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The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of accuracy, atom count (spatial scale), and duration (temporal scale). Since the mid-2000s, computer platforms have, however, failed to provide strong scaling for MD, as scale-out central processing unit (CPU) and graphics processing unit (GPU) platforms that provide substantial increases to spatial scale do not lead to proportional increases in temporal scale. Important scientific problems therefore remained inaccessible to direct simulation, prompting the development of increasingly sophisticated algorithms that present significant complexity, accuracy, and efficiency challenges. While bespoke MD-only hardware solutions have provided a path to longer timescales for specific physical systems, their impact on the broader community has been mitigated by their limited adaptability to new methods and potentials. In this work, we show that a novel computing architecture, the Cerebras wafer scale engine, completely alters the scaling path by delivering unprecedentedly high simulation rates up to 1.144 M steps/s for 200 000 atoms whose interactions are described by an embedded atom method potential. This enables direct simulations of the evolution of materials using general-purpose programmable hardware over millisecond timescales, dramatically increasing the space of direct MD simulations that can be carried out. In this paper, we provide an overview of advances in MD over the last 60 years and present our recent result in the context of historical MD performance trends. [ABSTRACT FROM AUTHOR]

The change of the vibrational energy within a molecule after collisions with another molecule plays an essential role in the evolution of molecular internal energy distributions, which is also the limiting process in the relaxation of gases toward equilibrium. Here, we investigate the energy transfer between the translational motion and the vibrational motion of the diatom during the atom–diatom collision, the simplest case involving the transfer between inter-molecular and intra-molecular energies. We are interested in the situation when the translational temperature of the gas is high, in which case, there are significant probabilities for the vibrational energy to change over widely separated energy levels after a collision. Data from quasi-classical trajectory simulations of the N + N2 system with ab initio potential energies suggest that the transition probability dependence on the collisional energy possesses an "activation-saturation" behavior and can be described by a simple model. The model allows for explicit evaluation of the vibrational state-to-state transition rate coefficients, from which the evolution of the vibrational energy distribution from any initial conditions can be solved by using the master equation approach. An example of the vibrational energy relaxation in the N + N2 system mimicking the gas behind strong shocks in a hypersonic flow is shown and the results are in good agreement with the available data. [ABSTRACT FROM AUTHOR]

We show that optimal control of the electron dynamics is able to prepare molecular ground states, within chemical accuracy, with evolution times approaching the bounds imposed by quantum mechanics. We propose a specific parameterization of the molecular evolution only in terms of interaction already present in the molecular Hamiltonian. Thus, the proposed method solely utilizes quantum simulation routines, retaining their favorable scalings. Due to the intimate relationships between variational quantum algorithms and optimal control, we compare, when possible, our results with state-of-the-art methods in the literature. We found that the number of parameters needed to reach chemical accuracy and algorithmic scaling is in line with compact adaptive strategies to build variational Ansätze. The algorithm, which is also suitable for quantum simulators, is implemented by emulating a digital quantum processor (up to 16 qubits) and tested on different molecules and geometries spanning different degrees of electron correlation. [ABSTRACT FROM AUTHOR]

The comprehension of nonadiabatic dynamics in polyatomic systems relies heavily on the simultaneous advancements in theoretical and experimental domains. The gas-phase ultrafast electron diffraction (UED) technique has attracted significant attention as a unique tool for monitoring photochemical and photophysical processes at the all-atomic level with high temporal and spatial resolutions. In this work, we simulate the UED spectra of cyclobutanone using the trajectory surface hopping method at the extended multi-state complete active space second order perturbation theory (XMS-CASPT2) level and thereby predict the results of the upcoming UED experiments in the Stanford Linear Accelerator Laboratory. The simulated results demonstrate that a few pathways, including the C2 and C3 dissociation channels, as well as the ring opening channel, play important roles in the nonadiabatic reactions of cyclobutanone. We demonstrate that the simulated UED signal can be directly interpreted in terms of atomic motions, which provides a unique way of monitoring the evolution of the molecular structure in real time. Our work not only provides numerical data that help to determine the accuracy of the well-known surface hopping dynamics at the high XMS-CASPT2 electronic-structure level but also facilitates the understanding of the microscopic mechanisms of the photoinduced reactions in cyclobutanone. [ABSTRACT FROM AUTHOR]

Background: Avian β-defensins (AvBDs) represent a key family of antimicrobial host defense peptides in birds. Accumulating evidence suggests that the evolutionary trajectory of β-defensin genes is specific to the gene, timescale, and species involved, implying that species-specific ecological and life-history differences drive divergent selective pressures on these genes. However, their evolutionary dynamics, particularly the interactions with ecological factors and life-history traits, remain insufficiently explored. Results: Through a comprehensive survey of 25 species spanning all major clades of Galliformes, 354 AvBD genes were identified. Comparative sequence analysis, genomic organization, and phylogenetic studies collectively reveal significant evolutionary diversification characterized by gene duplication, pseudogenization, and gene loss across these species. Notably, chicken AvBD3 exhibits significant differences in its coding regions, while AvBD6 and AvBD7 appear to have copy number variations, with species-specific paralogs of AvBD6 being especially prominent. Moreover, positive selection was more frequently observed in recently diverged gene lineages compared to ancestral ones. Using 70 samples from eight galliform species, the study further identified the prevalence of species-specific amino acid alleles. Phylogenetic comparative analysis demonstrated that the evolution of nine AvBD genes (AvBD2, -4, -5, -8, -9, -10, -11, -12, and -14) is significantly associated with specific ecological factors and life-history characteristics. Additionally, the evolutionary rates of these genes showed distinct relationship with inferred infection risk, likely reflecting the multifunctionality of β-defensins and potential trade-offs between immune defense and other biological functions. Conclusions: This cross-species identification and systematic evolutionary analysis of AvBDs in Galliformes deepen our understanding of the co-evolution of host defense peptides, offering valuable insights into their natural biology and evolution, and paving the way for future applications as alternatives to traditional antibiotics. [ABSTRACT FROM AUTHOR]

The common avian origin of many zoonotic infections and epidemics warrants investigation into the mechanism of respiratory surface protection in reservoir species such as birds. Our recent molecular investigations on the evolution and pulmonary expression of an ancient family of proteins, the C-type lectins, have revealed unique molecular adaptations in the surfactant proteins avian SP-A1 (aSP-A1), aSP-A2 and aSP-C coupled with the loss of surfactant protein-D (SP-D) in the avian lineage. As surfactant proteins are members of the collectin family, a subgroup of the C-type lectins, an in silico search for related non-surfactant collectin proteins (Collectin-10 (CL-10) and Collectin-11 (CL-11)) in the NCBI genome database was conducted to understand their evolution in the avian lineage. In addition, both CL-10 and CL-11 gene expression in the lungs and other organs of zebra finches and turkeys was confirmed by PCR. These PCR-confirmed zebra finch and turkey CL-10 and CL-11 sequences were compared with sequenced and in silico-predicted vertebrate homologues to develop a phylogenetic tree. Compared with avian surfactant proteins, CL-10 and CL-11 are highly conserved among vertebrates, suggesting a critical role in development and innate immune protection. The conservation of CL-11 EPN and collagen domain motifs may compensate to some extent for the loss of SP-D in the avian lineage. This article is part of the theme issue 'The biology of the avian respiratory system'. [ABSTRACT FROM AUTHOR]

Background: Convergent evolution is the independent evolution of similar traits in unrelated lineages across the Tree of Life. Various genomic signatures can help identify cases of convergent evolution at the molecular level, including changes in substitution rate in the same genes or gene networks. In this study, utilizing tarsus measurements of ~ 5400 species of birds, we identify independent shifts in tarsus length and use both comparative genomic and population genetic data to identify convergent evolutionary changes among focal clades with shifts to shorter optimal tarsus length. Results: Using a newly generated, comprehensive and broadly accessible set of 932,467 avian conserved non-exonic elements (CNEEs) and a whole-genome alignment of 79 birds, we find strong evidence for convergent acceleration in short-tarsus clades among 14,422 elements. Analysis of 9854 protein-coding genes, however, yielded no evidence of convergent patterns of positive selection. Accelerated elements in short-tarsus clades are concentrated near genes with functions in development, with the strongest enrichment associated with skeletal system development. Analysis of gene networks supports convergent changes in regulation of broadly homologous limb developmental genes and pathways. Conclusions: Our results highlight the important role of regulatory elements undergoing convergent acceleration in convergent skeletal traits and are consistent with previous studies showing the roles of regulatory elements and skeletal phenotypes. [ABSTRACT FROM AUTHOR]

The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture. Computing the likelihood of data observed at the leaves is costly as the size and complexity of the phylogeny grows. Efficient algorithms exist for trees, but cannot be applied to networks. We show that a vast array of models for trait evolution along phylogenetic networks can be reformulated as graphical models, for which efficient belief propagation algorithms exist. We provide a brief review of belief propagation on general graphical models, then focus on linear Gaussian models for continuous traits. We show how belief propagation techniques can be applied for exact or approximate (but more scalable) likelihood and gradient calculations, and prove novel results for efficient parameter inference of some models. We highlight the possible fruitful interactions between graphical models and phylogenetic methods. For example, approximate likelihood approaches have the potential to greatly reduce computational costs for phylogenies with reticulations. This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'. [ABSTRACT FROM AUTHOR]

Background: As diffuse midline glioma, H3K27 altered, is a rare tumor entity with poor prognosis and few therapeutic options, only little is known so far about the genetic factors that influence tumorigenesis and the course of tumor development. Presentation: We present the case of a 38-year-old female patient who suffered from nausea, fatigue, and intermittent walking impairment, which developed over the course of four weeks. Initial MRI showed an irregularly shaped, contrast-enhancing tumor around the third ventricle with central necrosis, most likely originating from the right thalamus. The patient underwent biopsy, followed by microsurgical resection with molecular analysis. Molecular neuropathology revealed the diagnosis of diffuse midline glioma with a H3K27M mutation WHO (World Health Organization) CNS (central nervous system) grade 4. Interestingly, MR imaging conducted for migraine diagnosis 6 years ago in retrospect already showed a small, nodular T2w hyperintense lesion in the right thalamus. Conclusion: Despite a more precise, molecularly driven classification of pediatric HGG (high-grade glioma) in the 5th edition of the WHO classification of CNS tumors, many genetic factors influencing the biological tumor development as well as the precise molecular evolution of tumors remain unclear. Given the highly aggressive clinical course of these tumors, with a median overall survival around 16 to 18 months, our report of a (presumable) precursor lesion years before clinical manifestation point towards a complex, multi-stage evolution of this tumor entity. Better understanding this molecular cascade might help to identify novel targets for individualized therapies. [ABSTRACT FROM AUTHOR]

Genetically encoded voltage indicators (GEVIs) allow for the cell-type-specific real-time imaging of neuronal membrane potential dynamics, which is essential to understanding neuronal information processing at both cellular and circuit levels. Among GEVIs, near-infrared-shifted GEVIs offer faster kinetics, better tissue penetration, and compatibility with optogenetic tools, enabling all-optical electrophysiology in complex biological contexts. In our previous work, we employed the directed molecular evolution of microbial rhodopsin Archaerhodopsin-3 (Arch-3) in mammalian cells to develop a voltage sensor called Archon1. Archon1 demonstrated excellent membrane localization, signal-to-noise ratio (SNR), sensitivity, kinetics, and photostability, and full compatibility with optogenetic tools. However, Archon1 suffers from low brightness and requires high illumination intensities, which leads to tissue heating and phototoxicity during prolonged imaging. In this study, we aim to improve the brightness of this voltage sensor. We performed random mutation on a bright Archon derivative and identified a novel variant, monArch, which exhibits satisfactory voltage sensitivity (4~5% ΔF/FAP) and a 9-fold increase in basal brightness compared with Archon1. However, it is hindered by suboptimal membrane localization and compromised voltage sensitivity. These challenges underscore the need for continued optimization to achieve an optimal balance of brightness, stability, and functionality in rhodopsin-based voltage sensors. [ABSTRACT FROM AUTHOR]

Background: The genus Pseudoroegneria (Nevski) Á.Löve contributes the St genome for more than 60% of perennial Triticeae species. However, the strong dominant character of the St genome makes it challenging to distinguish each species and/or even genus based on single or combined morphological traits. Moreover, the phylogeny and taxonomy of the St-genome containing polyploid genera remain controversial. Results: In this study, we used nuclear and chloroplast DNA-based phylogenetic analyses to reveal the systematic relationships between the St-genome containing polyploid species. The maximum likelihood (ML) tree based on nuclear ribosomal internal transcribed spacer region (nrITS) and three single-copy nuclear genes data (Acc1 + Pgk1 + DMC1) showed that polyploid species with the St genome were separated into seven genera with StStHH, StStYY, StStYYHH, StStYYPP, StStYYWW, StStPP, and StStEE genome constitutions, moreover, the polyploid species in Caucasus, America, and Australia have independent polyploidization events. The ML tree for the chloroplast DNA fragments (matK + rbcL + trnL-trnF) displayed that the P genome served as a maternal donor of Kengyilia melanthera and K. dingqinensis from the Hengduan Mountains region, while the St or StY genome served as the maternal donor of other St-genome containing species. Herein, we reported the genomic constitution of Kengyilia tibetica, K. changduensis, and K. dingqinensis with the StStYYPP genome for the first time. Conclusions: The St-genome-containing polyploid species should be treated as distinct genera according to different genome constitutions, and those species experienced independent allo-polyploidization events in different distribution regions and had two relatively independent maternal origins from the P or St/StY genomes. Besides, the Xp genome might have contributed to the unknown Y genome formation. [ABSTRACT FROM AUTHOR]

Ribosomes, vital for life, consist of a large subunit and a small subunit (SSU), the latter is crucial for translation initiation and mRNA binding. The SSU processome, a 71-protein multimer in humans, is an intermediate in ribosome formation. One of its constituents, WDR75 plays a pivotal role by binding to an evolutionary conserved motif in the external transcribed spacer region of the rRNA to help form the SSU. Herein, we explore mammalian WDR75 molecular evolution, 3D structure, and phylogeny in light of its essential role in the SSU processome. We predict to find the footprint of purifying selection, especially at sites that are essential for proper ribosome assembly. In our comparison of 70 mammalian WDR75 sequences, we found ~25% of sites with significant purifying selection and no evidence of positive selection. Purifying selection was ~5x stronger for sites folding into beta-sheets than those predicted to be coils. Phylogenetic analysis validated expected mammalian relationships and uncovered an unusually long branch leading to mouse-eared bats, exhibiting 18x more substitutions per site than the average mammalian substitution rate. In testing for molecular evolution among branches, we found no evidence for purifying selection along any individual branches, but unexpectedly detected significant diversifying selection solely among African great apes. [ABSTRACT FROM AUTHOR]

Background: The structure of chloroplast genomes (cpDNAs) in Fabaceae (Fab.) has undergone significant evolutionary modifications. Within the Papilionoideae (Pap.), the emergence of the Inverted Repeat-Lacking Clade (IRLC) represents a major genomic alteration. However, the molecular evolution and phylogenetic relationships within Pap. remain poorly resolved due to limited molecular data and incomplete research, highlighting the need for systematic investigation. Purpose: This study presents an in-depth analysis of the cpDNAs within the Pap., with the aim of unraveling the molecular evolution and phylogenetic interconnections among its species. Methods: Complete cpDNAs of 18 Pap. species were sequenced using the Illumina Novaseq 6000 platform, followed by assembly and annotation. Comparative genomic analyses were conducted to elucidate structural variations and phylogenetic relationships. Results: The research has uncovered significant differences in the structure and characteristics of the cpDNAs within the Pap.. The lengths of the cpDNAs of 18 species range from 121,190 bp to 158,539 bp, and they contain between 107 and 112 unique genes. Five species, namely Desmodium elegans and Indigofera bracteata, exhibit a typical quadripartite structure, while thirteen species from genera such as Astragalus (Ast.), Hedysarum (Hed.), and Caragana (Car.) are grouped within the Inverted Repeat-Lacking Clade (IRLC). Genetic characteristic analysis revealed a plentiful presence of SSR loci, with single-nucleotide repeats and dinucleotide (A/T) repeats being the most predominant. Notably, the cpDNAs of five species including D. elegans have experienced significant rearrangements. For example, an inversion of approximately 23 kilobase (kb) pairs was observed in Pueraria peduncularis and Sophora moorcroftiana. These species exhibit pronounced differences in their non-coding regions. Comparative genomic variations at cpDNA sites were identified. Moreover, by using D. elegans as a reference, six genes (ycf4, clpP, ycf1, trnI-GAU, accD, rpl32) displayed high nucleotide polymorphism (Pi > 0.1), and the Ka/Ks ratio for all protein-coding genes was determined to be less than 1. The topological structure of the constructed phylogenetic tree of 85 species was basically consistent with that of Pap.. Seven main clades were formed and relatively high bootstrap values were exhibited, further clarifying the evolutionary relationships among them. Conclusion: This study provides novel insights into the molecular evolution and phylogeny of Pap., offering a foundational resource for future taxonomic and evolutionary research. [ABSTRACT FROM AUTHOR]

The article "Advances in plant photobiology: let's light it up once again" from the Journal of Experimental Botany discusses the crucial role of light in regulating plant growth and development. It explores the molecular evolution of light signaling components, interactions with other signaling networks, and the integration of light signaling with temperature signaling and shade avoidance responses. The article also delves into the crosstalk between light signaling and phytohormone signaling, as well as the integration of light signaling with nutrient uptake. Additionally, it highlights the evolution of light signaling components and emphasizes the need for further research in the field of plant photobiology. [Extracted from the article]

Background: m6A RNA modifications are the most prevalent internal modifications in eukaryotic mRNAs and are crucial for plant growth and development, as well as for responses to biotic or abiotic stresses. The modification is catalyzed by writers, removed by erasers, and decoded by various m6A-binding proteins, which are readers. Brassica napus is a major oilseed crop. The dynamic regulation of m6A modifications by writers, erasers, and readers offers potential targets for improving the quality of this crop. Results: In this study, we identified 92 m6A-regulatory genes in B. napus, including 13 writers, 29 erasers, and 50 readers. A phylogenetic analysis revealed that they could be further divided into four, three, and two clades, respectively. The distribution of protein motifs and gene structures among members of the same clade exhibited notable similarity. During the course of evolution, whole genome duplication (WGD) and segmental duplication were the primary drivers of the expansion of m6A-related gene families. The genes were subjected to rigorous purification selection. Additionally, several sites under positive selection were identified in the proteins. RNA-seq and quantitative real-time PCR (qRT-PCR) expression analyses revealed that the identified Bnam6As exhibit tissue-specific expression patterns, as well as their expression patterns in response to various abiotic and biotic stresses. The 2000 bp sequence upstream of Bnam6As contained a number of cis-acting elements that regulate plant growth and environmental response. Furthermore, the protein interaction network revealed their interactions with a number of proteins of significant functional importance. Conclusion: The identification of m6A modifiers in oilseed rape and their molecular evolution and expression profiling have revealed potential functions and molecular mechanisms of m6A, thus establishing a foundation for further functional validation and molecular breeding. [ABSTRACT FROM AUTHOR]

Sex-linked and autosomal loci experience different selective pressures and evolutionary dynamics. X (or Z) chromosomes are often hemizygous in males (or females), as Y (or W) chromosomes often degenerate. Such hemizygous regions can be under greater efficacy of selection, as recessive mutations are immediately exposed to selection in the heterogametic sex leading to faster adaptation and faster divergence on the X chromosome (the so-called Faster-X or Faster-Z effect). However, in young nonrecombining regions, Y/W chromosomes often have many functional genes, and many X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on the X/Z by the Y/W homolog is expected to drive slower adaptation for diploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect has been studied extensively, much less is known empirically about the evolutionary dynamics of diploid X or Z chromosomes. Here, we took advantage of published population genomic data in the female-heterogametic human parasite Schistosoma japonicum to characterize the gene content and diversity levels of the diploid and hemizygous regions of the Z chromosome. We used different metrics of selective pressures acting on genes to test for differences in the efficacy of selection in hemizygous and diploid Z regions, relative to autosomes. We found consistent patterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both hemizygous and diploid Z regions. Moreover, relaxed selection was particularly pronounced for female-biased genes on the diploid Z, as predicted by recent theoretical work. [ABSTRACT FROM AUTHOR]

The bacterial protein quality control (PQC) network comprises a set of genes that promote proteostasis (proteome homeostasis) through proper protein folding and function via chaperones, proteases, and protein translational machinery. It participates in vital cellular processes and influences organismal development and evolution. In this review, we examine the mechanistic bases for how the bacterial PQC network influences molecular evolution. We discuss the relevance of PQC components to contemporary issues in evolutionary biology including epistasis, evolvability, and the navigability of protein space. We examine other areas where proteostasis affects aspects of evolution and physiology, including host-parasite interactions. More generally, we demonstrate that the study of bacterial systems can aid in broader efforts to understand the relationship between genotype and phenotype across the biosphere. [ABSTRACT FROM AUTHOR]

Simple Summary: Yunnan Province in southwestern China is home to a rich variety of grasshoppers, particularly from the Acrididae family, which play key roles in ecosystems and agriculture. However, understanding the phylogenetic relationships and evolution of these grasshoppers has been difficult using just their physical traits. To gain deeper insights, our study analyzed the mitochondrial DNA—the genetic material passed from mothers to offspring—of 17 different Acrididae species found in Yunnan. By comparing these new genetic sequences with those from 46 other Acrididae species, we were able to construct a detailed family tree showing how these grasshoppers are related. Our findings revealed that some groups previously thought to be closely related are not, suggesting that the existing classification needs to be updated. Additionally, we determined that the diversification of these grasshoppers occurred alongside significant geological and climate changes in the region over 50 million years ago. This research not only clarifies the evolutionary history of Yunnan's grasshoppers but also provides essential information for conserving their diverse populations. By improving our understanding of these insects, we can probe into their accurate phylogeny. Yunnan Province, a global biodiversity hotspot, hosts a diverse array of Acrididae grasshoppers essential for ecosystem dynamics and agriculture. To elucidate the phylogenetic relationships and evolutionary history of this group, we sequenced and analyzed complete mitochondrial genomes from 17 Acrididae species endemic to Yunnan, with genome lengths ranging from 15,403 to 15,943 base pairs. These data were integrated with mitochondrial sequences from 46 additional species to construct comprehensive phylogenetic trees. The maximum-likelihood tree identified four major clades with robust support (bootstrap values > 90%), revealing significant lineage diversification during the Early Eocene (51.94 million years ago, Mya) and subsequent radiations in the Miocene (~20 Mya) and Pliocene (~5 Mya). These divergence times correlate with major geological events and climatic shifts in the region, such as the uplift of the Tibetan Plateau and the intensification of the Asian monsoon. Notably, several species within the Coptacrinae and Oxyinae subfamilies, particularly Pseudodotraulia cornuata and Spathosternum prasiniferum, were found to be polyphyletic, indicating the necessity for taxonomic revisions. Further cluster analyses of codon usage bias and genetic distance support these taxonomic revisions within Acrididae. This robust phylogenetic framework underpins conservation strategies aimed at preserving Yunnan's rich grasshopper biodiversity and informs updates to their phylogeny. [ABSTRACT FROM AUTHOR]

Simple Summary: The mitochondrial genome has been widely used in biological phylogeny and evolutionary ecology due to its specific energy metabolism center and matrilineal inheritance. In this study, the mitochondrial genome of Chelonoidis vicina was assembled and annotated, and comparative mitochondrial genome, phylogenetic, and selection pressure analyses were used to examine the structure, phylogenetic status, and terrestrial adaptive evolution characteristics of C. vicina. These analyses can aid our understanding of the history of this ancient tortoise's adaptive evolution to a terrestrial environment from a molecular evolution standpoint. Background/Objectives: Mitochondrial genomes are widely used in phylogenetics and evolutionary and ecological research. Methods: In this study, the newest mitochondrial genome of Chelonoidis vicina was assembled and annotated. The comparative mitochondrial genome and selection pressure analyses were used to examine the terrestrial adaptive evolution characteristics of C. vicina and other terrestrial reptiles. Results: The results reveal that the mitochondrial genome of the tortoise C. vicina is consistent with that of other tortoise species, comprising 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs, and 1 noncoding control region (CR). The analysis of selection pressure reveals the presence of positive selection sites in the COX2, COX3, Cytb, ND3, ND4, ND4L, ND5, and ND6 genes of terrestrial reptiles. Of these, the COX2 and ND3 genes exhibited faster evolutionary rates. The mitochondrial genome structure of C. vicina is consistent with that of different terrestrial reptiles. The positive selection sites of COX2 and ND3 in terrestrial reptiles are closely related to a change in mitochondrial energy metabolism, which is possibly related to terrestrial adaptability. Conclusions: The results of this study provide new insights into the adaptive evolution of C. vicina to terrestrial niches from a mitogenomic perspective, as well as genetic resources for the protection of C. vicina. [ABSTRACT FROM AUTHOR]

One of the most important and difficult challenges in the research of molecular evolution is modeling the process of amino acid substitutions. Although single-matrix models, such as the LG model, are popular, their capability to properly capture the heterogeneity of the substitution process across sites is still questioned. Several mixture models with multiple matrices have been introduced and shown to offer advantages over single-matrix models. Current general mixture models assume the reversibility of the evolutionary process, implying that substitution rates between any two amino acids are equal in both forward and backward directions. This assumption is not based on biological properties but rather on computational simplicity. The well-known hypothesis is that more realistic models can yield more accurate evolutionary inferences; therefore, our aim is to estimate more biologically realistic models. To this end, we relax the assumption of reversibility and introduce two new general non-reversible 4-matrix mixture models, called nT4M and nT4X. Using alignments from HSSP and TreeBASE databases as data, our newly estimated models outperformed all single-matrix models and almost all reversible mixture models. Moreover, the new non-reversible mixture models enable us to infer rooted trees. [ABSTRACT FROM AUTHOR]

Recently, certain studies have claimed that cognitive features and pathologies unique to humans can be traced to certain changes in the nervous system. These are caused by genes that have likely evolved "from scratch," not having any coding precursors. The translated proteins would not appear outside of the human lineage and any orthologs in other species should be non-coding. This contrasts with research that has identified a decisive role for duplication, and modifications to regulatory sequences, for such phenotypic traits. Closer examination, however, reveals that the inferred lineage-specific emergence of at least two of these genes is likely a misinterpretation owing to a lack of peptide verification, experimental oversights, and insufficient species comparisons. A possible pseudogenic origin is proposed for one of them. The implications of these claims for the study of molecular evolution are discussed. [ABSTRACT FROM AUTHOR]

Expansion and losses of gene families are important drivers of molecular evolution. A recent survey of Fox genes in flatworms revealed that this superfamily of multifunctional transcription factors, present in all animals, underwent extensive losses and expansions during platyhelminth evolution. In this paper, I analyzed Fox gene complement in four additional species of platyhelminths, that represent early-branching lineages in the flatworm phylogeny: catenulids (Stenostomum brevipharyngium and Stenostomum leucops) and macrostomorphs (Macrostomum hystrix and Macrostomum cliftonense). Phylogenetic analysis of Fox genes from this expanded set of species provided evidence for multiple independent expansions of Fox gene families within flatworms. Notably, FoxG, a panbilaterian brain-patterning gene, appears to be the least susceptible to duplication, while FoxJ1, a conserved ciliogenesis factor, has undergone extensive expansion in various flatworm lineages. Analysis of the single-cell atlas of S. brevipharyngium, combined with RNA in situ hybridization, elucidated the tissue-specific expression of the selected Fox genes: FoxG is expressed in the brain, three of the Fox genes (FoxN2/3–2, FoxO4 and FoxP1) are expressed in the pharyngeal cells of likely glandular function, while one of the FoxQD paralogs is specifically expressed in the protonephridium. Overall, the evolution of Fox genes in flatworms appears to be characterized by an early contraction of the gene complement, followed by lineage-specific expansions that have enabled the co-option of newly evolved paralogs into novel physiological and developmental functions. [ABSTRACT FROM AUTHOR]

Sulfoxide synthase OvoA is the key enzyme involved in the biosynthesis of ovothiols (OSHs), secondary metabolites endowed with unique antioxidant properties. Understanding the evolution of such enzymes and the diversity of their metabolites should reveal fundamental mechanisms governing redox signaling and environmental adaptation. "Early-branching" animals such as Cnidaria display unique molecular diversity and symbiotic relationships responsible for the biosynthesis of natural products, however, they have been neglected in previous research on antioxidants and OSHs. In this work, we have integrated genome and transcriptome mining with biochemical analyses to study the evolution and diversification of OSHs biosynthesis in cnidarians. By tracing the history of the ovoA gene, we inferred its loss in the latest common ancestor of Medusozoa, followed by the acquisition of a unique ovoB/ovoA chimaeric gene in Hydrozoa, likely through a horizontal gene transfer from dinoflagellate donors. While Anthozoa (corals and anemones), bearing canonical ovoA genes, produced a striking variety of OSHs (A, B, and C), the multifunctional enzyme in Hydrozoa was related to OSH B biosynthesis, as shown in Clytia hemisphaerica. Surprisingly, the ovoA- lacking jellyfish Aurelia aurita and Pelagia noctiluca also displayed OSHs, and we provided evidence of their incorporation from external sources. Finally, transcriptome mining revealed ovoA conserved expression pattern during larval development from Cnidaria to more evolved organisms and its regulation by external stimuli, such as UV exposure. The results of our study shed light on the origin and diversification of OSH biosynthesis in basal animals and highlight the importance of redox-active molecules from ancient metazoans as cnidarians to vertebrates. [Display omitted] • Basal animals like Cnidaria represent an extraordinary example of molecular diversity in ovothiol biosynthesis. • Anthozoa (corals and anemones) display canonical ovo genes and produce a striking variety of OSHs (A, B, and C). • Besides ovoA gene lost in Medusozoa, some jellyfish Aurelia aurita and Pelagia noctiluca incorporate ovothiols through diet. • Hydrozoa e.g. Clytia hemisphaerica display a ovoB/ovoA chimeric gene, acquired through an HGT from dinoflagellates, and produce OSH B. • OvoA gene expression patterns are conserved during animal larval development and are regulated by environmental stressors. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome provides crucial information for comprehending gene rearrangement, molecular evolution, and phylogenetic analysis. Here, we have determined the complete mitogenome sequence of Gonatopsis borealis and Onychoteuthis compacta for the first time. Their genome sizes were 20,148 bp and 20,491 bp, respectively, including 18 protein-coding genes, COI-COIII, ATP6, and ATP8 are duplicated, 23 transfer RNA genes, and 2 ribosomal RNA (rRNA) genes (12S and 16S rRNA). Specifically, the overall A+T content is 70.69% and 72.67%. It shows a significant AT bias. The whole mitogenomes indicate positive AT skew (0.070 and 0.062). Furthermore, the gene order has been rearranged within Oegopsida. The tandem duplication random loss model was determined as most likely to explain the observed gene rearrangements. Phylogenetic analysis was performed, and the result tree was found to be consistent with the morphological identification classification. Estimation of divergence time for 35 species showed that the main differentiation of Oegopsida occurred in 140.70 Mya. These results will help to better understand the gene rearrangements and evolution of G. borealis and O. compacta and lay a foundation for further phylogeny genetic studies of Oegopsida. [ABSTRACT FROM AUTHOR]

In the dynamic field of gene therapy, recombinant adeno-associated viruses (rAAVs) have become leading viral vectors due to their safety, long-term expression, and wide-ranging cell and tissue tropism. With numerous FDA approvals and commercial products underscoring their potential, there is a critical need for efficient production processes to achieve high vector titers and quality. A major challenge in rAAV production is the efficient packaging of the genome into the viral capsid, with empty or partially filled capsids often representing over 90% of the produced material. To tackle this issue, we engineered the replication and packaging proteins of an AAV (Rep) to boost their functionality and improve vector titers. We subjected a complex Rep library derived from the AAV serotypes 1–13 to directed evolution in an AAV producer cell line. After each round of selection, single clones were analyzed, showing enrichment of specific hybrid Rep domains. Comparative analysis of these selected clones revealed considerable differences in their ability to package AAV2-based viral genomes, with hybrid Rep proteins achieving up to a 2.5-fold increase in packaging efficiency compared to their parental counterparts. These results suggest that optimizing rep gene variants through directed evolution is an effective strategy to enhance rAAV production efficiency. [ABSTRACT FROM AUTHOR]

Heterogeneous oxidation by gas-phase oxidants is an important chemical transformation pathway of secondary organic aerosol (SOA) and plays an important role in controlling the abundance, properties, as well as climate and health impacts of aerosols. However, our knowledge on this heterogeneous chemistry remains inadequate. In this study, the heterogeneous oxidation of α-pinene ozonolysis SOA by hydroxyl (OH) radicals was investigated under both low and high relative humidity (RH) conditions, with an emphasis on the evolution of molecular composition of SOA and its RH dependence. It is found that the heterogeneous oxidation of SOA at an OH exposure level equivalent to 12 hr of atmospheric aging leads to particle mass loss of 60% at 25% RH and 95% at 90% RH. The heterogeneous oxidation strongly changes the molecular composition of SOA. The dimer-to-monomer signal ratios increase dramatically with rising OH exposure, in particular under high RH conditions, suggesting that aerosol water stimulates the reaction of monomers with OH radicals more than that of dimers. In addition, the typical SOA tracer compounds such as pinic acid, pinonic acid, hydroxy pinonic acid and dimer esters (e.g., C 17 H 26 O 8 and C 19 H 28 O 7) have lifetimes of several hours against heterogeneous OH oxidation under typical atmospheric conditions, which highlights the need for the consideration of their heterogeneous loss in the estimation of monoterpene SOA concentrations using tracer-based methods. Our study sheds lights on the heterogeneous oxidation chemistry of monoterpene SOA and would help to understand their evolution and impacts in the atmosphere. [Display omitted] [ABSTRACT FROM AUTHOR]

The inverse problem of reconstructing two space-varying coefficients in a system of one-dimensional (1-d) time-dependent advection-diffusion-reaction (ADR) equations is considered. The ADR system can be used as a water quality model which describes the evolution of the biochemical oxygen demand (BOD) and dissolved oxygen (DO) in a river or stream. The coefficients to be reconstructed represents the effect of the deoxygenation and superficial reaeration processes on the DO and BOD concentration in water. Hölder stability estimates for the coefficients of interest are established using the Carleman estimate technique. [ABSTRACT FROM AUTHOR]

Human parainfluenza virus type 2 (HPIV2) is a clinically significant respiratory pathogen, which highlights the necessity of studies on its molecular evolution. This study investigated the evolutionary dynamics, phylodynamics, and structural characteristics of the HPIV2 fusion (F) gene using a comprehensive dataset spanning multiple decades and geographic regions. Phylogenetic analyses revealed two distinct clusters of HPIV2 F gene sequences, which were estimated to have diverged from a common ancestor approximately a century ago. Cluster 1 demonstrated a higher evolutionary rate and genetic diversity compared to the more stable cluster 2. Bayesian Skyline Plot analyses indicated a significant increase in the effective population size of the F gene between 2005 and 2015; potentially linked to enhanced diagnostic and surveillance capabilities. Structural modeling identified conserved conformational epitopes predominantly in the apex and stalk regions of the F protein. These findings underscore the evolutionary constraints and antigenic landscape of the HPIV2 F protein. [ABSTRACT FROM AUTHOR]

Heat stress affects various components of photosynthetic machinery of which Rubisco activation inhibition due to heat sensitive Rubisco activase (RCA) is the most prominent. Detailed comparison of RCA coding genes identified a tandem duplication event in the grass family lineage where the duplicated genes showed very different evolutionary pattern. One of the two genes showed high level of sequence conservation whereas the second copy, although present only 1.5 kb away, was highly variable among various plant species because of loss of introns, alternative splicing and loss of the last exon coding redox regulated C-terminal extension domain. Gene specific expression analysis, both at the transcription as well as the protein level, showed very different expression pattern of the two RCA copies. Expression of the highly conserved copy was higher under normal plant growing conditions that decreased many folds under heat stress with substantial genotypic variation, but the variable copy showed much higher expression under heat stress conditions across all grass species. The cultivated rice has only one functional gene as the second copy became nonfunctional due to multiple deletions but Oryza brachyantha and Oryza australiensis still have two functional Rca genes. Detailed analysis of the promoter region of the two copies among various plant species showed insertion of several transposable elements harboring heat responsive elements in the heat inducible copy of the gene. The conserved RCA copy of wheat didn’t have any transposable insertions whereas in that of maize has one heat shock element and sorghum had two. It would be interesting to study if the higher level of heat stress tolerance observed in sorghum and maize is associated with the differences observed for RCA. Key message This manuscript is reporting a grass family-specific tandem duplication event in RCA genes of cereals. The duplicated copies underwent neo-functionalization to evolve novel function to deal with heat stress. One copy of the tandem duplication maintained a high level of conservation whereas the second copy showed tremendous divergence to evolve species specific function of the gene. Specific function to respond to heat stress likely evolved via the insertion of various heat responsive elements carried by transposable elements.Key message: This manuscript is reporting a grass family-specific tandem duplication event in RCA genes of cereals. The duplicated copies underwent neo-functionalization to evolve novel function to deal with heat stress. One copy of the tandem duplication maintained a high level of conservation whereas the second copy showed tremendous divergence to evolve species specific function of the gene. Specific function to respond to heat stress likely evolved via the insertion of various heat responsive elements carried by transposable elements. [ABSTRACT FROM AUTHOR]

This review delves into the physio-chemical modeling of widely used (bio)degradable polymers such as polylactide (PLA), polyglycolide (PGA), and polycaprolactone (PCL), emphasizing the interplay between environmental conditions, chemical reactions, and material alterations. It utilizes structural equations and reaction–diffusion approaches to model changing structural properties during degradation. This review explores recent advances in physio-chemical modeling techniques, offering insights into predicting degradation kinetics, molecular weight evolution, and mass loss. This comprehensive understanding is essential for tailoring the degradation profiles of (bio)degradable polymers, optimizing their performance, and reducing environmental impact. Additionally, the review covers various other modeling approaches, including the multiscale method and the hybrid method, providing a holistic view of the current state of (bio)degradable polymer degradation modeling. [ABSTRACT FROM AUTHOR]

Introduction: Immunosuppressive diseases, such as chicken infectious anemia virus (CIAV), pose a major threat to livestock farming due to reduced disease resistance, poor vaccine response, and overall poor productivity. CIAV, recognized globally for decades, shows a significant genetic diversity, but its implications remain underexplored. Methods: This study analyzed over 1,000 VP1 sequences and examined CIAV's epidemiology, evolution, and spread with various phylodynamic and phylogeographic approaches. Results: Findings suggest that CIAV likely originated in Japan in the early 20th century, followed by worldwide diversification in two main clades. Both clades exhibited no significant competition and similar global patterns, characterized by a progressive increase until about 2000, when a transient decline was observed for some years, potentially reflecting the increasing use of vaccines. Accordingly, although significant selective pressures were shaping viral evolution, comparable strengths were estimated in the two viral populations. The phylogeographic analysis identified several connections involving also distantly related regions, and more generally, multiple introduction events occurred in several countries and were followed by local evolution, indicative of unconstrained viral circulation. Discussion: Overall, the study highlights the ongoing circulation and evolution of different CIAV variants worldwide, where biosecurity measures and vaccination appear insufficient to prevent viral presence and dispersal. [ABSTRACT FROM AUTHOR]

The effectiveness of poultry vaccination in preventing the transmission of highly pathogenic avian influenza viruses (AIVs) has been debated, and its impact on wild birds remains uncertain. Here, we reconstruct the movements of H5 subtype AIV lineages among vaccinated poultry, unvaccinated poultry, and wild birds, worldwide, from 1996 to 2023. We find that there is a time lag in viral transmission among different host populations and that movements from wild birds to unvaccinated poultry were more frequent than those from wild birds to vaccinated poultry. Furthermore, our findings suggest that the HA (hemagglutinin) gene of the AIV lineage that circulated predominately in Chinese poultry experienced greater nonsynonymous divergence and adaptive fixation than other lineages. Our results indicate that the epidemiological, ecological, and evolutionary consequences of widespread AIV vaccination in poultry may be linked in complex ways and that much work is needed to better understand how such interventions may affect AIV transmission to, within, and from wild birds. [ABSTRACT FROM AUTHOR]

Background: Haplotype networks are useful for investigating the genealogical relationships among haplotypes and have been extensively used in molecular evolution and population genetic studies. However, existing tools for visualizing haplotype networks lack comprehensive functionalities for data exploration and layout adjustments. Therefore, there is a need for a useful tool capable of constructing and visualizing haplotype networks, facilitating the exploration of data, particularly with datasets with large sample sizes. Results: We present HapNetworkView, a user-friendly tool that facilitates the construction and interactive visualization of haplotype networks, enabling users to explore haplotypes and mutation information effectively. HapNetworkView offers both automatic optimization and manual adjustment for haplotype network layouts. Additionally, HapNetworkView supports various input and output formats, as well as color customization. Conclusions: These comprehensive functionalities collectively satisfy various needs of users in haplotype network analysis, making HapNetworkView a valuable tool. [ABSTRACT FROM AUTHOR]

The evolution of metastasis, the spread of cancer to distal sites within the body, represents a lethal stage of cancer progression. Yet, the evolutionary dynamics that shape the emergence of metastatic disease remain unresolved. Here, using single-cell lineage tracing data in combination with phylogenetic statistical methods, we show that the evolutionary trajectory of metastatic disease is littered with bursts of rapid molecular change as new cellular subpopulations appear, a pattern known as punctuational evolution. Next, by measuring punctuational evolution across the metastatic cascade, we show that punctuational effects are concentrated within the formation of secondary tumours at distal metastatic sites, suggesting that qualitatively different modes of evolution may drive primary and metastatic tumour progression. Taken as a whole, our findings provide empirical evidence for distinct patterns of molecular evolution at early and late stages of metastatic disease and our approach provides a framework to study the evolution of metastasis at a more nuanced level than has been previously possible. [ABSTRACT FROM AUTHOR]

The evolution of brain-expressed genes is notably slower than that of genes expressed in other tissues, a phenomenon likely due to high-level functional constraints. One such constraint might be the integration of information by neuron assemblies, enhancing environmental adaptability. This study explores the physiological mechanisms of information integration in neurons through three types of synchronization: chemical, electromagnetic, and quantum. Chemical synchronization involves the diffuse release of neurotransmitters like dopamine and acetylcholine, causing transmission delays of several milliseconds. Electromagnetic synchronization encompasses action potentials, electrical gap junctions, and ephaptic coupling. Electrical gap junctions enable rapid synchronization within cortical GABAergic networks, while ephaptic coupling allows structures like axon bundles to synchronize through extracellular electromagnetic fields, surpassing the speed of chemical processes. Quantum synchronization is hypothesized to involve ion coherence during ion channel passage and the entanglement of photons within the myelin sheath. Unlike the finite-time synchronization seen in chemical and electromagnetic processes, quantum entanglement provides instantaneous non-local coherence states. Neurons might have evolved from slower chemical diffusion to rapid temporal synchronization, with ion passage through gap junctions within cortical GABAergic networks potentially facilitating both fast gamma band synchronization and quantum coherence. This mini-review compiles literature on these three synchronization types, offering new insights into the physiological mechanisms that address the binding problem in neuron assemblies. [ABSTRACT FROM AUTHOR]

The family Hepeviridae has seen an explosive expansion in its host range in recent years, yet the evolutionary trajectory of this zoonotic pathogen remains largely unknown. The emergence of rat hepatitis E virus (HEV) has introduced a new public health threat due to its potential for zoonotic transmission. This study investigated 2  464 wild small mammals spanning four animal orders, eight families, 21 genera, and 37 species in Yunnan Province, China. Using broadly reactive reverse transcription-polymerase chain reaction (RT-PCR), we systematically screened the presence and prevalence of Orthohepevirus and identified 192 positive specimens from 10 species, corresponding to an overall detection rate of 7.79%. Next-generation sequencing enabled the recovery of 24 full-length genomic sequences from eight host species, including Bandicota bengalensis, Eothenomys eleusis, and Episoriculus caudatus, representing newly reported host species for Orthohepevirus strains. Phylogenetic and sequence analyses revealed extensive genetic diversity within orthohepeviruses infecting rodents and shrews. Notably, among the identified strains, 20 were classified as Rocahepevirus ratti C1, two as C3, and one as Rocahepevirus eothenomi, while the remaining strain exhibited significant divergence, precluding classification. Evolutionary analyses highlighted close associations between orthohepeviruses and their respective host taxa, with distinct phylogenetic clustering patterns observed across different host orders. These findings emphasize the critical roles of co-speciation and cross-species transmission in shaping the evolutionary trajectories of the genera Paslahepevirus and Rocahepevirus. [ABSTRACT FROM AUTHOR]

Late embryogenesis abundant (LEA) proteins are a class of proteins associated with osmotic regulation and plant tolerance to abiotic stress. However, studies on the LEA gene family in the alpine cold-tolerant herb are still limited, and the phylogenetic evolution and biological functions of its family members remain unclear. In this study, we conducted genome-wide identification, phylogenetic evolution, and abiotic stress response analyses of LEA family genes in Notopterygium species, alpine cold-tolerant medicinal herbs in the Qinghai–Tibet Plateau and adjacent regions. The gene family identification analysis showed that 23, 20, and 20 LEA genes were identified in three Notopterygium species, N. franchetii, N. incisum, and N. forrestii, respectively. All of these genes can be classified into six LEA subfamilies: LEA_1, LEA_2, LEA_5, LEA_6, DHN (Dehydrin), and SMP (seed maturation protein). The LEA proteins in the three Notopterygium species exhibited significant variations in the number of amino acids, physical and chemical properties, subcellular localization, and secondary structure characteristics, primarily demonstrating high hydrophilicity, different stability, and specific subcellular distribution patterns. Meanwhile, we found that the members of the same LEA subfamily shared similar exon–intron structures and conserved motifs. Interestingly, the chromosome distributions of LEA genes in Notopterygium species were scattered. The results of the collinearity analysis indicate that the expansion of the LEA gene family is primarily driven by gene duplication. A Ka/Ks analysis showed that paralogous gene pairs were under negative selection in Notopterygium species. A promoter cis-acting element analysis showed that most LEA genes possessed multiple cis-elements connected to plant growth and development, stress response, and plant hormone signal transduction. An expression pattern analysis demonstrated the species-specific and tissue-specific expression of NinLEAs. Experiments on abiotic stress responses indicated that the NinLEAs play a crucial role in the response to high-temperature and drought stresses in N. franchetii leaves and roots. These results provide novel insights for further understanding the functions of the LEA gene family in the alpine cold-tolerant Notopterygium species and also offer a scientific basis for in-depth research on the abiotic stress response mechanisms and stress-resistant breeding. [ABSTRACT FROM AUTHOR]