Survey on phylogenetic tree construction using machine learning.

Since DNA sequencing has become commonplace, the development of efficient methods and tools to explore gene sequences has become indispensable. In particular, despite photosynthetic eukaryotes constituting the largest percentage of terrestrial biomass, computational functional characterization of gene sequences in these organisms still predominantly relies on comparisons with Arabidopsis thaliana and other angiosperms. This paper introduces PharaohFUN, a web application designed for the evolutionary and functional analysis of protein sequences in photosynthetic eukaryotes, leveraging orthology relationships between them. PharaohFUN incorporates a homogeneous representative sampling of key species in this group, bridging clades that have traditionally been studied separately, thus establishing a comprehensive evolutionary framework to draw conclusions about sequence evolution and function. For this purpose, it incorporates modules for exploring gene tree evolutionary history, expansion and contraction events, ancestral states, domain identification, multiple sequence alignments, and diverse functional annotation. It also incorporates different search modes to facilitate its use and increase its reach within the community. Tests were performed on the whole transcription factor toolbox of A. thaliana and on CCA1 protein to assess its utility for both large-scale and fine-grained phylogenetic studies. These exemplify how PharaohFUN accurately traces the corresponding evolutionary histories of these proteins by unifying results for land plants, streptophyte and chlorophyte microalgae. Thus, PharaohFUN democratices access to these kinds of analyses in photosynthetic organisms for every user, independently of their prior training in bioinformatics.

In this work, the polarity balance of a novel two-dimensional hyperchaotic map is considered, and thus the corresponding manifold of conditional symmetry is coined. The unique map has a simple structure but provides direct 2-D offset boosting, which brings the possibility for the construction of conditional symmetry by introducing an absolute value function. The corresponding evolution of the discrete sequences from the system is verified by the circuit implementation based on the microcontroller of CH32V307. The pseudorandom data from the map increases its adaptability for applications in information security. The hyperchaotic sequence-injected Ant Colony Optimization (ACO), Grey Wolf Optimizer (GWO), and Sparrow Search Algorithm (SSA) show their improved performance in the optimization algorithm. Robot path planning experiments confirm that all three algorithms exhibit superior convergence performance, global search capability, and path smoothness compared with the original algorithms.

Meiotic drivers are selfish genetic elements that gain transmission advantages by distorting equal, Mendelian segregation. For decades, biologists have considered meiotic drivers as interesting, albeit esoteric, case studies. It is now clear, however, that meiotic drive is more common and phylogenetically widespread than previously supposed. Indeed, intensive study of a few well-known cases has begun to reveal the evolutionary genomic consequences of meiotic drive. We argue here that many features of genome evolution, content, and organization that are seemingly inexplicable by organismal adaptation or nearly neutral processes are instead best accounted for by recurrent histories of meiotic drive. We review how meiotic drive can affect the evolution of sequences, gene copy numbers, genes with functions in meiosis and gametogenesis, signatures of "selection", chromosome rearrangements, and karyotype evolution. We also explore the interactions of meiotic drive elements with other classes of selfish genetic elements, including satellite DNAs, transposable elements, and with the endogenous host genes involved in drive suppression. Finally, we argue that some aspects of drive-mediated genome evolution are now sufficiently well established that we might reverse the direction of discovery- rather than ask how drive affects genome evolution, we can use genome data to discover new putative drive elements.

The host genetics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have 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 of 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 in an intron of ST6GAL1, a gene affecting immune development and function, connected to three other associated loci (harboring MUC1, MUC5AC and MUC16) through O-glycan biosynthesis. Our study provides robust evidence for individual genetic variation related to glycosylation, translating into susceptibility to SARS-CoV-2 infections with Omicron variants.

The “bauxite gas reservoir” in the Ordos Basin represents a novel exploration domain, yet the mechanisms governing its widespread aluminous fracture fillings remain unclear. This study integrates core observation, thin-section analysis, geochemical simulation, and rock physics to investigate the formation and impact of these fracture systems. Results identify a characteristic filling evolutionary sequence of “wall-lining film → oolitic/globular → plug-like → vermicular.” Geochemical simulations confirm that increasing pH and decreasing Eh driven by water–rock interactions are the key drivers for aluminous mineral precipitation. A distinct well log response model characterized by high GR, DEN, and CNL values coupled with low AC and RT is established for effective identification. Seepage experiments reveal that while Al–Si colloidal fracture fillings reduce permeability, they act as natural proppants to preserve effective flow channels, acting as a crucial high-permeability network for gas migration despite the mineral occlusion. These findings refine the accumulation theory for bauxite series reservoirs and provide geological evidence for deep tight gas exploration.

AIG1 (avrRpt2-induced gene 1)-like proteins are a class of GTPases that play crucial roles in plants, functioning both in chloroplast protein import and disease resistance. However, their evolutionary history and the mechanisms driving this functional diversification remain poorly understood. Here, we performed a comprehensive genomic and evolutionary analysis of this gene family across the plant kingdom. We identified 90 AIG1-like genes from 11 sequenced plant species, representing major lineages from green algae to angiosperms. Phylogenetic analysis revealed that plant AIG1-like proteins form three monophyletic lineages corresponding to the Toc34, Toc159, and IAN subfamilies, which originated via two ancient duplications predating the divergence of green algae and land plants. These lineages exhibit dramatically divergent evolutionary patterns. The Toc34 subfamily is evolutionarily conserved, maintaining stable copy numbers and gene structure, indicative of strong functional constraints in its core role in plastid import. In contrast, the Toc159 and IAN subfamilies have undergone dynamic expansion via lineage-specific duplication mechanisms, including segmental duplication and prolific tandem duplication, respectively. Notably, we uncovered a novel mechanism for generating head-to-head tandem duplicates in the IAN subfamily, mediated by recombination between inverted repeats. Our analysis of ancestral gene numbers and gene gain/loss dynamics further highlights that functional diversification was driven by both the acquisition of distinct C-terminal targeting domains (M and TM domains) and profound differences in evolutionary rates and duplication modes among subfamilies. This study provides the first full-scale evolutionary framework for plant AIG1-like genes, establishing that functional specialization is rooted in distinct modes of sequence and genomic evolution.

Abstract This paper proposes a computerized text analysis framework to examine the evolution of China’s industrial internet policies concerning SMEs. Analyzing a corpus of 310 policy documents concerning SMEs in industrial internet domain, we first investigated their external structure. Thematic sequence evolution analysis subsequently identified five key topics. Building on a pivotal policy issued in 2017, the evolution of China’s industrial internet policies concerning SMEs was categorized into two stages. The paper further explored the characteristics of the intergovernmental cooperation network, and examined the evolutionary paths of policy themes using a Sankey diagram. The findings indicate that the five topics in stage 2 are essentially the continuation and further development of the policy themes in stage 1, demonstrating strong policy coherence in industrial internet domain. Theoretically, this study addresses the IAD’s challenges in exploring the evolution of action situations and the diverse processes of structural changes over time, while overcoming the ACF’s limitations in interpreting the interactions of common belief systems and interests.

The Vindhyan basin (~1.7-1.0 Ga) is the largest Precambrian sedimentary succession, covering the central (Son Valley, Bundelkhand) and western (Rajasthan) parts of India. Stratigraphically, it is divided into Semri, Kaimur, Rewa and Bhander Groups, and is well exposed in both the Son Valley and the Rajasthan area. The present study aims to provide detailed geology and geochemistry of the Lower Kaimur Sequence (LKS), that is, Chittor Fort Sandstone (CFS; ~1.1 Ga) of Rajasthan, Western India, and to compare it with the so-called contemporaneous deposits preserved in the Son Valley, consisting of Sasaram Sandstone (SS), Ghurma Shale (GS) and Markundi Sandstone (MS), in order of superposition. The CFS of Rajasthan consists of three lithofacies, comprising alternating shale and sandstone. The SiO 2 /Al 2 O 3, K 2 O/Na 2 O, and CIA values from CFS, Rajasthan, indicate a moderate to high degree of chemical weathering in a warm, humid climate, leading to the derivation of compositionally mature sediments. The Th-Sc-Zr/10 and La/Sc-Ti/Zr diagrams imply that the sandstones of CFS belong to a passive margin setting, whereas the shales bear a signature of a continental island arc. The average trace element ratios, Th vs Sc and [Gd/Yb] N versus Eu/Eu*, indicate that the siliciclastics have post-Archean continental-to-intermediate compositions. The trace element ratio plots of La/Sc versus La/Co and La/Sc versus Th/Co revealed that the Hindoli Group (~1.8 Ga) of the Aravalli-Delhi Fold Belt (ADFB) is the source for the shales of the CFS of Rajasthan. The sandstones likely received detritus from the Berach granite (~2.5 Ga) of the Banded Gneissic Complex. At 1.6 Ga, due to this collisional activity, the compressional and extensional stresses caused the opening of the Vindhyan basin, which is separated from the Aravalli Fold Belts by the Great Boundary Fault (GBF). During the deposition of the LKS of Rajasthan/CFS the basin was active due to the reactivation of GBF. This caused a shift in provenance: the lower part of the Kaimur sequence received sediments from the Hindoli belt, while the upper part received sediment supply from the weathering of the Berach granite. Our study reveals that the LKS of Rajasthan has dissimilar lithology, geochemistry, provenance and tectonic setting from the contemporary sequence of the Son Valley. Our study thus suggests that a separate basin status should be given to the Rajasthan Vindhyans.

While graph-based pangenomes have become a standard and interoperable foundation for comparisons across multiple reference genomes, integrating protein-coding gene annotations across pangenomes in a single 'pangene set' remains challenging, both because of methodological inconsistency and biological presence-absence variation (PAV). Here, we review and experimentally evaluate the root of genome annotation and pangene set inconsistency using two polyploid plant pangenomes: cotton and soybean, which were chosen because of their existing diverse high-quality genomic resources and the known importance of gene PAV in their respective breeding programs. We first demonstrate that building pangene sets across different genome resources is highly error prone: PAV calculated directly from the genome annotations hosted on public repositories recapitulates structure in annotation methods and not biological sequence differences. Re-annotation of all genomes with a single identical pipeline largely resolves the broadest stroke issues; however, substantial challenges remain, including a surprisingly common case where exactly identical sequences have different gene model structural annotations. Combined, these results clearly show that pangenome gene model annotations must be carefully integrated before any biological inference can be made regarding sequence evolution, gene copy-number, or PAV.

As a tectonically stable and extensively superimposed basin situated in the North China Craton, the Ordos Basin hosts abundant reserves of oil, natural gas, and coal within its Paleozoic strata, rendering it a focal area in energy-related geological research. The basin’s evolutionary history provides a comprehensive record of key geological transitions—from an Early Paleozoic carbonate platform to Late Paleozoic marine–continental transitional deposits and ultimately to continental clastic sedimentation—largely governed by the regional tectonic dynamics associated with the North China Plate. This study presents a systematic review of the sedimentary and tectonic evolution of the Paleozoic sequence in the basin. Findings indicate that during the Early Paleozoic, the basin developed under a passive continental margin setting, characterized by widespread epicontinental marine carbonate deposition. By the Late Ordovician, subduction of the Qinqi Ocean triggered the Caledonian orogeny, resulting in regional uplift across the basin, widespread erosion, and a significant hiatus in Middle to Late Ordovician sedimentation, which facilitated the formation of paleo-weathered crust karst reservoirs. In the Late Paleozoic, the basin evolved into an intracratonic depression. From the Late Carboniferous to the Early Permian, the Hercynian tectonic event influenced the transformation from isolated rift basins to a broad epicontinental sea, leading to the deposition of critical coal-bearing strata within marine–continental transitional facies. Starting in the Middle Permian, the closure of surrounding oceanic domains induced widespread tectonic uplift, shifting the depositional environment to a terrestrial fluvial-lacustrine system and marking the termination of marine sedimentation in the region. Based on the comprehensive research findings, this study underscores that the superposition, inheritance, and interaction of multiple tectonic events are the primary controls on the paleogeographic architecture and sedimentary.

Reliable identification of allosteric binding sites remains a major bottleneck in structure-based drug discovery, particularly in protein kinase families where such sites are often structurally cryptic, evolutionarily non-conserved, and sparsely populated. In this work, we present a systematic analysis of binding site prediction across a rigorously curated dataset of human kinase-ligand complexes, encompassing 453 kinases and spanning five inhibitor classes: Type I, Type I.5, and Type II (orthosteric ATP-competitive) and Type III/IV (non-ATP allosteric) modulators. We employed the pretrained protein language model (PLM) ESM2-650M model that was fine-tuned for prediction of protein-ligand binding sites by replacing the original masked language modeling head with a token-level classification head that acts as a projection layer that maps the high-dimensional latent representation of each residue to a scalar probability score for a given protein residue to be part of the binding site. We employed this fine-tuned sequence-based PLM and structure-based detection approach P2Rank for identification of orthosteric and allosteric binding sites in protein kinases. Our analysis reveals a stark performance divergence: while both methods achieve high precision-recall (AUPR = 0.64-0.76) on orthosteric sites, PLM performance collapses on allosteric sites (AUPR = 0.06), despite retaining moderate ranking ability (AUROC = 0.70). This deficit persists even after strict control for sequence similarity, structural redundancy, and extreme class imbalance (allosteric residues constitute <3% of the kinase domain). To mechanistically interpret this discrepancy, we integrate large-scale local frustration analysis, a physics-based framework derived from energy landscape theory that quantifies the energetic stability of residue-residue interactions under mutational and conformational perturbations. We find that, although the global frustration landscape is conserved across kinase states dominated by neutral frustration (55-75% of residues), local binding sites exhibit fundamentally distinct mutational constraints. Orthosteric pockets are enriched in minimally frustrated residues, whereas allosteric sites are characterized by neutral mutational frustration, indicating evolutionary permissiveness and sequence degeneracy. This study reframes the performance of AI approaches in predicting protein binding sites as a reflection of functional design that can be rationalized through lens of the landscape-encoded protein frustration as an explainable AI framework.

Peculiar multi-stability observed in Yoshimura origami structures: Evolution and regulation of snapping sequence

Large-scale phylogenomics reveals convergent genome evolution across repeated transitions to endosymbiosis in Enterobacterales.

BackgroundThe molecular mechanisms that underlie adaptive divergence in complex traits can be assessed in traits like animal venoms where variation in gene sequence and expression levels can be directly linked to functional divergence in phenotypes. We used novel metrics for measuring functional divergence based on amino acid variation to assess the impact of coding sequence evolution, gene duplication and loss, and expression variation on the divergence in venom between sister species in two lineages of pitvipers.ResultsIn both lineages, coding sequence and expression variation made significant contributions to overall functional divergence whereas genic variation was less important. Locus-specific analyses of two multigene families that encode important venom proteins (serine proteases and metalloproteases) showed that (1) There were differences between lineages in the distributions of locus effect size on functional divergence between Sistrurus (many loci with similar effects) and Bothrops (loci with either small or large effects); (2) A small number of loci were under strong positive selection, but only in serine proteases was the intensity of selection positively correlated with contributions to functional divergence in venom. (3) Patterns of overall serine protease and metalloprotease expression differed between lineages, but there was no association between expression levels of individual genes and contributions to divergence.ConclusionsOur results show that the genetic underpinnings of early adaptive divergence in snake venoms are multifaceted and vary across lineages. Broadly, sequence and expression divergence both have substantial effects on functional divergence and each of these mechanisms has greater impacts than genic variation.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12915-025-02465-8.

Transposable elements (TEs) make up about half of the human and mouse genomes and play important regulatory roles in immune responses. However, the cis-regulatory contribution of TEs to immune cell development is less characterized. Here, we analyzed hundreds of chromatin accessibility, gene expression, transcription factor occupancy and DNA-DNA contact datasets in diverse mouse and human immune cells. We identified two rodent-specific TE subfamilies, ORR1E and ORR1D2 (collectively, ODE) that have transformed into cell type-specific enhancers across the mouse immune system. ODE loci acquired mutations post-insertion that enable differential binding of lineage-specifying transcription factors. ODEs show evidence of evolutionary sequence constraint and contact promoters of hundreds of genes in immune cells. ODE-targeted genes show cell type-specific and mouse-specific increases in expression compared to concordant human cell types. Thus, a single TE family can undergo functionalization after its genomic spread to generate batteries of cell-specific enhancers supporting a complex developmental cascade.

Microstructural evolution and characteristics of loess-paleosol sequences: a case study from the Liujiapo (LJP) profile, Southern loess Plateau, China

Cis-regulatory sequences, such as enhancers, play a crucial role in morphological evolution, but how their diversification leads to evolution of novel expression patterns that underpin diversity is still poorly understood. Recent work suggests that the function of enhancers is influenced by their genomic sequence context more than previously thought, further complicating our understanding of their contribution to diversity. To address these issues, we investigated the regulation of the RCO homeobox gene, which contributed to the evolution of complex leaves following its tandem duplication from LMI1. By characterizing seventeen regulatory alleles at the LMI1/RCO locus that we generated by genome editing, we found that the evolved RCO enhancer is subject to pronounced negative regulation that helps delimit the RCO expression domain. While the LMI1 enhancer was strictly required for LMI1 gene expression, the same was not true for the RCO enhancer, which caused only partial loss of function when deleted. We mapped both positively and negatively acting sequences within the RCO enhancer, validated them in reporter gene assays and showed that a repressive sequence arose in association with a nested duplication within the evolved RCO enhancer. This repressive sequence played a key role in shaping the specific RCO expression domain that underlies its role in leaf complexity, and we provide evidence that it helped to prevent potential pleiotropic effects arising from evolutionary diversification or RCO expression. Our findings highlight the regulatory features of a diversity-linked enhancer and show that the evolution of repressive sequences is a powerful force in regulatory evolution.

The DUF538 (Domain of Unknown Function 538) gene family plays critical roles in plant growth, development, and stress responses, yet its phylogenetic distribution, sequence evolution, and expression characteristics remain poorly understood. Here, we identified 196 DUF538 genes across 13 plants, all of which were specific to land plants. Phylogenetic analysis revealed four distinct subgroups within this family, with subgroups A and B likely originating from ancestral whole-genome duplication (WGD) events in angiosperms. The ancestral subgroups (C/D) exhibited distinct sequence features, biophysical properties, and selective pressures compared to subgroups A/B, whereas A/B underwent gene structure simplification, sequence divergence, and relaxation of selective constraints. In maize, co-expression networks analysis linked DUF538 genes to root development (e.g., flavonoid biosynthesis and kinase signaling) and leaf stress responses (e.g., hydrolase activity and defense signaling). Promoter and expression analyses revealed subgroup-specific enrichment of cis-elements, which correlated with differential expression patterns during development and under abiotic stress. Notably, under CaCl₂ stress, paralogs within subgroups were activated sequentially, sustaining a prolonged response while minimizing functional redundancy through temporal differentiation. Collectively, these findings demonstrate that DUF538 genes have achieved functional diversification through sequence divergence, relaxed selection, and spatiotemporal expression regulation, thereby providing potential targets for enhancing crop stress resilience.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-025-07741-x.

ABSTRACT A medium-resolution spectroscopic survey of helium-rich hot subdwarfs has been carried out using the Southern African Large Telescope. Objectives include the discovery of exotic hot subdwarfs, resolving distinct subclasses, identifying evolutionary sequences, and establishing the past and future histories of many of these unusual stars. This paper extends the sample to 697 stars. It describes the selection criteria and presents spectral classifications based on the MK-like Drilling system. The sample includes 283 extremely helium-rich hot subdwarfs, 17 extreme helium stars, 110 intermediate helium-rich hot subdwarfs, as well as 21 helium-rich stars of other types. It now represents the largest homogeneous sample of both ‘normal’ He-sdOs and ‘luminous’ or ‘hot’ He-sdOs. Interesting stars discovered include magnetic hot subdwarfs, extremely hot pre-white dwarfs and hot subdwarfs, including hot subdwarfs showing N v emission, one short-period binary, new extreme helium stars and several double-subdwarf candidates. The data form the basis for kinematic and model atmosphere analyses to follow.