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In the field of expensive optimization, numerous papers have proposed surrogate-assisted evolutionary algorithms (SAEAs) for a few thousand or even hundreds of function evaluations. However, in reality, low-cost simulations suffice for a lot of real-world problems, in which the number of function evaluations is moderately restricted, e.g., to several thousands. In such moderately restricted scenario, SAEAs become unnecessarily time-consuming and tend to struggle with premature convergence. In addition, tuning the SAEA parameters becomes impractical under the restricted budgets of function evaluations—in some cases, inadequate configuration may degrade performance instead. In this context, this paper presents a fast and auto-tunable evolutionary algorithm for solving moderately restricted expensive optimization problems. The presented algorithm is a variant of adaptive differential evolution (DE) algorithms, and is called emulation-based adaptive DE or EBADE. The primary aim of EBADE is to emulate the principle of sample-efficient optimization, such as that in SAEAs, by adaptively tuning the DE parameter configurations. Specifically, similar to Expected Improvement-based sampling, EBADE identifies parameter configurations that may produce expected-to-improve solutions, without using function evaluations. Further, EBADE incepts a multi-population mechanism and assigns a parameter configuration to each subpopulation to estimate the effectiveness of parameter configurations with multiple samples carefully. This subpopulation-based adaptation can help improve the selection accuracy of promising parameter configurations, even when using an expected-to-improve indicator with high uncertainty, by validating with respect to multiple samples. The experimental results demonstrate that EBADE outperforms modern adaptive DEs and is highly competitive compared to SAEAs with a much shorter runtime. [ABSTRACT FROM AUTHOR]

This paper focuses on the maximum speed at which biological evolution can occur. I derive inequalities that limit the rate of evolutionary processes driven by natural selection, mutations, or genetic drift. These rate limits link the variability in a population to evolutionary rates. In particular, high variances in the fitness of a population and of a quantitative trait allow for fast changes in the trait's average. In contrast, low variability makes a trait less susceptible to random changes due to genetic drift. The results in this article generalize Fisher's fundamental theorem of natural selection to dynamics that allow for mutations and genetic drift, via trade-off relations that constrain the evolutionary rates of arbitrary traits. The rate limits can be used to probe questions in various evolutionary biology and ecology settings. They apply, for instance, to trait dynamics within or across species or to the evolution of bacteria strains. They apply to any quantitative trait, e.g., from species' weights to the lengths of DNA strands. [ABSTRACT FROM AUTHOR]

The first microbial culture collection was established in 1890, and subsequently, over the course of the twentieth century, the number of culture collections grew substantially. One such collection was the CABI-IMI Genetic Resources Collection, informally initiated at the origins of the Commonwealth Mycological Institute in 1920 and established as a UK National Collection in 1947. Its holdings reflect the activities of CABI in agriculture and the environment. Like many collections, it was originally established as a taxonomic reference resource. Over the years, deposits have included strains isolated from disease outbreaks in major crops from all parts of the world. Recent developments in genome sequencing technology and bioinformatic analysis have opened up the potential to characterise historic strains to shed more insights on their biology and evolution. In this paper we describe how the resources held within the CABI-IMI culture collection have helped track the emergence and divergence of Fusarium xylarioides, the coffee wilt pathogen, with a specific focus on the evolution of pathogenicity. Such studies illustrate the value held within the world's culture collections—their importance in underpinning science and developing our understanding and evolution of plant diseases as well as how the impact of disease can be mitigated in response to climate change, in order to increase yields and feed the world's burgeoning population. [ABSTRACT FROM AUTHOR]

This paper revisits Fleeming Jenkin's anonymous review of Charles Darwin's Origin of Species, published in the North British Review in June 1867. This review is usually revered for its impact on Darwin's theory of descent with modification. Its classical interpretation states that Jenkin, a Professor of Engineering at the University of Edinburgh, made a compelling case against natural selection based on the fact of "blending inheritance" and the "swamping" of advantageous variations. Those themes, however, are strikingly absent from Jenkin's text. They were later read into Jenkin's text by scholars trying to explain how Darwinian selection was reconciled with Mendelian genes and the birth of the Modern Synthesis. While many scholars have tried to measure Jenkin's effect on Darwin, the value of the 1867 review remains unclear. This paper re-examines its content and concludes that Jenkin's "able review" was in fact written by an engineer whose competencies in biology were very low. Focusing on the figure of the shipwrecked white sailor isolated on an island inhabited by Black people, this paper also underlines the racial assumptions behind Jenkin's review. "Blending inheritance" is thus a theme linked to theoretical reworkings on the question of race and skin colors, taking its root in Galton's typology of heredity. Darwin was probably mostly unimpressed by Jenkin's review. The problems raised by the review were not so much "blending inheritance" and "swamping" but a conundrum of problems related to the effects of intercrossing on variation and reversion. [ABSTRACT FROM AUTHOR]

An equidistantX-cactus is a type of rooted, arc-weighted, directed acyclic graph with leaf set X, that is used in biology to represent the evolutionary history of a set X of species. In this paper, we introduce and investigate the space of equidistant X-cactuses. This space contains, as a subset, the space of ultrametric trees on X that was introduced by Gavryushkin and Drummond. We show that equidistant-cactus space is a CAT(0)-metric space which implies, for example, that there are unique geodesic paths between points. As a key step to proving this, we present a combinatorial result concerning ranked rooted X-cactuses. In particular, we show that such graphs can be encoded in terms of a pairwise compatibility condition arising from a poset of collections of pairs of subsets of X that satisfy certain set-theoretic properties. As a corollary, we also obtain an encoding of ranked, rooted X-trees in terms of partitions of X, which provides an alternative proof that the space of ultrametric trees on X is CAT(0). We expect that our results will provide the basis for novel ways to perform statistical analyses on collections of equidistant X-cactuses, as well as new directions for defining and understanding spaces of more general, arc-weighted phylogenetic networks. [ABSTRACT FROM AUTHOR]

To improve the quality and efficiency of machine translation (MT) for low-resource languages (LRLs), this paper analyzes the application of genetic algorithm (GA) under the background of cloud computing (CC). By using GA to optimize MT for LRL, this study aims to address the limitations and challenges of traditional methods on LRL. Firstly, GA under the background of the CC platform is analyzed in detail. The CC platform offers powerful computing and storage capabilities that provide the basis for large-scale optimization using GA. GA is an optimization algorithm based on the principle of biological evolution, which seeks the optimal solution by simulating genes' genetic and evolutionary processes. In MT of LRL, GA can be used to optimize model parameters, select translation rules, and improve translation quality, thereby improving translation results. Secondly, the present situation of MT for LRL is described. Finally, the traditional LRL-oriented MT and the GA-optimized LRL-oriented MT are compared and analyzed. The results reveal that the traditional LRL-oriented MT has low accuracy and low customer satisfaction (CS). Considering the translation time, accuracy, and resource utilization rate (RUR), the highest rate is only about 47%. In contrast, GA-optimized LRL-oriented MT significantly improves translation accuracy and CS, reaching approximately 94%. The final evaluation results indicate that the accuracy of the model is usually above 70%, and up to 94%. Therefore, GA plays an important role in optimization for LRL-oriented MT. This paper provides technical support for optimizing LRL-oriented MT and contributes to the further development of MT technology. By applying GA, the limitations of traditional methods in LRL can be overcome and the quality and efficiency of translation can be improved. It is of great significance to improve the development of translation technology of LRL, enhance cross-language communication, and promote global cultural exchange. [ABSTRACT FROM AUTHOR]

Differential evolution (DE) is one of the most efficient evolution algorithms (ES) for dealing with nonlinear, complicated and difficult global optimization problems. The main contribution of this paper can be summarized in three directions: Firstly, a novel crossover rate (CR) generation scheme based on the zscore value of fitness, named fcr, is introduced. For a minimization problem, the proposed CR generation strategy always assigns a smaller CR value to individual with smaller fitness value. Therefore, the parameters of individuals with better fitness are inherited by their offspring with high probability. In the second direction, the control parameters are adjusted by unused bimodal settings in which each parameter setting is selected according to the evolution status of individual. The third direction of our work is introducing the L1 norm distance as the weights for updating the mean value of crossover rate and scale factor. Theoretically, compared with L2 norm, L1-norm is more efficient to suppress outliers in the difference vector. These modifications are first integrated with the mutation strategy of JADE, then a modified version, named JADEfcr, is proposed. In addition, to improve the optimization ability further, another variant LJADEfcr by using a linear population reduction mechanism is considered. So as to confirm and examine the performance of JADEfcr and LJADEfcr, numerical experiments are conducted on 29 optimization problems defined by CEC2017 benchmark. For JADEfcr, its experimental results are made a comparison with twelve state-of-the-art algorithms. The comparative study demonstrates that in terms of robustness, stability and solution quality, JADEfcr are better and highly competitive with these well-known algorithms. For LJADEfcr, its results are compared with JADEfcr and other nine powerful algorithms including four recent algorithms and five top algorithms on CEC2017 competition. Experimental results indicate that LJADEfcr is superior and statistically competitive with these excellent algorithms in terms of robustness, stability and the quality of the obtained solutions. [ABSTRACT FROM AUTHOR]

A recent publication in Nature has generated much heated discussion about evolution, its tendency towards increasing diversity and complexity, and its potential status above and beyond the known laws of fundamental physics. The argument at the heart of this controversy concerns assembly theory, a method to detect and quantify the influence of higher-level emergent causal constraints in computational worlds made of basic objects and their combinations. In this short essay, I briefly review the theory, its basic principles and potential applications. I then go on to critically examine its authors' assertions, concluding that assembly theory has merit but is not nearly as novel or revolutionary as claimed. It certainly does not provide any new explanation of biological evolution or natural selection, or a new grounding of biology in physics. In this regard, the presentation of the paper is starkly distorted by hype, which may explain some of the outrage it created. [ABSTRACT FROM AUTHOR]

Intertidal algae may adapt to environmental challenges by acquiring genes from other organisms and relying on symbiotic microorganisms. Here, we obtained a symbiont-free and chromosome-level genome of Pyropia haitanensis (47.2 Mb), a type of intertidal algae, by using multiple symbiont screening methods. We identified 286 horizontal gene transfer (HGT) genes, 251 of which harbored transposable elements (TEs), reflecting the importance of TEs for facilitating the transfer of genes into P. haitanensis. Notably, the bulked segregant analysis revealed that two HGT genes, sirohydrochlorin ferrochelatase and peptide-methionine (R)-S-oxide reductase, play a significant role in the adaptation of P. haitanensis to heat stress. Besides, we found Pseudomonas, Actinobacteria, and Bacteroidetes are the major taxa among the symbiotic bacteria of P. haitanensis (nearly 50% of the HGT gene donors). Among of them, a heat-tolerant actinobacterial strain (Saccharothrix sp.) was isolated and revealed to be associated with the heat tolerance of P. haitanensis through its regulatory effects on the genes involved in proline synthesis (proC), redox homeostasis (ggt), and protein folding (HSP20). These findings contribute to our understanding of the adaptive evolution of intertidal algae, expanding our knowledge of the HGT genes and symbiotic microorganisms to enhance their resilience and survival in challenging intertidal environments. A symbiont-free and chromosome-level genome of Pyropia haitanensis and the corresponding metagenome revealed insights into horizontally transferred genes and bacterial symbionts helping this intertidal algae to combat stress. [ABSTRACT FROM AUTHOR]

The rhizome concept proposed by Gilles Deleuze and Félix Guattari offers a novel perspective on the organization and interdependence of complex constellations of heterogeneous entities, their mapping and their ruptures. The emphasis of the present study is placed on the dynamics of contacts and communication among such entities that arise from experimentation, without any favored hierarchy or origin. When applied to biological evolution, the rhizome concept integrates all types of heterogeneity resulting from "symbiotic" relationships among living beings (or their genomic material), horizontal genetic transfer, recombination and mutation, and breaks away from the approach that gives rise to the phylogenetic tree of life. It has already been applied to describe the dynamics and evolution of RNA viruses. Thus, here we introduce a novel framework for the interpretation the viral quasispecies concept, which explains the evolution of RNA virus populations as the result of dynamic interconnections and multifaceted interdependence between highly heterogeneous viral sequences and its inherently heterogeneous host cells. The rhizome network perspective underlines even further the medical implications of the broad mutant spectra of viruses that are in constant flow, given the multiple pathways they have available for fitness loss and gain. [ABSTRACT FROM AUTHOR]

Plagiognathops microlepis is an economic freshwater fish in the subfamily Xenocyprinae of Cyprinidae. It is widely distributed in the freshwater ecosystem of China, with moderate economic value and broad development prospects. However, the lack of genomic resources has limited our understanding on the genetic basis, phylogenetic status and adaptive evolution strategies of this fish. Here, we assembled a chromosome-level reference genome of P. microlepis by integrating Pacbio HiFi long-reads, Illumina short-reads and Hi-C sequencing data. The size of this genome is 1004.34 Mb with a contig N50 of 38.80 Mb. Using Hi-C sequencing data, 99.59% of the assembled sequences were further anchored to 24 chromosomes. A total of 578.91 Mb repeat sequences and 28,337 protein-coding genes were predicted in the current genome, of which, 26,929 genes were functionally annotated. This genome provides valuable information for investigating the phylogeny and evolutionary history of cyprinid fishes, as well as the genetic basis of adaptive strategies and special traits in P. microlepis. [ABSTRACT FROM AUTHOR]

An international collection of Staphylococcus aureus of clonal complex (CC) 398 from diverse hosts spanning all continents and a 30 year-period is studied based on whole-genome sequencing (WGS) data. The collection consists of publicly available genomic data from 2994 strains and 134 recently sequenced Swiss methicillin-resistant S. aureus (MRSA) CC398 strains. A time-calibrated phylogeny reveals the presence of distinct phylogroups present in Asia, North and South America and Europe. European MRSA diverged from methicillin-susceptible S. aureus (MSSA) at the beginning of the 1950s. Two major European phylogroups (EP4 and EP5), which diverged approximately 1974, are the main drivers of MRSA CC398 spread in Europe. Within EP5, an emergent MRSA lineage spreading among the European horse population (EP5-Leq) diverged approximately 1996 from the pig lineage (EP5-Lpg), and also contains human-related strains. EP5-Leq is characterized by staphylococcal cassette chromosome mec (SCCmec) IVa and spa type t011 (CC398-IVa-t011), and EP5-Lpg by CC398-SCCmecVc-t011. The lineage-specific antibiotic resistance and virulence gene patterns are mostly mediated by the acquisition of mobile genetic elements like SCCmec, S. aureus Genomic Islands (SaGIs), prophages and transposons. Different combinations of virulence factors are present on S. aureus pathogenicity islands (SaPIs), and novel antimicrobial resistance gene containing elements are associated with certain lineages expanding in Europe. This WGS-based analysis reveals the actual evolutionary trajectory and epidemiological trend of the international MRSA CC398 population considering host, temporal, geographical and molecular factors. It provides a baseline for global WGS-based One-Health studies of adaptive evolution of MRSA CC398 as well as for local outbreak investigations. Authors perform a whole genome sequencing-based analysis of an international MRSA CC398 population, revealing the evolutionary trajectory and epidemiological trend considering host, temporal, geographical and molecular factors as well as lineage-associated mobile genetic elements. [ABSTRACT FROM AUTHOR]

The incidence of beta-lactam resistance among clinical isolates is a major health concern. A key method to study the emergence of antibiotic resistance is adaptive laboratory evolution. However, in the case of the beta-lactam ampicillin, bacteria evolved in laboratory settings do not recapitulate clinical-like resistance levels, hindering efforts to identify major evolutionary paths and their dependency on genetic background. Here, we used the Microbial Evolution and Growth Arena (MEGA) plate to select ampicillin-resistant Escherichia coli mutants with varying degrees of resistance. Whole-genome sequencing of resistant isolates revealed that ampicillin resistance was acquired via a combination of single-point mutations and amplification of the gene encoding beta-lactamase AmpC. However, blocking AmpC-mediated resistance revealed latent adaptive pathways: strains deleted for ampC were able to adapt through combinations of changes in genes involved in multidrug resistance encoding efflux pumps, transcriptional regulators, and porins. Our results reveal that combinations of distinct genetic mutations, accessible at large population sizes, can drive high-level resistance to ampicillin even independently of beta-lactamases. Bacterial resistance to beta-lactam antibiotics is on the rise, but laboratory evolution studies do not always recapitulate clinical resistance levels. Here, the authors select Escherichia coli mutants with varying degrees of beta-lactam resistance, showing that combinations of distinct genetic mutations, accessible at large population sizes, can drive high-level resistance independently of beta-lactamases. [ABSTRACT FROM AUTHOR]

Muslim students have a high perceived conflict between religion and evolution. For this reason, constructivist teaching was implemented to emphasise the balance of the nature of science (NOS) on evolution and creationism theory within the conceptual ecology for biological evolution (CEBE) framework. This study explored changes in students' CEBE and how perceived conflict, NOS, and religion contributed to the evolution of acceptance during the course. This research followed a one-group pre-test and post-test design to gather data. Data collection tools used in this study included a questionnaire and a reflective essay. The study group consisted of third-year undergraduate biology students aged 20–22 from Universitas Islam Negeri Maulana Malik Ibrahim Malang in Indonesia. Questionnaire responses were analysed using statistical methods, including paired t-tests, correlation, and hierarchical regression, while reflective essays were analysed using content analysis. The study found that students' acceptance increased after the course and was correlated with their knowledge, religiosity, understanding of NOS, and perceived impact. The understanding of NOS was the primary factor influencing the acceptance of the theory of evolution, while perceived conflict has the least impact. In addition, reflective essays showed that while most students had a naive knowledge of evolutionary reasoning, they could explain the nature of science. The students were able to establish a complex relationship between science and religion using the chimpanzee-human relationship explanation. This study has provided an example of a learning method to minimise students' perceived conflict in the evolution course. [ABSTRACT FROM AUTHOR]

Theory predicts that compensatory genetic changes reduce negative indirect effects of selected variants during adaptive evolution, but evidence is scarce. Here, we test this in a wild population of Hawaiian crickets using temporal genomics and a high-quality chromosome-level cricket genome. In this population, a mutation, flatwing, silences males and rapidly spread due to an acoustically-orienting parasitoid. Our sampling spanned a social transition during which flatwing fixed and the population went silent. We find long-range linkage disequilibrium around the putative flatwing locus was maintained over time, and hitchhiking genes had functions related to negative flatwing-associated effects. We develop a combinatorial enrichment approach using transcriptome data to test for compensatory, intragenomic coevolution. Temporal changes in genomic selection were distributed genome-wide and functionally associated with the population's transition to silence, particularly behavioural responses to silent environments. Our results demonstrate how 'adaptation begets adaptation'; changes to the sociogenetic environment accompanying rapid trait evolution can generate selection provoking further, compensatory adaptation. Theory predicts that adaptive mutations can have indirect negative effects on fitness. This study demonstrates how 'adaptation begets adaptation': changes to the sociogenetic environment accompanying rapid adaptation in wild crickets provoked genome-wide compensatory adaptation. [ABSTRACT FROM AUTHOR]

The cold-water species Ophiura sarsii, a brittle star, is a key echinoderm in the Arctic continental shelf region, highly sensitive to climate change. However, the absence of a high-quality genome has hindered a thorough understanding of its adaptive evolution. In this study, we reported the first chromosome-level genome assembly of O. sarsii. The genome assembly totalled 1.57 Gb, encompassing 19 chromosomes with a GC content of 37.11% and a scaffold N50 length of 78.03 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment yielded a completeness estimate of 93.5% for this assembly. We predicted a total of 27,099 protein-coding genes, with 25,079 functionally annotated. The genome was comprised of 58.09% transposable elements. This chromosome-level genome of O. sarsii contributes to our understanding of the origin and evolution of marine organisms. [ABSTRACT FROM AUTHOR]

Ficus species (Moraceae) play pivotal roles in tropical and subtropical ecosystems. Thriving across diverse habitats, from rainforests to deserts, they harbor a multitude of mutualistic and antagonistic interactions with insects, nematodes, and pathogens. Despite their ecological significance, knowledge about the genomic background of Ficus remains limited. In this study, we report a chromosome-level reference genome of F. hirta, with a total size of 297.27 Mb, containing 28,625 protein-coding genes and 44.67% repeat sequences. These findings illuminate the genetic basis of Ficus responses to environmental challenges, offering valuable genomic resources for understanding genome size, adaptive evolution, and co-evolution with natural enemies and mutualists within the genus. [ABSTRACT FROM AUTHOR]

Osimertinib (Osi) is a widely used epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI). However, the emergence of resistance is inevitable, partly due to the gradual evolution of adaptive resistant cells during initial treatment. Here, we find that Osi treatment rapidly triggers adaptive resistance in tumor cells. Metabolomics analysis reveals a significant enhancement of oxidative phosphorylation (OXPHOS) in Osi adaptive-resistant cells. Mechanically, Osi treatment induces an elevation of NCOA4, a key protein of ferritinophagy, which maintains the synthesis of iron-sulfur cluster (ISC) proteins of electron transport chain and OXPHOS. Additionally, active ISC protein synthesis in adaptive-resistant cells significantly increases the sensitivity to copper ions. Combining Osi with elesclomol, a copper ion ionophore, significantly increases the efficacy of Osi, with no additional toxicity. Altogether, this study reveals the mechanisms of NCOA4-mediated ferritinophagy in Osi adaptive resistance and introduces a promising new therapy of combining copper ionophores to improve its initial efficacy. The mechanisms leading to acquired resistance to targeted therapy in cancer are not completely understood. Here, the authors show that ferritinophagy mediates adaptive resistance to Osimertinib, and that combining this EGFR tyrosine kinase inhibitor with copper ionophores improves its therapeutic efficacy in preclinical models of non-small cell lung cancer. [ABSTRACT FROM AUTHOR]

The formation of extracellular DNA traps (ETosis) is a first response mechanism by specific immune cells following exposure to microbes. Initially characterized in vertebrate neutrophils, cells capable of ETosis have been discovered recently in diverse non-vertebrate taxa. To assess the conservation of ETosis between evolutionarily distant non-vertebrate phyla, we observed and quantified ETosis using the model ctenophore Mnemiopsis leidyi and the oyster Crassostrea gigas. Here we report that ctenophores – thought to have diverged very early from the metazoan stem lineage – possess immune-like cells capable of phagocytosis and ETosis. We demonstrate that both Mnemiopsis and Crassostrea immune cells undergo ETosis after exposure to diverse microbes and chemical agents that stimulate ion flux. We thus propose that ETosis is an evolutionarily conserved metazoan defense against pathogens. Identifying core mechanisms of immune cells is critical for understanding the evolution of animal immune function. Here, Vandepas et al. report that ctenophore immune-like cells release extracellular DNA traps when exposed to microbes. [ABSTRACT FROM AUTHOR]

Escherichia coli MLB (MG1655 ΔpflB ΔldhA), which can hardly grow on glucose with little succinate accumulation under anaerobic conditions. Two-stage fermentation is a fermentation in which the first stage is used for cell growth and the second stage is used for product production. The ability of glucose consumption and succinate production of MLB under anaerobic conditions can be improved significantly by using acetate as the solo carbon source under aerobic condition during the two-stage fermentation. Then, the adaptive laboratory evolution (ALE) of growing on acetate was applied here. We assumed that the activities of succinate production related enzymes might be further improved in this study. E. coli MLB46-05 evolved from MLB and it had an improved growth phenotype on acetate. Interestingly, in MLB46-05, the yield and tolerance of succinic acid in the anaerobic condition of two-stage fermentation were improved significantly. According to transcriptome analysis, upregulation of the glyoxylate cycle and the activity of stress regulatory factors are the possible reasons for the elevated yield. And the increased tolerance to acetate made it more tolerant to high concentrations of glucose and succinate. Finally, strain MLB46-05 produced 111 g/L of succinic acid with a product yield of 0.74 g/g glucose. Synopsis: [ABSTRACT FROM AUTHOR]

This review first presents the origin and species of wild discus fish (Symphysodon spp.), as well as discus propagation and domestication. The phenotypic characteristics, with particular emphasis on primary and secondary colors, stress bars, stripes and spots, eye features, the "D" area, markings and rims, body and fin shapes, forehead types, and gill plates, are described. The domesticated discus varieties are then classified on the basis of their primary base color and distinct phenotypic characteristics. Major malformation features that affect the value of the discus are described. These details are of fundamental importance in helping aquaculturists, discus hobbyists, and researchers to understand the general background characteristics, as well as to identify common and new discus varieties based on their phenotypic appearance. The review concludes with recommendations for a few critical research topics that could be carried out in the near future to benefit understanding of this important ornamental fish species for the aquaculture industry, with a focus on the incorporation of transcriptomic and genomic tools that allow researchers to understand and predict putative functional genes and pathways at the molecular level. [ABSTRACT FROM AUTHOR]

To broaden the substrate scope of microbial cell factories towards renewable substrates, rational genetic interventions are often combined with adaptive laboratory evolution (ALE). However, comprehensive studies enabling a holistic understanding of adaptation processes primed by rational metabolic engineering remain scarce. The industrial workhorse Pseudomonas putida was engineered to utilize the non-native sugar D-xylose, but its assimilation into the bacterial biochemical network via the exogenous xylose isomerase pathway remained unresolved. Here, we elucidate the xylose metabolism and establish a foundation for further engineering followed by ALE. First, native glycolysis is derepressed by deleting the local transcriptional regulator gene hexR. We then enhance the pentose phosphate pathway by implanting exogenous transketolase and transaldolase into two lag-shortened strains and allow ALE to finetune the rewired metabolism. Subsequent multilevel analysis and reverse engineering provide detailed insights into the parallel paths of bacterial adaptation to the non-native carbon source, highlighting the enhanced expression of transaldolase and xylose isomerase along with derepressed glycolysis as key events during the process. Pseudomonas putida is becoming a host of choice for the valorization of lignocellulosic substrates. Here, the authors provide insight into the adaptation of this bacterium to the non-native substrate D-xylose, enabled by metabolic engineering and adaptive laboratory evolution. [ABSTRACT FROM AUTHOR]

Candida auris has become a serious threat to public health. The mechanisms of how this fungal pathogen adapts to the mammalian host are poorly understood. Here we report the rapid evolution of an adaptive C. auris multicellular aggregative morphology in the murine host during systemic infection. C. auris aggregative cells accumulate in the brain and exhibit obvious advantages over the single-celled yeast-form cells during systemic infection. Genetic mutations, specifically de novo point mutations in genes associated with cell division or budding processes, underlie the rapid evolution of this aggregative phenotype. Most mutated C. auris genes are associated with the regulation of cell wall integrity, cytokinesis, cytoskeletal properties, and cellular polarization. Moreover, the multicellular aggregates are notably more recalcitrant to the host antimicrobial peptides LL-37 and PACAP relative to the single-celled yeast-form cells. Overall, to survive in the host, C. auris can rapidly evolve a multicellular aggregative morphology via genetic mutations. Bing et al. report that Candida auris undergoes rapid evolution via de novo genetic mutations and forms multicellular aggregates that exhibit a survival advantage over the single-celled yeast-form phenotype during host infection. [ABSTRACT FROM AUTHOR]

Differential evolution (DE) is a robust optimizer designed for solving complex domain research problems in the computational intelligence community. In the present work, a multi-hybrid DE (MHDE) is proposed for improving the overall working capability of the algorithm without compromising the solution quality. Adaptive parameters, enhanced mutation, enhanced crossover, reducing population, iterative division and Gaussian random sampling are some of the major characteristics of the proposed MHDE algorithm. Firstly, an iterative division for improved exploration and exploitation is used, then an adaptive proportional population size reduction mechanism is followed for reducing the computational complexity. It also incorporated Weibull distribution and Gaussian random sampling to mitigate premature convergence. The proposed framework is validated by using IEEE CEC benchmark suites (CEC 2005, CEC 2014 and CEC 2017). The algorithm is applied to four engineering design problems and for the weight minimization of three frame design problems. Experimental results are analysed and compared with recent hybrid algorithms such as laplacian biogeography based optimization, adaptive differential evolution with archive (JADE), success history based DE, self adaptive DE, LSHADE, MVMO, fractional-order calculus-based flower pollination algorithm, sine cosine crow search algorithm and others. Statistically, the Friedman and Wilcoxon rank sum tests prove that the proposed algorithm fares better than others. [ABSTRACT FROM AUTHOR]

High reproductive compatibility between crops and their wild relatives can provide benefits for crop breeding but also poses risks for agricultural weed evolution. Weedy rice is a feral relative of rice that infests paddies and causes severe crop losses worldwide. In regions of tropical Asia where the wild progenitor of rice occurs, weedy rice could be influenced by hybridization with the wild species. Genomic analysis of this phenomenon has been very limited. Here we use whole genome sequence analyses of 217 wild, weedy and cultivated rice samples to show that wild rice hybridization has contributed substantially to the evolution of Southeast Asian weedy rice, with some strains acquiring weed-adaptive traits through introgression from the wild progenitor. Our study highlights how adaptive introgression from wild species can contribute to agricultural weed evolution, and it provides a case study of parallel evolution of weediness in independently-evolved strains of a weedy crop relative. Genome-wide evidence to support that wild rice can contribute to weedy rice evolution by hybridization and adaptive introgression is very limited. Here, the authors sequence the weedy rice genomes and show reproductively compatible wild rice can contribute to weedy rice evolution. [ABSTRACT FROM AUTHOR]

Due to the harsh operating environment and ultralong operating hours of wireless sensor networks (WSNs), node failures are inevitable. Ensuring the reliability of the data collected by the WSN necessitates the utmost importance of diagnosing faults in nodes within the WSN. Typically, the initial step in the fault diagnosis of WSN nodes involves extracting numerical features from neighboring nodes. A solitary data feature is often assigned a high weight, resulting in the failure to effectively distinguish between all types of faults. Therefore, this study introduces an enhanced variant of the traditional belief rule base (BRB), called the belief rule base with adaptive attribute weights (BRB-AAW). First, the data features are extracted as input attributes for the model. Second, a fault diagnosis model for WSN nodes, incorporating BRB-AAW, is established by integrating parameters initialized by expert knowledge with the extracted data features. Third, to optimize the model's initial parameters, the projection covariance matrix adaptive evolution strategy (P-CMA-ES) algorithm is employed. Finally, a comprehensive case study is designed to verify the accuracy and effectiveness of the proposed method. The results of the case study indicate that compared with the traditional BRB method, the accuracy of the proposed model in WSN node fault diagnosis is significantly improved. [ABSTRACT FROM AUTHOR]

This manuscript presents an algorithmic approach to cooperation in biological systems, drawing on fundamental ideas from statistical mechanics and probability theory. Fisher's geometric model of adaptation suggests that the evolution of organisms well adapted to multiple constraints comes at a significant complexity cost. By utilizing combinatorial models of fitness, we demonstrate that the probability of adapting to all constraints decreases exponentially with the number of constraints, thereby generalizing Fisher's result. Our main focus is understanding how cooperation can overcome this adaptivity barrier. Through these combinatorial models, we demonstrate that when an organism needs to adapt to a multitude of environmental variables, division of labor emerges as the only viable evolutionary strategy. [ABSTRACT FROM AUTHOR]

Animals synthesize simple lipids using a distinct fatty acid synthase (FAS) related to the type I polyketide synthase (PKS) enzymes that produce complex specialized metabolites. The evolutionary origin of the animal FAS and its relationship to the diversity of PKSs remain unclear despite the critical role of lipid synthesis in cellular metabolism. Recently, an animal FAS-like PKS (AFPK) was identified in sacoglossan molluscs. Here, we explore the phylogenetic distribution of AFPKs and other PKS and FAS enzymes across the tree of life. We found AFPKs widely distributed in arthropods and molluscs (>6300 newly described AFPK sequences). The AFPKs form a clade with the animal FAS, providing an evolutionary link bridging the type I PKSs and the animal FAS. We found molluscan AFPK diversification correlated with shell loss, suggesting AFPKs provide a chemical defense. Arthropods have few or no PKSs, but our results indicate AFPKs contributed to their ecological and evolutionary success by facilitating branched hydrocarbon and pheromone biosynthesis. Although animal metabolism is well studied, surprising new metabolic enzyme classes such as AFPKs await discovery. Much is still unknown of the evolution of animal metabolic enzymes. This study describes a new enzyme family bridging the production of polyketides and membrane lipids. This expands the known biochemical repertoire of animals for making ecologically and biomedically important natural products. [ABSTRACT FROM AUTHOR]

Professor Claus Nielsen, a renowned zoologist, passed away on January 18th, 2024. He was known for his influential work in the field of invertebrate biology, particularly in the study of bryozoan embryology and systematics. Claus was highly regarded for his research on ecto- and entoprocts and their relationship, as well as his contributions to the understanding of animal evolution. He was also recognized for his role as an editor for Acta Zoologica and for his efforts in promoting the field of zoological morphology. Claus will be remembered for his friendly demeanor, his dedication to teaching, and his significant impact on the field of invertebrate zoology. [Extracted from the article]