Species-specific accumulation and biomagnification of PFASs in aquatic and terrestrial organisms from the Xisha Islands.

UAV-based deep learning for biodiversity monitoring: Advances, applications, and future directions

The effect of some ecological characteristics (climate, soil, water content, and altitude) on the quality and antibacterial activity of Stachys inflata Benth. essential oil based on the indigenous knowledge of Iranian people

Ecological and Geographical Features of the Structural and Functional Status of Soil Microbial Cenosis in Old-Age Spruce Stands in Eastern Fennoscandia

Abstract Trophic level, which serves as a basic determinant of the evolutionary pathway of animals, including humans, emerges as, primarily, a product of relative energetic returns and food items availability. The concept of trophic level flexibility during the Paleolithic period for the highly adaptable human species represents a prevailing paradigm in the field of paleoanthropology. This paradigm largely relies on the observed variability of trophic levels among recent hunter-gatherer societies. We examine various methodological aspects involved in using ethnographic quantitative data as an analogical source for reconstructing the energetic returns of humans during the Paleolithic period and, consequently, their trophic level. By analyzing datasets from several studies, we highlight potential limitations that may arise when applying such analogies. In the past we argued that Paleolithic humans preferred to acquire the largest available prey. This assertion met with objection, based on ethnographic analogies. In addition to pointing out the limitations to the validity of such analogies, we propose that archaeofaunal records provide detectable reflection of prey ranking and thus their relative energetic returns without the need for detailed numerical reconstruction of energetic returns based on the ethnographic record. We introduce the Kakwani Concentration Index, originally developed in Economics to measure directionality and strength of inequality, as a measure of directionality and strength in the size ranking of prey in Archaeological assemblages to test preference for large prey. We propose that the paradigm of flexibility is based on adaptations that occurred following the Late Quaternary Megafaunal Extinctions during and after which prey size availability patterns have markedly changed. In contrast, as evidenced by the technological persistence of simple hunting tools and assemblages with large herbivores throughout the Lower and Middle Paleolithic, subsistence strategies likely centered on large prey, which can be deduced by the lack of composite projectile hunting tools for a substantial portion of human evolution. The paper re-emphasizes that ethnoarchaeological analogies should be treated as testable hypotheses, and they may hold potential validity for behaviors that exhibit cross-cultural correlates. Ultimately, it suggests that no such correlates are present in some influential hunting energetic returns and human trophic level reconstructions. We argue that the technological, ecological and cognitive non-analog features of ethnographic energetic returns datasets are too great to be predictive of the Paleolithic nutritional pattern.

Caudata (salamanders) is a highly threatened taxonomic group with over 60% of species estimated to be threatened. However, the species traits and extrinsic factors underlying their population decline and high extinction risk remain unclear. We conducted the first global comparative analysis to investigate which factors are associated with an increased risk of decline and extinction in salamanders. We addressed the following questions: Is extinction risk randomly distributed among salamander families, and if not, which families contain more threatened species than would be expected by chance; which species traits and extrinsic factors are important in determining the extinction risk in salamanders; and are the key factors for population decline consistent with those for extinction risk in salamanders? To determine which ecological characteristics and extrinsic factors best predict extinction risk and population decline in salamanders, we employed phylogenetic generalized least squares (PGLS) models and phylogenetic logistic regression (PGLM) models, respectively. Threatened salamanders were nonrandomly distributed across nine families, among which Cryptobranchidae and Hynobiidae contained significantly more threatened species than expected. Key predictors of salamander extinction risk were breeding strategy, geographic range size, minimum elevation, human threat index, and protected area coverage. Although geographic range size, climate change, and human threats were the most important predictors of salamander extinction risk and population decline, the effect of geographic range size was the opposite between the PGLS and PGLM models. Our results suggest that priority management should focus on extinction-prone families, particularly Cryptobranchidae and Hynobiidae, and salamanders with small range sizes and sensitivity to human disturbance or climate instability.

Wetlands are diminishing world-wide. Ramsar Convention has played a noteworthy role to designate the wetlands with ecological, socio-economic and cultural significance as Ramsar sites. However, unsustainable anthropogenic activities continue to threaten both Ramsar sites and other wetland complexes without any legal designation, particularly diminishing the diversity of various flora and fauna. Conservation resources are limited. Therefore, it is crucial to identify the priority areas and allocate the available resources in order to ensure optimum protection of biodiversity thriving in those wetlands. Despite this urgency, systematic approaches for prioritizing conservation areas within heterogeneous wetland landscapes remain poorly explored. To address this gap we designed a coalescing framework which integrates multiple components- wetland degradation mapping, wetland biodiversity hotspot (considering bird as indicator species), identification of important habitats, habitat quality and connectivity assessments to identify the conservation priority zones in wetland landscapes. We implemented our framework at East Kolkata Wetlands to address where and what should be protected within this heterogeneous wetland landscape. We identified 12.83 km2 as top 10% priority area as the best part of this wetland landscape for biodiversity conservation. In addition, we also identified areas falling under 50-90% conservation priority zones. Protection and maintenance of these areas will increase the overall habitat quality and habitat connectivity ultimately influencing the sustenance of overall biodiversity. As <50% conservation priority area has relatively lower priority values thus, can be used for sustainable economic activities without degrading the ecological characteristics of existing wetlands. Such multicomponent framework will produce more comprehensive and realistic conservation prioritization scenarios than any single method or partial combination. It can be broadly applicable for guiding biodiversity conservation at wetland landscapes situated adjacent to urban areas across the globe.

The commensal microbiome in respiratory tract tumors: From oncogenic mechanisms to clinical translation.

The aim of this work was to examine the causes and mechanisms by which plastic microparticles that have entered a water body are trapped in macrophyte thickets. The retention rate of plastic microparticles by macrophytes depends on the material of their origin; particle hardness, size, and concentration; the material density; and the morphological and ecological characteristics of the plants. For various species of macrophytes, the retention rate of microparticles in the size range of 1–5 mm ranges from 22% to 100%. The appearance of additional resistance to the movement of water and air masses promotes the slowing of the movement of microparticles, their sedimentation, and their retention by plants. Decreasing the kinetic energy of wind waves and raindrops via thickets of macrophytes prevents the repeated movement of already trapped microparticles. Mechanical retention of plastic microparticles occurs as a result of irregularities in the structure of plants, sieve-like structures made of interweaving stems and leaves, the bulk of plant litter, and the adhesion of plant surfaces and microparticles, which is enhanced by the sticky surfaces of the periphyton. The attraction and adhesion of plastic microparticles to plants and to each other occur as a result of the interaction of electric fields.

Enterotypes refer to the different bacterial clusters in the gut microecosystem, which are closely related to host physiology, digestion, disease, and other phenotypes. However, whether there are clear clusters in the silage microecosystem, and the fermentation quality and characteristics of unique cluster silage remain unknown. To determine whether distinct bacterial clusters exist in the silage microecosystem and to characterize their fermentation properties, we analyzed the bacterial community composition and fermentation quality of 156 silage samples, and further explored their underlying microbial ecological features. We confirmed three distinct clusters in the silage microbiome, which were named according to their dominant bacterial taxa: the E-cluster (characterized by a higher abundance of unclassified Enterobacteriaceae (UG)), the P-cluster (enriched with Pseudomonas and Janthinobacterium), and the L-cluster (dominated by Lactobacillus). These microbial clusters were closely associated with fermentation quality: the L-cluster exhibited superior silage quality compared to the E- and P-clusters. Meanwhile, the microbial functional profiles differed significantly among the three clusters of silage. Numerous pathways were significantly enriched in the P-cluster, such as the Biosynthesis of other secondary metabolites, etc. Moreover, bacterial co-occurrence networks of three clusters silage displayed cooperative interactions mainly, P-cluster silage network was more complex and tighter, E-cluster silage has more functional microbial units and more stable. Furthermore, the assembly of microbial communities in the three silage clusters was dominated by stochastic processes. Specifically, the E-cluster and L-cluster were governed by ecological drift, while dispersal limitation was more influential in the P-cluster. Overall, we found in our study that the silage microbiome can be divided into three clusters, and different clusters have significant differences in fermentation quality, microbial diversity and compositions, functional profiles, microbial network characteristics and community assembly mechanisms. These results could broaden our comprehension of the silage microbial ecology processes and also provide a scientific basis on which to develop a method to precisely regulate silage quality.

In the flora of Ukraine, 48 findings of the spontaneous spread of the alien species Nepeta racemosa Lam. were recorded: 30 records within the introduction centers and 18 outside the boundaries of cultivation. A brief morphological description of the plants is provided, and their ecological and biological features are investigated. It was found that all the habitats of this species in Ukraine were confined to synanthropic biotopes: decorative cultivated biotopes (parks, squares, lawns, flower gardens), residential and technotopes (biotope complexes of built-up areas, garbage and solid waste landfills). Most often, the plants grow in cracks in sidewalks and asphalt. According to time of introduction, N. racemosa belongs to neophytes, and according to method of introduction to ergasiophytes. The species requires further monitoring to assess the likelihood of its further spread within and beyond urban environments.

Bats are reservoirs for many emerging viruses, yet broad-scale spatial patterns of bat viromes and their ecological determinants remain unclear, limiting spillover risk assessment. To address this, we conducted a standardized survey across central to southern China. During 2022-2023, fecal samples were collected from 527 bats representing 17 species at 21 caves in seven provinces. Using each cave as the analytical unit, samples from all species at a site were pooled to construct 21 fecal RNA virome libraries for metatranscriptomic sequencing; viral-like contigs were annotated, and viral alpha/beta diversity was quantified at the genus level. Sites were grouped by geographic distance and latitude to evaluate spatial differentiation and to relate virome patterns to host community attributes and environmental factors. We annotated 56 viral families, including 19 vertebrate-associated families, with multiple families and genera shared across geographic groupings. Vertebrate-associated viral diversity showed limited evidence of geographic isolation within the study region but suggested gradual turnover with latitude. Host species richness was the strongest correlate of virome diversity, exceeding the effects of evaluated environmental variables (e.g., climate and human activity). These results support prioritization of species-rich bat habitats for surveillance and risk assessment.

Staphylococcus species are frequently detected during traditional Korean soybean fermentations, yet their ecological roles, metabolic functions, and safety characteristics remain poorly defined. In this study, we conducted an integrated genome-resolved and phenotypic analysis of Staphylococcus strains associated with traditional Korean soybean fermentation to clarify their functional significance and safety relevance. Using 23 controlled fermentation batches prepared with region-specific raw materials, we isolated 66 Staphylococcus strains and generated 47 non-redundant representative genomes. Species-level community analysis identified eight Staphylococcus species, with S. xylosus, S. shinii, S. equorum, and S. nepalensis representing the major taxa during fermentation. Genome-based metabolic reconstruction, enzymatic assays, and carbohydrate utilization tests revealed pronounced species- and strain-level heterogeneity. Although protease and amylase activities were generally limited, lipase and β-glucosidase activities were relatively high and highly variable, indicating potential functional roles in soybean fermentation. The strains encoded diverse carbon metabolic pathways and conserved biosynthetic and transport systems for the compatible solutes glycine betaine and proline, supporting adaptation to high-salinity fermentation environments. Safety assessment integrating antimicrobial susceptibility testing with genome-based analyses showed that most strains were coagulase-negative, non-hemolytic, and susceptible to clinically important antibiotics. However, the identification of S. saprophyticus, a known pathogen, harboring mobile resistance elements, including SCCmec-associated genes, underscores the need for strain-level safety evaluation despite overall low phenotypic resistance rates. Overall, this study provides a comprehensive genome-resolved and strain-level evaluation of Staphylococcus associated with traditional Korean soybean fermentation.

Ecosystem services (ESs) support human well-being, but their integrated assessment in urban green spaces remains challenging, particularly at the project scale, where finer spatial resolution (tens of meters) is required. Historical parks are complex socio-ecological systems with non-linear ES interactions. This study develops a design-oriented framework to assess how restoration interventions influence regulation, maintenance, and cultural ES potential provision. Indicators derived from field surveys and established models were selected according to CICES V5.2 and adapted to ecological and cultural features of historical parks. Survey units were defined for each ES section to enable a spatially explicit comparison between current and design scenarios. A normalized scoring system was applied to evaluate category-level changes and overall interaction patterns. The framework was tested on the restoration project of Monza Park (northern Italy). Results show a marked increase in cultural and regulation services (+28% and +17%, respectively), while maintenance services exhibited a slight decrease (−3%). These trends are reflected in the Cumulative Indicator Score (CIS), indicating an overall positive balance of ES provision in the design scenario. The Design Effectiveness Score (DES) showed consistently non-negative values (DES ≥ 0), reaching maximum effectiveness in transitions to woody vegetation (DES ≈ 1). The Synergy–Trade-off Score (STS) confirmed a general increase in ES supply across all categories, with a clear prevalence of synergies over trade-offs. The proposed framework supports the data-driven, spatially explicit evaluation of design alternatives and can guide decision-making in historical park restoration.

Objective: Quantitative analysis of the spatial distribution and ecological niche differentiation characteristics of the major evolutionary clades of Francisella tularensis subsp. holarctica (Fth), elucidate the mechanism of epidemiological heterogeneity. Methods: A systematic search of public databases was conducted to collect and curate whole-genome sequences and metadata of 415 Fth strains. A maximum-likelihood phylogenetic tree was constructed using core-genome single-nucleotide polymorphisms,and an additional 1 047 strains with complete metadata from public databases were integrated to perform geographic analysis by incorporating geographic information. A Bayesian molecular clock model was used to infer the divergence history of the major evolutionary clades. A 4×3 contingency table was constructed using 126 representative strains to determine niche preferences among evolutionary clades and isolation origins. Fisher's exact test was applied to examine general associations, and adjusted standardized residuals (ASR) were computed to determine the source-specific preference for each clade (|ASR| >1.96 implies a statistically significant difference). Results: The Phylogenetic analysis for the Fth strains indicated that there are subgenomic B.4, B.6, B.12, and B.16, which show evident geographic groups. Bayesian molecular clock analysis of the most recent common ancestor of Fth yielded an estimate of about 2276 years Before Common Era Fisher's exact test showed a powerful relationship between Fth clade types and sources of isolation (P<0.001). ASR analysis revealed that clade B.12 was significantly overrepresented in animal sources (ASR=4.95) and underrepresented in human sources (ASR=-4.77), and that clade B.6 was significantly overrepresented in human sources (ASR=2.88) and underrepresented in animal sources (ASR=-2.50). Conclusions: The two main Fth clades, B.6 and B.12, have distinct and opposite niche differentiation. Clade B.12 has a strong "zoonotic affinity", and clade B.6 has a significant "human affinity", indicating that B.6 is a zoonotic lineage that is more prone to infecting humans and poses a greater threat to public health. These will conclude the importance of the clade type in future disease monitoring and risk assessment for targeted disease prevention and control.

The western Himalayan region, particularly the Union Territory of Jammu &amp; Kashmir and Ladakh, was home to many freshwater lakes that represented ecologically critical systems sustaining high biodiversity and various essential ecosystem services, including nutrient cycling, climate regulation, and livelihood support. These lakes differed in size, altitude, and ecological characteristics. They contained diverse species of plankton and fish, which were key components of the aquatic food web, served as bioindicators of water quality, and played a crucial role in ecosystem functioning. This review aimed to assess the biodiversity and ecological integrity of freshwater lakes, with a focus on understanding the relationship between biological diversity, water quality, and environmental stressors. A systematic literature review was conducted in accordance with PRISMA guidelines. For data collection, Google Scholar, PubMed, ResearchGate, Scopus, and ScienceDirect databases were searched using relevant keywords. Studies published between 2010 and 2025 focusing on freshwater lakes of Jammu &amp; Kashmir and Ladakh were included, addressing ecological integrity, including water quality, biodiversity, trophic status, and pollution. The review revealed that these lakes supported diverse and functionally important planktonic and fish communities that regulated primary productivity and acted as reliable bioindicators of water quality. However, increasing anthropogenic pressures, including pollution, urbanisation, overexploitation, and unregulated tourism, were degrading water quality and disrupting ecological balance. Climate change, particularly glacial retreat and shifting precipitation regimes, further exacerbated these impacts, accelerating ecosystem instability and biodiversity loss. Overall, the freshwater lakes of the Himalayan region were under significant stress due to anthropogenic effects and climate change, resulting in declining water quality and biodiversity loss. To prevent further biodiversity loss and maintain ecological integrity, effective conservation strategies, strict policy implementation, and community participation were required to ensure long-term ecological sustainability.

Cognitive biases are widely discussed in the medical literature as systematic deviations from rational judgment and as significant contributors to diagnostic error. However, the prevailing view of cognitive biases as inherently epistemically detrimental may be challenged by recent research highlighting their potential utility. In this paper, we argue that the impact of cognitive biases in medicine depends not only on their internal cognitive structure, but also on the ecological characteristics of the medical environments in which they operate. We develop a conceptual framework that distinguishes between three types of cognitive biases: (1) those that are epistemically reliable (and practically useful) in so-called "safe cognitive environments", where ecological informational structures reliably support the use of "fast and frugal" heuristics; (2) those that are practically useful in "pragmatically permeable contexts" such as emergency care or public health, where time pressure, uncertainty, or resource constraints justify decisions that are epistemically suboptimal but action-guiding; and (3) those that are neither epistemically nor pragmatically defensible, and thus constitute clear targets for mitigation. By offering this taxonomy, we aim to clarify when and why cognitive biases hinder or support medical reasoning and practical actions. Our analysis also emphasizes the need to reframe some traditional assumptions in medical epistemology and education. Rather than attempting to eliminate all cognitive biases, we advocate for a more nuanced, context-sensitive, and ecologically informed approach in medicine. We conclude by outlining the implications of this framework for improving diagnostic accuracy, professional training, and institutional practices in healthcare.

Hybridization is a powerful force shaping the evolutionary trajectories of species, yet its outcomes are highly variable both across taxa and within a pair of species. In this study, we examine the processes shaping variation in the extent of hybrid ancestry, both among populations and across the genome. We use low-coverage sequencing data to infer local ancestry across the genome for 782 individuals from multiple populations across two geographic regions within the broadly overlapping range of Mimulus guttatus and Mimulus nasutus . We find that the extent of hybrid ancestry is variable across populations, supporting disparate historical patterns of hybridization. However, genomic patterns of hybrid ancestry are correlated across groups, indicating they are shaped by parallel processes. Correlations are highest in geographically proximal populations, including between sympatric and allopatric locations, providing evidence that introgression is not locally constrained but spreads via migration across the landscape. We find that features of the genome are predictive of hybrid ancestry and its correlations among populations. However, contrary to findings in some other species, these patterns are likely not driven by simple linked selection against hybrid ancestry. Genomic outliers for high hybrid ancestry are often shared among populations, suggesting a role for parallel positive selection on ancestry. However, known loci associated with reproductive isolation are poor predictors of ancestry variation across populations, indicating that selection acting in natural hybrid populations is highly polygenic and that the underlying genetic architecture varies across space. Overall, this study demonstrates how ecological, demographic, and genomic features all interact to shape the outcomes of hybridization.

Long-term eutrophication remains one of the major pressures affecting freshwater lake ecosystems in Europe. Lake Durowskie (north-western Poland) has experienced sustained nutrient loading from agricultural runoff, urban activities, and hydrological connections with upstream lakes, resulting in a hypertrophic state. Since 2009, restoration measures combined with systematic ecological monitoring have been implemented to improve the lake’s ecological condition. This study evaluates long-term phytoplankton and periphyton dynamics as indicators of ecological recovery in Lake Durowskie during 2008–2025. Samples were collected from multiple lake and inflow sites and analysed in terms of taxonomic composition, abundance, biomass, and ecological characteristics. Ecological status was assessed using biological indices, including the Shannon–Wiener diversity index (H′), Pielou evenness index (E), Jaccard similarity index, Nygaard mixed trophic index, and the diatom index (DI). The results indicate relatively high phytoplankton diversity and evenness across the lake. Chlorophyta and Bacillariophyceae contributed most to species richness, whereas total biomass was largely influenced by dinoflagellates, particularly Ceratium hirundinella and Peridiniopsis berolinense. Long-term observations revealed increasing algal species richness since 2022 and low Jaccard similarity values (17–25%), indicating significant community restructuring. Although the Nygaard index consistently classified the lake as hypertrophic, improvements in the periphyton diatom index at several sites suggest gradual ecological improvement. Overall, the results indicate a transitional recovery phase under persistent eutrophic pressure and confirm the value of phytoplankton and periphyton as indicators for long-term monitoring of hypertrophic lake ecosystems.

Abstract Migration is the synchronized movement of a large part of a population from breeding grounds to nonbreeding grounds driven by seasonal variation of resources and avoidance of harsh winter conditions. Migration is a central component of many species' life histories, including birds, mammals, fishes, and invertebrates. However, the interplay of ecological and evolutionary drivers of migration has long intrigued biologists and remains contentious. Shorebirds represent a valuable group for testing multiple predictors of migration, as they demonstrate a range of morphological and ecological characteristics (e.g., wing shape and habitat breadth) and a large proportion of shorebird species migrate. Here we tested whether breeding site climate, wing shape, body mass, and number of habitats occupied can predict migration across 196 shorebird species using novel Bayesian regression modeling allowing explicit decomposition of trait correlations into both phylogenetic and nonphylogenetic components. Increasing climate seasonality and pointier wing shapes favoring dispersal appeared strongly associated with migration, matching our predictions and potentially reflecting resource availability optimization and the energetic costs of migration. Higher number of habitats occupied also appeared associated with migration, perhaps reflecting selection to decrease the specific habitat requirements of migration transits. The lack of a significant relationship for body mass may reflect conflicting selection pressures, as migration efficiency (energetics) increases with body size but migration duration (and time that can be spent at breeding sites) decreases.