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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]

Purine alkaloids are naturally occurring nitrogenous methylated derivatives of purine nucleotide degradation products, having essential roles in medicine, food and various other aspects of our daily lives. They are generated through convergent evolution in different plant species. The pivotal reaction steps within the purine alkaloid metabolic pathways have been largely elucidated, and the convergent evolution of purine alkaloids has been substantiated through bioinformatic, biochemical and other research perspectives within S-adenosyl-ʟ-methionine-dependent N-methyltransferases. Currently, the biological and ecological roles of purine alkaloids, further refinement of the purine alkaloid metabolic pathways and the investigation of purine alkaloid adaptive evolutionary mechanisms continue to attract widespread research interest. The exploration of the purine alkaloid metabolic pathways also enhances our comprehension of the biochemical mechanism, providing insights into inter-species interactions and adaptive evolution and offering potential value in drug development and agricultural applications. Here, we review the progress of research in the distribution, metabolic pathway elucidation and regulation, evolutionary mechanism and ecological roles of purine alkaloids in plants. The opportunities and challenges involved in elucidating the biochemical basis and evolutionary mechanisms of the purine alkaloid metabolic pathways, as well as other research aspects, are also discussed. This article is part of the theme issue 'The evolution of plant meta-bolism'. [ABSTRACT FROM AUTHOR]

Comprehensive Summary: Kagome lattices have garnered significant attention due to their promising applications in catalysis, electronics, and magnetics. Although many efforts have been paid to the design and synthesis of Kagome lattices, there is a limited focus on constructing this lattice by multiple interaction forces. In this work, we employ 2,7‐dibromo‐carbazole as precursors to successfully fabricate the two‐dimensional self‐assembly Kagome lattices stabled by multiple interaction forces on Au(111) substrate. Using low‐temperature scanning tunneling microscopy, non‐contact atomic force microscopy and density functional theory calculation, we visualize and identify the four interaction forces within Kagome lattices: Au—N coordination bonds, Au—H hydrogen bonds, Br—Br halogen bonds, and Br—H hydrogen bonds, respectively. This study provides a basic understanding for designing and constructing more complex Kagome lattices. [ABSTRACT FROM AUTHOR]

The impact of plasma temperature on the formation and evolution of distinct and unique molecular species recorded as molecular signatures from laser induced plasma (LIP) was examined in this study. A definitive correlation between plasma temperature and the formation of molecular species has been established through a comprehensive temporal analysis of BO and BO2 molecular bands. The utilization of the signal-to-envelope ratio diagrams allowed for pinpointing the optimal temperature range for molecule emission. Notably, the molecule BO exhibited an ideal temperature range of 10,000–11,000 K for the proper formation of molecular emission bands, while BO2 preferred temperatures between 8,000–9,000 K. These optimal temperature ranges remained consistent regardless of the laser irradiation wavelength or ambient gas conditions of Ar, air or He studied in this work. These key findings highlight the significant influence of plasma temperature in shaping the molecular species observed in LIP. [ABSTRACT FROM AUTHOR]

A novel rosarin di-Cu complex 2Cu-1 and a linear six-pyrrolic mono-copper complex 1Cu-1 were synthesized using rosarin as the ligand. The molecular conformations of these complexes were confirmed by X-ray crystallography. The optical study of 1Cu-1 indicated NIR-II absorption due to the long six-pyrrolic ligand and the ICT effect. The 2Cu-1 complex exhibited a very narrow electronic reduction–oxidation gap of 0.50 eV, attributed to the antiaromatic characteristics of the rosarin ring. The first HER study of the di-copper rosarin complex 2Cu-1 indicated that the multi-metal poly-pyrrolic complexes are promising molecular hydrogen evolution reaction catalysts. [ABSTRACT FROM AUTHOR]

Clevelandellids are highly diversified and widespread unicellular eukaryotic organisms inhabiting the digestive tract of a broad spectrum of invertebrates and vertebrates. Time‐calibrated phylogeny of clevelandellids was built to reconstruct their ancestral hosts using stochastic mapping, investigate their coevolution with animal hosts using an event‐based tree reconciliation approach and examine the impact of hosts on their diversification dynamics and molecular evolution using the MuSSE method and phylogenetic regression. The progenitor of the analysed representatives of the order Clevelandellida colonized the hindgut of anurans in the Late Jurassic. Later on, clevelandellids switched from anuran to other terrestrial poikilotherm vertebrate and invertebrate hosts. Panesthiine cockroaches served as a source for at least four independent colonization waves into millipedes and non‐panesthiine cockroaches. Duplication events, duplications followed by host switching and inertia were recognized as the most relevant coevolutionary processes shaping the common history of clevelandellids and their animal hosts over geological time. Clevelandellids associated with panesthiine cockroaches were revealed to have significantly higher net‐diversification rates than ciliates living in millipedes, non‐panesthiine cockroaches and poikilotherm vertebrates. Clevelandellids show some interesting macroevolutionary trends, including clustering specific for higher taxa of their hosts, no backward transfers from invertebrate to vertebrate hosts and host‐dependent diversification dynamics. [ABSTRACT FROM AUTHOR]

The major organelles of the endomembrane system were in place by the time of the last eukaryotic common ancestor (LECA) (~1.5 billion years ago). Their acquisitions were defining milestones during eukaryogenesis. Comparative cell biology and evolutionary analyses show multiple instances of homology in the protein machinery controlling distinct interorganelle trafficking routes. Resolving these homologous relationships allows us to explore processes underlying the emergence of additional, distinct cellular compartments, infer ancestral states predating LECA, and explore the process of eukaryogenesis itself. Here, we undertake a molecular evolutionary analysis (including providing a transcriptome of the jakobid flagellate Reclinomonas americana), exploring the origins of the machinery responsible for the biogenesis of lysosome-related organelles (LROs), the Biogenesis of LRO Complexes (BLOCs 1,2, and 3). This pathway has been studied only in animals and is not considered a feature of the basic eukaryotic cell plan. We show that this machinery is present across the eukaryotic tree of life and was likely in place prior to LECA, making it an underappreciated facet of eukaryotic cellular organisation. Moreover, we resolve multiple points of ancient homology between all three BLOCs and other post-endosomal retrograde trafficking machinery (BORC, CCZ1 and MON1 proteins, and an unexpected relationship with the “homotypic fusion and vacuole protein sorting” (HOPS) and “Class C core vacuole/endosomal tethering” (CORVET) complexes), offering a mechanistic and evolutionary unification of these trafficking pathways. Overall, this study provides a comprehensive account of the rise of the LROs biogenesis machinery from before the LECA to current eukaryotic diversity, integrating it into the larger mechanistic framework describing endomembrane evolution. [ABSTRACT FROM AUTHOR]

The difficulty of designing simple autocatalysts that grow exponentially in the absence of enzymes, external drives or ingenious internal mechanisms severely constrains scenarios for the emergence of evolution by natural selection in chemical and physical systems. Here, we systematically analyze these difficulties in the simplest and most generic autocatalyst: a dimeric molecule that duplicates by templated ligation. We show that despite its simplicity, such an autocatalyst can achieve exponential growth autonomously. We also show, however, that it is possible to design as simple sub-exponential autocatalysts that have an advantage over exponential autocatalysts when competing for a common resource. We reach these conclusions by developing a theoretical framework based on kinetic barrier diagrams. Besides challenging commonly accepted assumptions in the field of the origin of life, our results provide a blueprint for the experimental realization of elementary autocatalysts exhibiting a form of natural selection, whether on a molecular or colloidal scale. Autocatalysis plays an important role in the origin of life and molecular evolution, however, designing simple autocatalysts that grow exponentially remains challenging. Here, the authors computationally design simple autocatalysts-- dimeric molecules that duplicate by templated ligation, --and show that these autocatalysts can achieve exponential growth autonomously. [ABSTRACT FROM AUTHOR]

Aims Methods Results Conclusion Contralateral axillary lymph node metastasis (CAM) is a rare clinical condition in patients with breast cancer (BC). CAM can be either a locoregional event or a distant metastasis. Molecular application for clonal evolution in BC has not been reported in CAM cases.We studied six patients with CAM with clinical, pathological and/or molecular evidence of distant metastasis; those patients had poor outcomes.Two cases with molecular analysis of paired primary and CAM established clonal evolution of the CAM with its corresponding primary with additional molecular alteration, increased tumour mutation burden, and copy number variations (CNVs) in the CAMs. Four cases containing alterations from genes potentially modulate chromatin organization, supporting chromatin and subsequent transcriptional signature changes are essential in CAM. Molecular analysis is critical to establish the connection between CAM and its primary counterpart. Distant CAM shows clonal evolution compared with its corresponding primary with additional molecular alterations, increased mutation burden and/or copy number variations.CAM should be evaluated individually and handled in a personalized fashion. Evidence of a true metastatic CAM can be supported by distant metastasis to other organs, specific morphological features and/or clonal evolution. [ABSTRACT FROM AUTHOR]

We have explored the reaction of a three‐components mixture of aminomalononitrile, urea and α‐amino acid methyl esters for the multicomponent synthesis substituted purines resembling PNA's building blocks. 2,6‐diamino‐purines, 6‐amino‐3,9‐dihydro‐2H‐purin‐2‐one (iso‐guanines), and 3,9‐dihydro‐6H‐purin‐6‐one derivatives, selectively decorated at C(8)‐position of the purine ring with different amino acid residues, were obtained from acceptable to good yields. The regio‐selectivity of the transformation was controlled by the use of urea in the ternary mixture and by the annulation agent involved in the ring‐closure of amino‐imidazole carbonitrile intermediates. Solvent free conditions, microwave irradiation and simple one‐carbon containing reagents further satisfied the major requirement of atom economy and sustainable chemistry. Due to the prebiotic nature of the three‐components mixture and of annulation agents, it also embodies the possibility for the synthesis of novel PNAs bearing purine nucleobases decorated at C(8)‐position of the imidazole ring as alternative RNA analogues in molecular evolution. [ABSTRACT FROM AUTHOR]

Background: Lithospermeae is the largest tribe within Boraginaceae. The tribe has been the focus of multiple phylogenetic studies over the last 15 years, with most focused on one genus or a few genera. In the present study, we newly sequenced 69 species of Lithospermeae and relatives to analyze the phylogenomic relationships among its members as well as the evolution of the plastid genome. Results: The phylogeny of Lithospermeae resolved from the plastid genome and nrDNA cistron is generally congruent with prior studies, but is better resolved and supported. Increasing character sampling across the plastid genome results in gradually more similar trees to that from the entire plastid genome. Overall, plastid genome structure was quite consistent across Lithospermeae. Codon Usage Bias (CUB) analyses demonstrate that across Lithospermeae plastid genomes were rich in AT and poor in GC. Mutation may play a greater role than selection across the plastid genome of Lithospermeae. The present study is the first to highlight the CUB characteristics of Lithospermeae species, which can help elucidate the mechanisms underlying patterns of molecular evolution and improve the expression levels of exogenous genes by codon optimization. Conclusions: This study provides a comprehensive phylogenomic analysis of Lithospermeae, significantly enhancing our understanding of the phylogenetic relationships and plastid genome evolution within this largest tribe of Boraginaceae. By utilizing an expanded genomic sampling approach, we have achieved increased resolution and support among the evolutionary relationships of the tribe, in line with but improving upon previous studies. The analyses of plastid genome structure revealed consistency across Lithospermeae, with a notable CUB. This study marks the first investigation into the CUB of Lithospermeae species and sets the stage for further research on the molecular evolution of plastid genomes across Boraginaceae. [ABSTRACT FROM AUTHOR]

Background: Mitochondrial genes and nuclear genes cooperate closely to maintain the functions of mitochondria, especially in the oxidative phosphorylation (OXPHOS) pathway. However, mitochondrial genes among arthropod lineages have dramatic evolutionary rate differences. Haplodiploid arthropods often show fast-evolving mitochondrial genes. One hypothesis predicts that the small effective population size of haplodiploid species could enhance the effect of genetic drift leading to higher substitution rates in mitochondrial and nuclear genes. Alternatively, positive selection or compensatory changes in nuclear OXPHOS genes could lead to the fast-evolving mitochondrial genes. However, due to the limited number of arthropod genomes, the rates of evolution for nuclear genes in haplodiploid species, besides hymenopterans, are largely unknown. To test these hypotheses, we used data from 76 arthropod genomes, including 5 independently evolved haplodiploid lineages, to estimate the evolutionary rates and patterns of gene family turnover of mitochondrial and nuclear genes. Results: We show that five haplodiploid lineages tested here have fast-evolving mitochondrial genes and fast-evolving nuclear genes related to mitochondrial functions, while nuclear genes not related to mitochondrion showed no significant evolutionary rate differences. Among hymenopterans, bees and ants show faster rates of molecular evolution in mitochondrial genes and mitochondrion-related nuclear genes than sawflies and wasps. With genome data, we also find gene family expansions and contractions in mitochondrion-related genes of bees and ants. Conclusions: Our results reject the small population size hypothesis in haplodiploid species. A combination of positive selection and compensatory changes could lead to the observed patterns in haplodiploid species. The elevated evolutionary rates in OXPHOS complex 2 genes of bees and ants suggest a unique evolutionary history of social hymenopterans. [ABSTRACT FROM AUTHOR]

ABSTRACT It is a global priority to better manage the biosphere, but action must be informed by comprehensive data on the abundance and distribution of species. The acquisition of such information is currently constrained by high costs. DNA barcoding can speed the registration of unknown animal species, the most diverse kingdom of eukaryotes, as the BIN system automates their recognition. However, inexpensive sequencing protocols are critical as the census of all animal species is likely to require the analysis of a billion or more specimens. Barcoding involves DNA extraction followed by PCR and sequencing with the last step dominating costs until 2017. By enabling the sequencing of highly multiplexed samples, the Sequel platforms from Pacific BioSciences slashed costs by 90%, but these instruments are only deployed in core facilities because of their expense. Sequencers from Oxford Nanopore Technologies provide an escape from high capital and service costs, but their low sequence fidelity has, until recently, constrained adoption. However, the improved performance of its latest flow cells (R10.4.1) erases this barrier. This study demonstrates that a MinION flow cell can characterise an amplicon pool derived from 100,000 specimens while a Flongle flow cell can process one derived from several thousand. At $0.01 per specimen, DNA sequencing is now the least expensive step in the barcode workflow. [ABSTRACT FROM AUTHOR]

Summary Marchantia polymorpha, occupying a basal position in the monophyletic assemblage of land plants, displays a notable expansion of plant U‐box (PUB) proteins compared with those in animals. We elucidated the roles of MpPUB9 in regulating salt stress tolerance in M. polymorpha. MpPUB9 expression was rapidly induced by high salinity and dehydration. MpPUB9 possessed an intact U‐box domain in the N‐terminus. MpPUB9‐Citrine localized to punctate structures and was peripherally associated with microsomal membranes. Phenotypic analyses demonstrate that the hyponastic and epinastic thallus growth phenotypes, which were induced by the overexpression and suppression of MpPUB9, may provoke salt stress‐resistant and ‐susceptible phenotypes, respectively. MpPUB9 was also found to directly interact with the exocyst protein MpEXO70.1, leading to its ubiquitination. Under high‐salinity conditions, though the stability of MpPUB9 was dramatically increased, MpEXO70.1 showed slightly faster turnover rates. Transcriptome analyses showed that salt treatment and the overexpression of MpPUB9 co‐upregulated the genes related to the modulation of H2O2 and cell wall organization. Overall, our results suggest that MpPUB9 plays a crucial role in the positive regulation of salt stress tolerance, resulting from its interaction with MpEXO70.1 and modulating turnover of the protein under high‐salt conditions via the coordination of UPS with autophagy. [ABSTRACT FROM AUTHOR]

ABSTRACT Understanding the molecular mechanisms of thermal adaptation is crucial to predict the impacts of global warming. However, there is still a lack of research on the effects of rising temperatures over time and of studies involving different populations from the same species. The present study focuses on these two aspects, which are of great importance in understanding how organisms cope and adapt to ongoing changes in their environment. This study investigates the impact of global warming on the gene expression patterns of Drosophila subobscura populations from two different latitudinal locations after 23 generations of evolution. Our results indicate that evolutionary changes depend on the genetic background of the populations, with different starting points for thermal evolution, and that high‐latitude populations show more pronounced evolutionary changes, with some evidence of convergence towards low‐latitude populations. We found an interplay between plasticity and selection, with the high‐latitude population showing fewer initial plastic genes and lower levels of adaptive plasticity, but a greater magnitude of change in both plastic and selective responses during evolution under warming conditions compared with its low‐latitude counterpart. A substantial proportion of the transcriptome was observed to be evolving, despite the lack of observable response at higher‐order phenotypic traits. The interplay between plasticity and selection may prove to be an essential component in shaping species’ evolutionary responses to climate change. Furthermore, the value of conducting studies on multiple populations of the same species is emphasised, given the identification of differences between populations with different backgrounds in several contexts. [ABSTRACT FROM AUTHOR]

ABSTRACT Genetic mechanisms have been at the forefront of our exploration into the substrate of adaptive evolution and phenotypic diversification. However, genetic variation only accounts for a fraction of phenotypic variation. In the last decade, the significance of RNA modification mechanisms has become more apparent in the context of organismal adaptation to rapidly changing environments. RNA m6A methylation, the most abundant form of RNA modification, is emerging as a potentially significant player in various biological processes. Despite its fundamental function to regulate other major post‐transcriptional mechanisms such as microRNA and alternative splicing, its role in ecology and evolution has been understudied. This review highlights the potential importance of m6A RNA methylation in ecological adaptation, emphasising the need for further research, especially in natural systems. We focus on how m6A not only affects mRNA fate but also influences miRNA‐mediated gene regulation and alternative splicing, potentially contributing to organismal adaptation. The aim of this review is to synthesise key background information to enhance our understanding of m6A mechanisms driving species survival in dynamic environments and motivate future research into the dynamics of adaptive RNA methylation. [ABSTRACT FROM AUTHOR]

Polygonati Rhizoma and Polygonati odorati Rhizoma, known as "Huangjing" and "Yuzhu" in China, are medicinal Polygonatum species resources with top-grade medical and edible properties. The chloroplast (cp) genome has been used to study species diversity, evolution, and breeding of species for applications in genetic engineering. Codon usage bias (CUB), a common and complex natural phenomenon, is essential for studies of codon optimization of exogenous genes, genetic engineering, and molecular evolution. However, the CUB of medicinal Polygonatum species chloroplast genomes has not been systematically studied. In our study, a detailed analysis of CUB was performed in the medicinal Polygonatum species chloroplast genomes. We investigated the codon bias of 204 plastid protein-coding genes (PCGs) in 4 medicinal Polygonatum species using CodonW and CUSP online software. Through the analysis of the codon bias index, we found that the medicinal Polygonatum species chloroplast genomes had weak codon usage bias. In addition, our results also showed a high preference for AT bases in medicinal Polygonatum species chloroplast genomes, and the preference to use AT-ending codons was observed in these species chloroplast genomes. The neutrality plot, ENC plot, PR2-Bias plot, and correspondence analysis showed that compared with mutation pressure, natural selection was the most important factor of CUB. Based on the comparative analysis of high-frequency codons and high expression codons, we also determined the 10-11 optimal codons of investigative medicinal Polygonatum species. Furthermore, the result of RSCU-based cluster analysis showed that the genetic relationship between different medicinal Polygonatum species could be well reflected. This study provided an essential understanding of CUB and evolution in the medicinal Polygonatum species chloroplast genomes. [ABSTRACT FROM AUTHOR]

Low-molecular-mass organic chemicals are widely discussed as potential indicators of life in extraterrestrial habitats. However, demarcation lines between biotic chemicals and abiotic chemicals have been difficult to define. Here, we have analyzed the potential utility of the quantum chemical property, HOMO-LUMO gap (HLG), as a novel proxy variable of life, since a significant trend towards incrementally smaller HLGs has been described in the genetically encoded amino acids. The HLG is a zeroth-order predictor of chemical reactivity. Comparing a set of 134 abiotic organic molecules recovered from meteorites, with 570 microbial and plant secondary metabolites thought to be exclusively biotic, we found that the average HLG of biotic molecules was significantly narrower (−10.4 ± 0.9 eV versus −12.4 ± 1.6 eV), with an effect size of g = 1.87. Limitation to hydrophilic molecules (XlogP < 2) improved the separation of biotic from abiotic compounds (g = 2.52). The "hydrophilic reactivity" quadrant defined by |HLG| < 11.25 eV and XlogP < 2 was populated exclusively by 183 biotic compounds and 6 abiotic compounds, 5 of which were nucleobases. We conclude that hydrophilic molecules with small HLGs represent valuable indicators of biotic activity, and we discuss the evolutionary plausibility of this inference. [ABSTRACT FROM AUTHOR]

Australian elapid snake venoms are uniquely procoagulant, utilizing blood clotting enzyme Factor Xa (FXa) as a toxin, which evolved as a basal trait in this clade. The subsequent recruitment of Factor Va (FVa) as a toxin occurred in the last common ancestor of taipans (Oxyuranus species) and brown snakes (Pseudonaja species). Factor II (prothrombin) activation has been stated as the primary mechanism for the lethal coagulopathy, but this hypothesis has never been tested. The additional activation of Factor VII (FVII) by Oxyuranus/Pseudonaja venoms has historically been considered as a minor, unimportant novelty. This study aimed to investigate the significance of toxic FVII activation relative to prothrombin activation by testing a wide taxonomical range of Australian elapid species with procoagulant venoms. The activation of FVII or prothrombin, with and without the Factor Va as a cofactor, was assessed, along with the structural changes involved in these processes. All procoagulant species could activate FVII, establishing this as a basal trait. In contrast, only some lineages could activate prothrombin, indicating that this is a derived trait. For species able to activate both zymogens, Factor VII was consistently more strongly activated than prothrombin. FVa was revealed as an essential cofactor for FVII activation, a mechanism previously undocumented. Species lacking FVa in their venom utilized endogenous plasma FVa to exert this activity. The ability of the human FXa:FVa complex to activate FVII was also revealed as a new feedback loop in the endogenous clotting cascade. Toxin sequence analyses identified structural changes essential for the derived trait of prothrombin activation. This study presents a paradigm shift in understanding how elapid venoms activate coagulation factors, highlighting the critical role of FVII activation in the pathophysiological effects upon the coagulation cascade produced by Australian elapid snake venoms. It also documented the novel use of Factor Va as a cofactor for FVII activation for both venom and endogenous forms of FXa. These findings are crucial for developing better antivenoms and treatments for snakebite victims and have broader implications for drug design and the treatment of coagulation disorders. The research also advances the evolutionary biology knowledge of snake venoms. [ABSTRACT FROM AUTHOR]

Millipedes have long been known to produce a diverse array of chemical defense agents that deter predation. These compounds, or their precursors, are stored in high concentration within glands (ozadenes) and are released upon disturbance. The subterclass Colobognatha contains four orders of millipedes, all of which are known to produce terpenoid alkaloids—spare the Siphonophorida that produce terpenes. Although these compounds represent some of the most structurally-intriguing millipede-derived natural products, they are the least studied class of millipede defensive secretions. Here, we describe the chemistry of millipede defensive secretions from three species of Brachycybe: Brachycybe producta, Brachycybe petasata, and Brachycybe rosea. Chemical investigations using mass spectrometry-based metabolomics, chemical synthesis, and 2D NMR led to the identification of five alkaloids, three of which are new to the literature. All identified compounds are monoterpene alkaloids with the new compounds representing indolizidine (i.e. hydrogosodesmine) and quinolizidine alkaloids (i.e. homogosodesmine and homo-hydrogosodesmine). The chemical diversity of these compounds tracks the known species phylogeny of this genus, rather than the geographical proximity of the species. The indolizidines and quinolizidines are produced by non-sympatric sister species, B. producta and B. petasata, while deoxybuzonamine is produced by another set of non-sympatric sister species, B. rosea and Brachycybe lecontii. The fidelity between the chemical diversity and phylogeny strongly suggests that millipedes generate these complex defensive agents de novo and begins to provide insights into the evolution of their biochemical pathways. [ABSTRACT FROM AUTHOR]

The Period genes (Per) play essential roles in modulating the molecular circadian clock timing in a broad range of species, which regulates the physiological and cellular rhythms through the transcription-translation feedback loop. While the Period gene paralogs are widely observed among vertebrates, the evolutionary history and the functional diversification of Per genes across vertebrates are not well known. In this study, we comprehensively investigated the evolution of Per genes at the copy number and sequence levels, including de novo binding motif discovery by comparative genomics. We also determined the lineage-specific transcriptome landscape across tissues and developmental stages and phenotypic effects in public RNA-seq data sets of model species. We observed multiple lineage-specific gain and loss events Per genes, though no simple association was observed between ecological factors and Per gene numbers in each species. Among salmonid fish species, the per3 gene has been lost in the majority, whereas those retaining the per3 gene exhibit not a signature of relaxed selective constraint but rather a signature of intensified selection. We also determined the signature of adaptive diversification of the CRY-binding region in Per1 and Per3 , which modulates the circadian rhythm. We also discovered putative regulatory sequences, which are lineage-specific, suggesting that these cis-regulatory elements may have evolved rapidly and divergently across different lineages. Collectively, our findings revealed the evolution of Per genes and their fine-tuned contribution to the plastic and precise regulation of circadian rhythms in various vertebrate taxa. [ABSTRACT FROM AUTHOR]

The principle of continuity demands the existence of prior molecular states and common ancestors responsible for extant macromolecular structure. Here, we focus on the emergence and evolution of loop prototypes – the elemental architects of protein domain structure. Phylogenomic reconstruction spanning superkingdoms and viruses generated an evolutionary chronology of prototypes with six distinct evolutionary phases defining a most parsimonious evolutionary progression of cellular life. Each phase was marked by strategic prototype accumulation shaping the structures and functions of common ancestors. The last universal common ancestor (LUCA) of cells and viruses and the last universal cellular ancestor (LUCellA) defined stem lines that were structurally and functionally complex. The evolutionary saga highlighted transformative forces. LUCA lacked biosynthetic ribosomal machinery, while the pivotal LUCellA lacked essential DNA biosynthesis and modern transcription. Early proteins therefore relied on RNA for genetic information storage but appeared initially decoupled from it, hinting at transformative shifts of genetic processing. Urancestral loop types suggest advanced folding designs were present at an early evolutionary stage. An exploration of loop geometric properties revealed gradual replacement of prototypes with α-helix and β-strand bracing structures over time, paving the way for the dominance of other loop types. AlphFold2-generated atomic models of prototype accretion described patterns of fold emergence. Our findings favor a ‛processual' model of evolving stem lines aligned with Woese's vision of a communal world. This model prompts discussing the 'problem of ancestors' and the challenges that lie ahead for research in taxonomy, evolution and complexity. [ABSTRACT FROM AUTHOR]

Development of chiral aggregation‐induced emission (AIE) materials toward hierarchical self‐assembly is crucial to reveal the origin and evolution of life. In this work, a pair of chiral AIE enantiomers is fabricated by attaching the typical AIE units to the chiral binaphthyl core via a single bond linkage. The AIE behavior is inherited from the introduced AIE unit while the binaphthyl unit can not only improve the photo‐physical properties but also provide the whole molecules with chirality. Moreover, as driven by the dipolar structure and chirality of the AIEgens, the hierarchical self‐assembly with different morphologies such as spheres, ribbons or fibers, flowers, and even bigger structures with various sizes can be dynamically monitored with the assembled time, which provided a favorable evidence to study the structural evolution from molecular level to a higher‐level structure. On the other hand, these AIEgens can act strong electronic acceptors due to the introduced AIE unit. By complexing them with strong electronic donors, the resulting intermolecular charge transfer can induce remarkable red emissions with the tunable properties which is much different from their individuals. This enabled it as a facile, economic, and flexible approach to develop organic photoelectric materials. [ABSTRACT FROM AUTHOR]

SUMMARY: Plants produce a staggering array of chemicals that are the basis for organismal function and important human nutrients and medicines. However, it is poorly defined how these compounds evolved and are distributed across the plant kingdom, hindering a systematic view and understanding of plant chemical diversity. Recent advances in plant genome/transcriptome sequencing have provided a well‐defined molecular phylogeny of plants, on which the presence of diverse natural products can be mapped to systematically determine their phylogenetic distribution. Here, we built a proof‐of‐concept workflow where previously reported diverse tyrosine‐derived plant natural products were mapped onto the plant tree of life. Plant chemical‐species associations were mined from literature, filtered, evaluated through manual inspection of over 2500 scientific articles, and mapped onto the plant phylogeny. The resulting "phylochemical" map confirmed several highly lineage‐specific compound class distributions, such as betalain pigments and Amaryllidaceae alkaloids. The map also highlighted several lineages enriched in dopamine‐derived compounds, including the orders Caryophyllales, Liliales, and Fabales. Additionally, the application of large language models, using our manually curated data as a ground truth set, showed that post‐mining processing can largely be automated with a low false‐positive rate, critical for generating a reliable phylochemical map. Although a high false‐negative rate remains a challenge, our study demonstrates that combining text mining with language model‐based processing can generate broader phylochemical maps, which will serve as a valuable community resource to uncover key evolutionary events that underlie plant chemical diversity and enable system‐level views of nature's millions of years of chemical experimentation. Significance Statement: This study introduces a novel workflow to map the distribution of natural products onto a phylogeny. It also demonstrates the effectiveness of combining text mining of the literature with large language model evaluation for constructing a "phylochemical" database that can organize vast portions of the chemical diversity present across the plant tree of life. [ABSTRACT FROM AUTHOR]

Evolution requires selection. Molecular/chemical/preDarwinian evolution is no exception. One molecule must be selected over another for molecular evolution to occur and advance. Evolution, however, has no goal. The laws of physics have no utilitarian desire, intent or proficiency. Laws and constraints are blind to "usefulness." How then were potential multi-step processes anticipated, valued and pursued by inanimate nature? Can orchestration of formal systems be physico-chemically spontaneous? The purely physico-dynamic self-ordering of Chaos Theory and irreversible non-equilibrium thermodynamic "engines of disequilibria conversion" achieve neither orchestration nor formal organization. Natural selection is a passive and after-the-fact-of-life selection. Darwinian selection reduces to the differential survival and reproduction of the fittest already-living organisms. In the case of abiogenesis, selection had to be 1) Active, 2) Pre-Function, and 3) Efficacious. Selection had to take place at the molecular level prior to the existence of non-trivial functional processes. It could not have been passive or secondary. What naturalistic mechanisms might have been at play? [ABSTRACT FROM AUTHOR]

South Pacific archipelagos are central in the biogeographic debate on the relative importance of vicariance and dispersal in shaping the distribution of species. However, each taxonomic group was subject to different processes and histories, and here, we reveal the historical biogeography of the diverse Eumolpinae leaf beetles, widely distributed in the region. Extensive taxon sampling focusing on South Pacific Eumolpinae was used to infer the first molecular phylogeny of the group using three single‐copy protein‐coding nuclear and two mitochondrial markers. Upon assessing the clade of interest for lineage‐specific variation in substitution rates, the age of the most recent common ancestors was estimated using out‐group calibration and multi‐gamma site models (MGSMs). Biogeographic analyses used standard event‐based inferences also incorporating phylogenetic uncertainty. Zealandian Eumolpinae are monophyletic and appear to have split from their global relatives in the transition from the Cretaceous to the Paleogene. Variation in the rates of molecular evolution affected the in‐group stem branch, with a significant drop in the substitution rate, and the MGSM correction recovered the crown age of Zealandian Eumolpinae during the Late Eocene–Oligocene transition. Biogeographic inference resolved the origin of the radiation in New Caledonia, favouring a null model without island age constraints, and repeated dispersal events to the other islands, including three independent but synchronous colonisations of New Zealand during the Miocene. New Caledonia, with a highly diverse Eumolpinae fauna of uncertain origin, acted as a hub and pump of biodiversity of these beetles in the entire South Pacific region, sending migrants to other islands through long‐distance dispersal with lineages establishing when land became available. [ABSTRACT FROM AUTHOR]

Simple Summary: Peste des petits ruminants (PPR) is a highly contagious viral disease affecting small ruminants, posing significant economic challenges, especially in Africa. This study focused on understanding the genetic stability of the live-attenuated Peste des petits ruminant's vaccine Nigeria 75/1 strain, which is an essential tool for the eradication program. A nucleotide sequence comparison of the hypervariable region (C-terminus domain) of the nucleoprotein of the PPR vaccine from 10 different African vaccine manufacturers was conducted. Data analysis revealed 100% nucleotide homology between vaccine samples and the master seed, indicating the genetic stability of the PPR vaccine Nigeria 75/1 over decades. This research contributes to ongoing efforts to control Peste des petits ruminants outbreaks and ensures the efficacy of vaccination programs, ultimately benefiting animal health and agricultural sustainability. Peste des petits ruminants virus (PPRV), which is the only member of the Morbillivirus caprinae species and belongs to the genus Morbillivirus within the Paramyxoviridae family, causes the highly contagious viral sickness "Peste des petits ruminants (PPR)." PPR is of serious economic significance for small ruminant production, particularly in Africa. Control of this critical disease depends highly on successful vaccination against the PPRV. An in-depth understanding of the genetic evolution of the live-attenuated PPR vaccine Nigeria 75/1 strain used in Africa is essential for the successful eradication of this disease by 2030. Therefore, this study investigated the possible genetic evolution of the PPR vaccine produced by various African laboratories compared with the master seed available at AU-PANVAC. RT-PCR was performed to amplify a segment of the hypervariable C-terminal part of the nucleoprotein (N) from commercial batches of PPR vaccine Nigeria 75/1 strain. The sequences were analyzed, and 100% nucleotide sequence identity was observed between the master seed and vaccines produced. The results of this study indicate the genetic stability of the PPR vaccine from the Nigeria 75/1 strain over decades and that the vaccine production process used by different manufacturers did not contribute to the emergence of mutations in the vaccine strain. [ABSTRACT FROM AUTHOR]

Diarrhea is one of the major public health issues worldwide. Although the infections of individual enteric virus have been extensively studied, elucidation of the coinfection involving multiple viruses is still limited. In this study, we identified the coinfection of human adenovirus (HAdV) and human astrovirus (HAstV) in a child with acute gastroenteritis, analyzed their genotypes and molecular evolution characteristics. The sample was collected and identified using RT‐PCR and subjected to whole‐genome sequencing on the NovaSeq (Illumina) platform. Obtained sequences were assembled into the complete genome of HAdV and the ORF1 of HAstV. We conducted phylogenetic analysis using IQ‐TREE software and conducted recombination analysis with the Recombination Detection Program. The sequenced HAdV was confirmed to be genotype 41, and was genetically close to some European strains. Phylogenetic analysis revealed that the HAstV was genetically close to both HAstV‐2 and HAstV‐4 and was different from the genotype prevalent in Shenzhen before. The recombination analysis confirmed that the sequenced HAstV strain is a recombinant of HAstV‐2 and HAstV‐4. Our analysis has shown that the strains in this coinfection are both uncommon variants in this geographical region, instead of dominant subtypes that have prevailed for years. This study presents a coinfection of HAdV and HAstV and conducts an evolutionary analysis on involved viruses, which reveals the genetic diversity of epidemic strains in Southern China and offers valuable insights into vaccine and medical research. [ABSTRACT FROM AUTHOR]

Hydrogen evolution reaction (HER) from water splitting using renewable energy provides a promising solution to the global energy crisis and environmental problems. However, the lack of in‐depth understanding of the reaction mechanism and clear identification of the catalytic active site has hindered the further development of low‐cost, high‐performance, and long‐life efficient electrocatalysts. Through in situ characterization techniques, the activity and stability of catalysts can be monitored in real‐time, track the structural evolution of catalytic reaction intermediates, and obtain a deep understanding of catalytic reaction mechanism, so as to feedback and guide the development and utilization of the catalyst. In this review, advanced development of in situ characterization techniques in electrocatalytic HER in recent years is summarized. In situ spectroscopy can be used to track the behavior of reaction intermediates such as adsorption, desorption, and structural evolution at the molecular level to reveal the electrocatalytic HER mechanism. The imaging techniques can be used to observe the evolution of material structure during HER in situ, which provides valuable information for the understanding of visualization of catalytic hydrogen evolution at atomic level. This review contributes to theadvanced development of in situ characterization technique for electrocatalytic HER. [ABSTRACT FROM AUTHOR]

Pectin is a vital component of plant cell walls and its methylation process is regulated by pectin methylesterase inhibitors (PMEIs). PMEIs regulate the structural and functional modifications of cell walls in plants and play an important role in plant processes such as seed germination, fruit ripening, and stress response. Although the PMEI gene family has been well characterized in model plants, the understanding of its molecular evolution and biological functions in watermelon remains limited. In this study, 60 ClPMEI genes were identified and characterized, revealing their dispersion on multiple chromosomes. Based on a systematic developmental analysis, these genes were classified into three subfamilies, which was further supported by the exon, intron, and conserved motif distribution. Analysis of cis-elements and expression patterns indicated that ClPMEIs might be involved in regulating the tolerance of watermelon to various abiotic stresses. Moreover, distinct ClPMEI genes exhibit specific functions under different abiotic stresses. For example, ClPMEI51 and ClPMEI54 showed a significant upregulation in expression levels during the late stage of drought treatments, whereas ClPMEI3 and ClPMEI12 displayed a significant downregulation under low-temperature induction. Subcellular localization prediction and analysis revealed that the ClPMEI family member proteins were localized to the cell membrane. This study provided an important foundation for the further exploration of the functions of ClPMEI genes in watermelon. [ABSTRACT FROM AUTHOR]

[Display omitted] Ion channel activation upon ligand gating triggers a myriad of biological events and, therefore, evolution of ligand gating mechanism is of fundamental importance. TRPM2, a typical ancient ion channel, is activated by adenosine diphosphate ribose (ADPR) and calcium and its activation has evolved from a simple mode in invertebrates to a more complex one in vertebrates, but the evolutionary process is still unknown. Molecular evolutionary analysis of TRPM2s from more than 280 different animal species has revealed that, the C-terminal NUDT9-H domain has evolved from an enzyme to a ligand binding site for activation, while the N-terminal MHR domain maintains a conserved ligand binding site. Calcium gating pattern has also evolved, from one Ca2+-binding site as in sea anemones to three sites as in human. Importantly, we identified a new group represented by olTRPM2, which has a novel gating mode and fills the missing link of the channel gating evolution. We conclude that the TRPM2 ligand binding or activation mode evolved through at least three identifiable stages in the past billion years from simple to complicated and coordinated. Such findings benefit the evolutionary investigations of other channels and proteins. [ABSTRACT FROM AUTHOR]

The domestication of plants and animals has resulted in one of the most significant cultural and socio‐economical transitions in human history. Domestication of animals, including human‐supervised reproduction, largely uncoupled particular animal species from their natural, evolutionary history driven by environmental and ecological factors. The primary motivations for domesticating animals were, and still are, producing food and materials (e.g. meat, eggs, honey or milk products, wool, leather products, jewelry and medication products) to support plowing in agriculture or in transportation (e.g. horse, cattle, camel and llama) and to facilitate human activities (for hunting, rescuing, therapeutic aid, guarding behavior and protecting or just as a companion). In recent years, decoded genetic information from more than 40 domesticated animal species have become available; these studies have identified genes and mutations associated with specific physiological and behavioral traits contributing to the complex genetic background of animal domestication. These breeding‐altered genomes provide insights into the regulation of different physiological areas, including information on links between e.g. endocrinology and behavior, with important pathophysiological implications (e.g. for obesity and cancer), extending the interest in domestication well beyond the field. Several genes that have undergone selection during domestication and breeding encode specific G protein‐coupled receptors, a class of membrane‐spanning receptors involved in the regulation of a number of overarching functions such as reproduction, development, body homeostasis, metabolism, stress responses, cognition, learning and memory. Here we summarize the available literature on variations in G protein‐coupled receptors and their ligands and how these have contributed to animal domestication. [ABSTRACT FROM AUTHOR]

The Entada landrace of enset (Ensete ventricosum (Welw.) Chessman) is probably the most unique indigenous crop in Ethiopia, being maintained and utilized by the Ari people in the South of Ethiopia. Here we describe genetic diversity, selection signatures and relationship of Entada with cultivated and wild enset using 117 Entada genotypes collected from three Entada growing regions in Ethiopia (Sidama, South and North Ari). A total number of 1,617 high-quality SNP markers, obtained from ddRAD-sequences, were used for the diversity studies. Phylogenetic analysis detected a clear distinction between cultivated enset, Entada and wild enset with Entada forming a completely separated clade. However, extremely short branch lengths among the Entada genotypes indicate very little molecular evolution in the Entada lineages. Observed and expected heterozygosities were high, 0.73 and 0.50, respectively. Overall, our results strongly indicate that the Entada genotypes we have studied originated from one or a few clonal lineages that have been propagated and spread among farmers as clones. Prolonged clonal propagation of heterozygous genotypes from a single or few founding lineages has led to populations with very little or no diversity between genotypes, and high heterozygosity within genotypes. Signatures of directional selection were identified at eight loci based on an FST outlier analysis. Four candidate genes detected are involved in axillary shoot growth and might be involved in controlling natural sucker formation in Entada. [ABSTRACT FROM AUTHOR]

Fishborne trematode (FBT) is an important group of parasites that are endemic worldwide to a certain extent. However, despite the epidemiological significance, the species and phylogenetic evolution characteristics of FBT metacercariae have not been well studied. In this study, a total of 600 Pseudorasbora parva (P. parva) specimens were collected from Qiqihar, 61.8% (371/600) were found to be infected with trematode metacercariae. A total of three kinds of trematodes metacercariae were obtained, and they were identified as Clonorchis sinensis (C. sinensis), Metorchis orientalis (M. orientalis), and Metorchis taiwanensis (M. taiwanensis) by morphological and phylogenetic analysis with infection rates of 47.7% (286/600), 15.5% (93/600), and 23.7% (142/600), respectively. Meanwhile, a survey of the three trematodes metacercariae showed that the infection rate of C. sinensis metacercariae was the highest in September, up to 66% (66/100), and the lowest in June at 26% (26/100). The infection rate of M. orientalis metacercariae was the highest in October at 26% (26/100) and the lowest in June at 5% (5/100). The infection rate of M. taiwanensis metacercariae was at its peak in November at 36% (36/100) and the lowest in July at 15% (15/100). The co-infection of metacercariae of C. sinensis and M. taiwanensis was the most common and reached a peak in October, and their infection rate was higher in autumn than in summer. The peak of infection intensity of metacercariae for C. sinensis, M. orientalis, and M. taiwanensis were different: C. sinensis was 24/g in September, M. orientalis was 7/g in October, and M. taiwanensis was 10/g in November. From the above results, it was confirmed that three species of trematodes metacercaria played an important role in infection of second intermediate hosts in Qiqihar region. Studying the morphological characteristics and sequencing the ITS2 gene for a phylogenetic tree of them will be useful for future molecular evolution, biology, and ecology of trematode metacercariae. [ABSTRACT FROM AUTHOR]

The relative importance of various sensory modalities can shift in response to evolutionary transitions, resulting in changes to underlying gene families encoding their reception systems. The rapid birth‐and‐death process underlying the evolution of the large olfactory receptor (OR) gene family has accelerated genomic‐level change for the sense of smell in particular. The transition from the land to sea in marine mammals is an attractive model for understanding the influence of habitat shifts on sensory systems, with the retained OR repertoire of baleen whales contrasting with its loss in toothed whales. In this study, we examine to what extent the transition from a terrestrial to a marine environment has influenced the evolution of baleen whale OR repertoires. We developed Gene Mining Pipeline (GMPipe) (https://github.com/AprilJauhal/GMPipe), which can accurately identify large numbers of candidate OR genes. GMPipe identified 707 OR sequences from eight baleen whale species. These repertoires exhibited distinct family count distributions compared to terrestrial mammals, including signs of relative expansion in families OR10, OR11 and OR13. While many receptors have been lost or show signs of random drift in baleen whales, others exhibit signs of evolving under purifying or positive selection. Over 85% of OR genes could be sorted into orthologous groups of sequences containing at least four homologous sequences. Many of these groups, particularly from family OR10, presented signs of relative expansion and purifying selective pressure. Overall, our results suggest that the relatively small size of baleen whale OR repertoires result from specialisation to novel olfactory landscapes, as opposed to random drift. [ABSTRACT FROM AUTHOR]

Previous studies on horseshoe bats (Rhinolophus spp.) have described many coronaviruses related to SARS‐CoV (SARSCoVr) in China and only a few coronaviruses related to SARS‐CoV‐2 (SARSCoV2r) in Yunnan (southern China), Cambodia, Laos and Thailand. Here, we report the results of several field missions carried out in 2017, 2021 and 2022 across Vietnam during which 1218 horseshoe bats were sampled from 19 locations. Sarbecoviruses were detected in 11% of faecal RNA extracts, with much more positives among Rhinolophus thomasi (46%). We assembled 38 Sarbecovirus genomes, including 32 SARSCoVr, four SARSCoV2r, and two recombinants of SARSCoVr and SARSCoV2r (RecSar), one showing a Spike protein very similar to SARS‐CoV‐2. We detected a bat co‐infected with four coronaviruses, including two sarbecoviruses. Our analyses revealed that Sarbecovirus genomes evolve in Vietnam under strong geographical and host constraints. First, we found evidence for a deep separation between viruses from northern Vietnam and those from central and southern Vietnam. Second, we detected only SARSCoVr in Rhinolophus thomasi, both SARSCoVr and SARSCoV2r in Rhinolophus affinis, and only RecSar in Rhinolophus pusillus captured close to the border with China. Third, the bias in favour of Uracil in synonymous third codon positions of SARSCoVr extracted from R. thomasi showed a negative correlation with latitudes. Our results also provided support for an emergence of SARS‐CoV in horseshoe bats from northern Yunnan and emergence of SARS‐CoV‐2 in horseshoe bats from northern Indochina subtropical forests (southern Yunnan, northern Laos and north‐western Vietnam). [ABSTRACT FROM AUTHOR]

The origin of translation is one of the most difficult problems of molecular evolution. Identifying molecular systems that translate an RNA sequence into a peptide sequence in the absence of ribosomes and enzymes is a challenge. Recently, single‐nucleotide translation via coupling of 5′ phosphoramidate‐linked amino acids to 2′/3′‐aminoacyl transfer‐NMPs, as directed by the sequence of an RNA template, was demonstrated for three of the four canonical nucleotides. How single‐nucleotide translation could be expanded to include all four bases and to produce longer peptides without translocation along the template strand remained unclear. Using transfer strands of increasing length containing any of the four bases that interrogate adjacent positions along the template, we now show that pentapeptides can be produced in coupling reactions and subsequent hydrolytic release in situ. With 2′/3′‐aminoacylated mono‐, di‐, tri‐ and tetranucleotides we thus show how efficient translation can be without biomacromolecules. [ABSTRACT FROM AUTHOR]

The study of nano-scratching under water lubrication is helpful to understand the role of lubrication mechanism in the machining of single crystal γ-TiAl alloy. In this paper, through the comparative analysis of nano-scratching under different thicknesses of water layers, it was found that under a water layer thickness of 1 nm, nano-scratching not only improves the surface quality but also achieves multiple reductions in scratch force, stress, temperature and subsurface structural damage. In order to deeply reveal the internal mechanism of workpiece temperature variation under different thicknesses of water layer lubrication, a fitting formula was innovatively adopted to conduct quantitative analysis. In addition, with the increase of the thickness of the water layer, it was observed that the water film effect was continuously enhanced, and this change caused the matrix stress to gradually increase, which hindered the forward motion of the nanoscratch, ultimately resulting in an increase in the friction coefficient. These findings provide valuable insights into the nanoscratching mechanism of monocrystalline γ-TiAl alloy in the presence of water film, and provide a new perspective for understanding the complex mechanism of nanoscratch behaviour under water lubrication, thus promoting the understanding of nanoscale lubrication effects. [ABSTRACT FROM AUTHOR]

Simarouba, a neotropical genus in the family Simaroubaceae, currently lacks comprehensive genomic data in existing databases. This study aims to fill this gap by providing genomic resources for three Simarouba species, S. amara, S. versicolor, and S. glauca. It also aims to perform comparative molecular evolutionary analyses in relation to other species within the order Sapindales. The analysis of these three Simarouba species revealed the presence of the typical quadripartite structure expected in plastomes. However, some pseudogenization events were identified in the psbC, infA, rpl22, and ycf1 genes. In particular, the CDS of the psbC gene in S. amara was reduced from 1422 bp to 584 bp due to a premature stop codon. Nucleotide diversity data pointed to gene and intergenic regions as promising candidates for species and family discrimination within the group, specifically matK, ycf1, ndhF, rpl32, petA-psbJ, and trnS-trnG. Selection signal analyses showed strong evidence for positive selection on the rpl23 gene. Phylogenetic analyses indicated that S. versicolor and S. glauca have a closer phylogenetic relationship than S. amara. We provide chloroplast genomes of three Simaruba species and use them to elucidate plastome evolution, highlight the presence of pseudogenization, and identify potential DNA barcode regions. [ABSTRACT FROM AUTHOR]

Pancreatic ribonuclease (RNase1), a digestive enzyme produced by the pancreas, is associated with the functional adaptation of dietary habits and is regarded as an attractive model system for studies of molecular evolution. In this study, we identified 218 functional genes and 48 pseudogenes from 114 species that span all four Cetartiodactyla lineages: two herbivorous lineages (Ruminantia and Tylopoda) and two non‐herbivorous lineages (Cetancodonta and Suoidea). Multiple RNase1 genes were detected in all species of the two herbivorous lineages, and phylogenetic and genomic location analyses demonstrated that independent gene duplication events occurred in Ruminantia and Tylopoda. In Ruminantia, the gene duplication events occurred in the ancestral branches of the lineage in the Middle Eocene, a time of increasing climatic seasonality during which Ruminantia rapidly radiated. In contrast, only a single RNase1 gene was observed in the species of the two non‐herbivorous lineages (Cetancodonta and Suoidea), suggesting that the previous Cetacea‐specific loss hypothesis should be rejected. Moreover, the duplicated genes of RNase1 in the two herbivorous lineages (Ruminantia and Tylopoda) may have undergone functional divergence. In combination with the temporal coincidence between gene replication and the enhanced climatic seasonality during the Middle Eocene, this functional divergence suggests that RNase1 gene duplication was beneficial for Ruminantia to use the limited quantities of sparse fibrous vegetation and adapt to seasonal changes in climate. In summary, the findings indicate a complex and intriguing evolutionary pattern of RNase1 in Cetartiodactyla and demonstrate the molecular mechanisms by which organisms adapt to the environment. [ABSTRACT FROM AUTHOR]

The nearly neutral theory of molecular evolution posits variation among species in the effectiveness of selection. In an idealized model, the census population size determines both this minimum magnitude of the selection coefficient required for deleterious variants to be reliably purged, and the amount of neutral diversity. Empirically, an 'effective population size' is often estimated from the amount of putatively neutral genetic diversity and is assumed to also capture a species' effectiveness of selection. A potentially more direct measure of the effectiveness of selection is the degree to which selection maintains preferred codons. However, past metrics that compare codon bias across species are confounded by among-species variation in %GC content and/or amino acid composition. Here, we propose a new Codon Adaptation Index of Species (CAIS), based on Kullback-Leibler divergence, that corrects for both confounders. We demonstrate the use of CAIS correlations, as well as the Effective Number of Codons, to show that the protein domains of more highly adapted vertebrate species evolve higher intrinsic structural disorder. [ABSTRACT FROM AUTHOR]

Background Information Results Conclusion and Significance Microvilli are finger‐like, straight, and stable cellular protrusions that are filled with F‐actin and present a stereotypical length. They are present in a broad range of cell types across the animal tree of life and mediate several fundamental functions, including nutrient absorption, photosensation, and mechanosensation. Therefore, understanding the origin and evolution of microvilli is key to reconstructing the evolution of animal cellular form and function. Here, we review the current state of knowledge on microvilli evolution and perform a bioinformatic survey of the conservation of genes encoding microvillar proteins in animals and their unicellular relatives.We first present a detailed description of mammalian microvilli based on two well‐studied examples, the brush border microvilli of enterocytes and the stereocilia of hair cells. We also survey the broader diversity of microvilli and discuss similarities and differences between microvilli and filopodia. Based on our bioinformatic survey coupled with carefully reconstructed molecular phylogenies, we reconstitute the order of evolutionary appearance of microvillar proteins. We document the stepwise evolutionary assembly of the “molecular microvillar toolkit” with notable bursts of innovation at two key nodes: the last common filozoan ancestor (correlated with the evolution of microvilli distinct from filopodia) and the last common choanozoan ancestor (correlated with the emergence of inter‐microvillar adhesions).We conclude with a scenario for the evolution of microvilli from filopodia‐like ancestral structures in unicellular precursors of animals. [ABSTRACT FROM AUTHOR]

Background: The tribe Ampelopsideae plants are important garden plants with both medicinal and ornamental values. The study of codon usage bias (CUB) facilitates a deeper comprehension of the molecular genetic evolution of species and their adaptive strategies. The joint analysis of CUB in chloroplast genomes (cpDNA) offers valuable insights for in-depth research on molecular genetic evolution, biological resource conservation, and elite breeding within this plant family. Results: The base composition and codon usage preferences of the eighteen chloroplast genomes were highly similar, with the GC content of bases at all positions of their codons being less than 50%. This indicates that they preferred A/T bases. Their effective codon numbers were all in the range of 35–61, which indicates that the codon preferences of the chloroplast genomes of the 18 Ampelopsideae plants were relatively weak. A series of analyses indicated that the codon preference of the chloroplast genomes of the 18 Ampelopsideae plants was influenced by a combination of multiple factors, with natural selection being the primary influence. The clustering tree generated based on the relative usage of synonymous codons is consistent with some of the results obtained from the phylogenetic tree of chloroplast genomes, which indicates that the clustering tree based on the relative usage of synonymous codons can be an important supplement to the results of the sequence-based phylogenetic analysis. Eventually, 10 shared best codons were screened on the basis of the chloroplast genomes of 18 species. Conclusion: The codon preferences of the chloroplast genome in Ampelopsideae plants are relatively weak and are primarily influenced by natural selection. The codon composition of the chloroplast genomes of the eighteen Ampelopsideae plants and their usage preferences were sufficiently similar to demonstrate that the chloroplast genomes of Ampelopsideae plants are highly conserved. This study provides a scientific basis for the genetic evolution of chloroplast genes in Ampelopsideae species and their suitable strategies. [ABSTRACT FROM AUTHOR]

The evolution of CO2 nanobubbles generated by gas–hydrate dissociation is comprehensively studied in this research, employing a synergistic approach that combines laboratory experiments and molecular dynamics simulations. The results show that a higher concentration of nanobubbles can be observed in the early stages of hydrate dissociation, while smaller, thus‐generated, nanobubbles are less stable and prefer to amalgamate into larger bubbles through coalescence or Ostwald ripening. From the high Laplace pressure inside some nanobubbles as well as their higher local densities, they may transform into nanodroplets by densification fluctuations. Thus, the dynamic coexistence of nanobubbles and ‐droplets is confirmed from both experimental and simulation measurements. The number and size of the nanobubbles in the system affects the interaction between water molecules and their movements so that the water molecules diffuse faster upon this condition. The water–water interactions become more pronounced in the presence of nanobubbles and the hydrogen bond network is better preserved in the bulk. This study provides new insights into the microscale mechanisms of gas–hydrate dissociation and highlights the complex interactions between nanobubbles/ ‐droplets, and the aqueous environment after CO2–hydrate dissociation. [ABSTRACT FROM AUTHOR]

Visual signals are involved in many fitness‐related tasks and are therefore essential for survival in many species. Aquatic organisms are ideal systems to study visual evolution, as the high diversity of spectral properties in aquatic environments generates great potential for adaptation to different light conditions. Flatfishes are an economically important group, with over 800 described species distributed globally, including halibut, flounder, sole, and turbot. The diversity of flatfish species and wide array of environments they occupy provides an excellent opportunity to understand how this variation translates to molecular adaptation of vision genes. Using models of molecular evolution, we investigated how the light environments inhabited by different flatfish lineages have shaped evolution in the rhodopsin gene, which is responsible for mediating dim‐light visual transduction. We found strong evidence for positive selection in rhodopsin, and this was correlated with both migratory behavior and several fundamental aspects of habitat, including depth and freshwater/marine evolutionary transitions. We also identified several mutations that likely affect the wavelength of peak absorbance of rhodopsin, and outline how these shifts in absorbance correlate with the response to the light spectrum present in different habitats. This is the first study of rhodopsin evolution in flatfishes that considers their extensive diversity, and our results highlight how ecologically‐driven molecular adaptation has occurred across this group in response to transitions to novel light environments. [ABSTRACT FROM AUTHOR]

Understanding the combined effects of environmental heterogeneity and evolutionary processes on marine populations is a primary goal of seascape genomic approaches. Here, we utilized genomic approaches to identify local adaptation signatures in Littoraria flava , a widely distributed marine gastropod in the tropical West Atlantic population. We also performed molecular evolution analyses to investigate potential selective signals across the genome. After obtaining 6,298 and 16,137 single nucleotide polymorphisms derived from genotyping-by-sequencing and RNA sequencing, respectively, 69 from genotyping-by-sequencing (85 specimens) and four from RNA sequencing (40 specimens) candidate single nucleotide polymorphisms were selected and further evaluated. The correlation analyses support different evolutionary pressures over transcribed and non-transcribed regions. Thus, single nucleotide polymorphisms within transcribed regions could account for the genotypic and possibly phenotypic divergences in periwinkles. Our molecular evolution tests based on synonymous and non-synonymous ratio (kN/kS) showed that genotype divergences containing putative adaptive single nucleotide polymorphisms arose mainly from synonymous and/or UTR substitutions rather than polymorphic proteins. The distribution of genotypes across different localities seems to be influenced by marine currents, pH, and temperature variations, suggesting that these factors may impact the species dispersion. The combination of RNA sequencing and genotyping-by-sequencing derived datasets provides a deeper understanding of the molecular mechanisms underlying selective forces responses on distinct genomic regions and could guide further investigations on seascape genomics for non-model species. [ABSTRACT FROM AUTHOR]

A thorough understanding of adaptation and speciation requires model organisms with both a history of ecological and phenotypic study as well as a complete set of genomic resources. In particular, high-quality genome assemblies of ecological model organisms are needed to assess the evolution of genome structure and its role in adaptation and speciation. Here, we generate new genomes of cactophilic Drosophila , a crucial model clade for understanding speciation and ecological adaptation in xeric environments. We generated chromosome-level genome assemblies and complete annotations for seven populations across Drosophila mojavensis , Drosophila arizonae , and Drosophila navojoa. We use these data first to establish the most robust phylogeny for this clade to date, and to assess patterns of molecular evolution across the phylogeny, showing concordance with a priori hypotheses regarding adaptive genes in this system. We then show that structural evolution occurs at constant rate across the phylogeny, varies by chromosome, and is correlated with molecular evolution. These results advance the understanding of the D. mojavensis clade by demonstrating core evolutionary genetic patterns and integrating those patterns to generate new gene-level hypotheses regarding adaptation. Our data are presented in a new public database (cactusflybase.arizona.edu), providing one of the most in-depth resources for the analysis of inter- and intraspecific evolutionary genomic data. Furthermore, we anticipate that the patterns of structural evolution identified here will serve as a baseline for future comparative studies to identify the factors that influence the evolution of genome structure across taxa. [ABSTRACT FROM AUTHOR]

Low dissolved oxygen (hypoxia) is recognized as a major threat to aquatic ecosystems worldwide. Because oxygen is paramount for the energy metabolism of animals, understanding the functional and genetic drivers of whole-animal hypoxia tolerance is critical to predicting the impacts of aquatic hypoxia. In this study, we investigate the molecular evolution of key genes involved in the detection of and response to hypoxia in ray-finned fishes: the prolyl hydroxylase domain (PHD)–hypoxia-inducible factor (HIF) oxygen-sensing system, also known as the EGLN (egg-laying nine)– HIF oxygen-sensing system. We searched fish genomes for HIFA and EGLN genes, discovered new paralogs from both gene families, and analyzed protein-coding sites under positive selection. The physicochemical properties of these positively selected amino acid sites were summarized using linear discriminants for each gene. We employed phylogenetic generalized least squares to assess the relationship between these linear discriminants for each HIFA and EGLN and hypoxia tolerance as reflected by the critical oxygen tension (P crit) of the corresponding species. Our results demonstrate that P crit in ray-finned fishes correlates with the physicochemical variation of positively selected sites in specific HIFA and EGLN genes. For HIF2A , two linear discriminants captured more than 90% of the physicochemical variation of these sites and explained between 20% and 39% of the variation in P crit. Thus, variation in HIF2A among fishes may contribute to their capacity to cope with aquatic hypoxia, similar to its proposed role in conferring tolerance to high-altitude hypoxia in certain lineages of terrestrial vertebrates. [ABSTRACT FROM AUTHOR]

Tree diagrams are the prevailing form of visualization in biological classification and phylogenetics. Already during the time of the so-called Systematist Wars from the mid-1960s until the 1980s most journal articles and textbooks published by systematists contained tree diagrams. Although this episode of systematics is well studied by historians and philosophers of biology, most analyses prioritize scientific theories over practices and tend to emphasize conflicting theoretical assumptions. In this article, I offer an alternative perspective by viewing the conflict through the lens of representational practices with a case study on tree diagrams that were used by numerical taxonomists (phenograms) and cladists (cladograms). I argue that the current state of molecular phylogenetics should not be interpreted as the result of a competition of views within systematics. Instead, molecular phylogenetics arose independently of systematics and elements of cladistics and phenetics were integrated into the framework of molecular phylogenetics, facilitated by the compatibility of phenetic and cladistic practices with the quantitative approach of molecular phylogenetics. My study suggests that this episode of scientific change is more complex than common narratives of battles and winners or conflicts and compromises. Today, cladograms are still used and interpreted as specific types of molecular phylogenetic trees. While phenograms and cladograms represented different forms of knowledge during the time of the Systematist Wars, today they are both used to represent evolutionary relationships. This indicates that diagrams are versatile elements of scientific practice that can change their meaning, depending on the context of use within theoretical frameworks. [ABSTRACT FROM AUTHOR]