risk for infection, culture data are rarely used in clinical decision-making. Culture-positivity in open fractures is believed to indicate higher wound bioburden, but this hypothesis remains unconfirmed. This study aimed to correlate culture positivity and quantitative wound bioburden using next-generation sequencing (NGS) and to characterize patterns of bioburden and bacterial diversity amongst patients with open fracture and Fracture Related Infection. We hypothesized that higher wound bioburden would be associated with culture positivity. This secondary analysis of the METRC Bioburden Study included 78 patients with severe open tibia fractures who underwent standardized tissue sampling at definitive wound closure and at later fracture site revision surgery. DNA extracted from intraoperative tissue was analyzed via 16S rRNA gene amplicon sequencing. Quantitative bioburden metrics included bacterial read percentage and bacteria-to-human read ratio (BHR). Associations between sequencing-based bioburden, culture results, and clinical infection (CDC-defined) were evaluated using Mann-Whitney U tests, McNemars chi-squared tests, and unsupervised clustering analyses. Culture-positive samples exhibited significantly higher bacterial read percentages and higher log(BHR) values than culture-negative samples. Optimal thresholds yielded high sensitivity and specificity for both bacterial reads and BHR for predicting culture positivity. Neither baseline culture nor NGS positivity predicted later infection. However, follow-up samples from patients with established infection showed significantly higher bioburden and distinct microbiome structures. Clustering analyses identified two infection-associated microbial profiles: one with high bioburden and high diversity (polymicrobial infection) and one with low bioburden and low diversity (single-dominant pathogen). Culture positivity in open fractures correlates strongly with increased bacterial bioburden, indicating that positive cultures may primarily reflect microbial load rather than specific pathogens. Quantitative NGS-based measures, including bacterial read proportion and BHR, may offer a biologically grounded approach to assess wound contamination and may inform infection risk. Distinct bioburden-diversity patterns suggest heterogeneous infection phenotypes that may require tailored surgical and antimicrobial strategies.

Despite being a topic of early experimental studies, the effects of immersion-emersion cycles and temperature on the heart rate of intertidal Mytilus mussels have not been fully characterized. Using a recently released intertidal chamber paired with our own software package, we conducted a multiday experiment and continuously monitored the heart rate of the blue mussel Mytilus edulis. Under normal conditions, we detected a subtle spike in heart rate upon emersion before the eventual decline, as well as an overshoot upon reimmersion. Additionally, heart rate was sensitive to temperature changes during immersion but less responsive during emersion. These patterns were markedly altered following an unintended prolonged emersion event, which led to the loss of the emersion spike, an extended reimmersion overshoot, and heightened thermal sensitivity on top of an overall elevation in heart rate. However, the heart rate gradually returned to the pre-event baseline over the following days, demonstrating the significant resilience of the mussels. Our study highlights the potential of high-resolution physiological data in assessing the effects of environmental stressors on coastal ecosystems.

Ground-nesting wild bees require suitable soil conditions for their below-ground development and overwintering life stages. Understanding how soil translocation and disturbance affect individuals and the following generations of bees is important for identifying conservation measures for ground-nesting wild bees. We investigated the effects of soil translocation and disturbance on the ground-nesting solitary spring mining bee Colletes cunicularius. In a replicated controlled design, we compared the effects of soil translocation with different degrees of disturbance on the number of surviving bees and the emergence time. We found that soil translocation and disturbance reduced bee survival but did not result in complete mortality, with some individuals surviving even under severe soil disturbance. There was no evidence that soil disturbance affected the timing of spring emergence, suggesting that disturbance is unlikely to alter the timing of nest construction and, consequently, the production of the next generation. Our results indicate that translocating soil containing overwintering bees could be a promising conservation measure to compensate for habitat loss caused by land conversion.

Climate change is threatening coral reef ecosystems around the world, causing significant declines in reef organisms, including sponges. The health of sponges is intimately linked to their symbiosis with microorganisms, yet little is known about their integrated response to ocean warming. Here, we present a comprehensive view of the effect of elevated sea surface temperatures (SST) on the model sponge Ianthella basta. I. basta individuals were exposed to temperatures up to 32 {degrees}C, 2-3 {degrees}C above the mean annual maxima. Host gene expression profiles showed an initial response to heat stress after 2 days, and a decreased expression of genes involved in maintaining tissue integrity, pumping capacity, vitamin transport, and stable symbioses after 4 to 8 days. Congruently, heat stressed samples started to show tissue regression and a reduced abundance of the dominant symbionts after 4 days. A significant loss of the symbionts occurred after 8 days, together with a reduction in microbially driven nitrogen cycling and amino-acid transport and an introduction of opportunistic microbes, which could lead to nutrient imbalance and further destabilisation of the holobiont. Together, this work provides important insights into the avenues through which future SST can impact host-microbe interactions in coral reef sponges.

Selection-intensity estimates from RELAX are reported as a point value of K with a likelihood-ratio P. We report that, at default settings and on data of ordinary size, the program does not reproduce its own fits. Of 27 enzyme entries refitted under two optimiser configurations, none reproduced its log-likelihood to within 0.01 units; the median change was 103 units, the largest over 3,400, and four verdicts reversed. Eighty null orthologues reproduced none. A byte-identical command returned a distinct likelihood on every repetition, single-threaded, across three releases, and on alignments simulated under the fitted model, where 3.3 per cent of replicates reproduced. The documented random-number seed never reaches the generator when assigned on the command line, yet reads back as the value supplied. PAML localises the cause: its two-ratio model, without site classes, reproduced its log-likelihood for all 288 genes; its site-class models agreed for 27 to 67 per cent. The instability follows the mixture over sites, not the program. The output does not show it: 46 of 410 fits ended with a negative likelihood-ratio statistic, impossible under convergence, and 123 of 410 report a K re-estimated under a domain restriction rather than the unconstrained maximum. Of 234 published studies using RELAX, none reported a seed. Seeding while holding the thread count at one reproduced sixty of sixty runs on twenty genes under two releases; the seed alone reproduced none of five, and no documentation states the second condition. We recommend that fits be repeated and their dispersion published.

Objective Based on the bioinformatics method of multi-database integration, this study systematically analyzes the expression characteristics, clinical pathological correlation, prognostic value, potential molecular mechanisms, and immune infiltration patterns of hepatocyte growth factor receptor (MET) in gastric cancer. Methods The UALCAN and GEPIA databases were employed to examine the differential expression of MET between gastric cancer and normal gastric mucosal tissues, as well as its associations with clinicopathological features. Kaplan-Meier Plotter was utilized to evaluate the impact of MET expression on overall survival (OS) and progression-free survival (PFS). Protein-protein interaction (PPI) network was constructed via LinkedOmics, followed by Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of co-expressed genes. Four algorithms, TIMER, CIBERSORT, EPIC, and MCPcounter, were used to cross evaluate the correlation between MET expression and immune cell infiltration; Further validate the cell type specific expression of MET using the gastric cancer single-cell sequencing queues (GSE134520, GSE167297) built into the TISCH database. Results MET expression was significantly elevated in gastric cancer tissues compared with normal gastric mucosa (P < .05), and its expression level was significantly correlated with tumor grade and TNM stage. Patients with high MET expression exhibited significantly poorer OS and PFS than those with low MET expression (P < .05). The PPI network revealed that MET could interact with 20 key proteins, including EGFR, ERBB2, HGF, STAT3, and GRB2 etc. GO enrichment analysis suggests that differentially expressed genes are significantly enriched in functions such as the ERBB signaling pathway, cadherin binding, and DNA repair complexes; KEGG enrichment analysis showed that MET related genes were significantly enriched in pathways such as homologous recombination, nuclear cytoplasmic transport, mismatch repair, and oxidative phosphorylation. Immune infiltration analysis showed that the negative association between MET and B cells infiltration has cross algorithm robustness, while the association with neutrophils, CD8+ T cells, CD4+ T cells, and macrophages exhibits algorithmic heterogeneity or insignificance; There is no significant correlation between MET and common immune checkpoint molecules such as PD-1, PD-L1, CTLA4, etc. Single cell validation further confirmed that MET is mainly enriched in malignant epithelial cells and endothelial cells, and is almost not expressed in immune cells. Conclusions Multidimensional bioinformatic analyses demonstrate that elevated MET expression serves as an independent risk factor for unfavorable prognosis in gastric cancer. MET may mediate dual drug resistance in gastric cancer via crosstalk with multiple signaling molecules (including EGFR, ERBB2, HGF, STAT3 and GRB2) and dysregulation of the homologous recombination repair pathway. Results from multiple-algorithm immune infiltration analysis, single-cell dataset analysis and immune checkpoint correlation analysis indicate that MET exerts only modest direct regulatory effects on the gastric cancer immune microenvironment. This exploratory study offers systematic bioinformatic evidence supporting MET as a candidate prognostic biomarker and potential therapeutic target for gastric cancer. Further functional experiments and prospective cohort studies are required to validate its molecular mechanisms and clinical utility.

The sex ratio at birth (SRB), or secondary sex ratio, is stable, with more boys born alive, but shifts after major events. Acute stress may reduce SRB through disproportionate male fetal loss, while sexual intercourse patterns around conception are associated with offspring sex. We examined whether Brazil's April 2021 Gamma-wave mortality peak was followed by an SRB decline within the previously reported stress-sensitive 3-5 month window. We analysed >81 million live births (1997-2024) from Brazil's Live Birth Information System (SINASC) using pre-pandemic autoregressive forecasts with 95% prediction intervals (PIs). In July 2021, SRB was 50.951% versus 51.185% expected, below the 95% PI (50.968-51.402%), indicating fewer boys. All five macroregions were below expectation, largest in the North, including Amazonas, where Gamma was first identified. Monte Carlo simulation showed that, under usual SRB patterns, a decline with this timing and consistency across Brazil would occur about once in 200 simulations (probability 0.00467), making July 2021 unusual. In February 2023, SRB was 51.441% versus 51.220% expected, above the 95% PI (51.003-51.438%), indicating more boys, nine months after Brazil ended its COVID-19 emergency, suggesting increased sexual intercourse after pandemic relaxation. In April 2023, SRB was 50.956% versus 51.221% expected, below the 95% PI (51.004-51.439%), indicating fewer boys, four months after Pele's death. A comparable UK decline followed Princess Diana's death 4-5 months later. Gamma was prespecified; later observations are hypothesis-generating. These findings highlight SRB's population-level utility and warrant investigation of stress-related and behavioural pathways; ecological design precludes causality.

Motivation: Tree sets appear naturally when performing model based phylogenetic analyses. When tracking host-parasite co-evolution, testing sensitivity of different model assumptions, or even just checking convergence of individual runs of the same analysis, the question arises: are a given pair of tree sets the same? And if they are not the same, how do they differ? Results: We provide DensiTree 3, an interactive tool for inspecting pairs of sets of trees that allow visualising both tree sets using a single panel. Incorporation of CCDs provide better summary trees, taxon orderings and extra functionality like rogue detection, making it easier to interpret tree samples. Furthermore, a clade comparison graph allows inspection of differences in clade support and clade heights linked to the double-DensiTree panel. Together, these visualisations of tree sets make it easy to identify potential differences in the tree sets and interactively inspect these differences. Furthermore, recent advances in conditional clade distributions (CCDs) to represent tree distributions have been incorporated in DensiTree 3, and the most visible part of the user interface has been updated for a more modern look. Availability: DensiTree 3 is freely available from https://cs.auckland.ac.nz/~remco/DensiTree/. The program is licensed under GPL and source code is available via the link above.

Pterocarpus erinaceus Poir. (Fabaceae), the barwood or vene, is at the heart of one of the most severe conservation crises currently affecting tropical timber species. It has become the most heavily traded timber species in the world by volume, at the centre of an illegal rosewood trade to Asia that has driven the species to near-total disappearance in several countries despite its listing on CITES Appendix II since 2016. Faced with this urgency, ex situ conservation and restoration programmes often rest on the untested assumption that selecting seed trees by size improves the quality of the offspring produced in the nursery. This study rigorously tests this hypothesis against the competing one of a determinism dominated by the planting site, using six complementary analytical approaches (continuous regression, linear mixed models with a site x seed-tree interaction, seed-mass mediation analysis, non-linear growth modelling of height and diameter, between-site phenotypic plasticity, and multi-predictor allometric equations), across two contrasting bioclimatic sites in COte d'Ivoire (Korhogo: dry zone; Daloa: humid zone) and six seed-tree categories. Site exerts a decisive influence on growth at all ages (ANOVA, p<0.001 for height, diameter and biomass), whereas germination does not differ significantly between sites (70.3% at Daloa versus 61.6% at Korhogo; X2=1.95; p=0.162). Seed-tree DBH does not affect growth in any of the tests (continuous regression, p>0.30; mixed model, p>0.07), and the seed-mass mediation analysis remains inconclusive, seed mass varying only slightly among seed trees in this species (0.07-0.08 g). The exponential growth model provides the best fit for height and diameter at both sites, and two-predictor allometric equations explain 96.2% of biomass variance compared with 89.9% for the single-predictor model. These results indicate that ex situ conservation and compensatory reforestation programmes for this endangered species would benefit from prioritising the choice of planting site over the dendrometric selection of seed trees. A recommendation directly applicable to conservation nurseries established in response to the rosewood crisis.

The identification and use of stress-tolerant coral in outplanting efforts has been proposed as a method of restoring and bolstering reef health under increasing environmental change. Prior research has focused on understanding survival in cross-reef transplantation, but evidence of long term resiliency of outplanted corals remains limited. Here, we report data at a five-year timepoint of a reciprocal transplant study of the stress-tolerant Caribbean corals Pseudodiploria strigosa and Siderastrea siderea between a nearshore and offshore site in Belize. Extreme marine heat wave conditions in August of 2024 revealed species and site-specific bleaching patterns. Through assessments of mortality, energy reserves, and chlorophyll concentrations, P. strigosa appear to be more limited in long-term acclimatization potential to the nearshore environment while S. siderea maintain acclimatization capacity displayed 17 months post transplant to nearshore. This work conveys information relevant to managers in selecting species for restoration efforts based on short-term growth and long-term resilience in native versus non-native sites, offers insight into potential mechanisms driving these trends, and takeaways on site specific management decisions for successful coral outplanting success.

Urban protected areas (PAs) have become important habitats for wildlife in rapidly expanding human-dominated landscapes. These PAs may provide refuge and continuously abundant resources, which may enable some adaptable carnivores to persist and attain high abundances. However, little is known about the population ecology and interactions between carnivores sharing such spatially restricted and disturbed urban habitats. We evaluated the densities and spatio-temporal interactions of leopards (Panthera pardus) and striped hyenas (Hyaena hyaena) in Jhalana-Amagarh Conservation Reserve, a protected area (PA) embedded within the metropolis of Jaipur, India. During May-July 2025, we deployed 30 paired camera-traps and used spatially explicit capture-recapture models to estimate density and individual activity centres. We further quantified their diel activity and temporal overlap using kernel density estimation. Leopard density was estimated at 7.03 {+/-} 1.31 individuals/10 km sq and striped hyena density at 4.06 {+/-} 0.96 individuals/10 km sq, with activity centres of both species occurring in close proximity and frequently towards the reserve periphery. Both species were predominantly nocturnal and showed high temporal overlap ({Delta}4 = 0.801, CI=0.73-0.86). Our results report exceptionally high leopard and striped hyena densities in an urban PA and exemplify the importance of small PAs within rapidly expanding cities, stressing the need for finer-scale studies more broadly to understand the mechanisms shaping interactions between the two species. However, such systems require careful management of food subsidies, habitat quality and connectivity along with long-term monitoring of population viability, disease dynamics and human-wildlife conflict.

Background: This systematic review and meta-analysis evaluated the prognostic value of Hippo signaling pathway biomarkers in oral squamous cell carcinoma. Methods: Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, electronic database searches identified 17 eligible studies involving 1,194 patients. Associations between the immunohistochemical expression of Hippo pathway effectors, primarily YAP and TAZ, and clinicopathological characteristics were assessed. Meta-analyses using random-effects models estimated pooled hazard ratios for overall survival. Results: Predominantly nuclear expression of YAP and TAZ was consistently associated with adverse clinicopathological features, including advanced clinical stage, lymph node metastasis, and poorer histological differentiation. Meta-analysis demonstrated that YAP overexpression was associated with worse overall survival (hazard ratio, 1.918; 95% confidence interval, 1.036 to 3.549; p = 0.038). TAZ overexpression was similarly associated with poorer overall survival (hazard ratio, 2.845; 95% confidence interval, 1.682 to 4.811; p < 0.001). Although substantial between-study heterogeneity was observed, the direction of the prognostic association remained consistent across studies. Conclusions: Increased nuclear expression of YAP and TAZ is consistently associated with more aggressive disease and poorer overall survival in oral squamous cell carcinoma. These findings support the prognostic value of Hippo pathway biomarkers, although methodological heterogeneity warrants cautious interpretation.

1. Organisms rely on environmental cues, such as moonlight illumination and weather, to modulate nocturnal behaviors that reduce predation risk and conserve energy during demanding periods. Urbanization can alter the reliability of cues, potentially impairing organisms' ability to respond appropriately with consequences in increasingly urbanized landscapes. 2. We leveraged the Motus Wildlife Tracking System to identify roost initiation, roost departure and nocturnal restlessness of dark-eyed juncos (Junco hyemalis) overwintering along an urban to rural gradient to determine if activity patterns are affected by weather, moonlight illumination, and urbanization. 3. Nocturnal behavior of overwintering juncos varied with environmental factors, including moonlight illumination and temperature. However, the strength of these responses differed among sites, suggesting that natural cues of moonlight illumination were masked in urban areas, where individuals were more responsive to temperature. 4. Our results suggest that urbanization weakens birds' responsiveness to natural light cues, likely because artificial lighting reduces the visibility of moonlight; representing a key mechanism by which human-altered landscapes can disrupt nocturnal ecology in birds.

The genus Phakellia comprises predominantly fan-shaped deep-sea sponges, but its species diversity and boundaries remain unresolved. Here, we use an integrative approach combining morphological and molecular data to investigate the Phakellia robusta species complex and describe two new species, Phakellia pallida sp. nov. and Phakellia pusilla sp. nov. Overlap in external and spicular morphology makes these taxa challenging to identify. Molecular analyses based on mitochondrial (cox1) and nuclear (28S) markers support the recognition of the three taxa as distinct species, and reveal their close evolutionary relationship. The two new species co-occur in the NE Atlantic Ocean and the Mediterranean Sea, with overlapping depth ranges, although P. pallida sp. nov. is generally found at greater depths. Our results also suggest that several previous records of P. robusta from the Mediterranean and southern parts of the NE Atlantic may instead correspond to either P. pallida sp. nov. or P. pusilla sp. nov., indicating that its distribution requires reassessment. In addition, a group I intron previously reported in the cox1 gene of P. robusta was polymorphically detected at the same insertion site in some, but not all, individuals of P. pusilla sp. nov., but it was absent from P. pallida sp. nov. individuals. Overall, our results reveal pseudocryptic diversity within Phakellia and highlight the value of integrative approaches for resolving species boundaries and reassessing deep-sea sponge diversity and distributions.

Deep learning (DL) applied to haematoxylin and eosin (H&E)-stained pathology images can predict microsatellite instability (MSI) in gastric cancer (GC). We evaluated its diagnostic accuracy and discriminative performance. PubMed, Embase, Cochrane Library and Web of Science were searched for studies applying DL to H&E images for MSI prediction in GC. The protocol was prospectively registered in PROSPERO (CRD420261503140). Risk of bias was assessed with QUADAS-2. Pooled sensitivity and specificity were estimated with a bivariate random-effects model, with subgroup analyses by validation strategy and data source; slide-level areas under the curve (AUCs) were pooled after logit transformation. Prespecified scenario analyses assessed robustness. Ten studies were included; seven independent datasets from six studies entered the primary synthesis. Pooled sensitivity, specificity and summary receiver operating characteristic AUC were 0.78 (95% CI 0.63-0.88), 0.85 (95% CI 0.77-0.90) and 0.89 (95% CI 0.86-0.91); nine studies contributed to the secondary AUC synthesis (pooled AUC 0.85, 95% CI 0.80-0.89). Hospital-derived cohorts showed numerically higher sensitivity (0.86) and diagnostic odds ratio (39.8) than TCGA-derived cohorts (0.71 and 11.5), but subgroup differences were limited by the small number of studies and substantial heterogeneity. DL models show good diagnostic accuracy for MSI prediction in GC, but clinical utility still requires confirmation in standardised multicentre, independent external and prospective studies.