Search Results (591)

Arid Central Asia (ACA) is a major source of atmospheric dust in the Northern Hemisphere; however, the evolutionary models and driving mechanisms of Holocene aeolian activity in this region remain debated. Based on 13 reliable AMS ¹⁴C dates from the Sayram Lake SLM2009 sediment core, this study reconstructs the Holocene sequence in aeolian activity through end-member modeling analysis (EMMA). It evaluates its relationship with regional atmospheric circulation. Four end-members were identified from base to top: EM1, with a modal grain size of 7.58 μm, represents low-energy suspension deposition; EM2 (26.30 μm) reflects lacustrine hydrodynamic processes; while EM3 (52.48 μm) and EM4 (416.86 μm) serve as proxies for regional aeolian activity. The results indicate that aeolian activity was relatively strong during the early Holocene (reaching peaks at 11.7–11.2 and 9.2–8.1 cal ka BP), significantly intensified during the mid-Holocene (7.3–5.3 cal ka BP), and gradually weakened in the late Holocene (since 4.0 cal ka BP). Comparison of the aeolian record from Lake Sayram with Greenland ice cores, North Atlantic ice-rafted debris events, and the GISP2 K⁺ record indicates that variations in aeolian activity in arid Central Asia are closely linked to the Northern Hemisphere climate system. We propose that these variations were primarily modulated by large-scale atmospheric circulation, driven by the synergistic interaction between the Siberian High and the mid-latitude westerlies. Full article

Background: PYR/PYL/RCAR proteins are core abscisic acid (ABA) receptors that play essential roles in ABA signal transduction, plant growth and development, and abiotic stress responses. However, the PYL gene family in watermelon (Citrullus lanatus) has not been systematically characterized, limiting our understanding of ABA-mediated stress adaptation in this economically important crop. Methods: A genome-wide analysis was performed to identify ClPYL genes in watermelon using a hidden Markov model search. Phylogenetic relationships were reconstructed using the maximum likelihood method. Segmental duplication events were analyzed using synteny analysis. Conserved motifs, gene structures, and promoter cis-acting elements were characterized using MEME and PlantCARE. Expression profiles under drought, salt, and cold stresses were examined by quantitative real-time PCR (qRT-PCR) with three biological replicates. Results: In this study, 15 ClPYL genes were identified in watermelon through genome-wide analysis. Phylogenetic reconstruction classified these genes into four subfamilies, with subfamily II being exclusively present in cucurbits—a lineage-specific feature not observed in Arabidopsis. Synteny analysis revealed eight segmental duplication events involving members of subfamilies I, III, and IV, while subfamily II members were not associated with these duplications. Members within the same subfamily share similar exon-intron structures and conserved motifs. Promoter analysis revealed that ClPYL genes are enriched with various cis-acting elements associated with hormone signaling and abiotic stress responses. Expression profiling demonstrated that ClPYL genes exhibit diverse and dynamic expression patterns under drought, high-salinity, and cold stresses. Notably, genes such as ClPYL5 under drought, ClPYL02 under salt, and ClPYL15 under cold stress displayed persistent stress-responsive expression. Conclusions: These findings reveal the evolutionary conservation and diversification of the PYL family in watermelon and provide a set of candidate genes for functional studies aimed at dissecting ABA-mediated stress adaptation. This work establishes a genomic framework for developing stress-resilient watermelon varieties through molecular breeding. Full article

This article examines Max Nordau’s Entartung (Degeneration) (1892/93) at the intersection of fin-de-siècle cultural critique and contemporary psychopathology. It argues that Nordau did not simply denounce modern art, but transferred an established psychiatric vocabulary—centred on degeneration, hysteria, and neurasthenia—into the sphere of aesthetic judgement. Interpreting a range of literary and cultural phenomena as symptoms of pathological degeneration, Nordau sought to diagnose the psychological condition of modern culture through the works of contemporary writers and intellectuals. Situating Entartung within the broader nineteenth-century degeneration paradigm and within contemporary evolutionary debates, the article analyses how scientific discourse was mobilised to authorise cultural evaluation. Rather than assessing the validity of Nordau’s diagnoses, it reconstructs the epistemic logic through which psychiatric categories were transformed into instruments of cultural criticism. In doing so, it repositions Nordau within the history of the human sciences, highlighting his role in the consolidation of expert authority in late nineteenth-century cultural debates. By foregrounding the structural migration of psychiatric categories into cultural criticism, the article contributes to a more nuanced understanding of the alliance between scientific knowledge and normativity at the fin de siècle. Full article

Increasing genomic data are driving changes in the selection of phylogenetic markers and analysis strategies. Databases enable the extraction of established markers, such as single and multilocus sequence typing (MLST), but are often limited by the number of informative sites or availability with respect to incomplete source data sets or reductive evolution in bacteria such as the Mollicutes. Genome-wide analyses like average nucleotide identity (ANI) often overcome these problems but also depend on the alignment percentage. Complementary analyses help validate results and address limitations of primary approaches. However, how genome-wide compositional signals and reduced core gene sets affect phylogenomic resolution across a large and taxonomically diverse dataset of complete Mollicutes genomes remains unclear. Therefore, we applied an advanced MLST approach based on single-copy orthologs (SCOs), alongside codon usage analysis. The reliability and impact of these approaches were first analyzed using Acholeplasmatales as the foundation, with 16S rRNA gene, ANI, SCOs, and codon usage. Codon usage analysis revealed lineage-associated compositional signatures across the 52 strains that were broadly consistent with current genus and subgroup assignments, whereas ANI and 16S rRNA gene identified species with ≥96.5% and ≥97%, respectively. Among these, SCOs showed the most matches to the current taxonomy, supporting the approach being extended to Mollicutes. Applied to 807 Mollicutes strains, the analysis revealed 16 shared SCOs. Concatenation of this core set significantly enhanced phylogenomic resolution, providing a robust framework for reconstructing evolutionary relationships within Mollicutes. Full article

We propose a coupling-aware equivalent source reconstruction framework for reproducing complex three-dimensional electromagnetic (EM) environments inside an anechoic chamber. A measured or simulated target field is represented by a finite set of physically realizable equivalent source antennas whose positions and complex excitations are identified by solving a nonlinear high-dimensional inverse problem. To ensure physical fidelity, the forward model explicitly accounts for mutual coupling through a full-wave Method-of-Moments (MoM) formulation, avoiding the inaccuracies of idealized uncoupled superposition. The inverse problem is efficiently solved using a hybrid evolutionary optimization scheme that combines an adaptive differential evolution strategy with stagnation-triggered CMA-ES refinement, augmented by a lightweight surrogate-based pre-screening to reduce expensive full-wave evaluations. The optimized source configuration is directly deployed in a microwave anechoic chamber, where the reconstructed field is measured on an observation plane and compared against the target field. The experimental results demonstrate close agreement in both amplitude and spatial distribution, while the proposed optimization pipeline substantially reduces the number of full-wave evaluations required for convergence. This work enables accurate repeatable chamber emulation of outdoor or in situ EM scenarios for robust system-level testing and evaluation. Full article

Codon usage bias is important for regulating protein translation efficiency and accuracy. The HSP90 gene, a pivotal gene in plants, maintains homeostasis in plant protein stress responses and organelle immune defense functions. We systematically examine codon usage preferences in six forage grass species and the regulatory mechanisms of the HSP90 gene in governing codon preference. A set of metrics is evaluated, including effective codon number (ENC), codon adaptation index, and relative synonymous codon usage. Neutral evolutionary trajectories reveal usage preferences for six plant codons, with natural selection serving as the primary driving factor. The correlation between the ENC–GC3 curve (ENC relative to third-position GC content in synonymous codons) and codon bias index reveals these genes to exhibit moderate codon bias. The phenomenon of evolutionary constraints is exemplified by a propensity for C/G-terminating codons, concomitant with a suppression of NUA/NCG codons (NUA is an abbreviation for UA dinucleotide, and NCG is an abbreviation for CG dinucleotide). Phylogenomic reconstruction reveals a conserved diversification pathway, positioning P. giganteum A. Rich. at the basal node of the evolutionary framework. This study identified through systematic assessment that natural selection is the primary evolutionary force driving the biased use of codons in grass HSP90 genes. This finding provides actionable insights for enhancing abiotic stress tolerance in forage germplasm through precise codon engineering. Full article

Rana kukunoris is an amphibian species endemic to the Qinghai-Xizang Plateau and adapted to high-elevation environments. To clarify its genetic diversity and phylogeographic structure, mitochondrial cytochrome b (Cytb) sequences from multiple localities across the northeastern plateau were analyzed. The results indicate moderate haplotype diversity coupled with low nucleotide variation, suggesting a demographic history shaped by historical bottlenecks and limited expansion. Furthermore, population genetic analyses reveal restricted gene flow and notable genetic differentiation among geographically separated localities. Phylogenetic reconstruction supports the presence of two major lineages, corresponding to northern and southern groups divided by an elevational boundary at approximately 3200 m. Historical demographic inference further suggests regionally distinct population dynamics rather than a pronounced, synchronous expansion. Overall, these findings demonstrate that plateau topography and Quaternary climatic oscillations have played key roles in shaping the evolutionary history and current genetic structure of R. kukunoris. 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

PRRSV-2 represents a major threat to the swine industry. Canada is one of the world’s leading pork producers and a major trading partner of live pigs with the United States, yet PRRSV-2 evolutionary dynamics in these two countries are often studied independently, partly due to limited publicly available sequence data from Canada. We analyzed more than 3000 PRRSV-2 ORF5 sequences collected between 2000 and 2024 from five Canadian provinces. Thirteen previously described sub-lineages were detected in Canada, while approximately one-third of the sequences could not be assigned to any known sub-lineage. Phylogenetic analyses incorporating global reference sequences revealed that most unclassified sequences clustered into four distinct monophyletic clades, exhibiting genetic distances greater than 9.5% from recognized sub-lineages. We propose two new sub-lineages, 1K and 1L, corresponding to clades that were prevalent and persistent over time, whereas the remaining two clades were rare and last detected in 2021. We reconstructed cross-border transmission histories and found that sub-lineages 1C, 1H, 1I, 1K, and 1L originated in Canada, whereas 1A, 1B, 1E, and 1F originated in the United States. Transmission patterns varied across sub-lineages, ranging from unidirectional to bidirectional movement. Our findings refine PRRSV-2 classification and provide insights to inform targeted surveillance, particularly at national borders. Full article

Codon usage bias (CUB) in mitochondrial genomes reflects evolutionary forces such as mutation, selection, and genetic drift, yet its dynamics in early-diverging fungal lineages like Conidiobolus (Zoopagomycota) remain unclear. This study systematically analyzed mitochondrial core protein-coding genes (PCGs) from eight Conidiobolus species to elucidate the drivers of CUB and phylogenomic patterns. Nucleotide composition revealed pronounced AT richness (73.32% ± 3.38%) and low GC3 (13.40% ± 5.11%), indicating a preference for A/T-ending codons. Neutrality and ENC-GC3s plots demonstrated that natural selection, rather than mutation pressure, predominantly shaped codon bias, supported by weak GC12-GC3 correlations (slopes: 0.037–0.335) and significant ENC deviations from mutation-driven expectations. PR2-bias analysis further highlighted a strong bias toward A over T and C over G. Correspondence analysis linked major codon usage variations to GC3s, CAI, and FOP indices. Phylogenetic reconstructions based on relative synonymous codon usage (RSCU) and concatenated mitochondrial sequences revealed discordant topologies, particularly in the placement of C. polytocus and C. polyspermus, suggesting divergent evolutionary trajectories. Optimal codon analysis identified species-specific preferences dominated by A/T termini. These findings underscore natural selection as the primary force driving AT-biased mitochondrial CUB in Conidiobolus, while phylogenomic discordance highlights complex evolutionary pressures in this ecologically diverse fungal genus. This study provides foundational insights into mitochondrial genome evolution and codon adaptation mechanisms in early-diverging fungi. Full article

Riptortus pedestris (Hemiptera, Alydidae) is widely distributed across East Asia, where significant genetic differentiation may occur among geographic populations. To understand the genetic structure, historical dynamics, and formation of geographic distribution patterns in China, we conducted a phylogeographic analysis using three mitochondrial genes (COI, COII, Cytb) from 35 populations. After PCR amplification, we performed genetic diversity analysis, Fst/Nm estimation, phylogenetic reconstruction (ML, BI, NJ), haplotype network, AMOVA, neutrality tests, mismatch distribution, and molecular dating. Results revealed high genetic diversity (Hd > 0.81, π > 0.011), an AT-rich base composition, and faster evolution at the first codon position. Genetic and geographic distances were significantly correlated, with high Fst values indicating strong differentiation, especially between southwestern/southern and other populations. Two main clades were identified: Clade 1 (mainly southern and southwestern China) and Clade 2 (central, northern, northwestern, and northeastern China). A star-like haplotype network and neutrality tests suggested a rapid expansion around 0.019–0.022 Ma (Last Glacial Maximum), and molecular dating estimated the main split at ~0.029 Ma. AMOVA and Gst/Nst confirmed significant phylogeographic structure with most variation among populations. This study provides initial evidence for the genetic differentiation and evolutionary history of R. pedestris in China, demonstrating that its population structure was shaped by climatic changes and geographical isolation, providing key insights into its adaptive evolution and dispersal. Full article

Background/Objectives: We analyzed the whole-genome sequences of ciprofloxacin-resistant (CIP-R) enteropathogenic Escherichia coli (EPEC) ST752 isolates in South Korea to characterize their molecular epidemiology. This lineage has emerged as the predominant CIP-R EPEC clone in South Korea, accounting for 28.8% of human clinical isolates and circulating within the One Health interface. Methods: We performed whole-genome sequencing (WGS) and reference-based core-genome single-nucleotide polymorphism (SNP) analysis on 26 CIP-R EPEC ST752 isolates (19 human clinical and 7 poultry-derived isolates). To elucidate their evolutionary history and transmission dynamics, Bayesian phylodynamic and phylogeographic reconstructions were implemented by integrating domestic isolates with a global genome dataset (n = 508). Results: Isolates from human and poultry sources clustered together with an identical virulence profile and minimal genetic distance. The Bayesian molecular clock analysis estimated that the time to the most recent common ancestor of the South Korean clade was 2000.65. Moreover, the phylogeographic analysis supported statistical evidence (Bayes factor 32.16) for the introduction of this lineage into South Korea from Denmark and revealed a strongly supported host transition from humans to poultry (Bayes factor > 10,000), although this requires cautious interpretation due to limited temporal sampling of poultry isolates. Conclusions: Continued integrated One Health surveillance across human, animal, and environmental reservoirs is needed to monitor and prevent the spread of high-risk antimicrobial-resistant clones. Full article

Bovine viral diarrhea (BVD) is a major cause of economic losses in the global cattle industry, particularly in countries characterized by intensive livestock production systems. Pestivirus tauri, formerly known as Bovine viral diarrhea virus type 2 (BVDV-2), is the current taxonomic designation according to the International Committee on Taxonomy of Viruses (ICTV). Between 2005 and 2018, Pestivirus tauri was detected in cattle herds in mainland Italy, particularly in the Lombardy region. Four viral strains were successfully isolated in cell cultures and subjected to whole-genome sequencing. Phylogenetic reconstruction placed all Italian isolates within the Pestivirus tauri subgenotype c, a lineage encompassing strains reported in Asia, Europe and the United States. Consistently, comparative sequence identity analyses indicated the highest similarity with the Parker strain (USA, 1991) and the Potsdam 1600 strain (Germany, 2000). These results contribute to a more detailed understanding of Pestivirus tauri genomic architecture and evolutionary dynamics, providing a valuable resource for comparative genomic studies. Such data are crucial for exploring viral diversity and evolution, optimizing the design of diagnostic primers and probes, and advancing insights into the molecular epidemiology of Pestivirus. Full article

Intrabasinal low uplifts in lacustrine rift basins are key targets for sedimentological and petroleum geological research, as they can act as local source areas and exert critical controls on intrabasinal “source-to-sink” systems. Due to the discontinuous sediment supply, these systems often demonstrate the subtle and intermittent nature, and their roles in the development of depositional systems are usually overlooked. To clarify the controlling effect of intrabasinal local provenances on sedimentary system evolution, this study reconstructed the dynamic tectonic evolution of the Weixinan Low Uplift in the Beibuwan Basin, and systematically analyzed its control on “source-to-sink” systems and sedimentary filling using integrated high-resolution 3D seismic, core, well logging and geochemical data. Our results demonstrate that the activity of Fault 3 dominated the paleogeomorphic evolution of the Weixinan Low Uplift and its surrounding areas, which further governed the spatiotemporal development of the “source-to-sink” system and the distribution of sedimentary systems, with distinct evolutionary stages as follows: During the Ls2 Member stage (48.6–40.4 Ma), Fault 3 was inactive, the Weixinan Low Uplift was manifested as a gently dipping subaqueous slope under the influence of regional lacustrine transgression, and only small-scale braided river deltas were developed on the slope belt with weak sediment supply from the Qixi Uplift. During the Ls1 Member stage (40.4–33.9 Ma), the Ls13 Sub-member stage (lower Ls1 Member stage) was characterized by initiation of Fault 3 with segmented activity, triggering the formation of the Eastern Sub-sag of the Haizhong Sag and subaqueous uplift of the Weixinan Low Uplift; clastic sediments from the central Qixi Uplift were transported northeastward, developed braided river deltas and large-scale basin-floor lacustrine fans. In the Ls12 Sub-member stage (middle Ls1 Member stage), Fault 3 continued to propagate and was gradually linked, leading to further uplift of the Weixinan Low Uplift and expansion of the Haizhong Sag; Clastic materials from the central Qixi Uplift were almost entirely trapped in the Eastern Sub-sag of the Haizhong Sag. During the Ls11 Sub-member stage (upper Ls1 Member stage), further intensification of Fault 3 activity caused the Weixinan Low Uplift to be subaerially exposed and evolve into an intrabasinal local provenance, which supplied clastic sediments to surrounding sags and developed braided river deltas on the gentle slope belts and small-scale lacustrine fans on the lower slope. This study demonstrates that the tectonic evolution of the Weixinan Low Uplift has induced prominent changes in the basin paleogeomorphology, which in turn triggered dynamic shifts in the provenance and sediment transport pathways, and thus gave rise to complex local “source-to-sink” systems and depositional styles. Full article

The genus Xylaria comprises numerous species, particularly prevalent in tropical ecosystems such as those of Ecuador. Despite its ecological importance, the taxonomy of the genus remains challenging, and much of its diversity in the Neotropics remains under-documented. This study provides a preliminary characterization of the Xylaria diversity at the Estación Científica San Francisco, an Andean biodiversity hotspot in Southern Ecuador. Through an integrated approach including detailed macro- and micro-morphological descriptions and nuclear ribosomal DNA (nrDNA ITS and LSU) phylogenetic analyses, 20 Xylaria specimens were examined. As a result, ten species were recognized: Xylaria adscendens, X. cf. anisopleura, X. apiculata, X. curta, X. enterogena, X. fissilis, X. globosa, X. aff. telfairii, X. tuberoides, and X. aenea, the latter representing a new record for Ecuador. The phylogenetic analysis presented here serves as a preliminary systematic positioning of these specimens within the genus rather than a comprehensive global reconstruction. While these ribosomal markers provided preliminary insights into species relationships, partial incongruence with morphospecies highlights the evolutionary complexity of certain lineages and underscores the need for future multilocus studies. Furthermore, four additional phylotypes found in their anamorphic state are documented, suggesting that local diversity exceeds current records. By providing detailed morphological documentation supported by preliminary barcode data from a poorly sampled region, this study contributes vital information to the global understanding of Xylaria and underscores the importance of Southern Ecuador as a reservoir of fungal diversity. Full article