Rate Of Evolution Research Articles

Genetic species concept as applied to multilocus nuclear data

Using the example of multiple species groups and species complexes, it is empirically shown that the resolving power of a set of 10–20 nuclear loci is insufficient for the study of their genetic differentiation. For the adequate analysis of phylogenetic relationships (including reticulation events) and assessment of divergence levels within such groups of closely related species, it is necessary to multiply the number of nuclear loci and transit to high-throughput next-generation deep sequencing. However, the question of the genomic coverage required for the purposes of such study remains open. In other words, exactly how many genes in a set are needed to measure the genetic distance resolving the relationships between branches on the phylogenetic tree reconstruction of a complex of closely related species? We chose protein-coding sequences as a standard set of markers. Distances for 160–180 genes with a combined length of 270 000–300 000 bp were used to estimate the divergence levels of closely related mammalian species. In most cases, the interspecific distances are within the 0.15–0.75% range (median of 0.33%). The range of distances between semi-species is 0.12–0.28% (median of 0.14%). Intraspecific distances are always lower than 0.11%. Rodents show higher values of interspecific distances, 0.25–2.3% (median of 0.72%); distances between half-species range from 0.1 to 0.35%. To determine the number of nuclear loci and their combined length sufficient for the calculation of a genetic distance, we use simulations based on a model that included the following parameters: the average rate of gene evolution, its dispersion, and the level of polymorphism in the modern and ancestral populations. We performed a preliminary analysis of the distribution of loci evolution rates among mammalian taxa based on the data on ~50 thousand nuclear markers. It is shown that a relative error of 10–15%, comparable to the same value for mitochondrial distances between close species based on individual genes (approximately 1000 bp in length), is achieved using approximately 100 loci of 300 bp in length. Based on these data, we propose the following working hypothesis: the threshold of interspecific/intraspecific genetic distance calculated on the basis of the exons most frequently used in mammalian molecular phylogenetics is approximately 0.15%. This hypothesis assumes a species rank for the forms in statu nascendi. It should be noted that not all “good” species have significant genetic distances, since in some cases reproductive barriers form faster than substitutions accumulate in the genome.

Whether niche changes promote the evolution of species: a case study of Paeonia in Asia and North America

Ecological changes have been observed to promote rates of lineage diversification, yet the precise roles of ecological factors, species evolution, and environmental variability in driving species diversity remain research hot spots. The association between ecological change and lineage diversification, particularly with regard to the size of the time scale, remains poorly understood. To explore whether ecological change facilitates species evolution, we focused on the unique family Paeoniaceae, which encompasses both herbaceous and woody taxa, to investigate the evolutionary rates. As a unique family characterized by a single genus of angiosperms and comprising various climatic types, the ecological niche changes of Paeoniaceae are closely associated with the evolution, making it an ideal model for conducting association analysis. In this study, we integrated the molecular fragments and ecological factors to explore the relationship between species evolution and niche changes in Paeoniaceae. The phylogenetic tree revealed that Paeoniaceae forms a sister relationship with Penthoraceae, Haloragidaceae, Iteaceae, Crassulaceae, and Saxifragaceae, constituting an independent clade based on the positive selection of molecular fragments including two protein-coding genes and eight non-coding regions. The divergence time was estimated to be between 102 and 116 Mya (Million years ago). The phylogenetic tree within Paeonia revealed a clear division into three groups: sections of Paeonia, Moutan, and Onaepia with high support values for each branch based on the ten positive selection of molecular fragments. The rapid rate of evolution observed in Paeonia, about 0-5 Mya. In addition, ecological niche modeling showed that the potential distributions for Paeonia expanded from middle Asia to eastern Asia, and from central North America to the Northern part of North America during the Last Glacial Maximum (LGM) to Mid Holocene (MID) period. This suggests that Paeonia continuously adapted to changing ecological environments over time. Compared to the rate of climatic niche divergence and lineage diversification, the ecological niche of Paeonia underwent significant changes during the period of 3-11 Mya, occurring 5 Mya earlier than the period of evolutionary rate change. These findings offer comprehensive insights into the relationship between niche change and the evolution of species, providing valuable perspectives for further ecological cultivation efforts.

Quantifying the impact of vaccination on transmission and diversity of influenza A variants in pigs.

Global evolutionary dynamics of influenza A virus (IAV) are fundamentally driven by the extent of virus diversity generated, transmitted, and shaped in individual hosts. How vaccination affects the degree of IAV genetic diversity that can be transmitted and expanded in pigs is unknown. To evaluate the effect of vaccination on the transmission of genetically distinct IAV variants and their diversity after transmission in pigs, we examined the whole genome of IAV recovered from the nasal cavities of pigs vaccinated with different influenza immunization regimens after being infected simultaneously by H1N1 and H3N2 IAVs using a seeder pig model. We found that the seeder pigs harbored more diversified virus populations than the contact pigs. Among contact pigs, H3N2 and H1N1 viruses recovered from pigs vaccinated with a single dose of an unmatched modified live vaccine generally accumulated more extensive genetic mutations than non-vaccinated pigs. Furthermore, the non-sterilizing immunity elicited by the single-dose-modified live vaccine may have exerted positive selection on H1 antigenic regions as we detected significantly higher nonsynonymous but lower synonymous evolutionary rates in H1 antigenic regions than non-antigenic regions. In addition, we observed that the vaccinated pigs shared significantly less proportion of H3N2 variants with seeder pigs than unvaccinated pigs. These results indicated that vaccination might reduce the impact of transmitted influenza variants on the overall diversity of IAV populations harbored in recipient pigs and that within-host genetic selection of IAV is more likely to occur in pigs vaccinated with improperly matched vaccines.IMPORTANCEUnderstanding how vaccination shapes the diversity of influenza variants that transmit and propagate among pigs is essential for designing effective IAV surveillance and control programs. Current knowledge about the transmission of IAV variants has primarily been explored in humans during natural infection. However, how immunity elicited by improperly matched vaccines affects the degree of IAV genetic diversity that can be transmitted and expanded in pigs at the whole-genome level is unknown. We analyzed IAV sequences from samples collected daily from experimentally infected pigs vaccinated with various protocols in a field-represented IAV co-infection model. We found that vaccine-induced non-sterilizing immunity might promote genetic variation on the IAV genome and drive positive selection at antigenic sites during infection. In addition, a smaller proportion of H3N2 viral variants were shared between seeder pigs and vaccinated pigs, suggesting the influence of vaccination on shaping the virus genomic diversity in recipient pigs during the transmission events.

High‐Selectivity Tandem Photocatalytic Methanation of CO2 by Lacunary Polyoxometalates‐Stabilized *CO Intermediate

AbstractStabilizing specific intermediates to produce CH4 remains a main challenge in solar‐driven CO2 reduction. Herein, g‐C3N4 is modified with saturated and lacunary phosphotungstates (PWx, x=12, 11, 9) to tailor the CO2 reduction pathway to yield CH4 in high selectivity. Increased lacuna of phosphotungstates leads to higher CH4 yield and selectivity, with a superior CH4 selectivity of 80 % and 40.8 μmol ⋅ g−1 ⋅ h−1 evolution rate for PW9/g‐C3N4. Conversely, g‐C3N4 and PWx alone show negligible CH4 production. The conversion of CO2 to CH4 follows a tandem catalytic process. CO2 is initially activated on g‐C3N4 to form *CO intermediates, meanwhile photogenerated electrons derived from g‐C3N4 transfer to PWx. Then the reduced PWx captures *CO, which is subsquently hydrogenated to CH4. With the injection of two photogenerated electrons, PW9 is capable of adsorbing and activating *CO. However, the reduced PW12 and PW11 are incapable of adsorbing *CO due to the small energy of occupied molecular orbitals, which is the reason for the poorer activity of PWx/g‐C3N4 (x=12, 11) compared with that of PW9/g‐C3N4. This work provides new insights to regulate highly selective CO2 photoreduction to CH4 by utilizing lacuna of polyoxometalates to enhance the interaction of metals in polyoxometalates with key intermediates.

Inguinal hernia recurrence after laparoscopic mesh removal for chronic pain: a single-center experience with 11years of practice.

Up to 12% of patients undergoing minimally invasive inguinal hernia repair may develop chronic postoperative inguinal pain (CPIP), possibly explained by the presence of mesh. Recent studies reported that laparoscopic mesh removal is feasible and safe. However, the risk of a hernia recurrence is unknown. This observational study describes the rate of hernia recurrence and evolution in pain score following laparoscopic mesh removal for CPIP after preperitoneal inguinal hernia repair. Prospectively collected questionnaires and operative notes of consecutive patients undergoing a laparoscopic mesh removal for CPIP in our center of expertise between November 2011 and July 2022 were studied. Pain scores were quantified using the Numeric Pain Rating Scale (NRS, 0-10). The presence of a hernia recurrence was based on patient history and clinical findings. A total of 89 patients underwent laparoscopic mesh removal, and data of 83 patients (93% response rate) were available for analysis. Median decrease in pain score (NRS) after mesh removal was 4 (range + 2 to -9). After a median 4.3years follow up period, a hernia recurrence was present in 18 patients (21.7%). Of these, eight were symptomatic requiring correction using a Lichtenstein repair with a favorable outcome whereas a wait-and-see approach was successfully followed in the remaining 10 patients. Laparoscopic mesh removal for CPIP following preperitoneal inguinal hernia repair resulted in an inguinal hernia recurrence in one of five patients requiring remedial surgery in one in ten patients. This knowledge may inform the preoperative counseling process.

OGU: A Toolbox for Better Utilising Organelle Genomic Data.

Organelle genomes serve as crucial datasets for investigating the genetics and evolution of plants and animals, genome diversity, and species identification. To enhance the collection, analysis, and visualisation of such data, we have developed a novel open-source software tool named Organelle Genome Utilities (OGU). The software encompasses three modules designed to streamline the handling of organelle genome data. The data collection module is dedicated to retrieving, validating and organising sequence information. The evaluation module assesses sequence variance using a range of methods, including novel metrics termed stem and terminal phylogenetic diversity. The primer module designs universal primers for downstream applications. Finally, a visualisation pipeline has been developed to present comprehensive insights into organelle genomes across different lineages rather than focusing solely on individual species. The performance, compatibility and stability of OGU have been rigorously evaluated through benchmarking with four datasets, including one million mixed GenBank records, plastid genomic data from the Lamiaceae family, mitochondrial data from rodents, and 308 plastid genomes sourced from various angiosperm families. Based on software capabilities, we identified 30 plastid intergenic spacers. These spacers exhibit a moderate evolutionary rate and offer practical utility comparable to coding regions, highlighting the potential applications of intergenic spacers in organelle genomes. We anticipate that OGU will substantially enhance the efficient utilisation of organelle genomic data and broaden the prospects for related research endeavours.

2D/2D Hydrogen-Bonded Organic Frameworks/Covalent Organic Frameworks S-scheme Heterojunctions for Photocatalytic Hydrogen Evolution.

Hydrogen-bonded organic frameworks (HOFs) demonstrate significant potential for application in photocatalysis. However, the low efficiency of electron-hole separation and limited stability inhibit their practical utilization in photocatalytic hydrogen evolution from water splitting. Herein, the novel dual-pyrene-base supramolecular HOF/COF 2D/2D S-scheme heterojunction between HOF-H4TBAPy (Py-HOF, H4TBAPy represents the 1,3,6,8-tetrakis (p-benzoic acid) pyrene) and Py-COF was successfully established using a rapid self-assembly solution dispersion method. Experimental and theoretical investigations confirm that the size-matching of two crystalline porous materials enables the integrated heterostructure material with abundant surface reaction sites, strong interaction, and an enhanced S-scheme built-in electric field, thus significantly improving the efficiency of photogenerated charge carrier separation and stability. Notably, the optimal HOF/COF heterojunction achieves a photocatalytic hydrogen evolution rate of 390.68 mmol g-1 h-1, which is 2.28 times higher than that of pure Py-HOF and 9.24 times higher than that of pure COF. These findings precisely acquire valuable atomic-scale insights into the ingenious design of dual-pyrene-based S-scheme heterojunction. This work presents an innovative perspective for forming supramolecular S-scheme heterojunctions over HOF-based semiconductors, offering a protocol for designing the powerful and strong-coupling S-scheme built-in electric fields for efficient solar energy utilization.

2D/2D Hydrogen‐Bonded Organic Frameworks/Covalent Organic Frameworks S‐scheme Heterojunctions for Photocatalytic Hydrogen Evolution

Hydrogen‐bonded organic frameworks (HOFs) demonstrate significant potential for application in photocatalysis. However, the low efficiency of electron‐hole separation and limited stability inhibit their practical utilization in photocatalytic hydrogen evolution from water splitting. Herein, the novel dual‐pyrene‐base supramolecular HOF/COF 2D/2D S‐scheme heterojunction between HOF‐H4TBAPy (Py‐HOF, H4TBAPy represents the 1,3,6,8‐tetrakis (p‐benzoic acid) pyrene) and Py‐COF was successfully established using a rapid self‐assembly solution dispersion method. Experimental and theoretical investigations confirm that the size‐matching of two crystalline porous materials enables the integrated heterostructure material with abundant surface reaction sites, strong interaction, and an enhanced S‐scheme built‐in electric field, thus significantly improving the efficiency of photogenerated charge carrier separation and stability. Notably, the optimal HOF/COF heterojunction achieves a photocatalytic hydrogen evolution rate of 390.68 mmol g−1 h−1, which is 2.28 times higher than that of pure Py‐HOF and 9.24 times higher than that of pure COF. These findings precisely acquire valuable atomic‐scale insights into the ingenious design of dual‐pyrene‐based S‐scheme heterojunction. This work presents an innovative perspective for forming supramolecular S‐scheme heterojunctions over HOF‐based semiconductors, offering a protocol for designing the powerful and strong‐coupling S‐scheme built‐in electric fields for efficient solar energy utilization.

Molecular evolution and genetic diversity of defective chorion 1 in Anastrepha fraterculus and Anastrepha obliqua (Diptera, Tephritidae).

The family Tephritidae comprises numerous fruit fly species, some of which are economically significant, such as several in the genus Anastrepha. Most pest species in this genus belong to the fraterculus group, characterized by closely related species that are difficult to differentiate due to recent divergence and gene flow. Identifying genetic markers for their study is paramount for understanding the group's evolution and eventual phytosanitary control. Because there is variation in eggshell morphology among species in the genus, the study of the rapidly evolving defective chorion 1 (dec-1) gene, which is crucial for chorion formation and reproduction, could provide relevant information for Anastrepha differentiation. We compared transcriptome sequences of dec-1 from two of the most important pest species in the genus, Anastrepha fraterculus and Anastrepha obliqua to dec-1 sequences from Anastrepha ludens, which was used for structure prediction. Furthermore, we amplified a conserved exon across populations of these species. These data revealed three alternative transcripts in A. fraterculus and A. obliqua, consistent with patterns found in other Tephritidae; we obtained orthologous sequences for these other tephritids from NCBI to investigate patterns of selection affecting this gene at different hierarchical levels using different methods. These analyses show a general pattern of purifying selection across the whole gene and throughout its history at different hierarchical levels, from populations to more distantly related species. That notwithstanding, we still found evidence of positive and episodic diversifying selection at different levels. Different parts of the gene have shown distinct evolutionary rates, which were associated with the diverse proproteins produced by posttranslational changes of DEC-1, with proproteins that are incorporated in the chorion earlier in egg formation being in general more conserved than others that are incorporated later. This correlation appears more evident in certain lineages, including the branch that separates Anastrepha, as well as other internal branches that differentiate species within the genus. Our data showed that this gene shows remarkable variation across its different exons, which has proven to be informative at different evolutionary levels. These changes hold promise not only for studying differentiation in Anastrepha but also for the eventual management of selected pest species.

A superlattice interface and S-scheme heterojunction for ultrafast charge separation and transfer in photocatalytic H2 evolution

The rapid recombination of photoinduced charge carriers in semiconductors fundamentally limits their application in photocatalysis. Herein, we report that a superlattice interface and S-scheme heterojunction based on Mn0.5Cd0.5S nanorods can significantly promote ultrafast charge separation and transfer. Specifically, the axially distributed zinc blende/wurtzite superlattice interfaces in Mn0.5Cd0.5S nanorods can redistribute photoinduced charge carriers more effectively when boosted by homogeneous internal electric fields and promotes bulk separation. Accordingly, S-scheme heterojunctions between the Mn0.5Cd0.5S nanorods and MnWO4 nanoparticles can further accelerate the surface separation of charge carriers via a heterogeneous internal electric field. Subsequent capture of the photoelectrons by adsorbed H2O is as fast as several picoseconds which results in a photocatalytic H2 evolution rate of 54.4 mmol·g−1·h−1 without any cocatalyst under simulated solar irradiation. The yields are increased by a factor of ~5 times relative to control samples and an apparent quantum efficiency of 63.1% at 420 nm is measured. This work provides a protocol for designing synergistic interface structure for efficient photocatalysis.

Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal.

Our understanding of the evolution of many microbes has been revolutionised by the molecular clock, a statistical tool to infer evolutionary rates and timescales from analyses of biomolecular sequences. In all molecular clock models, evolutionary rates and times are jointly unidentifiable and 'calibration' information must therefore be used. For many organisms, sequences sampled at different time points can be employed for such calibration. Before attempting to do so, it is recommended to verify that the data carry sufficient information for molecular dating, a practice referred to as evaluation of temporal signal. Recently, a fully Bayesian approach, BETS (Bayesian Evaluation of Temporal Signal), was proposed to overcome known limitations of other commonly used techniques such as root-to-tip regression or date randomisation tests. BETS requires the specification of a full Bayesian phylogenetic model, posing several considerations for untangling the impact of model choice on the detection of temporal signal. Here, we aimed to (i) explore the effect of molecular clock model and tree prior specification on the results of BETS and (ii) provide guidelines for improving our confidence in molecular clock estimates. Using microbial molecular sequence data sets and simulation experiments, we assess the impact of the tree prior and its hyperparameters on the accuracy of temporal signal detection. In particular, highly informative priors that are inconsistent with the data can result in the incorrect detection of temporal signal. In consequence, we recommend: (i) using prior predictive simulations to determine whether the prior generates a reasonable expectation of parameters of interest, such as the evolutionary rate and age of the root node, (ii) conducting prior sensitivity analyses to assess the robustness of the posterior to the choice of prior, and (iii) selecting a molecular clock model that reasonably describes the evolutionary process.

Genetic diversity and spread of recombinant coxsackievirus A4 in hand, foot, and mouth disease cases in Bangkok, Thailand: 2017–2023

Coxsackievirus A4 (CVA4) has recently become one of the most common causative agents of hand, foot, and mouth disease. The current study investigated the genetic diversity and spread of recombinant CVA4 by analyzing circulating genotypes and recombinant strains in Bangkok, Thailand, from 2017 to 2023. Partial VP1, 3Dpol, and whole genome sequencing of CVA4 samples collected from collaborating hospitals were conducted. Phylogenetic analysis of CVA4 VP1 and 3Dpol genome regions revealed discordance, indicating recombination. The predominant CVA4 genotype was C3, primarily observed in 2019. The predominant genotype in 2017 was C1. D2, commonly found in China, was occasionally observed. In nucleotide similarity analysis, intertypic recombination between CVA4 and EV-A during the evolutionary history of the virus was evident, particularly in the nonstructural region. The estimated emergence of genotypes C1 and C3 in Thailand occurred around 2014, with an evolutionary rate of 5.8 × 10− 3 nucleotide substitutions per site per year. Genotype D2 exhibited notable variability across both the entire genome and the structural protein region compared to genotype C. Monitoring the genetic diversity and circulation of recombinant CVA4 is crucial for identifying newly emerging virus strains, enabling prompt public health responses and containment efforts, and enhancing surveillance in Thailand.

Sustainable Scalable Mechanochemical Synthesis of CdS/Bi2S3 Nanocomposites for Efficient Hydrogen Evolution

In the present study, a green, scalable, and environmentally friendly approach was developed for the fabrication of Bi2S3-decorated CdS nanoparticles with an efficient hydrogen generation ability from the water. As a sulfur source, thiourea was used. The process was completed in two stages: mechanical activation and thermal annealing. The presence of spherical CdS nanoparticles and Bi2S3 nanorods in the CdS/Bi2S3 nanocomposite was confirmed and proved by XRD, Raman spectroscopy, SEM-EDS, and TEM. The synthesized CdS/Bi2S3 nanocomposites were evaluated for their photocatalytic hydrogen evolution capabilities. The CdS/Bi2S3 photocatalyst exhibited 25% higher photocatalytic activity compared to CdS, reaching a hydrogen evolution rate of 996.68 μmol h−1g−1 (AQE 0.87%) after 3.5 h under solar-light irradiation.

ITSxpress version 2: software to rapidly trim internal transcribed spacer sequences with quality scores for amplicon sequencing.

The nuclear ribosomal RNA (rRNA) internal transcribed spacer (ITS) regions are commonly used to identify fungi and other eukaryotic taxa in amplicon sequencing. The highly conserved rRNA regions flanking the ITS are often trimmed before being used for taxonomic assignment. The Python software package ITSxpress rapidly trims single-end or paired-end sequences in FASTQ format for use in amplicon sequence variant clustering methods like DADA2. This new major release of ITSxpress improves the paired-end merging method, simplifies installation of the QIIME 2 ITSxpress plugin, removes major dependencies, adds use cases, and is compatible with newer compression formats. This article discusses the modifications to ITSxpress that improve the output and user experience, leading to a major version increase.IMPORTANCEITSxpress is a sequence trimming method applied to internal transcribed spacer (ITS) amplicon sequences before calling amplicon sequence variants (ASVs). The ITS region is used to understand the composition of eukaryotic microbial communities. ITS sequences provide good taxonomic resolution due to their hypervariability, but are flanked by conserved regions that allow their primers to be more universal. Amplicons generated with such primers contain regions with different evolutionary rates, and trimming these conserved regions results in better taxonomic classification and a more valid set of ASVs. This package can be used for most amplicon sequencing methods including for newer long-read sequencing formats, such as PacBio. ITSxpress can be installed from Bioconda, used as a Docker image, or installed from source code. The package works well with high-performance computing clusters or laptops due to its low-resource requirements.

The diversity of glycan chains in jellyfish mucin of three Cubozoan species: the contrast in molecular evolution rates of the peptide chain and Glycans.

The O-glycan composition of jellyfish (JF) mucin (qniumucin: Q-mucin) extracted from three Cubozoan species was studied after the optimization of the purification protocol. Application of a stepwise gradient of ionic strength to anion exchange chromatography (AEXC) was effective for isolating Q-mucin from coexisting impurities. In the three species, the amino acid sequence of the tandem repeat (TR) region in Q-mucin in all three Cubozoans seemed to remain the same as that in all Scyphozoans, although their glycan chains seemed to exhibit clear diversity. In particular, the amounts of acidic moieties on the glycan chains of Q-mucin from the Cubozoans markedly varied even in these genetically close species. In two of the three Cubozoan species, the fraction of disaccharides was large, showing a sharp contrast to that of the glycans of Q-mucin in Scyphozoans. This study also indicates that the simple sequence of TR commonly inherited in all Cubozoan and Scyphozoan JF species after the long term of evolution over 500Myears. According to this research, the glycans and the TR of mucin-type glycoproteins (MTGPs), forming a hierarchical structure, appear to complement each other in the evolutionary changes because the time required for their hereditary conversion is considerably different. The cooperation of these mechanisms is a strategy to achieve the contradictory functions of biosystems, namely species conservation and diversity acquisition.

Photothermal Induced Dual-Interface: Accelerating Sustainable Hydrogen Evolution from Formic Acid.

Formic acid (FA), a liquid hydrogen storage carrier, can release hydrogen via photothermal catalysis, providing a clean and sustainable solution toward a carbon-neutral energy cycle. Despite recent advances in the design of efficient catalysts, the development of advanced systems with high H2 yield, stability, and durability remains challenging due to the inefficient photothermal conversion and mass transfer in the traditional liquid-solid bulk system, as well as the trade-off between hydrogen storage density and dehydrogenation rate. Here, we address these challenges by creating a photothermal-induced dual-interface characterized by high spectral absorption and low heat loss, a facile supply of FA, and vaporization of FA to minimize the energy barrier of the reaction. As a result, a record hydrogen evolution rate (200.9 mmol g-1 h-1) is achieved in a high concentration (26 M) of FA, which is about 15 times higher than the liquid-solid bulk system. In addition, it can be operated continuously for more than 192 h without additive addition and energy consumption, providing a strategy for accelerating interfacial mass transfer to improve catalytic activity, and also presents a reference for sustainable hydrogen production.

The complete mitochondrial genome of Dimorphopterus japonicus (Hidaka, 1959) (Hemiptera, Lygaeoidea) and phylogenetic relationships within the Lygaeoidea superfamily

Dimorphopterus japonicus is a kind of pest which seriously harms sorghum and millet. In this study, we sequenced the mitochondrial whole genome of D. japonicus (Hidaka, 1959), and characterized and analyzed the mitogenome. The D. japonicus genome length is 15,473 bp, and it exhibits a typical high A + T content (77.6%). The mitogenomic structure of D. japonicus is highly conservative and there are no gene rearrangements. The evolutionary rates of the PCGs are in the order of atp8 > nad3 > nad6 > nad2 > nad5 > atp6 > nad4 > nad4L > cox2 > nad1 > cytb > cox3 > cox1. By using the Bayesian inference and maximum likelihood methods, we inferred the phylogenetic relationships within Lygaeoidea and estimated their divergence times based on concatenated mitogenome genes. The stable clades of (Oxycarenidae + Piesmatidae), (Malcidae + Colobathristidae), (Meschiidae + Berytidae), and (Blissidae+(Cymidae + Ninidae)) were consistently recovered in all analyses. Estimated divergence times revealed that the divergence time of the Lygaeoidea was 99.4 Ma (95% HPD: 83.4-124.8 Ma), and most lygaeoid families diverged during the early Cretaceous to late Paleogene. Berytidae is the latest differentiation in the lygaeoid families, and the genus Dimorphopterus was differentiated in 45.9 Ma (95% HPD: 39.8–47.7 Ma). This study is of great significance for reconstructing the phylogeny of Lygaeoidea and providing insights into its evolutionary history.

13 C-MFA helps to identify metabolic bottlenecks for improving malic acid production in Myceliophthora thermophila

BackgroundMyceliophthora thermophila has been engineered as a significant cell factory for malic acid production, yet strategies to further enhance production remain unclear and lack rational guidance. 13C-MFA (13C metabolic flux analysis) offers a means to analyze cellular metabolic mechanisms and pinpoint critical nodes for improving product synthesis. Here, we employed 13C-MFA to investigate the metabolic flux distribution of a high-malic acid-producing strain of M. thermophila and attempted to decipher the crucial bottlenecks in the metabolic pathways.ResultsCompared with the wild-type strain, the high-Malic acid-producing strain M. thermophila JG207 exhibited greater glucose uptake and carbon dioxide evolution rates but lower oxygen uptake rates and biomass yields. Consistent with these phenotypes, the 13C-MFA results showed that JG207 displayed elevated flux through the EMP pathway and downstream TCA cycle, along with reduced oxidative phosphorylation flux, thereby providing more precursors and NADH for malic acid synthesis. Furthermore, based on the 13C-MFA results, we conducted oxygen-limited culture and nicotinamide nucleotide transhydrogenase (NNT) gene knockout experiments to increase the cytoplasmic NADH level, both of which were shown to be beneficial for malic acid accumulation.ConclusionsThis work elucidates and validates the key node for achieving high malic acid production in M. thermophila. We propose effective fermentation strategies and genetic modifications for enhancing malic acid production. These findings offer valuable guidance for the rational design of future cell factories aimed at improving malic acid yields.

Evolution mechanism of physical morphology of oxbow lake in the middle Yangtze River

Oxbow lakes, formed through river meandering cutoffs, are recognized as key components of river ecosystems, characterized by both fluvial and lacustrine features. The focus of previous research has been placed primarily on post-disconnection changes, leaving gaps in the understanding of their long-term morphological evolution. This gap is addressed through a comparative analysis of gate-controlled and naturally connected oxbow lakes over a 30-year period. In this study, Tian’ezhou Lake (gate-controlled) and Shangchewan Lake (naturally connected), located in the middle Yangtze River, are investigated. Key morphological parameters such as curvature, shoreline development index, and shrinkage rate were measured using Google Earth Engine (GEE). The influence of hydrological and meteorological factors on lake morphology was analyzed through Redundancy Analysis (RDA). Significant morphological changes were observed from 1990 to 2000. During this period, Tian’ezhou’s curvature was found to increase by 0.003/year, while Shangchewan’s curvature decreased by 0.011/year. After the construction of the Three Gorges Dam (TGD), a reduction in the rate of morphological evolution was detected, particularly between 2000 and 2010, when Tian’ezhou’s curvature decreased by 0.071/year and Shangchewan’s increased by 0.04/year. Post-2010, no significant changes in planar morphology were recorded in either lake. It was revealed by RDA that annual precipitation from 1990 to 1999 played a dominant role in influencing the morphological evolution of both lakes. From 2000 to 2020, water level fluctuations and hydrological connectivity emerged as the primary drivers. Gate control at Tian’ezhou Lake mitigated extreme water level fluctuations, contributing to a more stable environment and a slower rate of morphological evolution compared to Shangchewan. The findings underscore the importance of balanced water management strategies, integrating both natural and engineered hydrological interventions. Practical guidance is provided for ecological restoration and river management, with an emphasis on maintaining stable habitats and ensuring ecosystem resilience in response to hydrological changes.

Two methods to analyze radial diffusion ensembles: The perils of space- and time-dependent diffusion

Particle dynamics in Earth's outer radiation belt can be modeled using a diffusion framework, where large-scale electron movements are captured by a diffusion equation across a single adiabatic invariant, L*(L). While ensemble models are promoted to represent physical uncertainty, as yet there is no validated method to analyze radiation belt ensembles. Comparisons are complicated by the domain dependent diffusion, since diffusion coefficient DLL is dependent on L. We derive two tools to analyze ensemble members: time to monotonicity tm and mass/energy moment quantities N,E. We find that the Jacobian (1/L2) is necessary for radiation belt error metrics. Components of ∂E/∂t are explicitly calculated to compare the effects of outer and inner boundary conditions, and loss, on the ongoing diffusion. Using tm, N, and E, we find that: (a) different physically motivated choices of outer boundary condition and location result in different final states and different rates of evolution; (b) the gradients of the particle distribution affect evolution more significantly than DLL; (c) the enhancement location, and the amount of initial background particles, are both significant factors determining system evolution; (d) loss from pitch-angle scattering is generally dominant; it mitigates but does not remove the influence of both initial conditions and outer boundary settings, which are due to the L-dependence of DLL. We anticipate that this study will promote renewed focus on the distribution gradients, on the location and nature of the outer boundary in radiation belt modeling, and provide a foundation for systematic ensemble modeling.