Sequence Evolution Research Articles

Crossover Operator Inspired by the Selection Operator for an Evolutionary Task Sequencing Algorithm

This paper proposes a novel crossover operator for evolutionary algorithms in task sequencing and verifies its efficacy. Unlike the conventional blind and entirely stochastic selection of sequence fragments exchanged with the second individual, the proposed operator employs a method where the probability of fragment selection is influenced by the total cost of internal connections within the exchanged fragments. At the same time, the new operator retains its stochastic nature and is not a deterministic operator, which reduces the risk of the evolutionary algorithm getting stuck in a local minimum. The idea of the proposed crossover operator was based on the main mechanism of the evolutionary algorithm that determines the success of this type of algorithm selection. To assess its effectiveness, the new operator was compared against previously employed crossover operators using a traveling salesman problem (TSP) instance in a multidimensional space in order to map the problem of symmetric sequencing tasks described with multiparameters (e.g., a symmetric variant of production tasks sequencing).

Variant pathogenicity prediction based on the ESGMM algorithm

Modeling the functional impact of sequence variation is a critical issue for both understanding and developing proteins. An Evolutionary Sequence and Gaussian Mixture Model (ESGMM) for predicting variant pathogenicity is presented in this paper. The model is trained on 2715 clinical proteins and their homologous sequences, using a Transformer-based protein language model to discover evolutionary patterns of amino acids from multiple sequence alignment (MSA). To fully mine deep information of MSA two-dimensional data, an axial attention mechanism is introduced during training. The model estimates the probability of all variants compared to the wild type and calculates variant scores. To categorize variations as pathogenic or benign, a global–local Gaussian mixture model is then constructed for each variant, and ESGMM scores are produced for each variant employing a combination of global and local information. Particle swarm optimization (PSO) is introduced to optimize the local Gaussian mixture model and further quantify the uncertainty of the classification, which enhances the model prediction precision. Experimental results demonstrate the superiority of the optimized ESGMM algorithm in predicting the pathogenicity of variants.

Smoothing-Based Aftershock Probabilistic Seismic Hazard Assessment Using the Spatiotemporal ETAS Model

ABSTRACT Probabilistic seismic hazard analysis (PSHA) is generally based on computing time-invariant occurrence rates of mainshocks using the Poisson process. However, aftershock probabilistic seismic hazard analysis (APSHA) allows for assessing time-varying aftershock occurrence rates within a short-term seismic hazard mitigation framework. Our proposed methodology of APSHA develops a smoothing-based analytical formulation to capture the spatial distribution and temporal evolution of aftershock sequences using the spatiotemporal epidemic-type aftershock sequence model. This approach is tested on case studies of the 2013 Bushehr, 2021 and 2022 Hormozgan seismic events, and characterizes the aftershocks’ hierarchical structure to improve the reliability of aftershock hazard assessments. Then, the results of APSHA (aftershock ground-motion hazard at specific sites) based on smoothing are compared with conventional PSHA (pre-mainshock ground-motion hazard at specific sites). This comparative analysis highlights the importance of considering aftershock effects when assessing ground-motion hazards because PSHA does not fully account for aftershock hazard increases following major earthquakes.

Evolution of sequence, structural and functional diversity of the ubiquitous DNA/RNA-binding Alba domain

The DNA/RNA-binding Alba domain is prevalent across all kingdoms of life. First discovered in archaea, this protein domain has evolved from RNA- to DNA-binding, with a concomitant expansion in the range of cellular processes that it regulates. Despite its widespread presence, the full extent of its sequence, structural, and functional diversity remains unexplored. In this study, we employed iterative searches in PSI-BLAST to identify 15,161 unique Alba domain-containing proteins from the NCBI non-redundant protein database. Sequence similarity network (SSN) analysis clustered them into 13 distinct subgroups, including the archaeal Alba and eukaryotic Rpp20/Pop7 and Rpp25/Pop6 groups, as well as novel fungal and Plasmodium-specific Albas. Sequence and structural conservation analysis of the subgroups indicated high preservation of the dimer interface, with Alba domains from unicellular eukaryotes notably exhibiting structural deviations towards their C-terminal end. Finally, phylogenetic analysis, while supporting SSN clustering, revealed the evolutionary branchpoint at which the eukaryotic Rpp20- and Rpp25-like clades emerged from archaeal Albas, and the subsequent taxonomic lineage-based divergence within each clade. Taken together, this comprehensive analysis enhances our understanding of the evolutionary history of Alba domain-containing proteins across diverse organisms.

Central role of glycosylation processes in human genetic susceptibility to SARS-CoV-2 infections with Omicron variants.

The host genetics of SARS-CoV-2 has previously been studied based on cases from the earlier waves of the pandemic in 2020 and 2021, identifying 51 genomic loci associated with infection and/or severity. SARS-CoV-2 has shown rapid sequence evolution increasing transmissibility, particularly for Omicron variants, which raises the question whether this affected the host genetic factors. We performed a genome-wide association study of SARS-CoV-2 infection with Omicron variants including more than 150,000 cases from four cohorts. We identified 13 genome-wide significant loci, of which only five were previously described as associated with SARS-CoV-2 infection. The strongest signal was a single nucleotide polymorphism (SNP) intronic of ST6GAL1, a gene affecting immune development and function, and connected to three other associated loci (harboring MUC1, MUC5AC and MUC16) through O-glycan biosynthesis. We also found further evidence for an involvement of blood group systems in SARS-CoV-2 infection, as we observed association 1) for a different lead SNP in the ABO locus indicating a protective effect of blood group B against Omicron infection, 2) for the FUT2 SNP tagging secretor status also reported for SARS-CoV-2 infection with earlier variants, and 3) for the strongest expression quantitative trait locus (eQTL) for FUT3 (Lewis gene). Our study provides robust evidence for individual genetic variation related to glycosylation translating into susceptibility to SARS-CoV-2 infections with Omicron variants.

Impact of gradient zero-valent iron pollution from steel works on soil microaggregate geochemical processes and dissipative structures

Abstract: Zero-valent iron (ZVI) contamination from steel works poses significant threats to soil quality and ecosystem health, particularly affecting soil microaggregates, which are fundamental to soil structure and function. In this study, we systematically investigated the impact of gradient ZVI pollution on the organic geochemical environment of soil microaggregates around steel works located in the core water source area of the Middle Route of the South-to-North Water Diversion Project in China. Advanced analytical techniques, including X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), X-ray fluorescence spectroscopy (XRF), inductively coupled plasma optical emission spectroscopy (ICP-OES), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR), were employed to comprehensively characterize the geochemical processes, mineralogy, and organic matter environment of soil microaggregates. The findings revealed that soils near the steel works were acidified and strongly oxidized, with heavy metal contents, particularly Fe, significantly decreasing with increasing distance from the steel works (Fe content decreased from 27,516.2 mg/kg to 23,492.6 mg/kg). The pH of soils near the steel works was lower, while oxidation-reduction potential (ORP) and electrical conductivity were higher. XPS analysis indicated a higher content of reactive oxygen species (ROS) near the steel works and significantly lower soil organic matter content. The iron valence distribution showed spatial differences, with higher Fe2⁺ content on the surface of soil microaggregates near the steel works and Fe³⁺ dominating in areas farther away. These results suggest an evolutionary sequence of ZVI from Fe (0) oxidation to Fe(II) and then to Fe(III). The formation of dissipative structures in soil microaggregates due to ZVI contamination significantly affects soil physicochemical properties and the organic environment. This study provides valuable insights into the multifaceted impacts of industrial activities on soil ecosystems and offers a scientific basis for soil conservation and remediation strategies.

Reawakening of Voragine, the Oldest of Etna’s Summit Craters: Insights from a Recurrent Episodic Eruptive Behavior

Paroxysmal explosive activity at Etna volcano (Italy) has become quite frequent over the last three decades, raising concerns with the civil protection authorities due to its significant impact on the local population, infrastructures, viability and air traffic. Between 4 July and 15 August 2024, during the tourist season peak when the local population doubles, Etna volcano gave rise to a sequence of six paroxysmal explosive events from the summit crater named Voragine. This is the oldest and largest of Etna’s four summit craters and normally only produces degassing, with the previous explosive sequences occurring in December 2015 and May 2016. In this paper, we use thermal images recorded by the monitoring system maintained by the Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Etneo (INGV–OE), and an automatic procedure previously tested in order to automatically define the eruptive parameters of the six lava fountain episodes. These data allowed us to infer the eruptive processes and gain some insights on the evolution of the explosive sequences that are useful for hazard assessment. Specifically, our results lead to the hypothesis that the Voragine shallow storage has a capacity of ~12–15 Mm3, which was not completely emptied with the last two paroxysmal events. It is thus possible that one or two additional explosive paroxysmal events could occur in the future. It is noteworthy that an additional paroxysmal episode occurred at Voragine on 10 November 2024, after the submission of this paper, thus confirming our hypothesis.

Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination

Recent genomic analyses have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars), but the mechanisms that create and maintain these units remain unclear. By analyzing closely-related isolate genomes from the same or related samples and identifying recent recombination events using a novel bioinformatics methodology, we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection-driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on greater similarity in temporal abundance patterns of genomes of the same vs. different units, and recombination was shown to affect all sizable segments of the genome (i.e., be genome-wide) and have two times or greater impact on sequence evolution than point mutations. These results were observed in both Salinibacter ruber, an environmental halophilic organism, and Escherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or recombination, but not necessarily their synergistic effect, and answer an important question for microbiology: what a species and a subspecies are.

Double red giant branch and red clump features of Galactic disc stellar populations with Gaia gspspec

The bimodality of the Milky Way disc, in the form of a thick short disc and a thinner more radially extended one, encrypts the complex internal evolution of our Galaxy and its interaction with the environment. To disentangle the different competing physical processes at play in Galactic evolution, a detailed chrono-chemical-kinematical and dynamical characterisation of the disc bimodality is necessary, including high number statistics. Here, we make use of an extremely precise sub-sample of the Gaia DR3 catalogue of stellar chemo-physical parameters. The selected database is composed of 408 800 stars with a median uncertainty of 10 K, 0.03, and 0.01 dex in and respectively. The stellar parameter precision allows us to break the age-metallicity degeneracy of disc stars. For the first time, the disc bimodality in the Kiel diagram of giant stars is observed, getting rid of interstellar absortion issues. This bimodality produces double red giant branch sequences and red clump features for mono-metallicity populations. A comparison with BaSTI isochrones allows us to demonstrate that an age gap is needed to explain the evolutionary sequence separation, in agreement with previous age-metallicity relations obtained using sub-giant stars. A bimodal distribution in the stellar mass- plane is observed at constant metallicity. Finally, a selection of stars with 0.03 dex shows that the most metal-rich population in the Milky Way disc presents an important proportion of stars with ages in the range of 5-13 Gyr, in agreement with previous literature findings. This old, extremely metal-rich population is possibly a mix of migrated stars from the internal Galactic regions, and old disc stars formed before the last major merger of the Milky Way. The Gaia Kiel diagrams of disc mono-abundance stellar populations reveal a complex, non-linear age-metallicity relation crafted by internal and external processes of Galactic evolution. Their detailed analysis opens new opportunities to reconstruct the puzzle of the Milky Way disc bimodality.

Plasticity and environment-specific relationships between gene expression and fitness in Saccharomyces cerevisiae

The environment influences how an organism’s genotype determines its phenotype and how this phenotype affects its fitness. Here, to better understand this dual role of environment in the production and selection of phenotypic variation, we determined genotype–phenotype–fitness relationships for mutant strains of Saccharomyces cerevisiae in four environments. Specifically, we measured how promoter mutations of the metabolic gene TDH3 modified expression level and affected growth for four different carbon sources. In each environment, we observed a clear relationship between TDH3 expression level and fitness, but this relationship differed among environments. Mutations with similar effects on expression in different environments often had different effects on fitness and vice versa. Such environment-specific relationships between phenotype and fitness can shape the evolution of phenotypic plasticity. We also found that mutations disrupting binding sites for transcription factors had more variable effects on expression among environments than those disrupting the TATA box, which is part of the core promoter. However, mutations with the most environmentally variable effects on fitness were located in the TATA box, because of both the lack of plasticity of TATA box mutations and environment-specific fitness functions. This observation suggests that mutations affecting different molecular mechanisms contribute unequally to regulatory sequence evolution in changing environments.

Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors.

We describe an effort ("Codebook") to determine the sequence specificity of 332 putative and largely uncharacterized human transcription factors (TFs), as well as 61 control TFs. Nearly 5,000 independent experiments across multiple in vitro and in vivo assays produced motifs for just over half of the putative TFs analyzed (177, or 53%), of which most are unique to a single TF. The data highlight the extensive contribution of transposable elements to TF evolution, both in cis and trans , and identify tens of thousands of conserved, base-level binding sites in the human genome. The use of multiple assays provides an unprecedented opportunity to benchmark and analyze TF sequence specificity, function, and evolution, as further explored in accompanying manuscripts. 1,421 human TFs are now associated with a DNA binding motif. Extrapolation from the Codebook benchmarking, however, suggests that many of the currently known binding motifs for well-studied TFs may inaccurately describe the TF's true sequence preferences.

Semantic variation and semantic change in the color lexicon

Abstract Color terms show a remarkable variation in their possible lexicalization patterns across different languages. In the literature, the interest has been especially to describe the color lexicon of a certain language and to determine whether it may abide or not by Berlin and Kay’s universal evolutionary sequence, e.g., whether a certain color denomination may be considered as a basic color term, or whether a certain color category is lexicalized by more than one basic color term, by which criteria, etc. It has not been established, however, which are the most common lexical sources of basic color terms on a comparative basis, and which semantic changes are more common in this semantic field. On the basis of data drawn from 70 ancient and modern Indo-European languages, we aim at answering precisely these research questions concerning the origin and the development of basic color terms. We discuss the various lexical sources of the basic color terms for white, black, red, green, yellow, blue, brown, gray, orange, pink, and purple, and we show the most important semantic changes leading to these color meanings. We also discuss to which extent these terms are likely to be inherited or borrowed. All this aims at being a contribution to the study of diachronic semantics.

Variation and evolution analysis of SARS-CoV-2 using self-game sequence optimization.

The evolution of SARS-CoV-2 has precipitated the emergence of new mutant strains, some exhibiting enhanced transmissibility and immune evasion capabilities, thus escalating the infection risk and diminishing vaccine efficacy. Given the continuous impact of SARS-CoV-2 mutations on global public health, the economy, and society, a profound comprehension of potential variations is crucial to effectively mitigate the impact of viral evolution. Yet, this task still faces considerable challenges. This study introduces DARSEP, a method based on Deep learning Associates with Reinforcement learning for SARS-CoV-2 Evolution Prediction, combined with self-game sequence optimization and RetNet-based model. DARSEP accurately predicts evolutionary sequences and investigates the virus's evolutionary trajectory. It filters spike protein sequences with optimal fitness values from an extensive mutation space, selectively identifies those with a higher likelihood of evading immune detection, and devises a superior evolutionary analysis model for SARS-CoV-2 spike protein sequences. Comprehensive downstream task evaluations corroborate the model's efficacy in predicting potential mutation sites, elucidating SARS-CoV-2's evolutionary direction, and analyzing the development trends of Omicron variant strains through semantic changes. Overall, DARSEP enriches our understanding of the dynamic evolution of SARS-CoV-2 and provides robust support for addressing present and future epidemic challenges.

Linking the primordial composition of planet building disks to the present-day composition of rocky exoplanets

The composition of rocky planets is strongly driven by the primordial materials in the protoplanetary disk, which can be inferred from the abundances of the host star. Understanding this compositional link is crucial for characterizing exoplanets. We aim to investigate the relationship between the compositions of low-mass planets and their host stars. We determined the primordial compositions of host stars using high-precision present-day stellar abundances and stellar evolutionary models. These primordial abundances were then input into a stoichiometric model to estimate the composition of planet-building blocks. Additionally, we employed a three-component planetary interior model (core, mantle, and water in different phases) to estimate planetary compositions based only on their radius and mass. We find that although stellar abundances vary over time, relevant abundance ratios such as Fe/Mg remain relatively constant during the main sequence evolution for low temperature stars. A strong correlation is found between the iron-to-silicate mass fraction of protoplanetary disks and planets, while no significant correlation was observed for water mass fractions. The Fe/Mg ratio varies significantly between planets and their stars, indicating substantial disk-driven compositional diversity, and this ratio also correlates with planetary radius. While stellar abundances, as a proxy of the composition of protoplanetary disk, provide a baseline for planetary composition, significant deviations arise due to complex disk processes, challenging the assumption of a direct, one-to-one elemental relationship between stars and their planets.

A Uniformitarian Solution to the Appearance of Small-Bodied Hominins, Dwarfs, Pathologies, and Self-Domestication: Theories of New Discoveries

A variety of new finds has produced a new set of species classified to the _Homo_ clade. Some of these appear to represent very small hominins with a variety of traits that are often seen in pathologies. The group of traits, however, do not associate with any known suite or any single condition, either genetic or induced by chemicals, radiation or other means. The first find of a hominin, the Neandertal, was considered a pathological modern human at first. Some claimed hominin finds were fakes that displayed so unusual traits, but whose status was supported by prominent scientists, that only a few questioned their authenticity. The lack of fit into the evolutionary sequence known at a given time has not been considered a single factor in rejecting a find, as the consideration of the Taung fossil eventually proved. Nevertheless, repeated finds of the same kind of fossil in different parts of the world, in different contexts by the same investigator does seem remarkable. Placing these finds in a phylogenetic setting is in order, but the distance and time frames are as challenging as is the problem of coincidence. Reference to pathological conditions producing several types of dwarfism are discussed in the context of these small-bodied finds. This paper proposes a hypothesis that a unique infection in several _Homo erectus _populations could offer a potential explanation for the developmental anomalies seen in small-bodied hominins.

Elucidating Evolutionary Mechanisms and Variants of the Hammerhead Ribozyme Using In Vitro Selection.

The Hammerhead Ribozyme (HHR) is a ubiquitous RNA enzyme that catalyzes site-specific intramolecular cleavage. While mutations to its catalytic core have traditionally been viewed as detrimental to its activity, several discoveries of naturally occurring variants of the full-length ribozyme challenge this notion, suggesting a deeper understanding of HHR evolution and functionality. By systematically introducing mutations at key nucleotide positions within the catalytic core, we generated single-, double-, and triple-mutation libraries to explore the sequence requirements and evolution of a full-length HHR. In vitro selection revealed many novel hammerhead variants, some of which possess mutations at nucleotides previously considered to be essential. We also demonstrate that the evolutionary trajectory of each nucleotide in the catalytic core directly correlates with their functional importance, potentially giving researchers a novel method to assess the sequence requirements of functional nucleic acids.

Orphan genes are not a distinct biological entity.

The genome sequencing revolution has revealed that all species possess a large number of unique genes critical for trait variation, adaptation, and evolutionary innovation. One widely used approach to identify such genes consists of detecting protein-coding sequences with no homology in other genomes, termed orphan genes. These genes have been extensively studied, under the assumption that they represent valid proxies for species-specific genes. Here, we critically evaluate taxonomic, phylogenetic, and sequence evolution evidence showing that orphan genes belong to a range of evolutionary ages and thus cannot be assigned to a single lineage. Furthermore, we show that the processes generating orphan genes are substantially more diverse than generally thought and include horizontal gene transfer, transposable element domestication, and overprinting. Thus, orphan genes represent a heterogeneous collection of genes rather than a single biological entity, making them unsuitable as a subject for meaningful investigation of gene evolution and phenotypic innovation.

The currently observed clumps cannot be the “direct” precursors of the currently observed open clusters

We categorized clumps, embedded clusters, and open clusters and conducted a comparative analysis of their physical properties. Overall, the radii of open clusters are significantly larger than those of embedded clusters and clumps. The radii of embedded clusters are larger than those of clumps, which may be due to the expansion of embedded clusters. The open clusters have significantly higher masses than embedded clusters, by about one order of magnitude. Given the current mass distribution of clumps in the Milky Way, the evolutionary sequence from a single clump evolving into an embedded cluster and subsequently into an open cluster cannot account for the observed open clusters with old ages and high masses, which is also supported by N-body simulations of individual embedded clusters. To explain the mass and radius distributions of the observed open clusters, initial embedded clusters with masses higher than 3000 M⊙ are necessary. However, the upper limit of the embedded cluster sample is less than 1000 M⊙, and only a few ATLASGAL clumps have a mass higher than 3000 M⊙. Thus, the currently observed clumps cannot be the “direct” precursors of the currently observed open clusters. If the Milky Way has a burst-like and time-dependent star formation history, the currently observed open clusters with old ages and high masses may come from massive clumps in the past. There is also a very real possibility that these open clusters originate from post-gas expulsion coalescence of multiple embedded clusters. We compared the separation of open clusters and the typical size of molecular clouds, and find that most molecular clouds may only form one open cluster, which supports the scenario of post-gas expulsion coalescence. Further study is necessary to distinguish between the different scenarios.

Spectral cluster supertree: fast and statistically robust merging of rooted phylogenetic trees.

The algorithms for phylogenetic reconstruction are central to computational molecular evolution. The relentless pace of data acquisition has exposed their poor scalability and the conclusion that the conventional application of these methods is impractical and not justifiable from an energy usage perspective. Furthermore, the drive to improve the statistical performance of phylogenetic methods produces increasingly parameter-rich models of sequence evolution, which worsens the computational performance. Established theoretical and algorithmic results identify supertree methods as critical to divide-and-conquer strategies for improving scalability of phylogenetic reconstruction. Of particular importance is the ability to explicitly accommodate rooted topologies. These can arise from the more biologically plausible non-stationary models of sequence evolution. We make a contribution to addressing this challenge with Spectral Cluster Supertree, a novel supertree method for merging a set of overlapping rooted phylogenetic trees. It offers significant improvements over Min-Cut supertree and previous state-of-the-art methods in terms of both time complexity and overall topological accuracy, particularly for problems of large size. We perform comparisons against Min-Cut supertree and Bad Clade Deletion. Leveraging two tree topology distance metrics, we demonstrate that while Bad Clade Deletion generates more correct clades in its resulting supertree, Spectral Cluster Supertree's generated tree is generally more topologically close to the true model tree. Over large datasets containing 10,000 taxa and 500 source trees, where Bad Clade Deletion usually takes 2 h to run, our method generates a supertree in on average 20 s. Spectral Cluster Supertree is released under an open source license and is available on the python package index as sc-supertree.

Convergence and divergence of diploid and tetraploid cotton genomes.

Polyploidy is an important driving force in speciation and evolution; however, the genomic basis for parallel selection of a particular trait between polyploids and ancestral diploids remains unexplored. Here we construct graph-based pan-genomes for diploid (A2) and allotetraploid (AD1) cotton species, enabled by an assembly of 50 genomes of genetically diverse accessions. We delineate a mosaic genome map of tetraploid cultivars that illustrates genomic contributions from semi-wild forms into modern cultivars. Pan-genome comparisons identify syntenic and hyper-divergent regions of continued variation between diploid and tetraploid cottons, and suggest an ongoing process of sequence evolution potentially linked to the contrasting genome size change in two subgenomes. We highlight 43% of genetic regulatory relationships for gene expression in diploid encompassing sequence divergence after polyploidy, and specifically characterize six underexplored convergent genetic loci contributing to parallel selection of fiber quality. This study offers a framework for pan-genomic dissection of genetic regulatory components underlying parallel selection of desirable traits in organisms.