Context Of Evolution Research Articles

DDMut-PPI: predicting effects of mutations on protein-protein interactions using graph-based deep learning.

Protein-protein interactions (PPIs) play a vital role in cellular functions and are essential for therapeutic development and understanding diseases. However, current predictive tools often struggle to balance efficiency and precision in predicting the effects of mutations on these complex interactions. To address this, we present DDMut-PPI, a deep learning model that efficiently and accurately predicts changes in PPI binding free energy upon single and multiple point mutations. Building on the robust Siamese network architecture with graph-based signatures from our prior work, DDMut, the DDMut-PPI model was enhanced with a graph convolutional network operated on the protein interaction interface. We used residue-specific embeddings from ProtT5 protein language model as node features, and a variety of molecular interactions as edge features. By integrating evolutionary context with spatial information, this framework enables DDMut-PPI to achieve a robust Pearson correlation of up to 0.75 (root mean squared error: 1.33 kcal/mol) in our evaluations, outperforming most existing methods. Importantly, the model demonstrated consistent performance across mutations that increase or decrease binding affinity. DDMut-PPI offers a significant advancement in the field and will serve as a valuable tool for researchers probing the complexities of protein interactions. DDMut-PPI is freely available as a web server and an application programming interface at https://biosig.lab.uq.edu.au/ddmut_ppi.

The Free-Running Circasemilunar Period Is Determined by Counting Circadian Clock Cycles in the Marine Midge Clunio Marinus.

Semilunar rhythms are found in numerous marine organisms, but the molecular mechanism and functional principles of endogenous circasemilunar clocks remain elusive. Here, we explore the connection between the free-running circasemilunar clock and the circadian clock in the marine midge Clunio marinus with three different chronobiological assays. First, we found that the free-running circasemilunar period of the adult emergence rhythm in C. marinus changes linearly with diel T-cycle length, supporting a day-counting mechanism. Second, under LD 6:6, periods of circasemilunar and circadian emergence were comparable to those under LD 12:12, indicating that the circasemilunar counter in C. marinus relies on endogenous circadian oscillations rather than external T-cycles. Finally, when desynchronizing the circadian clock with constant light, the free-running circasemilunar emergence rhythm disappeared as well, suggesting that it requires a synchronized circadian clock. These results oppose the long-held view that C. marinus' free-running circasemilunar clock operates independently of the circadian clock. In a broader evolutionary context, our results strengthen the idea that the circasemilunar clocks of dipterous insects are based on different functional principles compared to the circasemilunar or circalunar clocks of marine annelids and algae. These divergent clock principles may indicate multiple evolutionary origins of circasemilunar and circalunar clocks.

Osmophore Structure and Labellum Micromorphology in Ophrys speculum (Orchidaceae): New Interpretations of Floral Features and Implications for a Specific Sexually Deceptive Pollination Interaction

Pollination by sexual deception specifically attracts male insects, through the floral scent and particular morphological features of the flower that serve as visual and tactile stimuli. The unique bond between the Ophrys speculum orchid and the male Dasyscolia ciliata wasp primarily stems from a few distinctive semiochemicals that mimic the female wasp’s sex pheromone, although the floral scent comprises a variety of compounds. An osmophore producing highly volatile compounds has been documented in four close relatives of O. speculum and is now being also investigated in this species. Given the existing debates regarding the structure of the labellum and stigmatic cavity in O. speculum, this study details their micromorphology. Additionally, comparisons of O. speculum flowers and female D. ciliata wasps under stereomicroscopy and scanning electron microscopy are conducted to seek new evidence of visual and tactile mimicry. The findings confirm that (i) an osmophore is present at the apical margin of the labellum in O. speculum flowers; (ii) the labellum features a distinct basal field homologous to those found in other Ophrys species; and (iii) the basal labellum region closely mimics the female wasp’s thorax and wings. The implications of these novel floral features are discussed within an evolutionary context.

Echinoagave nievesiorum (Agavaceae, Asparagales): A new species from the Sierra Madre Occidental, Jalisco, Mexico

Echinoagave nievesiorum (Agavaceae, Asparagales), a new species endemic to the Sierra Wixárika (Huichola), part of the Sierra Madre Occidental, Jalisco, Mexico, is described. This species shares morphological characteristics with Echinoagave rzedowskiana but it differs from the latter by having narrower and striate leaves; leaf sheaths shorter, triangular and wider at the base; narrower ovary width; shorter tube length; tepal lobes at anthesis converging and tightening the filaments; larger filament length to flower length ratio; fruiting spikes thicker and denser with the peduncle covered by the capsules and the bracts usually deciduous; capsules broadly ellipsoid with dorsally blackish valves. A distribution map with biogeographic provinces is provided to place the species in an ecological and evolutionary context.

Organ-specific proteomes of Selaginella convoluta provide insights into its desiccation tolerance mechanisms

Selaginella convoluta is a desiccation-tolerant lycophyte capable of enduring water deprivation by arresting its metabolism when dry and reactivating it upon rehydration. Mechanisms to mitigate the harmful effects of desiccation have been investigated in an evolutionary context; however, plants have additional species-specific strategies refined by environmental conditions. Previous metabolome analysis pointed out S. convoluta as a source of chemodiversity. Shotgun proteomic analysis, conducted using an Orbitrap Elite and analyzed with PatternLab for proteomics, compared shoots and roots under two hydration conditions. Our approach identified 1,176 proteins. Proteins associated with photosynthesis, stress, and defense (primarily Reactive Oxygen Species scavengers and chaperones) were enriched in the shoots’ proteome in both hydrated and desiccated states. Post-hydration, roots exhibited exclusive proteins involved in defense, metabolism, and protein trafficking (notably 14-3-3-like proteins, and a putative Bet_v_1 domain-containing protein, which was 15.6 times more abundant in dehydrated roots). These results demonstrate that S. convoluta, when harvested in its dried state from its natural habitat, serves as a valuable source of molecular data, reflecting a realistic multifactorial environmental scenario.

Genome Evolution and Introgression in the New Zealand mud Snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa.

We have sequenced, assembled, and analyzed the nuclear and mitochondrial genomes and transcriptomes of Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa, two prosobranch snail species native to New Zealand that together span the continuum from estuary to freshwater. These two species are the closest known relatives of the freshwater species Potamopyrgus antipodarum-a model for studying the evolution of sex, host-parasite coevolution, and biological invasiveness-and thus provide key evolutionary context for understanding its unusual biology. The P. estuarinus and P. kaitunuparaoa genomes are very similar in size and overall gene content. Comparative analyses of genome content indicate that these two species harbor a near-identical set of genes involved in meiosis and sperm functions, including seven genes with meiosis-specific functions. These results are consistent with obligate sexual reproduction in these two species and provide a framework for future analyses of P. antipodarum-a species comprising both obligately sexual and obligately asexual lineages, each separately derived from a sexual ancestor. Genome-wide multigene phylogenetic analyses indicate that P. kaitunuparaoa is likely the closest relative to P. antipodarum. We nevertheless show that there has been considerable introgression between P. estuarinus and P. kaitunuparaoa. That introgression does not extend to the mitochondrial genome, which appears to serve as a barrier to hybridization between P. estuarinus and P. kaitunuparaoa. Nuclear-encoded genes whose products function in joint mitochondrial-nuclear enzyme complexes exhibit similar patterns of nonintrogression, indicating that incompatibilities between the mitochondrial and the nuclear genome may have prevented more extensive gene flow between these two species.

Single-cell RNA-seq of Drosophila miranda testis reveals the evolution and trajectory of germline sex chromosome regulation.

Although sex chromosomes have evolved from autosomes, they often have unusual regulatory regimes that are sex- and cell-type-specific such as dosage compensation (DC) and meiotic sex chromosome inactivation (MSCI). The molecular mechanisms and evolutionary forces driving these unique transcriptional programs are critical for genome evolution but have been, in the case of MSCI in Drosophila, subject to continuous debate. Here, we take advantage of the younger sex chromosomes in D. miranda (XR and the neo-X) to infer how former autosomes acquire sex-chromosome-specific regulatory programs using single-cell and bulk RNA sequencing and ribosome profiling, in a comparative evolutionary context. We show that contrary to mammals and worms, the X down-regulation through germline progression is most consistent with the shutdown of DC instead of MSCI, resulting in half gene dosage at the end of meiosis for all 3 X's. Moreover, lowly expressed germline and meiotic genes on the neo-X are ancestrally lowly expressed, instead of acquired suppression after sex linkage. For the young neo-X, DC is incomplete across all tissue and cell types and this dosage imbalance is rescued by contributions from Y-linked gametologs which produce transcripts that are translated to compensate both gene and protein dosage. We find an excess of previously autosomal testis genes becoming Y-specific, showing that the neo-Y and its masculinization likely resolve sexual antagonism. Multicopy neo-sex genes are predominantly expressed during meiotic stages of spermatogenesis, consistent with their amplification being driven to interfere with mendelian segregation. Altogether, this study reveals germline regulation of evolving sex chromosomes and elucidates the consequences these unique regulatory mechanisms have on the evolution of sex chromosome architecture.

Between social cognition and material engagement: the cooperative body hypothesis

AbstractIn recent years, social cognition approaches to human evolution and Material Engagement Theory have offered new theoretical resources to advance our understanding of the prehistoric hominin mind. To date, however, these two approaches have developed largely in isolation from one another. I argue that there is a gap between social- and material-centred approaches, and that this is precisely the sociomateriality of the appearance of ancestral hominin bodies, which evolved under selective pressure to develop increasingly complex, cooperative sociality. To get this sociomaterial body in focus, I develop an esthesiological framework, appropriated from Merleau-Ponty (2003), for interpreting the expressive body in an evolutionary and comparative context. The guiding hypothesis of esthesiology is that before being rationality (social or material), “humanity is another corporeity” (Merleau-Ponty, 2003, p. 208). Esthesiology studies the appearance of the body and its sense organs as an intertwining locus of a sensing power (the ability to see, to touch, etc.) and a sensible character (the visible, touchable body). It is this dual-aspect character of the body that facilitates the most basic affective and sensorimotor modes of sociality. Examining these features from a comparative perspective, we find that the human body is distinctively suited to prosocial communication and cooperation: a more cooperative eye, an exposed and communicative skin. I thus propose a cooperative body hypothesis, by analogy with the cooperative eye hypothesis (Tomasello et al., 2007). Esthesiology provides a framework for integrating and interpreting a wide range of otherwise disconnected facts concerning human and nonhuman animal bodies, forms of life, cognition, and evolution, thereby bridging the gap between social cognition and material engagement perspectives. In doing so, however, it not only solves problems and proposes new directions of investigation, but also demands theoretical revisions from each.

Floral scent of eastern skunk cabbage (Symplocarpus foetidus: Araceae)

Symplocarpus foetidus (L.) Salisb. (eastern skunk cabbage) occurs across a broad geographic range of northeastern North America, blooming in winter between December and March. The inflorescences are well-known for their thermogenic and thermoregulatory metabolic capabilities. The perceptual qualities of their fetid floral aroma have been described widely in the literature, but to date the floral volatile composition remained largely unknown. Here we present a detailed study of the floral scent produced by S. foetidus collected from intact female- and male-stage inflorescences and from dissected floral parts. Our results show a large range of biosynthetically diverse volatiles including nitrogen- and sulfur-containing compounds, monoterpenes, benzenoids, and aliphatic esters and alcohols. We document high inter-individual variation with some organ-specific volatile trends but no clear strong variation based on sexual stage. Multivariate data analysis revealed two distinct chemotypes from our study populations that are not defined by sexual stage or population origin. The chemotype differences may explain the bimodal perceptual descriptions in earlier work which vary between highly unpleasant/fetid and pleasant/apple-like. We discuss the results in ecological contexts including potential for floral mimicry, taking into account existing pollination studies for the species. We also discuss the results in evolutionary contexts, comparing our scent data to published scent data from the close sister species Symplocarpus renifolius. Future work should more closely examine the chemotype occurrence and frequency within these and other populations, and the impact these chemotypes may have on pollinator attraction and reproductive success.

The multidimensional spectrum of eco-evolutionary relationships between sharks and remoras.

Remoras are a highly specialised group of fishes known to associate with a range of marine megafauna, including elasmobranchs, cetaceans and marine reptiles. Remoras appear to benefit from these interspecific interactions through consumption of host dermal parasites or reduced cost of transport. Shark-remora associations are widely documented, yet our understanding of the costs and benefits involved in these interactions is poor. Studies frequently make claims about mutualistic, commensalistic or parasitic relationships without providing the necessary quantitative information necessary to make these claims. Here I explain why this approach is problematic, and proceed to examine shark-remora interactions in a rigorous eco-evolutionary framework. These interactions cannot be properly classified without considering net evolutionary fitness and context dependence. In reality, shark-remora interactions are best defined by a multidimensional spectrum of fitness consequences, with net fitness outcomes shifting between mutualism and parasitism (and vice versa) through space and time.

Species-aware DNA language models capture regulatory elements and their evolution

BackgroundThe rise of large-scale multi-species genome sequencing projects promises to shed new light on how genomes encode gene regulatory instructions. To this end, new algorithms are needed that can leverage conservation to capture regulatory elements while accounting for their evolution.ResultsHere, we introduce species-aware DNA language models, which we trained on more than 800 species spanning over 500 million years of evolution. Investigating their ability to predict masked nucleotides from context, we show that DNA language models distinguish transcription factor and RNA-binding protein motifs from background non-coding sequence. Owing to their flexibility, DNA language models capture conserved regulatory elements over much further evolutionary distances than sequence alignment would allow. Remarkably, DNA language models reconstruct motif instances bound in vivo better than unbound ones and account for the evolution of motif sequences and their positional constraints, showing that these models capture functional high-order sequence and evolutionary context. We further show that species-aware training yields improved sequence representations for endogenous and MPRA-based gene expression prediction, as well as motif discovery.ConclusionsCollectively, these results demonstrate that species-aware DNA language models are a powerful, flexible, and scalable tool to integrate information from large compendia of highly diverged genomes.

Probing the interstellar medium of the quasar BRI 0952−0115

Context. The extent of the effect of active galactic nuclei (AGN) on their host galaxies at high-redshift is not apparent. The processes governing the co-eval evolution of the stellar mass and the mass of the central supermassive black hole, along with the effects of the supermassive black hole on the host galaxy, remain unclear. Studying this effect in the distant universe is a difficult process as the mechanisms of tracing AGN activity can often be inaccurately associated with intense star formation and vice versa. Aims. Our aim is to better understand the processes governing the interstellar medium (ISM) of the quasar BRI 0952−0952 at z = 4.432, specifically with regard to the individual heating processes at work and to place the quasar in an evolutionary context. Methods. We analyzed ALMA archival bands 3, 4, and 6 data and combined the results with high-resolution band-7 ALMA observations of the quasar. We detected [C I](2–1), [C II](2P3/2 − 2P1/2), CO(5–4), CO(7–6), CO(12–11), OH 2Π1/2(3/2 − 1/2), and H2O(211 − 202), and we report a tentative detection of OH+. We updated the lensing model and we used the radiative transfer code MOLPOP-CEP to produce line emission models which we compared with our observations. Results. We used the [C I] line emission to estimate the total molecular gas mass in the quasar. We present results from the radiative transfer code MOLPOP-CEP constraining the properties of the CO emission and suggest different possible scenarios for heating mechanisms within the quasar. We extended our results from MOLPOP-CEP to the additional line species detected in the quasar to place stronger constraints on the ISM properties. Conclusions. Modeling from the CO SLED suggests that there are extreme heating mechanisms operating within the quasar in the form of star formation or AGN activity; however, with the current data, it remains unclear which of the two is the preferred mechanism as both models reasonably reproduce the observed CO line fluxes. The updated lensing model suggests a velocity gradient across the [C II] line, suggestive of ongoing kinematical processes within the quasar. We find that the H2O emission in BRI 0952 is likely correlated with star-forming regions of the ISM. We used the molecular gas mass from [C I] to calculate a depletion time for the quasar. We conclude that BRI 0952−0952 is a quasar with a significant AGN contribution while also showing signs of extreme starburst activity, indicating that the quasar could be in a transitional phase between a starburst-dominated stage and an AGN-dominated stage.

Towards the Exploration and Evolution of Insulin-like Venoms in Actiniaria (Sea anemones).

Recent studies have elucidated the diversity of genes encoding venom in Sea anemones. However, most of those genes are yet to be explored in an evolutionary context. Insulin is a common peptide across metazoans and has been coopted into a predatory venom in many venomous lineages. In this study, we focus on the diversity of insulin-derived venoms in Sea anemones and on elucidating their evolutionary history. We sourced data for 34 species of Sea anemones and found sequences belonging to two venom families which have Insulin PFAM annotations. Our findings show that both families have undergone duplication events. Members of each of the independently evolving clades have consistent predicted protein structures and distinct dN/dS values. Our work also shows that sequences allied with VP302 are part of a multidomain venom contig and have experienced a secondary gain into the venom system of cuticulate Sea anemones.

Insights into adaptive behavioural plasticity from the guppy model system.

Behavioural plasticity allows organisms to respond to environmental challenges on short time scales. But what are the ecological and evolutionary processes that underlie behavioural plasticity? The answer to this question is complex and requires experimental dissection of the physiological, neural and molecular mechanisms contributing to behavioural plasticity as well as an understanding of the ecological and evolutionary contexts under which behavioural plasticity is adaptive. Here, we discuss key insights that research with Trinidadian guppies has provided on the underpinnings of adaptive behavioural plasticity. First, we present evidence that guppies exhibit contextual, developmental and transgenerational behavioural plasticity. Next, we review work on behavioural plasticity in guppies spanning three ecological contexts (predation, parasitism and turbidity) and three underlying mechanisms (endocrinological, neurobiological and genetic). Finally, we provide three outstanding questions that could leverage guppies further as a study system and give suggestions for how this research could be done. Research on behavioural plasticity in guppies has provided, and will continue to provide, a valuable opportunity to improve understanding of the ecological and evolutionary causes and consequences of behavioural plasticity.

The past, present, and future of crowdsourcing and innovation: A bibliometric analysis and future research agenda

This research article addresses the current status and emerging trends in the literature at the intersection of crowdsourcing and innovation. While separate reviews exist for crowdsourcing and innovation individually, a comprehensive literature review specific to their intersection is lacking. Therefore, this study conducts a bibliometric meta-analysis of the extensive body of literature in the field of innovation and crowdsourcing, aiming to fill this research gap. The analysis encompasses all articles in Elsevier's Scopus database that incorporate relevant terms in their titles, abstracts, or keywords, resulting in a sample of 180 articles. VosViewer and Bibliometrix package in R are employed for the analysis. The analysis reveals three key research clusters, including the role of crowdsourcing in fostering organizational innovation, crowdsourcing-based social capital formation and its impact on organizational value creation, and the role of crowdsourcing platforms in facilitating engagement between the crowd and the organization. Adopting a holistic perspective, this research contributes new insights into the interconnections between crowdsourcing and innovation research fields. Additionally, the analysis provides clarity on research content, evolutionary context, and reveals emerging research trends in this domain.

Dynamics of Learning in Neural Networks: A Gaussian Profile Approach

This article explores the impact of learning on the connection strengths between nodes in a recurrent associative attractor network, utilizing a Gaussian firing profile to simulate the adaptive nature of neural connections. Initially, the network exhibits uniform connec- tion strengths, symbolizing a naive state without prior learning. Through a computational model, we demonstrate how learning processes can dynamically adjust these connec- tions, emphasizing the strengthening of associations between spatially or functionally proximate nodes. The model employs a Gaussian function to adjust connection strengths based on node proximity, effectively mimicking biological learning mechanisms. Post- learning, nodes are reordered based on their connection strengths to reveal the emergent network structure, offering insights into how neural networks can evolve to represent and recall associative memories. This study not only sheds light on the fundamental aspects of neural plasticity but also provides a computational framework for simulating learning and memory formation in artificial neural networks.

The Molecular Characterization of the Cyprinid herpesvirus 3 (CyHV-3) ORF24 Protein and its effect on the expression of immune genes (in vitro)

Cyprinid herpesvirus 3 (CyHV-3), known as koi herpesvirus (KHV), is highly contagious and lethal. In this study, we aimed to characterize the ORF24-encoding protein of CyHV-3, investigate its sub-cellular localization, and determine its impact on the expression of immune factors through in vitro experiments. The results showed that the CyHV-3 ORF24 protein comprises 579 amino acids. Interestingly, multiple comparisons with homologous proteins from three carp herpesvirus origins showed no significant similarity. The fluorescence localization experiment showed that the green fluorescence signal, representing the protein pEGFP-ORF24, was primarily diffused in the cytoplasm. Notably, the overexpression of ORF24 effectively suppressed the expression of immune factors in both CCO (Channel catfish ovary) and FHM (Fathead minnow muscle cell line) cells. Bioinformatic analysis indicated that the CyHV-3 ORF24 gene exhibited significant differences from the corresponding genes in the other two carp herpesviruses. This suggests its unique functional role in the evolutionary context. Moreover, our findings demonstrated that overexpression of CyHV-3 ORF24 can effectively inhibit the expression of immune factors, underscoring its crucial role as a viral immune escape factor. These results provide further insights into the immune function of the CyHV-3 ORF24 protein and offer a theoretical foundation for developing new vaccines against CyHV-3 virus infections.

Prediction of protein-ATP binding residues using multi-view feature learning via contextual-based co-attention network

Accurately predicting protein-ATP binding residues is critical for protein function annotation and drug discovery. Computational methods dedicated to the prediction of binding residues based on protein sequence information have exhibited notable advancements in predictive accuracy. Nevertheless, these methods continue to grapple with several formidable challenges, including limited means of extracting more discriminative features and inadequate algorithms for integrating protein and residue information. To address the problems, we propose ATP-Deep, a novel protein-ATP binding residues predictor. ATP-Deep harnesses the capabilities of unsupervised pre-trained language models and incorporates domain-specific evolutionary context information from homologous sequences. It further refines the embedding at the residue level through integration with corresponding protein-level information and employs a contextual-based co-attention mechanism to adeptly fuse multiple sources of features. The performance evaluation results on the benchmark datasets reveal that ATP-Deep achieves an AUC of 0.954 and 0.951, respectively, surpassing the performance of the state-of-the-art model. These findings underscore the effectiveness of assimilating protein-level information and deploying a contextual-based co-attention mechanism grounded in context to bolster the prediction performance of protein-ATP binding residues.

Lake water chemistry and local adaptation shape NaCl toxicity in Daphnia ambigua.

The increasing application of road deicing agents (e.g., NaCl) has caused widespread salinization of freshwater environments. Chronic exposure to toxic NaCl levels can impact freshwater biota at genome to ecosystem scales, yet the degree of harm caused by road salt pollution is likely to vary among habitats and populations. The background ion chemistry of freshwater environments may strongly impact NaCl toxicity, with greater harm occurring in ion-poor, soft water conditions. In addition, populations exposed to salinization may evolve increased NaCl tolerance. Notably, if organisms are adapted to the water chemistry of their natal environment, toxicity responses may also vary among populations in a given test medium. We examined the potential for this evolutionary and environmental context to interact in shaping NaCl toxicity with a pair of laboratory reciprocal transplant toxicity experiments, using natural populations of the water flea Daphnia ambigua collected from three lakes that vary in ion availability and composition. We observed a strong effect of the lake water environment on NaCl toxicity in both trials. NaCl caused a much greater decline in reproduction and r in lake water from a low-ion/calcium-poor environment (20 μS/cm specific conductance; 1.7 mg/L Ca2+) compared with water from both a Ca2+-rich lake (55 μS/cm; 7.2 mg/L Ca2+) and an ion-rich coastal lake (420 μS/cm; 3.4 mg/L Ca2+). Daphnia from this coastal lake were most robust to the effects of NaCl on reproduction and r. A significant interaction between the population and lake water environment shaped survival in both trials, suggesting that local adaptation to the test waters used may have contributed to toxicity responses. Our findings that the lake water environment, adaptation to that environment, and adaptation to a contaminant of interest may shape toxicity demonstrate the importance of considering environmental and biological complexity in mitigating pollution impacts.

Uniformity and diversity of language in an evolutionary context

The paper explores a view on language that is in line with the Strong Minimalist Thesis and that derives an evolutionary scenario predicting language variation in time and space. A stable and uniform UG making available recursive Merge shaped by laws of nature such as simplicity and efficiency has been integrated by a sudden rewiring of the brain into an existing biological system which is comparable to the concept of the faculty of language in the broad sense. The basic oppositions such as symmetry and asymmetry, internal language/thought and externalization, uniformity and diversity, universality and particular languages are derived as an automatic consequence of the architecture of the grammar as it evolved in the human species in concert with general principles of nature. A stable and simple system can be reconciled with a dynamic complex one.