Evolutionary Function Research Articles

Improved Barnacle Mating Optimizer-Based Least Square Support Vector Machine to Predict COVID-19 Confirmed Cases with Total Vaccination

Abstract Every country must have an accurate and efficient forecasting model to avoid and manage the epidemic. This paper suggests an upgrade to one of the evolutionary algorithms inspired by nature, the Barnacle Mating Optimizer (BMO). First, the exploration phase of the original BMO is enhanced by enforcing and replacing the sperm cast equation through Levy flight. Then, the Least Square Support Vector Machine (LSSVM) is partnered with the improved BMO (IBMO). This hybrid approach, IBMO-LSSVM, has been deployed effectively for time-series forecasting to enhance the RBF kernel-based LSSVM model since vaccination started against COVID-19 in Malaysia. In comparison to other well-known algorithms, our outcomes are superior. In addition, the IBMO is assessed on 19 conventional benchmarks and the IEEE Congress of Evolutionary Computation Benchmark Test Functions (CECC06, 2019 Competition). In most cases, IBMO outputs are better than comparison algorithms. However, in other circumstances, the outcomes are comparable.

Genome-Wide Characterization of the Mitogen-Activated Protein Kinase Gene Family and Their Expression Patterns in Response to Drought and Colletotrichum Gloeosporioides in Walnut (Juglans regia).

Mitogen-activated protein kinases (MAPKs) are a family of Ser/Thr (serine/threonine) protein kinases that play very important roles in plant responses to biotic and abiotic stressors. However, the MAPK gene family in the important crop walnut (Juglans regia L.) has been less well studied compared with other species. We discovered 25 JrMAPK members in the Juglans genome in this study. The JrMAPK gene family was separated into four subfamilies based on phylogenetic analysis, and members of the same subgroup had similar motifs and exons/introns. A variety of cis-acting elements, mainly related to the light response, growth and development, stress response, and hormone responses, were detected in the JrMAPK gene promoters. Collinearity analysis showed that purification selection was the main driving force in JrMAPK gene evolution, and segmental and tandem duplications played key roles in the expansion of the JrMAPK gene family. The RNA-Seq (RNA Sequencing) results indicated that many of the JrMAPK genes were expressed in response to different levels of Colletotrichum gloeosporioides infection. JrMAPK1, JrMAPK3, JrMAPK4, JrMAPK5, JrMAPK6, JrMAPK7, JrMAPK9, JrMAPK11, JrMAPK12, JrMAPK13, JrMAPK17, JrMAPK19, JrMAPK20, and JrMAPK21 were upregulated at the transcriptional level in response to the drought stress treatment. The results of this study will help in further investigations of the evolutionary history and biological functions of the MAPK gene family in walnut.

Extending and refining the fearful ape hypothesis.

The fearful ape hypothesis (FAH) presents an evolutionary-developmental framework stipulating that in the context of cooperative caregiving, unique to human great ape group life, heightened fearfulness was adaptive. This is because from early in human ontogeny fearfulness expressed and perceived enhanced care-based responding and cooperation with mothers and others. This response extends and refines the FAH by incorporating the commentaries' suggestions and additional lines of empirical work, providing a more comprehensive and nuanced version of the FAH. Specifically, it encourages and hopes to inspire cross-species and cross-cultural, longitudinal work elucidating evolutionary and developmental functions of fear in context. Beyond fear, it can be seen as a call for an evolutionary-developmental approach to affective science.

Molecular evolution and structural analyses of proteins involved in metabolic pathways of volatile organic compounds in Petunia hybrida (Solanaceae).

The association between plants and their pollinators is essential for increasing the diversity in angiosperms. Morphological and physiological traits, mainly floral scent, can influence the pollination dynamics and select pollinators for each plant species. In this work, we studied two proteins involved in producing volatile organic compounds in plants, conyferyl alcohol acyltransferase (CFAT) and benzoyl-CoA:benzyl alcohol/phenyl ethanol benzoyl transferase (BPBT) genes. We aimed to understand these proteins with respect to evolutionary and structural aspects and functions in Solanaceae using phylogenetic methods and comparative molecular modeling. We used Bayesian inference to describe the proteins' evolutionary history using Petunia x hybrida as a query to search for homologs in the Solanaceae family. Theoretical 3D models were obtained for both proteins using Panicum virgatum as a template. The phylogenetic tree included several different enzymes with diverse biological roles in Solanaceae, displaying the transferase domain. We identified only one sequence of CFAT in the databases, which belongs to Petunia x hybrida, and found several BPBT sequences from the genera Nicotiana, Solanum, and Capsicum. The 3D structures of CFAT and BPBT have two different domains, and we have identified the amino acid residues essential for the enzymatic activity and interaction with substrates.

Optimizing boiler combustion parameters based on evolution teaching-learning-based optimization algorithm for reducing NOx emission concentration.

How to reduce a boiler's NOx emission concentration is an urgent problem for thermal power plants. Therefore, in this paper, we combine an evolution teaching-learning-based optimization algorithm with extreme learning machine to optimize a boiler's combustion parameters for reducing NOx emission concentration. Evolution teaching-learning-based optimization algorithm (ETLBO) is a variant of conventional teaching-learning-based optimization algorithm, which uses a chaotic mapping function to initialize individuals' positions and employs the idea of genetic evolution into the learner phase. To verify the effectiveness of ETLBO, 20 IEEE congress on Evolutionary Computation benchmark test functions are applied to test its convergence speed and convergence accuracy. Experimental results reveal that ETLBO shows the best convergence accuracy on most functions compared to other state-of-the-art optimization algorithms. In addition, the ETLBO is used to reduce boilers' NOx emissions by optimizing combustion parameters, such as coal supply amount and the air valve. Result shows that ETLBO is well-suited to solve the boiler combustion optimization problem.

Narratives of crisis: From affective structures to adaptive functions.

This commentary focuses on affective structures and the main adaptive functions of shared narratives to fill the gaps of the Conviction Narrative Theory. The transmission of narratives among individuals in highly uncertain situations is irrevocably tainted by affects and anchored in collective memory. Narratives have important evolutionary functions for human beings under threat and act as the social glue that creates and strengthens social bonds among individuals.

Аттракторы и циклические состояния в конечных динамических системах ориентаций полных графов

Graph models occupy an important place in information security tasks. Finite dynamic systems of complete graphs orientations are considered. States of a dynamic system (ΓKn , α), n ⩾ 1, are all possible orientations of a given complete graph Kn, and the evolutionary function transforms the complete graph orientation by reversing all arcs that go into sinks, and there are no other differences between the given and the next digraphs. The cyclic (belonging to attractors) states of the system are characterized, namely, state belongs to an attractor, if and only if it hasn’t a sink or its indegrees vector is (n − 1, n − 2, . . . , 0). A table is given with the number of cyclic and non-cyclic states in the systems of complete graphs orientations with the number of vertices from 1 to 8 inclusive. The formation of attractors of the system, their type and length are described, namely, there are attractors of length 1, each of which is formed by state without sink, and attractors of length n, each of which is formed by such states −→G ∈ ΓKn , in which indegrees vector is (n − 1, n − 2, . . . , 0), wherein each such attractor represents a circuit, in which each next state is obtained from the previous one as follows: if −→G has vector of indegrees of its vertices in the order of their enumeration (d −(v1), d−(v2), . . . , d−(vn)), then α( −→G) ∈ ΓKn has vector of indegrees of its vertices in the order of their enumeration (d −(v1) + 1, d−(v2) + 1, . . . , d−(vn) + 1), where the addition is calculated modulo n, and only these attractors. Note that in the considered finite dynamic systems the number of attractors of length n is equal to (n − 1)! and the number belonging to the attractors states is equal to n!. A table is given with the corresponding number of attractors in the systems of complete graphs orientations with the number of vertices from 1 to 8 inclusive.

Turning Heads on the Dance Floor: Synchrony and Social Interaction Using a Silent Disco Paradigm

Music and dance appear to have a social bonding effect, which some have theorized is part of their ultimate evolutionary function. Prior research has also found a social bonding effect of synchronized movement, and it is possible that interpersonal synchrony could be considered the “active ingredient” in the social bonding consequences of music or dance activity. The present study aimed to separate the effects of synchrony from other factors associated with joint experience of dancing by using a “silent disco” manipulation, in which the timing of a musical stimulus was varied within a dyad in a freestyle dance setting. Three conditions were included: synchrony, tempo-shifted (in which the tempo was stretched by 5% for one participant), and phase-shifted (in which the beat was offset by 90 degrees for one participant). It was found that, when participants were listening to music in time with each other, they gave higher subjective ratings of their experience interacting with their partner. Participants also were observed looking towards each other more in the synchrony condition, compared with the non-synchrony conditions. From this, it appears that sharing time may contribute to the social effects of joint dancing, independent of any other effects associated with sharing space on the dancefloor. Avenues for further research, and possibilities using this “silent disco” paradigm, are discussed.

Delphinieae flowers originated from the rewiring of interactions between duplicated and diversified floral organ identity and symmetry genes.

Species of the tribe Delphinieae (Ranunculaceae) have long been the focus of morphological, ecological, and evolutionary studies due to their highly specialized, nearly zygomorphic (bilaterally symmetrical) spiral flowers with nested petal and sepal spurs and reduced petals. The mechanisms underlying the development and evolution of Delphinieae flowers, however, remain unclear. Here, by conducting extensive phylogenetic, comparative transcriptomic, expression, and functional studies, we clarified the evolutionary histories, expression patterns, and functions of floral organ identity and symmetry genes in Delphinieae. We found that duplication and/or diversification of APETALA3-3 (AP3-3), AGAMOUS-LIKE6 (AGL6), CYCLOIDEA (CYC), and DIVARICATA (DIV) lineage genes was tightly associated with the origination of Delphinieae flowers. Specifically, an AGL6-lineage member (such as the Delphinium ajacis AGL6-1a) represses sepal spur formation and petal development in the lateral and ventral parts of the flower while determining petal identity redundantly with AGL6-1b. By contrast, two CYC2-like genes, CYC2b and CYC2a, define the dorsal and lateral-ventral identities of the flower, respectively, and form complex regulatory links with AP3-3, AGL6-1a, and DIV1. Therefore, duplication and diversification of floral symmetry genes, as well as co-option of the duplicated copies into the preexisting floral regulatory network, have been key for the origin of Delphinieae flowers.

Brain-to-BAT - and Back?: Crosstalk between the Central Nervous System and Thermogenic Adipose Tissue in Development and Therapy of Obesity.

The body of mammals harbors two distinct types of adipose tissue: while cells within the white adipose tissue (WAT) store surplus energy as lipids, brown adipose tissue (BAT) is nowadays recognized as the main tissue for transforming chemical energy into heat. This process, referred to as 'non-shivering thermogenesis', is facilitated by the uncoupling of the electron transport across mitochondrial membranes from ATP production. BAT-dependent thermogenesis acts as a safeguarding mechanism under reduced ambient temperature but also plays a critical role in metabolic and energy homeostasis in health and disease. In this review, we summarize the evolutionary structure, function and regulation of the BAT organ under neuronal and hormonal control and discuss its mutual interaction with the central nervous system. We conclude by conceptualizing how better understanding the multifaceted communicative links between the brain and BAT opens avenues for novel therapeutic approaches to treat obesity and related metabolic disorders.

Pain dynamics: an integrative roadmap for navigating through the experiential process

ABSTRACT The authors present a theoretical integrative model of pain-dynamics for the categorization and transformation of emotional pain in person-centered and experiential psychotherapies. Integrating data from research literature and clinical work, the model distinguishes between three types of emotional pain: basic emotional pain, relational pain, and self-pain. The authors show how each type of emotional pain has not only distinct developmental etiology and evolutionary function, but also how each type requires a fundamentally different transformational process to be healed. Though clients experience all three types of pain in their life, usually one particular pain is dominant in the session. The model provides markers for identifying the active pain in the session, directing the therapist to one of three transformational paths. It thus provides a focus for the work, but also leaves plenty of room for intuitive moment-to-moment tracking of emerging experience. Although this new conceptual model emerged from the integration of the authors’ AEDP practice with EFT principles, pain dynamics can help to systematically select interventions and techniques from a variety of experiential models. Conceptualizing the active pain in the session combines the advantages of case conceptualization and moment to moment work of process formulation.

An Overview of Harvey Whitehouse’s The Ritual Animal: Imitation and Cohesion in the Evolution of Social Complexity (2021)

In the book The Ritual Animal: Imitation and Cohesion in the Evolution of Social Complexity (2021), Harvey Whitehouse presents an interdisciplinary approach to the study of ritual that is remarkable in range and versatility. Embedded in evolutionary principles, his theories hold vast explanatory potential, asking pertinent questions about the evolutionary functions and psychological substrates of ritual behaviour and its pivotal role in the origins of cultural and social complexity. Moreover, he compellingly discusses how the research outlined, resulting from many collaborations over several decades, can serve as a basis for meaningful policy making as well as the bridging of various fields within academia, hence demonstrating its potential for making contributions toward some of the most pressing issues currently faced by humanity.

Genome-Wide Identification, Evolution, and Expression Characterization of the Pepper (Capsicum spp.) MADS-box Gene Family.

MADS domain transcription factors play roles throughout the whole lifecycle of plants from seeding to flowering and fruit-bearing. However, systematic research into MADS-box genes of the economically important vegetable crop pepper (Capsicum spp.) is still lacking. We identified 174, 207, and 72 MADS-box genes from the genomes of C. annuum, C. baccatum, and C. chinense, respectively. These 453 MADS-box genes were divided into type I (Mα, Mβ, Mγ) and type II (MIKC* and MIKCC) based on their phylogenetic relationships. Collinearity analysis identified 144 paralogous genes and 195 orthologous genes in the three Capsicum species, and 70, 114, and 10 MADS-box genes specific to C. annuum, C. baccatum, and C. chinense, respectively. Comparative genomic analysis highlighted functional differentiation among homologous MADS-box genes during pepper evolution. Tissue expression analysis revealed three main expression patterns: highly expressed in roots, stems, leaves, and flowers (CaMADS93/CbMADS35/CcMADS58); only expressed in roots; and specifically expressed in flowers (CaMADS26/CbMADS31/CcMADS11). Protein interaction network analysis showed that type II CaMADS mainly interacted with proteins related to flowering pathway and flower organ development. This study provides the basis for an in-depth study of the evolutionary features and biological functions of pepper MADS-box genes.

Hearing the physical condition: The relationship between sexually dimorphic vocal traits and underlying physiology.

A growing amount of research has shown associations between sexually dimorphic vocal traits and physiological conditions related to reproductive advantage. This paper presented a review of the literature on the relationship between sexually dimorphic vocal traits and sex hormones, body size, and physique. Those physiological conditions are important in reproductive success and mate selection. Regarding sex hormones, there are associations between sex-specific hormones and sexually dimorphic vocal traits; about body size, formant frequencies are more reliable predictors of human body size than pitch/fundamental frequency; with regard to the physique, there is a possible but still controversial association between human voice and strength and combat power, while pitch is more often used as a signal of aggressive intent in conflict. Future research should consider demographic, cross-cultural, cognitive interaction, and emotional motivation influences, in order to more accurately assess the relationship between voice and physiology. Moreover, neurological studies were recommended to gain a deeper understanding of the evolutionary origins and adaptive functions of voice modulation.

Examination of morphological traits of children's faces related to perceptions of cuteness using Gaussian process ordinal regression.

Konrad Lorenz, an ethologist, proposed that certain physical elements are perceived as cute and induce caretaking behavior in other individuals, with the evolutionary function of enhancing offspring survival. He called these features Kindchenschema, baby schema. According to his introspection, these include a large forehead, chubby round features, and chubby cheeks. Previous studies are limited to examining the effects of these facial features on perceived cuteness. However, other morphological factors may be related to perceived cuteness. This study uses Bayesian optimization, one of the global sequential optimization methods for estimating unknown functions, to search for facial morphological features that enhance the perceptions of facial cuteness. We applied Bayesian optimization incorporating Gaussian process ordinal regression (GPOR), which allows an estimation of the latent cuteness function based on evaluations using the Likert scale. A total of 96 preschool children provided the facial images used in this study. We summarized the facial shape variations using methodologies of geometric morphometrics and principal component analysis (PCA) up to the third principal component (PC), which we refer to as the face space. A total of 40 participants evaluated the images created by warping the average facial texture of the children's faces with randomly generated parameters in the face space. Facial traits related to perceived cuteness were estimated based on the averaged cuteness function. Perceived cuteness was linked to the relative lower position of facial components and narrower jawline but not to the forehead height.

An inducible gene from glycoside hydrolase one family of Plutella xylostella decreases larval survival when feeding on host plant.

Glycoside hydrolase family 1 (GH1) members exhibit a broad substrate spectrum and play important roles in insect-plant interactions, such as the defensive β-glucosidase and β-thioglucosidase (so-called myrosinase). However, knowledge about the expression profiling and function of glycoside hydrolase family 1 members in a specialist pest of crucifers Plutella xylostella is still limited. In this study, 13 putative glycoside hydrolase family 1 members of P. xylostella were identified based on the sequence characteristics, while no myrosinase activity was detectable in P. xylostella using gas chromatography-mass spectrometry (GC-MS). Expression profiling of these glycoside hydrolase family 1 members identified the midgut-specific gene Px008848 that is induced by host plant. Further experiments revealed that the in vitro expressed Px008848 protein had β-glucosidase activity and the survival rate of the larvae feeding on wounded Arabidopsis thaliana leaves declined when leaves were treated with purified Px008848 protein. When CRISPR/Cas9-based homozygous mutant larvae of Px008848 and wild-type larvae were respectively transferred onto the A. thaliana, the larval survival rate of the mutant larvae was significantly higher than that of the wild-type individuals. Our work showed that certain insect glycoside hydrolase family 1 gene may have negative effect on the development of larvae feeding on the host plant, which broadened our understandings on the evolutionary function of this gene family in the insect-plant interaction.

Reversible Wrinkling Surfaces for Enhanced Grip on Wet/Dry Conditions.

Friction is important in material design for robotic systems that need to perform tasks regardless of environmental changes. Generally, robotic systems lose their friction in wet environments and fail to accomplish their tasks. Despite the significance of maintaining friction in dry and wet environments, it is still challenging. Here, we report a smart switching surface, which helps to complete missions in both wet and dry environments. Inspired by the reversible wrinkling mechanism of a human finger, the surface reversibly generates and removes wrinkles to adapt to both environments using volume-changing characteristics of the Nafion film. The switchable surfaces with manipulated wrinkle morphologies via patterns of diverse densities, sizes, and shapes induce a relationship between the wrinkle morphologies and friction: wrinkles on denser and smaller hexagonal patterns generate six times more friction than non-switching flat surfaces in wet environments and a similar amount of friction to the flat surfaces in dry environments. In addition, the wrinkle morphologies according to the patterns are predicted through numerical simulation, which is in good agreement with experimental results. This work presents potential applications in robotic systems that are required to perform in and out of water and paves the way for further understanding of wrinkling dynamics, manipulation, and evolutionary function in skin.

Genome-Wide Identification, Evolution, and Expression Pattern Analysis of the GATA Gene Family in Tartary Buckwheat (Fagopyrum tataricum)

GATA is a transcription factor that exerts a vital function in plant growth and development, physiological metabolism, and environmental responses. However, the GATA gene family has rarely been studied in Tartary buckwheat since the completion of its genome. This study used bioinformatics methods to identify GATA genes of Tartary buckwheat and to analyze their subfamily classification, structural composition, and developmental evolution, as well as to discuss the expression patterns of FtGATA genes in different subfamilies. The twenty-eight identified FtGATA genes in the Tartary buckwheat genome were divided into four subfamilies and distributed on eight chromosomes. One pair of tandem repeat genes and eight pairs of fragments were found in chromosome mapping. Spatiotemporal expression patterns of eight FtGATA genes in different subfamilies indicated that the FtGATA gene family has regulatory roles in tissue specificity, fruit development, abiotic stress, and hormonal responses. This study creates a theoretical and scientific foundation for further research on the evolutionary relationship and biological function of FtGATA.

Predictive functional, statistical and structural analysis of CSNK2A1 and CSNK2B variants linked to neurodevelopmental diseases.

Okur-Chung Neurodevelopmental Syndrome (OCNDS) and Poirier-Bienvenu Neurodevelopmental Syndrome (POBINDS) were recently identified as rare neurodevelopmental disorders. OCNDS and POBINDS are associated with heterozygous mutations in the CSNK2A1 and CSNK2B genes which encode CK2α, a serine/threonine protein kinase, and CK2β, a regulatory protein, respectively, which together can form a tetrameric enzyme called protein kinase CK2. A challenge in OCNDS and POBINDS is to understand the genetic basis of these diseases and the effect of the various CK2⍺ and CK2β mutations. In this study we have collected all variants available to date in CSNK2A1 and CSNK2B, and identified hotspots. We have investigated CK2⍺ and CK2β missense mutations through prediction programs which consider the evolutionary conservation, functionality and structure or these two proteins, compared these results with published experimental data on CK2α and CK2β mutants, and suggested prediction programs that could help predict changes in functionality of CK2α mutants. We also investigated the potential effect of CK2α and CK2β mutations on the 3D structure of the proteins and in their binding to each other. These results indicate that there are functional and structural consequences of mutation of CK2α and CK2β, and provide a rationale for further study of OCNDS and POBINDS-associated mutations. These data contribute to understanding the genetic and functional basis of these diseases, which is needed to identify their underlying mechanisms.

Nvp63 and nvPIWIL1 Suppress Retrotransposon Activation in the Sea Anemone Nematostella vectensis.

The transcription factors p63 and p73 have high similarity to the tumor suppressor protein p53. While the importance of p53 in DNA damage control is established, the functions of p63 or p73 remain elusive. Here, we analyzed nvp63, the cnidarian homologue of p63, that is expressed in the mesenteries of the starlet sea anemone Nematostella vectensis and that is activated in response to DNA damage. We used ultraviolet light (UV) to induce DNA damage and determined the chromatin-bound proteome with quantitative, bottom-up proteomics. We found that genotoxic stress or nvp63 knockdown recruited the protein nvPIWIL1, a homologue of the piRNA-binding PIWI protein family. Knockdown nvPIWIL1 increased protein expression from open reading frames (ORFs) that overlap with class I and II transposable element DNA sequences in the genome of N. vectensis. UV irradiation induced apoptosis, and apoptosis was reduced in the absence of nvp63 but increased with the loss of nvPIWIL1. Loss of nvp63 increased the presence of class I LTR and non-LTR retrotransposon but not of class II DNA transposon-associated protein products. These results suggest that an evolutionary early function of nvp63 might be to control genome stability in response to activation of transposable elements, which induce DNA damage during reintegration in the genome.