Search Results (113)

The H9N2 avian influenza virus (AIV) is currently widespread globally and poses a serious threat to the poultry industry and public health; however, its global epidemiological characteristics and key molecular mutation patterns have not yet been systematically elucidated. Based on the NCBI Influenza Virus Resource Database, this study collected relevant data on the H9N2 AIV from around the world between 1966 and 2023. It conducted a comprehensive analysis of the geographic distribution of 11,933 strains, the temporal distribution of 11,824 strains, the host sources of 11,756 strains, and the genetic polymorphisms at key functional sites. The results showed that 90.14% of H9N2 AIV sequences in the dataset originated from Asia, with China contributing the largest number of sequences. The global sequence availability pattern underwent four phases: sporadic sequence availability, gradual increase, high sequence availability, and subsequent decline, with 2007–2018 representing a period of relatively high availability of publicly accessible sequences. Host analysis indicated that H9N2 AIV sequences were predominantly derived from poultry-related hosts, with chickens being the main host source in the dataset, and available sequences have also been reported from various mammals, including pigs and humans, as well as environmental media. Molecular analysis revealed that receptor-binding-related sites in the HA protein, such as Q226L and I155T, have become dominant variants, while mammalian-adaptive mutations such as PB2 E627K and D701N remain at low frequencies; M2 S31N is widely prevalent, whereas the detection rate of NA drug-resistance-associated mutations is low. This study systematically reveals the global distribution patterns of available H9N2 AIV sequences, host distribution characteristics, and key molecular mutation patterns of the H9N2 AIV, providing a scientific basis for cross-host transmission risk assessment, molecular surveillance, and targeted prevention and control. Full article

Distributional gaps in poorly documented Neotropical mammals often reflect the combined effects of ecological filtering, low detectability, taxonomic uncertainty, and incomplete sampling. We reassessed the documented distribution of L. brachyotis (Dobson, 1879), a rarely collected forest-dwelling phyllostomid bat, using an expanded occurrence dataset and specimen-based validation. Independently, we used ecological niche models to characterize climatic suitability under current and paleoclimatic conditions. We compiled 125 documentary or specimen records from published sources and museum material, including new voucher-based records from southern Ecuador and northern Colombia, and consolidated them into 121 reviewed unique locality-coordinate units. After environmental screening and cell-level deduplication, 115 unique presence cells were used for model calibration. The best-supported model used linear, quadratic, and hinge features with a regularization multiplier of 2.5 and performed significantly better than null-model expectations. Under current conditions, climatic suitability was broad but spatially heterogeneous across northern South America, with additional suitable areas in Mesoamerica, the Andean–Amazonian interface, central Brazil, and southeastern Brazil. Temporal projections identified recurrent areas of climatic suitability across northern South America, but were interpreted as climatic context rather than direct evidence of historical occupancy or demographic continuity. The new records indicate that the documented distribution remains incomplete along its margins. Our results support a revised interpretation of L. brachyotis as a rarely recorded humid-forest bat with a coherent Amazonian–Guianan core and peripheral extensions consistent with the combined influence of climatic suitability, habitat heterogeneity, and incomplete sampling. Full article

Skin is a highly specialized barrier organ, which serves essential barrier, immune, and sensory functions and exhibits conserved structure. In addition, each species exhibits a unique skin transcriptional profile for adapting distinct environmental conditions and physiological demands. However, these transcriptional profiles across mammals remain incompletely understood. In this study, we integrated 61 publicly available skin RNA-seq datasets from eight mammalian species: human (Homo sapiens), macaque (Macaca fascicularis), mouse (Mus musculus), sheep (Ovis aries), goat (Capra hircus), donkey (Equus asinus), rabbit (Oryctolagus cuniculus), and pig (Sus scrofa). We identified a large number (2286 to 4588) of differentially expressed genes (DEGs) based on 10,504 one-to-one orthologous genes in all pairwise species comparisons. A total of 44 conserved genes were identified by integrating tissue specificity, expression variability, and mean expression level, which were enriched in epidermal development, keratinocyte differentiation, and desmosome organization. We also identified species-specific genes and transcription factors, such as STMN1 (donkey), COL1A1 (goat), and ACTN2 (mouse), which are associated with the cell cycle, extracellular matrix, and muscle contraction pathways, respectively. WGCNA further revealed goat-associated module 2 (M2) enriched in the negative regulation of angiogenesis. Collectively, this study provides a comprehensive cross-species transcriptional profile resource for mammalian skin, providing a valuable resource for understanding the regulatory plasticity underlying skin evolution across mammals. Full article

Environmental temperature is a major ecological factor shaping physiological and molecular evolution in mammals. Fatty acid desaturase genes (FADS1 and FADS2) play essential roles in the biosynthesis of long-chain polyunsaturated fatty acids (PUFAs), which are critical for membrane structure and metabolic regulation. However, their evolutionary responses to climatic variation in wild mammals remain poorly understood. In this study, we analyzed 27 rodent species distributed across diverse climatic regions to investigate the relationship between environmental temperature and the evolutionary rates of the FADS1 and FADS2 genes. Phylogenetic comparative methods, including phylogenetic ANOVA, phylogenetic generalized least squares (PGLS), and branch model analyses, were applied to estimate ω (dN/dS) ratios and assess selection patterns. Branch-site model analyses were further performed to test for episodic positive selection acting on specific codons in low-temperature-associated lineages. Our results showed that species inhabiting lower-temperature environments exhibited significantly higher ω values for both FADS genes compared with those in warmer environments. PGLS analyses revealed consistent negative associations between temperature variables and evolutionary rates, particularly for BIO5, and branch model analyses further indicated elevated ω values in low-temperature-associated lineages relative to background branches. Branch-site analyses detected significant signatures of episodic positive selection in Spermophilus dauricus and Microtus oregoni, with candidate positively selected codons identified in both lineages. Similar temperature-associated evolutionary rate patterns were also observed in expanded mammalian datasets, suggesting a broader cross-taxa trend. Overall, these findings indicate that environmental temperature is associated with heterogeneous evolutionary rate patterns in FADS genes and suggest that lipid metabolism genes may be recurrently influenced by cold-related selective pressures across mammals. Full article

For this project, we surveyed small mammal communities in protected forest habitats of the Sintra-Cascais Natural Park, Portugal, to establish a robust baseline for conservation planning. Our study provides a dataset and accompanying information to support an empirical framework for assessing the environmental determinants of small mammal occurrence across diverse habitats. These habitats encompass the park’s main forested areas within the UNESCO-designated landscape of the Sintra Mountain Range. Field sampling was conducted in two periods (2018 and 2024–2025) across six areas, comprising a total of 43 sites representative of the dominant habitat types within each location. A combination of live trapping, hair sampling, and camera trapping was employed, which enabled the detection of ten small mammal species, four Eulipotyphla and six Rodentia. The final dataset, derived from an extensive sampling effort of 8820 trap-nights, comprises a total of 792 specimen records. The complementary sampling approaches contributed differently to species detection, with live trapping recording the highest species richness and camera trapping generating the greatest number of detections. Obtained data provide critical support to inform the design and implementation of integrated, evidence-based conservation actions to sustain stable small mammal populations over the long term. Full article

Guide-net marine mammal bycatch reduction devices (BRDs) are intended to reduce protected species interactions in trawl fisheries, but their use may also cause catch loss of commercial fish and cephalopods. We restructured June and September 2024 sea trial records into a final six-taxon BRD/COD modeling dataset containing 5641 individual records from 24 unique haul clusters. Logistic GLM, random forest, and XGBoost models were evaluated using haul-grouped cross-validation, and random forest SHAP and permutation analyses were used as exploratory variable contribution diagnostics. Model discrimination was modest and split-sensitive, but Brier score and accuracy were interpreted cautiously because the catch loss prevalence was 0.163 and trivial baselines were strong. Body length and headline height were the leading non-species contributors, while nominal guide-net angle remained a relevant design variable but ranked below several biological, tow condition, and realized gear geometry variables. Additional haul-clustered GEE sensitivity analyses treated nominal guide-net angle as a two-level categorical factor (30°/45°). Across four GEE specifications, the 45° angle term was consistently positive, but confidence intervals were wide, p-values were not significant, and the full species-adjusted model showed suspected quasi-separation in the hairtail term. These results indicate that nominal angle contribution cannot be cleanly isolated from species composition and realized gear geometry in this field dataset. We therefore interpret guide-net angle as an exploratory predictive contributor rather than as a causal factor of catch loss. Full article

Detailed knowledge of biodiversity is fundamental to supporting conservation and management strategies in protected natural areas, especially in mountain systems located in biogeographic transition zones (Chihuahuan Desert and Sierra Madre Oriental regions). The Sierra de Zapalinamé State Natural Reserve is a priority system in northeastern Mexico; however, comprehensive long-term inventories of its terrestrial vertebrate fauna have been limited. The objective of this study was to comprehensively characterize the richness and composition of the terrestrial vertebrate fauna of the Sierra de Zapalinamé State Natural Reserve using a long-term, multi-source dataset integrating systematic field surveys, biological collections, and citizen science records, and to assess the extent to which the reserve represents the vertebrate diversity of northeastern Mexico. A total of 415 terrestrial vertebrate species were recorded, comprising 299 birds, 67 mammals, 42 reptiles, and 7 amphibians. Despite its proximity to urban areas and industrial activities, the reserve maintains high levels of biodiversity, harboring a substantial proportion of the terrestrial vertebrate fauna of northeastern Mexico. The results emphasize the importance of the Sierra de Zapalinamé State Natural Reserve as a regional biodiversity hotspot and support the strengthening of long-term monitoring and management strategies to improve wildlife conservation in underrepresented ecoregions facing increasing environmental pressures. Full article

In 2022, the World Health Organization (WHO) published the Fungal Priority Pathogens List (FPPL), yet its application has remained largely focused on human medicine, with limited consideration of animal hosts and veterinary diagnostics. This retrospective study aimed to characterise the occurrence of WHO critical- and high-priority yeasts in veterinary clinical submissions in Portugal within an explicit One Health framework. All yeast-positive submissions received by a Portuguese veterinary diagnostic laboratory between 2019 and 2026 were reviewed. Isolates were identified phenotypically, by an automated identification system and by MALDI-TOF mass spectrometry. Data on host species, sample type and year of submission were analysed using standard descriptive and inferential statistics. Among 2033 mycological submissions, 219 were yeast-positive. Out of these, 82 isolates (37.4%) corresponded to WHO critical- or high-priority taxa, most frequently Candida albicans, followed by Nakaseomyces glabratus, Cryptococcus neoformans var. neoformans, the Candida parapsilosis complex and Candida tropicalis. The remaining 137 isolates (62.6%) corresponded to non-WHO taxa, among which the most frequent were Papiliotrema laurentii and Debaryomyces hansenii (n = 21 each; 15.3%), followed by the Stephanoascus ciferrii complex (n = 15; 11.0%), Meyerozyma guilliermondii and Candida sake (n = 12 each; 8.8%), and Wickerhamomyces anomalus (n = 9; 6.6%). WHO-prioritised taxa were recovered predominantly from ornamental birds, as well as from dogs, cats and marine mammals. These findings demonstrate that FPPL-listed yeasts are regularly detected among yeast-positive veterinary diagnostic submissions and highlight ornamental birds as prominent hosts within this dataset. Full article

Background/Objectives: Autophagy is an evolutionarily conserved intracellular degradation mechanism that is regulated by a set of autophagy-related (ATG) proteins. The only transmembrane protein among ATGs is the lipid scramblase ATG9, which exists in the form of two paralogs, ATG9A and ATG9B, in humans and other vertebrates. Methods: Here, we analyzed human and murine skin transcriptome and proteome datasets for the expression of ATG9 paralogs and performed comparative genomics to determine their conservation during the evolution of amniotes (mammals and sauropsids). Results: The expression of ATG9B, but not of ATG9A, is enriched in differentiated epidermal keratinocytes and in skin appendages of humans and mice. In contrast to the conservation of ATG9A in all major clades of amniotes, ATG9B has been lost in at least three phylogenetic lineages. Cetaceans, which have unique skin adaptations to aquatic life, harbor mutations that disrupt the open reading frame of ATG9B. Many or all species of turtles (Testudines) and crocodilians (Crocodylia) have entirely lost the ATG9B gene. Conclusions: ATG9B has undergone independent pseudogenization or gene loss in different subgroups of amniotes. In mammalian species that have retained the gene, its expression pattern indicates functions of ATG9B in the skin and skin appendages. Full article

Forest conversion from natural forests to secondary forests and plantations has significantly altered wildlife habitats in subtropical regions. However, the drivers of disparities in bird and mammal multidimensional diversity between these forest types remain poorly understood. We analyzed a four-year camera-trapping dataset to compare the taxonomic, functional, and phylogenetic diversity and community structure of birds and mammals. Our results indicated that forest conversion impacts biodiversity differently across taxa. Birds exhibited higher taxonomic and phylogenetic diversity in secondary forests than in plantations. A similar pattern was also evident for birds among different stand types. However, mammals exhibited considerable taxonomic diversity but showed higher phylogenetic diversity and structure in secondary forests. A similar pattern was also evident for mammals among different stand types. Beta diversity revealed significant differences in bird taxonomic composition and mammal phylogenetic composition between secondary and plantation forests. Furthermore, elevation primarily influenced bird taxonomic diversity, phylogenetic diversity and structure in secondary forests, whereas mammal functional diversity, phylogenetic diversity and structure were more sensitive to elevational changes in both secondary and plantation forests. These findings reveal that birds and mammals respond distinctively to forest conversion. We emphasize that management strategies must be group-specific. For birds, we recommend prioritizing the preservation of secondary forests as biodiversity refugia and transforming structurally simplified plantations into complex habitats by retaining legacy trees and native understory vegetation. For mammals, conservation should prioritize landscape-scale connectivity by protecting continuous forest corridors along altitudinal gradients. Practically, this requires restricting further fragmentation of high-altitude habitats and restoring native vegetation in degraded corridors to facilitate dispersal and maintain the phylogenetic integrity of mammal communities. Full article

Dolphins are widely recognized as intelligent marine mammals with sophisticated communication and echolocation. Accurately classifying their whistles is essential for understanding their communication patterns and monitoring their population size, structure, and distribution. In this study, we assembled a large, high-quality dataset of Indo-Pacific bottlenose dolphin (Tursiops aduncus) whistle signals collected at the Chimelong Ocean Kingdom. The dataset included multiple whistle categories, including a whistle type that has not previously been available for research. We then applied convolutional neural networks (CNNs) for classifying whistle signals, using five CNN architectures to analyze the signals. Model performance was evaluated using mean average precision (mAP), and the best-performing model achieved 0.929 in mAP on the test set, demonstrating that CNN-based approaches can effectively distinguish among different whistle classes. To probe robustness, we also introduced noise at defined SNR levels to increase testing complexity and assess the stability of the classifier. BELLHOP acoustic propagation modeling was used to generate channel impulse responses. These simulated signals were combined with the original signal data to construct an augmented training set. The results indicate that this augmentation enhanced the robustness of the classification model. Differentiating the whistle types is crucial as whistle categories may reflect variation in communication structure, behavioral context, or group-level acoustic patterns. Therefore, the proposed approach can support large-scale bioacoustic analysis and provide useful information for future studies on dolphin communication, behavior, and conservation. Full article

The primary aim of wildlife rehabilitation centres is the release of treated animals back into the wild after treatment. Data collected during rehabilitation can provide valuable insights into current trends and can help with conservation strategies aiming to reduce human-related negative impact. This review analyses records from past and currently operating wildlife rescue and rehabilitation centres in Lithuania over a 23-year period. Data were compiled for 7847 individual animals representing 216 species of birds, mammals, and reptiles. The study evaluates patterns of seasonal admission, taxonomic composition, known causes of injury or admission, and rehabilitation outcomes. The results showed that 83% of cases involved birds, mammals comprised 16%, and reptiles were recorded only infrequently (0.52%). Admissions peaked in summer, comprising 42% of all cases. Injuries of unknown origin were the most common (55%). Among cases with identified causes, a substantial proportion were associated with human activities, including road accidents (5% of all cases), collisions with anthropogenic structures (4%), and attacks by domestic cats or dogs (3%). The presence of a specialized rehabilitation centre, together with active public involvement in the rescue of injured wildlife, contributes to release rates reaching approximately 30% of admitted animals. Datasets such as those analyzed in this study may contribute to improved preparedness for managing unavoidable human–wildlife interactions in the future. Full article

Campylobacter jejuni is a major zoonotic pathogen that circulates among birds, livestock, humans, and environmental reservoirs, yet the genomic mechanisms that enable persistence and transmission across divergent hosts remain incompletely understood. Here, we sequenced 61 C. jejuni isolates recovered from multiple host-associated sources in Shenzhen, China, from 2016 to 2023, and analyzed them together with 312 dereplicated publicly available high-quality reference genomes. Phylogenomic analyses resolved three major clades, including one avian-restricted clade and two clades showing frequent cross-host occurrence. Human-associated isolates displayed lower coding density than mammal-associated isolates and significantly higher proteome-level carbon and nitrogen demands than avian-associated isolates. Comparative genomic analyses further revealed strong host-associated divergence in chromosome-encoded, plasmid-encoded, and horizontally acquired gene repertoires. In human-derived isolates, 11 dataset-specific human-unique KEGG genes and 48 human-unique virulence-associated genes were identified, and human-associated strains showed the strongest multidrug-resistance signal across both chromosome-encoded and mobile-gene compartments. Resistance-associated functions enriched in human-associated genomes included antibiotic inactivation, efflux-mediated resistance, target protection/replacement/alteration, reduced permeability, and nutrient-acquisition-associated resistance. By contrast, core host-interaction loci remained under strong purifying selection, indicating that major human-associated traits were linked more closely to mobile gene acquisition than to extensive mutation-driven diversification. Together, these findings support a proposed genome-partition framework of host adaptation in C. jejuni, in which relatively stable chromosomal backgrounds are complemented by rapid plasmid- and horizontal-transfer-mediated acquisition of high-impact accessory genes. Full article

Open-access biodiversity repositories such as the Global Biodiversity Information Facility (GBIF) are central to contemporary conservation research, yet their heterogeneous data sources introduce quality issues and spatial sampling biases that may compromise conservation analyses. This study evaluates the spatial and taxonomic quality of GBIF occurrence data for five protected species representing mammals and vascular plants in Central Europe. A transparent data-cleaning workflow was applied, including coordinate validation, removal of duplicate and erroneous locations, and taxonomic harmonization. Spatial sampling bias was quantified using nearest neighbor distance-based metrics, enabling comparison of clustering patterns before and after data cleaning. Raw datasets exhibited strong spatial clustering across all species, with nearest neighbor ratios (NNR) ranging from 0.06 to 0.73. Data cleaning reduced the number of retained records by approximately 15–57% and increased NNR values to 0.27–0.80, indicating the removal of extreme spatial artifacts. However, NNR values remained well below unity after cleaning, demonstrating persistent non-random spatial sampling structure related to uneven sampling effort. The strongest relative improvements were observed for plant species derived from herbarium records. These results highlight the need to distinguish between data quality errors and structural spatial bias in open biodiversity data and underscore the necessity of bias-aware methods beyond standard data-cleaning procedures in conservation analyses. Full article

Understanding animal actions and interactions is essential for behavior analysis and ecological monitoring. Although large-scale in-the-wild datasets have advanced animal action recognition, existing methods still struggle with fine-grained motion, spatial relations, and multi-individual interactions. To address these challenges, we introduce AIRA, a unified framework for Action and Interaction Recognition in Animals. Built upon a vision–language model (VLM), AIRA learns in an action-centered representation space defined by body parts and their corresponding motions, thereby improving robustness to background noise and enabling cross-species generalization via a unified mammal-centric part ontology. To model actions, we treat body parts and motion as primary cues and introduce Actionbit tokens—compact representations for parts and motions generated by a large language model (LLM) that encode which parts move and how. We further propose Part-Enhanced Prompt Fine-tuning (PEPF) to make the VLM explicitly sensitive to part and pose cues. Within PEPF, the Action–actionbit Alignment (AbA) module enriches action representations with fine-grained part–motion semantics, and Part-Vision Prompting (PVP) extracts keyframes through action-aware prompting. Experiments across multiple benchmarks show consistent improvements in both action and interaction recognition, highlighting the importance of action-centered adaptation and relational reasoning for understanding animal behavior in the wild. Full article