Search Results (198)

Water scavenger beetles (Coleoptera: Hydrophiloidea) exhibit remarkable adaptations to both aquatic and terrestrial habitats and play irreplaceable ecological roles, yet their higher-level phylogeny and the molecular basis of their adaptive evolution remain unresolved. Here, we sequenced four complete mitogenomes of C. unipunctatus from the Qinghai–Tibetan Plateau (QTP) and conducted a comprehensive mitogenomic analysis by integrating these new data with 22 publicly available Hydrophiloidea mitogenomes, representing three families and six subfamilies. Our analyses revealed highly conserved mitogenomic architecture across Hydrophiloidea, with structural variation confined to non-coding regions and AT content correlating with both habitat type and phylogenetic lineage. Phylogenetic reconstructions robustly resolved the higher-level relationships: Helophoridae and Hydrochidae formed the sister group to Hydrophilidae, within which Hydrophilinae and Sphaeridiinae were strongly supported as monophyletic clades. We detected positive selection in the energy metabolism genes cox3 and nad5 along the ancestral branch of the terrestrial subfamily Sphaeridiinae, providing the first molecular evidence linking mitochondrial adaptation to the aquatic-to-terrestrial habitat shift. However, no positive selection signals were found in high-altitude C. unipunctatus populations, suggesting that adaptation to extreme environments operates through alternative mechanisms (e.g., regulatory or structural variation) rather than protein-coding evolution. This study establishes a robust phylogenetic framework for Hydrophiloidea and reveals the diverse molecular pathways underlying their adaptive evolution, from protein-coding adaptation during aquatic–terrestrial shifts to non-coding responses in extreme high-altitude environments. Full article

Background: Velvet worms (Onychophora) occupy a pivotal phylogenetic position for deciphering the evolution of Panarthropoda, yet their exact placement within this clade remains debated. Furthermore, early studies in some onychophoran species revealed extensive gene rearrangements and the truncation or even loss of canonical transfer RNAs (tRNAs), features uncommon in other panarthropods. However, due to sparse representation, the pervasiveness and evolutionary significance of these genomic peculiarities across the phylum remain poorly understood. Methods: We sequenced and assembled three novel mitogenomes representing both extant onychophoran families (Epiperipatus barbadensis [Peripatidae]; Euperipatoides rowelli and Phallocephale tallagandensis [Peripatopsidae]) and conducted comparative analyses with five published species. Results: Onychophoran mitogenomes displayed high A+T content (mean 77.32%) but revealed a family-level divergence in GC skew. All genomes contained the standard 13 protein-coding genes (PCGs) and two ribosomal RNAs, yet tRNA counts varied significantly (ranging from 13 to 22), reflecting lineage-specific tRNA loss. Ancestral state reconstruction uncovered deep architectural divergence: Peripatopsidae retains the ancestral onychophoran gene arrangement, whereas Peripatidae exhibits a stable but derived gene order. Despite this architectural plasticity, synonymous codon usage patterns remained strictly conserved across the phylum, with all but one PCG evolving under strong purifying selection. Maximum likelihood phylogenetic reconstruction based on PCGs strongly supported Onychophora as the sister group to Arthropoda within Panarthropoda. Conclusions: Our findings provide robust molecular evidence supporting the Antennopoda hypothesis over the Tactopoda hypothesis for Panarthropoda phylogeny. Furthermore, we demonstrate extensive mitogenomic remodeling between the two extant onychophoran families, including divergent GC-skew patterns, tRNA contents, and gene arrangements. Full article

Mpox is a zoonosis caused by the monkeypox virus. Here, we report Mali’s index Mpox case, which was clinically identified at the Mali–Guinea border by the national telemedicine center and confirmed by PCR. The library prepared with NextGenPCR™ MPXV Sequencing Library Prep and sequenced on Minion MK1C revealed a genome length of 197,122 bp with an average depth of 1284.4×. The strain belonged to Clade IIb G1 lineage and exhibited 85 mutations relative to NC_063383.1. To decipher genomic epidemiology, genomes ≥ 195 kb were retrieved from NCBI and aligned with MAFFT. Time-resolved phylogenetic reconstruction and ancestral trait inference were performed with TreeTime v0.11.4. A median joining network was built with Popart v1.7. Phylogeographic analysis revealed clustering with Clade IIb (G.1 lineage) linked to the May 2025 outbreak in Sierra Leone. Full article

Amidst rapid urbanization and modernization, numerous traditional villages in China face severe challenges, including landscape homogenization and the erosion of their distinctive characteristics. Addressing this issue requires a method capable of systematically identifying, analyzing, and reconstructing both the landscape and its underlying cultural features. This study proposes a digital analytical approach that integrates multimodal artificial intelligence with landscape language theory to address the homogenization of cultural landscapes in traditional Chinese villages. Taking Xinye Village in Zhejiang Province as a case study, the research systematically decodes its landscape spatial narratives and underlying cultural genes. This framework systematically deconstructs village landscapes across four levels: “vocabulary, context, grammar, and semantics”. The village image database is first automatically recognized and statistically analyzed by computer vision technology, which extracts 31 core landscape vocabulary items from three main categories and nine subcategories. Second, Retrieval-augmented Generation technology is employed to synthesize from the constructed domain-specific corpus, a natural context structured around Yuhua Mountain and Daofeng Mountain, as well as a cultural context based on ancestral hall order, connected through folk activities, and idealized by farming and reading passed down through generations. Building on this framework, a multimodal model was used to examine the spatial composition and combinatorial laws of landscape features. Six essential dimensions—spatial layout, visual order, element combination, functional relationships, circulation layout, and scale correlations—revealed the spatial grammar of shuikou landscape. Lastly, the semantic values conveyed by the landscape vocabulary were thoroughly analyzed across three dimensions—form, function, and culture—by integrating a knowledge base. This work creates a landscape language atlas of Xinye Village by combining these studies and using a linguistic model of “character-word-sentence-paragraph”. By methodically deciphering the clan’s cultural code of “farming and reading passed down through generations”, this clearly reconstructs the spatial narrative logic from micro-elements to macro-patterns. This research not only advances the study of landscape language in traditional villages from qualitative description toward a systematic, digital, and interpretable paradigm but also provides an operational theoretical and methodological foundation for the in-depth interpretation, conservation, and transmission of traditional village cultural landscapes. Full article

The Neuroblastoma Breakpoint Family (NBPF) consists of 23 genes, 9 of which are pseudogenes, and is characterized by extensive duplication events and species-specific diversification in Homo sapiens, as well as by the presence of a unique protein domain known as Olduvai (also referred to as DUF1220 or the NBPF domain). Previous studies have attempted to define subfamilies based on the presence of HLS triplet domains; however, this classification has become increasingly unclear with the identification of additional NBPF members. The family remains poorly understood, and the functions of many genes are still unknown, although several have been hypothesized to play key roles in cell proliferation and developmental processes, particularly in neural and skeletal tissues. In this study, we systematically analyzed all available data on the NBPF gene family using the PRISMA-S methodology to infer the biological functions in which these genes may be involved. We also generated multiple phylogenetic trees to support the creation of coherent subfamilies and to correlate the origin of each subfamily with homologous genes in our last common ancestor with the Pan genus, providing what we believe to be one of the most comprehensive phylogenetic reconstructions including all currently annotated NBPF members. Through comparative genomic and phylogenetic analyses, we propose that the NBPF may have originated from a duplication of the PDE4DIP gene, with NBPF26 representing the ancestral member from which the remaining NBPF genes diverged via lineage-specific segmental duplications. In this systematic review and comparative genomic study, we present the first integrative synthesis of our knowledge of the NBPF, encompassing its evolutionary origins, structural dynamics, expression across tissues, and clinical associations. Full article

South China’s freshwater biodiversity has been shaped by Quaternary climatic oscillations and persistent geological barriers. We investigated the phylogeography and conservation implications of the primary freshwater fish Microphysogobio kachekensis across mainland China and Hainan Island using mitochondrial (cyt b and control region) and nuclear (RAG2 and rpS7-1) markers from 200 individuals. Mitochondrial analyses recovered two major lineages and multiple sublineages largely structured by drainage basins, whereas nuclear data resolved four geographically concordant lineages. Population differentiation was strong (high F_ST), and SAMOVA/AMOVA supported major barriers restricting gene flow, including the Qiongzhou Strait, Gulf of Tonkin, Yunkai Mountains, and Nanling Mountains. Ancestral-area reconstruction inferred the Pearl River region as the most likely source area, followed by dispersal to northern Hainan and subsequent expansion to southern Hainan and the Red River, with additional northward expansion to the Zhejiang–Fujian region. Despite high haplotype diversity, within-population nucleotide diversity was low, consistent with long-term river isolation and complex demographic history. We propose six ESUs and four MUs for evolutionarily informed conservation and to guide stock enhancement in southern China. Full article

The diversity of religious traditions and the increasing prevalence of religious pluralism, along with critical reflections on scientism and the relationship between philosophy and religion, have stimulated global scholarly discussions on Confucianism—its identity as a tradition of learning, its religious dimensions, and its relation to religion in general. These discussions have been further enriched by the discovery of early Confucian texts and renewed examination of existing Confucian classics. As the founder and chief architect of Confucianism, and as both a perceiver and teacher of its truths, Confucius demonstrated a distinct religious consciousness in his teachings and practices. This is reflected in his beliefs concerning spirits and deities, his views on sacrifice, and his ritual awareness—not only through his faith in Heaven and the Mandate of Heaven and his reverence for ancestral spirits, but also in his belief in natural deities. However, Confucius’s conception of natural deities and his associated sacrificial views remain relatively underexplored. This paper examines how Confucius distinguished between the physical and the divine aspects of nature, recognized the connection between the order (or disorder) of these two realms and political governance, maintained faith in natural deities, and advocated for corresponding ritual practices. By systematically reconstructing Confucius’s beliefs regarding natural deities, this study aims to fill a significant gap in current research. Full article

Background: This study presents the sequencing and analysis of mitochondrial DNA (mtDNA) genomes from nine early medieval horse remains excavated across archaeological sites in Silesia region in present day Poland. Methods: Using aDNA extraction protocols optimized for short fragments, combined with target enrichment and high-throughput sequencing, we reconstructed partial mtDNA sequences for seven of the specimens. Results: The authenticity of the aDNA was confirmed through damage pattern analysis. Phylogenetic reconstruction revealed that the specimens belonged to six distinct mtDNA lineages (B, D, E, G, L, and M), indicating a high level of mitochondrial diversity within medieval Silesian horse population. Conclusions: These findings highlight the extensive mtDNA variability among domestic horses, reflecting the diversity of their ancestral populations rather than modern breed differentiation. This research enhances our understanding of horse population structure in medieval Europe, emphasizing the genetic complexity present during this period. Full article

The bifunctional glutathione synthase (GshF) is able to catalyze glutathione synthesis and is favored for industrial application due to its lack of product inhibition. However, its practical use is limited by moderate catalytic efficiency and poor thermostability. Here, we applied ancestral sequence reconstruction (ASR) to engineer a more robust ancestral GshF (Anc427) with thermal denaturation temperature of 56.2 ± 0.2 °C, representing an increase of 10.8 ± 0.2 °C over the probe enzyme (St-GshF). Additionally, Anc427 exhibited a thermal half-life (t_1/2) of 3465.7 min at 40 °C, representing a 20-fold increase over that of St-GshF. Under optimal conditions (pH 7.0, 37 °C), Anc427 displayed a specific activity of 3.3 ± 0.02 U·mg⁻¹, representing a 20% enhancement compared to St-GshF. Structural modeling and molecular dynamics simulations indicated that the improved stability can be attributed to increased structural rigidity in Anc427. These findings demonstrate that ASR effectively enhances both thermostability and catalytic activity of GshF, significantly advancing its potential for industrial biocatalysis. Full article

This study presents an in silico proof of concept exploring whether deep learning models can perform conditional mitochondrial DNA (mtDNA) sequence prediction across species boundaries. A CNN–BiLSTM model was trained under a leave-one-species-out (LOSO) scheme on complete mitochondrial genomes from 21 vertebrate species, primarily archosaurs. Model behavior was evaluated through multiple complementary tests. Under context-conditioned settings, the model performed next-nucleotide prediction using overlapping 200 bp windows to assemble contiguous 2000 bp fragments for held-out species; the resulting high token-level accuracy (>99%) under teacher forcing is reported as a diagnostic of conditional modeling capacity. To assess leakage-free performance, a two-flank masked-span imputation task was conducted as the primary evaluation, requiring free-running reconstruction of 500 bp interior spans using only distal flanking context; in this setting, the model consistently outperformed nearest-neighbor and demonstrated competitive performance relative to flank-copy baselines. Additional robustness analyses examined sensitivity to window placement, genomic region (coding versus D-loop), and random initialization. Biological plausibility was further assessed by comparing predicted fragments to reconstructed ancestral sequences and against composition-matched null models, where observed identities significantly exceeded null expectations. Using the National Center for Biotechnology Information (NCBI) BLAST web interface, BLASTn species identification was performed solely as a biological plausibility check, recovering the correct species as the top hit in all cases. Although limited by dataset size and the absence of ancient DNA damage modeling, these results demonstrate the feasibility of conditional mtDNA sequence prediction as an initial step toward more advanced generative and evolutionary modeling frameworks. Full article

This article examines how the Park Chung Hee regime reshaped the public memory of the Neo-Confucian philosopher Yi I (penname Yulgok, 1536–1584) by recasting him as a model of patriotic nationalism. Beginning with the inauguration of the Yulgok Festival in 1962, Yi I was no longer commemorated solely as a scholar of the Chosŏn dynasty; instead, the regime portrayed him as a patriotic sage who advocated for military preparedness. Drawing on archival materials (presidential speeches, heritage management reports, newspaper articles), this study reconstructs the policy discourse surrounding Yulgok and traces the state-driven mechanisms that reframed his public image. The analysis shows that Yulgok’s image became embedded in political rituals, monumentalized in public spaces, circulated in everyday life through currency iconography, and materialized in physical heritage sites transformed to embody a purified, idealized vision of the past. Together, these initiatives positioned the state as the custodian of Yulgok’s memory, aligning his image with the ideological priorities of the militarist state. Full article

Bacteriophages are powerful drivers of microbial evolution and are increasingly explored as alternatives to antibiotics against multidrug-resistant pathogens such as Pseudomonas aeruginosa. Here, we describe the isolation, phenotypic characterization and genomic, structural and evolutionary analysis of Pseudomonas phage Adele, a lytic myovirus representing a novel species within the genus Pakpunavirus (family Vandenendeviridae). Phage Adele exhibits a short latent period of 20 min, a burst size of 59 ± 11 virions per infected cell and a high virulence index, efficiently lysing non-O11 Pseudomonas aeruginosa strains and reducing biofilm biomass. In vivo, Adele confers marked protection in a Galleria mellonella infection model. Phylogenetic reconstruction, synteny analysis and structural modeling demonstrate the relatedness of Vandenendeviridae to phages of the Andersonviridae and Vequintavirinae clades, pointing to a stable, ancestral virion architecture that has undergone lineage-specific elaborations, including the duplication and divergence of tail tube proteins. The tail assembly chaperone gene employs a conserved −1 programmed ribosomal frameshift. Phage Adele encodes an elaborate set of metabolic reprogramming and anti-defense systems, reflecting extensive horizontal gene transfer. The combination of a conserved structural architecture and mosaic genome establishes Adele as an exemplary system for studying modular evolution in phages, alongside its demonstrated therapeutic efficacy. Full article

The evolution of robust DNA repair mechanisms was a prerequisite for the conquest of land by plants, a transition that exposed them to harsh new environmental stressors. The poly (ADP-ribose) polymerase (PARP) family is central to this adaptation, as it orchestrates DNA repair and stress signaling pathways essential for coping with the elevated UV radiation and desiccation of terrestrial environments. Yet its early evolutionary origins are unknown. Here, we present a comprehensive reconstruction of the PARP family’s history across the plant kingdom. Our phylogenomic analysis reveals that PARP evolution ignited during the bryophyte radiation, expanding from a single ancestral algal gene into three distinct subfamilies (PARP1, PARP2, and PARP3). This diversification was driven by structural innovations in DNA-binding domains and a rewiring of transcriptional networks to respond to terrestrial challenges. We provide direct experimental support for this hypothesis through functional analysis of PARPs from the extremotolerant moss Syntrichia caninervis. We show that its PARP proteins provide multifaceted protection against UV radiation, heat, and genotoxic agents, and that recently duplicated PARP2 genes are already diverging in function. Our work pinpoints the molecular adaptations in a key DNA repair family that enabled the greening of Earth and uncovers novel genetic targets for enhancing crop resilience. Full article

Background/Objectives: Chromosomal inversions play an important role in the evolution of insects by forming genetic barriers between closely related species and facilitating local adaptation. Polymorphic inversions in malaria mosquitoes of the Maculipennis subgroup have been studied for over 50 years, yet the evolutionary ancestry of the gene orders remains unknown. In this study, we mapped the genes flanking the breakpoints of two polymorphic X-chromosome inversions in the cryptic species Anopheles messeae and Anopheles daciae of the Maculipennis subgroup. Methods: We used an iterative mapping approach to define the breakpoint regions, selecting flanking markers based on the genome assembly of the reference species, Anopheles atroparvus. To identify the ancestral X chromosomal arrangement in An. messeae and An. daciae, we developed and implemented the genomic inversion calculator (GIC), which uses greedy heuristics to determine the shortest evolutionary scenario of rearrangements. Results: Our knowledge of the relative genomic positions of the inversion breakpoints in An. daciae and An. messeae enabled us to use the An. atroparvus genome as an outgroup and the GIC tool to show that the X0 and X2 arrangements emerged independently along the evolutionary lineages of An. daciae and An. messeae, respectively, based on the X1 arrangement. Conclusions: These results refine the structure and boundaries of the X chromosome rearrangements and reconstruct the sequence of evolutionary events in the cryptic complex An. messeae–An. daciae, demonstrating that the X1 arrangement is ancestral. This study lays the groundwork for analyzing the molecular organization of breakpoints, the mechanisms of inversion formation, and their role in speciation. Full article

Currently, there remains a lack of systematic quantitative analysis of the acoustic impact mechanism of ancestral temple theatres in relation to their core function of opera performance. This paper takes the Zhaomutang—a typical ancestral temple theatre in northeast Jiangxi—as an example, and comprehensively uses on-site mapping, impulse response testing, and ODEON three-dimensional sound field simulation to conduct acoustic sensitivity analysis on five key spatial elements of the theatre. The results show that the theatre has a hierarchical sound field pattern along its depth, characterized by “high in the front, low in the rear, stronger on the sides and weaker in the middle”. The front patio and the Xiangtang support the clarity of Gan opera dialogue and the fullness of singing through early lateral reflections and moderate reverberation (EDT of 0.8–1.1 s, C₈₀ of 3.2–6.1 dB). However, the rear patio and the Qintang show apparent loudness deficiency (G of −1.5–3.2 dB) and lack of spatial immersion (LF₈₀ below 0.23). The most effective optimization comes from the reconstruction of the geometric relationship between performers and audience: moving the performers forward and appropriately raising the stage and audience area floor can significantly shorten the rear area EDT and increase C₈₀ and G; in contrast, the improvement in sound quality brought about by adding a patio cover and raising the gables is minimal, and the changes in various parameters are generally less than 1 JND. Based on this, the “schedule priority—reversible intervention” acoustic maintenance strategy for living heritage is proposed, and it is suggested that reversible reflective components be set in the side corridor to specifically enhance the sense of immersion in the rear area sound field. The study constructs a quantitative correlation framework of space, materials, and sound field, providing methodological support and parameter basis for the acoustic assessment and protective utilization of ancestral temple theatres. Full article