Selective Constraints Research Articles

Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species.

Genome structural variations within species are rare. How selective constraints preserve gene order and chromosome structure is a central question in evolutionary biology that remains unsolved. Our sequencing of several genomes of the appendicularian tunicate Oikopleura dioica around the globe reveals extreme genome scrambling caused by thousands of chromosomal rearrangements, although showing no obvious morphological differences between these animals. The breakpoint accumulation rate is an order of magnitude higher than in ascidian tunicates, nematodes, Drosophila, or mammals. Chromosome arms and sex-specific regions appear to be the primary unit of macrosynteny conservation. At the microsyntenic level, scrambling did not preserve operon structures, suggesting an absence of selective pressure to maintain them. The uncoupling of the genome scrambling with morphological conservation in O. dioica suggests the presence of previously unnoticed cryptic species and provides a new biological system that challenges our previous vision of speciation in which similar animals always share similar genome structures.

Transcriptome-wide expression landscape and starch synthesis pathway co-expression network in sorghum.

The gene expression landscape across different tissues and developmental stages reflects their biological functions and evolutionary patterns. Integrative and comprehensive analyses of all transcriptomic data in an organism are instrumental to obtaining a comprehensive picture of gene expression landscape. Such studies are still very limited in sorghum, which limits the discovery of the genetic basis underlying complex agricultural traits in sorghum. We characterized the genome-wide expression landscape for sorghum using 873 RNA-sequencing (RNA-seq) datasets representing 19 tissues. Our integrative analysis of these RNA-seq data provides the most comprehensive transcriptomic atlas for sorghum, which will be valuable for the sorghum research community for functional characterizations of sorghum genes. Based on the transcriptome atlas, we identified 595 housekeeping genes (HKGs) and 2080 tissue-specific expression genes (TEGs) for the 19 tissues. We identified different gene features between HKGs and TEGs, and we found that HKGs have experienced stronger selective constraints than TEGs. Furthermore, we built a transcriptome-wide co-expression network (TW-CEN) comprising 35 modules with each module enriched in specific Gene Ontology terms. High-connectivity genes in TW-CEN tend to express at high levels while undergoing intensive selective pressure. We also built global and seed-preferential co-expression networks of starch synthesis pathways, which indicated that photosynthesis and microtubule-based movement play important roles in starch synthesis. The global transcriptome atlas of sorghum generated by this study provides an important functional genomics resource for trait discovery and insight into starch synthesis regulation in sorghum.

Patterns of Change in Nucleotide Diversity Over Gene Length.

Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to estimate Effective population size based on the diversity of synonymous sites demand a better understanding of their selective constraints. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide diversity at synonymous sites and uncover a pattern of low diversity towards the translation initiation site of a gene. The degree of reduction in diversity at the translation initiation site and the length of this region of reduced diversity can be quantified as "Effect Size" and "Effect Length" respectively, using parameters of an asymptotic regression model. Estimates of Effect Length across bacteria covaried with recombination rates as well as with a multitude of translation-associated traits such as the avoidance of mRNA secondary structure around translation initiation site, the number of rRNAs, and relative codon usage of ribosomal genes. Evolutionary simulations under purifying selection reproduce the observed patterns and diversity-length correlation and highlight that selective constraints on the 5'-region of a gene may be more extensive than previously believed. These results have implications for the estimation of effective population size, and relative mutation rates, and for genome scans of genes under positive selection based on "silent-site" diversity.

Coherent long-term body-size responses across all Northwest Atlantic herring populations to warming and environmental change despite contrasting harvest and ecological factors.

Body size is a key component of individual fitness and an important factor in the structure and functioning of populations and ecosystems. Disentangling the effects of environmental change, harvest and intra- and inter-specific trophic effects on body size remains challenging for populations in the wild. Herring in the Northwest Atlantic provide a strong basis for evaluating hypotheses related to these drivers given that they have experienced significant warming and harvest over the past century, while also having been exposed to a wide range of other selective constraints across their range. Using data on mean length-at-age 4 for the sixteen principal populations over a period of 53 cohorts (1962-2014), we fitted a series of empirical models for temporal and between-population variation in the response to changes in sea surface temperature. We find evidence for a unified cross-population response in the form of a parabolic function according to which populations in naturally warmer environments have responded more negatively to increasing temperature compared with those in colder locations. Temporal variation in residuals from this function was highly coherent among populations, further suggesting a common response to a large-scale environmental driver. The synchrony observed in this study system, despite strong differences in harvest and ecological histories among populations and over time, clearly indicates a dominant role of environmental change on size-at-age in wild populations, in contrast to commonly reported effects of fishing. This finding has important implications for the management of fisheries as it indicates that a key trait associated with population productivity may be under considerably less short-term management control than currently assumed. Our study, overall, illustrates the need for a comparative approach within species for inferences concerning the many possible effects on body size of natural and anthropogenic drivers in the wild.

The evolution of seminal fluid gene expression and postmating reproductive isolation in Drosophila.

Seminal fluid protein (Sfp) genes show, in general, a higher rate of sequence divergence than genes from other categories, which is often attributed to forms of postcopulatory sexual selection or sexual conflict. Recently, the relaxation of selective constraints has been proposed as an alternative explanation for the rapid sequence evolution of Sfps and other genes with sex-limited expression. The expression of Sfp genes is a likely target of selection, but the evolution of differences in their expression levels is less understood. Here, we explore both polymorphism and divergence in Sfp gene expression between Drosophila melanogaster and Drosophila simulans, how selection might have influenced their expression, and whether changes in expression might trigger the evolution of reproductive isolating barriers. In our analysis, Sfp genes showed higher divergence, but not higher polymorphism, in expression than the average male reproductive glands gene. Sfp genes with reproductive-tissue-specific expression were enriched for both directional and stabilizing selection, while relaxed selection was the predominant mode of evolution among Sfp genes with any other nonreproductive tissue-specific or nontissue-specific expression. The knockdown of single genes known to affect intraspecific sperm competition, and with patterns of expression divergence and polymorphism suggestive of directional selection, was not enough to break down postmating reproductive isolation barriers between species. Our results identify the expression of male-specific Sfp genes as an enriched target of selection and suggest a complex molecular relationship between postcopulatory sexual selection on a single gene's expression and its effect on the onset of speciation.

Pervasive mimicry in flight behavior among aposematic butterflies

Flight was a key innovation in the adaptive radiation of insects. However, it is a complex trait influenced by a large number of interacting biotic and abiotic factors, making it difficult to unravel the evolutionary drivers. We investigate flight patterns in neotropical heliconiine butterflies, well known for mimicry of their aposematic wing color patterns. We quantify the flight patterns (wing beat frequency and wing angles) of 351 individuals representing 29 heliconiine and 9 ithomiine species belonging to ten color pattern mimicry groupings. For wing beat frequency and up wing angles, we show that heliconiine species group by color pattern mimicry affiliation. Convergence of down wing angles to mimicry groupings is less pronounced, indicating that distinct components of flight are under different selection pressures and constraints. The flight characteristics of the Tiger mimicry group are particularly divergent due to convergence with distantly related ithomiine species. Predator-driven selection for mimicry also explained variation in flight among subspecies, indicating that this convergence can occur over relatively short evolutionary timescales. Our results suggest that the flight convergence is driven by aposematic signaling rather than shared habitat between comimics. We demonstrate that behavioral mimicry can occur between lineages that have separated over evolutionary timescales ranging from <0.5 to 70 My.

The Wide-Area Coverage Path Planning Strategy for Deep-Sea Mining Vehicle Cluster Based on Deep Reinforcement Learning

The path planning strategy of deep-sea mining vehicles is an important factor affecting the efficiency of deep-sea mining missions. However, the current traditional path planning algorithms suffer from hose entanglement problems and small coverage in the path planning of mining vehicle cluster. To improve the security and coverage of deep-sea mining systems, this paper proposes a cluster-coverage path planning strategy based on a traditional algorithm and Deep Q Network (DQN). First, we designed a deep-sea mining environment modeling and map decomposition method. Subsequently, the path planning strategy design is based on traditional algorithms and DQN. Considering the actual needs of deep-sea mining missions, the mining vehicle cluster path planning algorithm is optimized in several aspects, such as loss function, neural network structure, sample selection mechanism, constraints, and reward function. Finally, we conducted simulation experiments and analysis of the algorithm on the simulation platform. The experimental results show that the deep-sea mining cluster path planning strategy proposed in this paper performs better in terms of security, coverage, and coverage rate.

Genetic analysis of ocular tumour-associated genes using large genomic datasets: insights into selection constraints and variant representation in the population

BackgroundLarge genomic databases enable genetic evaluation in terms of haploinsufficiency and prevalence of missense and synonymous variants. We explored these parameters in ocular tumour-associated genes.MethodsA curated list of ocular tumour-associated...

Pandangan dan Tantangan Guru dalam Penerapan Metode Socrates untuk Meningkatkan Keterampilan Berpikir Kritis Siswa Sekolah Dasar

Critical thinking skill is a major concern in education throughout the world, with the aim of preparing students for the learning context of the 21st century. However, many teachers have difficulty adopting this new teaching method. This qualitative research aims to investigate teachers' views and the obstacles they face when implementing the Socratic method, an inquiry-based learning approach, in the classroom. Researchers used a purposive sampling method to select five Indonesian language teachers and conducted semi-structured interviews. Data analysis shows that most teachers see positively the application of the Socratic method in improving students' critical thinking skills. However, they face challenges, especially related to knowledge of teaching materials, questioning skills, student participation, topic selection, and time constraints. Based on these findings, this research recommends the need for additional support for teachers, especially in terms of understanding Indonesian language subject matter and effective teaching skills while implementing the Socratic method in the classroom.

Critical Challenges and Frontiers in Cartilage Tissue Engineering.

Cartilage tissue engineeringhas witnessed considerable advancements since its establishment in 1977, evolving from rudimentary surgical interventions to more nuanced biotechnological approaches. The field has navigated various challenges encompassing cellular considerations, scaffold material selection, environmental factors, and ethical and regulatory constraints. Innovations in cell source diversification, including chondrocytes, mesenchymal stem cells, and induced pluripotent stem cells, have been instrumental but not without their limitations, such as restricted cell proliferation and ethical dilemmas. Scaffold materials offer a unique dichotomy between natural substrates, which provide biocompatibility, and synthetic matrices, which grant mechanical integrity. However, translational hurdles in clinical applicability persist. Environmental factors, such as growth factors and thermal and mechanical forces, have been recognized as influential variables in cellular behavior and tissue maturation. Despite these strides, integration with host tissue remains a significant challenge, involving mechanical and immunological complexities. Looking forward, emerging technologies such as 3D and 4D printing, nanotechnology, and molecular therapies hold the promise of refining scaffold design and enhancing tissue regeneration. As the field continues to mature, a multidisciplinary approach encompassing thorough scientific investigation and collaboration is indispensable for overcoming existing challenges and realizing its full clinical potential.

A Novel Approach for Simultaneous Localization and Dense Mapping Based on Binocular Vision in Forest Ecological Environment

The three-dimensional reconstruction of forest ecological environment by low-altitude remote sensing photography from Unmanned Aerial Vehicles (UAVs) provides a powerful basis for the fine surveying of forest resources and forest management. A stereo vision system, D-SLAM, is proposed to realize simultaneous localization and dense mapping for UAVs in complex forest ecological environments. The system takes binocular images as input and 3D dense maps as target outputs, while the 3D sparse maps and the camera poses can be obtained. The tracking thread utilizes temporal clue to match sparse map points for zero-drift localization. The relative motion amount and data association between frames are used as constraints for new keyframes selection, and the binocular image spatial clue compensation strategy is proposed to increase the robustness of the algorithm tracking. The dense mapping thread uses Linear Attention Network (LANet) to predict reliable disparity maps in ill-posed regions, which are transformed to depth maps for constructing dense point cloud maps. Evaluations of three datasets, EuRoC, KITTI and Forest, show that the proposed system can run at 30 ordinary frames and 3 keyframes per second with Forest, with a high localization accuracy of several centimeters for Root Mean Squared Absolute Trajectory Error (RMS ATE) on EuRoC and a Relative Root Mean Squared Error (RMSE) with two average values of 0.64 and 0.2 for trel and Rrel with KITTI, outperforming most mainstream models in terms of tracking accuracy and robustness. Moreover, the advantage of dense mapping compensates for the shortcomings of sparse mapping in most Smultaneous Localization and Mapping (SLAM) systems and the proposed system meets the requirements of real-time localization and dense mapping in the complex ecological environment of forests.

A three-dimensional lead iodide perovskite analog featuring hydrogen-bonded dual monovalent cations.

Three-dimensional (3D) halide perovskites have attracted considerable research interest, yet the selection of A-site cations is restricted by the Goldschmidt tolerance factor. To accommodate cations beyond this acceptable range, novel 3D perovskite analog structures with edge- and face-sharing motifs have been developed. Until now, these structures have been limited to divalent cations due to significant electrostatic repulsion when incorporating two monovalent cations. Herein, we employ a supramolecular synthon mechanism to address the issue and an effective hydrogen-bonding pattern is achieved in a novel 3D lead iodide hybrid perovskite, (ammonium)(morpholinium)Pb2I6 (1). The inorganic framework of 1 consists of two edge-shared [PbI6] octahedra connected via corner-sharing, thus forming a continuous 3D network. Structural analysis indicates that the spatial separation of N atoms and the existence of N-H⋯O hydrogen bonds effectively eliminate electrostatic repulsion. This work has demonstrated the potential to mitigate constraints of cation selection on 3D frameworks and could spur the development of novel 3D perovskite materials and related fields.

Selective orthotic constraint of lower limb movement during walking reveals new insights into neuromuscular adaptation.

A concern expressed by the clinical community is that the constraint of motion provided by an ankle foot orthosis (AFO) may lead the user to become dependent on its stiffness, leading to learned non-use. To examine this, we hypothesized that using an experimental AFO-footwear combination (exAFO-FC) that constrains ankle motion during walking would result in reduced soleus and tibialis anterior EMG compared to free (exAFO-FC) and control (no AFO, footwear only) conditions. A total of 14 healthy subjects walked at their preferred speed (1.34 ± 0.09 m·s-1) for 15 min, in three conditions, namely, control, free, and stop. During the stance phase of walking in the stop condition, ipsilateral soleus integrated EMG (iEMG) declined linearly, culminating in a 32.1% reduction compared to the control condition in the final 5 min interval of the protocol. In contrast, ipsilateral tibialis anterior iEMG declined in a variable fashion culminating in an 11.2% reduction compared to control in the final 5 min interval. During the swing phase, the tibialis anterior iEMG increased by 6.6% compared to the control condition during the final 5 min interval. The contralateral soleus and tibialis anterior exhibited increased iEMG in the stop condition. An AFO-FC functions as a biomechanical motion control device that influences the neural control system and alters the output of muscles experiencing constraints of motion.

The neglected floral polymorphism: mirror-image flowers emerge from the shadow of heterostyly

Abstract Morphological asymmetries in plants and animals raise intriguing questions concerning their function and how they have evolved. One of the most conspicuous asymmetries in plants involves mirror-image flowers (enantiostyly) in which styles are deflected to either the left or right sides (L or R, respectively) of the flower. Species with this floral polymorphism often possess two types of stamens (heteranthery): centrally located feeding anthers and a pollinating anther orientated in the opposite direction to the style (reciprocal enantiostyly). However, some species lack heteranthery and sex-organ reciprocity can be partial or absent (non-reciprocal enantiostyly). Many enantiostylous species have nectarless flowers and are ‘buzz-pollinated’ by pollen-collecting bees. In contrast to other stylar polymorphisms such as heterostyly, enantiostyly exists as either monomorphic or dimorphic conditions, with L and R flowers on the same plant in the former, and genetically determined floral morphs with either L or R flowers in the latter. Enantiostyly has been reliably reported from 11 angiosperm families, but in only two is there convincing evidence that dimorphic enantiostyly occurs. Various hypotheses concerning developmental or selective constraints attempt to explain the rarity of this genetic polymorphism. Experimental studies on the function of enantiostyly indicate that the reciprocity of stigmas and pollinating anthers promotes pollinator-mediated cross-pollination and limits geitonogamous selfing. Insufficient or inferior pollinator service can result in the evolutionary breakdown of enantiostyly, including reduced stigma–anther separation, increased selfing, and dissolution of heteranthery. In this article we review recent advances and knowledge gaps in understanding these curious asymmetries and discuss why they have received less attention than heterostyly.

A Study on the Differential Patterns of Selective Constraints in Different Ecological Niches

A Study on the Differential Patterns of Selective Constraints in Different Ecological Niches

Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa)

The APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) gene family plays vital roles in plants, serving as a key regulator in responses to abiotic stresses. Despite its significance, a comprehensive understanding of this family in lettuce remains incomplete. In this study, we performed a genome-wide search for the AP2/ERF family in lettuce and identified a total of 224 members. The duplication patterns provided evidence that both tandem and segmental duplications contributed to the expansion of this family. Ka/Ks ratio analysis demonstrated that, following duplication events, the genes have been subjected to purifying selection pressure, leading to selective constraints on their protein sequence. This selective pressure provides a dosage benefit against stresses in plants. Additionally, a transcriptome analysis indicated that some duplicated genes gained novel functions, emphasizing the contribution of both dosage effect and functional divergence to the family functionalities. Furthermore, an orthologous relationship study showed that 60% of genes descended from a common ancestor of Rosid and Asterid lineages, 28% from the Asterid ancestor, and 12% evolved in the lettuce lineage, suggesting lineage-specific roles in adaptive evolution. These results provide valuable insights into the evolutionary mechanisms of the AP2/ERF gene family in lettuce, with implications for enhancing abiotic stress tolerance, ultimately contributing to the genetic improvement of lettuce crop production.

A genomic mutational constraint map using variation in 76,156 human genomes.

The depletion of disruptive variation caused by purifying natural selection (constraint) has been widely used to investigate protein-coding genes underlying human disorders1-4, but attempts to assess constraint for non-protein-coding regions have proved more difficult. Here we aggregate, process and release a dataset of 76,156 human genomes from the Genome Aggregation Database (gnomAD)-the largest public open-access human genome allele frequency reference dataset-and use it to build a genomic constraint map for the whole genome (genomic non-coding constraint of haploinsufficient variation (Gnocchi)). We present a refined mutational model that incorporates local sequence context and regional genomic features to detect depletions of variation. As expected, the average constraint for protein-coding sequences is stronger than thatfor non-coding regions. Within the non-coding genome, constrained regions are enriched for known regulatory elements and variants that are implicated in complex human diseases and traits, facilitating the triangulation of biological annotation, disease association and natural selection to non-coding DNA analysis. More constrained regulatory elements tend to regulate more constrained protein-coding genes, which in turn suggests that non-coding constraint can aid the identification of constrained genes that are as yet unrecognized by current gene constraint metrics. We demonstrate that this genome-wide constraint map improves the identification and interpretation of functional human genetic variation.

Mitochondrial phylogenomics of bumblebees, Bombus (Hymenoptera: Apidae): a tale of structural variation, shifts in selection constraints, and tree discordance

Abstract The mitochondrial DNA (mtDNA) of bumblebees (Bombus) has been widely used for phylogenetic studies, but its evolution is still underexplored. Here we report a comprehensive analysis of 60 bumblebee mitogenomes, including 40 newly assembled ones, to investigate bumblebee mtDNA structure, composition, and informativeness under a phylogenetic framework. Our mtDNA dataset supports the monophyly of Bombus and its subgenera, although we found a high degree of tree discordance in deeper nodes when using different inference methods or matrix composition. Concerning mitogenome structure, our results show that tRNA genes were often rearranged, with unique rearrangements indicating shared ancestry across bumblebee subgenera, illustrating their potential for subgeneric classification. Our results also challenge the notion that faster evolving mtDNA exhibits higher gene rearrangement rates. Finally, we explicitly assessed shifts in selection constraints of mtDNA genes in obligate social parasites of subgenus Psithyrus and found that their mtDNA evolved under relaxed selective constraints. Our findings show the utility of mtDNA in providing insights into bumblebee phylogenetics, evolution, and genome trait diversification. We also highlight the potential for comparative mitogenomics to uncover previously unknown aspects of bumblebee evolution, offering exciting opportunities for future research in this field.

Magnetic tile fault detection of high‐voltage electric machines: A multiview feature selection method via consistent soft label

AbstractImage‐based scheme has attracted wide attention in the fault detection of high‐voltage permanent magnet motors, but it often suffers from the shooting conditions. Multiview feature selection allows multisource information to be fused, which can improve the accuracy and robustness of image detection. Therefore, we propose multiview unsupervised consistency via soft‐label feature selection (MUCSFS). This method constructs consistent pseudo labels through soft labels from clustering affinity of each view sample and builds the model by integrating selection constraints into the graph model. This model filters the fault data set to obtain the feature subset, which is used for clustering. We verify the method's effectiveness by simulating multiview data. The fault clustering experiment on the high‐voltage motors' magnetic tile fault data set confirm that our method can effectively cluster the fault categories.

Mitogenome sequences of domestic cats demonstrate lineage expansions and dynamic mutation processes in a mitochondrial minisatellite

BackgroundAs a population genetic tool, mitochondrial DNA is commonly divided into the ~ 1-kb control region (CR), in which single nucleotide variant (SNV) diversity is relatively high, and the coding region, in which selective constraint is greater and diversity lower, but which provides an informative phylogeny. In some species, the CR contains variable tandemly repeated sequences that are understudied due to heteroplasmy. Domestic cats (Felis catus) have a recent origin and therefore traditional CR-based analysis of populations yields only a small number of haplotypes.ResultsTo increase resolution we used Nanopore sequencing to analyse 119 cat mitogenomes via a long-amplicon approach. This greatly improves discrimination (from 15 to 87 distinct haplotypes in our dataset) and defines a phylogeny showing similar starlike topologies within all major clades (haplogroups), likely reflecting post-domestication expansion. We sequenced RS2, a CR tandem array of 80-bp repeat units, placing RS2 array structures within the phylogeny and increasing overall haplotype diversity. Repeat number varies between 3 and 12 (median: 4) with over 30 different repeat unit types differing largely by SNVs. Five SNVs show evidence of independent recurrence within the phylogeny, and seven are involved in at least 11 instances of rapid spread along repeat arrays within haplogroups.ConclusionsIn defining mitogenome variation our study provides key information for the forensic genetic analysis of cat hair evidence, and for the first time a phylogenetically informed picture of tandem repeat variation that reveals remarkably dynamic mutation processes at work in the mitochondrion.