Evolutionary Process Research Articles

Ecological and evolutionary processes involved in shaping microbial habitat generalists and specialists in urban park ecosystems.

Urban parks, as an important urban greenspace, play essential roles in ecosystem services and are important hotspots for microbes. Microbial diversity is driven by different ecological and evolutionary processes, while little is currently known about the distinct roles of ecological and evolutionary features in shaping microbial diversity in urban park ecosystems. We explored the ecological and evolutionary characteristics of prokaryotic and microeukaryotic habitat generalists and specialists in urban park ecosystems based on a representative set of different habitats. We found that different ecological and evolutionary drivers jointly maintained and regulated microbial diversity in urban park microbiomes through analyzing the community assembly process, ecological roles in hierarchical interaction, and species diversification potential. These findings significantly advance our understanding regarding the mechanisms governing microbial diversity in urban park ecosystems.

The role of satellite DNAs in the chromosomal rearrangements and the evolution of the rare XY1Y2 sex system in Harttia (Siluriformes: Loricariidae).

The underlying processes behind the formation, evolution, and long-term maintenance of multiple sex chromosomes have been largely neglected. Among vertebrates, fishes represent the group with the highest diversity of multiple sex chromosome systems and, with six instances, the Neotropical fish genus Harttia stands out by presenting the most remarkable diversity. However, although the origin mechanism of their sex chromosome systems is well discussed, little is known about the importance of some repetitive DNA classes in the differentiation of multiple systems. In this work, by employing a combination of cytogenetic and genomic procedures, we evaluated the satellite DNA composition of H. carvalhoi with a focus on their role in the evolution, structure, and differentiation process of the rare XY1Y2 multiple sex chromosome system. The genome of H. carvalhoi contains a total of 28 satellite DNA families, with the A+T content ranging between 38,1 and 68,1% and the predominant presence of long satellites. The in situ hybridization experiments detected 15 satellite DNAs with positive hybridization signals mainly on centromeric and pericentromeric regions of almost all chromosomes or clustered on a few pairs. Five of them presented clusters on X, Y1, and/or Y2 sex chromosomes which were therefore selected for comparative hybridization in the other three congeneric species. We found several conserved satellites accumulated on sex chromosomes and also in regions that were involved in chromosomal rearrangements. Our results provide a new contribution of satellitome studies in multiple sex chromosome systems in fishes and represent the first satellitome study for a Siluriformes species.

Limits on the evolutionary rates of biological traits.

This paper focuses on the maximum speed at which biological evolution can occur. I derive inequalities that limit the rate of evolutionary processes driven by natural selection, mutations, or genetic drift. These rate limits link the variability in a population to evolutionary rates. In particular, high variances in the fitness of a population and of a quantitative trait allow for fast changes in the trait's average. In contrast, low variability makes a trait less susceptible to random changes due to genetic drift. The results in this article generalize Fisher's fundamental theorem of natural selection to dynamics that allow for mutations and genetic drift, via trade-off relations that constrain the evolutionary rates of arbitrary traits. The rate limits can be used to probe questions in various evolutionary biology and ecology settings. They apply, for instance, to trait dynamics within or across species or to the evolution of bacteria strains. They apply to any quantitative trait, e.g., from species' weights to the lengths of DNA strands.

Evolutionary pathways to lower biomass allocation to the seed coat in crops: insights from allometric scaling.

Crops generally have seeds larger than their wild progenitors´ and with reduced dormancy. In wild plants, seed mass and allocation to the seed coat (a proxy for physical dormancy) scale allometrically so that larger seeds tend to allocate less to the coats. Larger seeds and lightweight coats might thus have evolved as correlated traits in crops. We tested whether 34 crops and 22 of their wild progenitors fit the allometry described in the literature, which would indicate co-selection of both traits during crop evolution. Deviations from the allometry would suggest that other evolutionary processes contribute to explain the emergence of larger, lightweight-coated seeds in crops. Crops fitted the scaling slope but deviated from its intercept in a consistent way: Seed coats of crops were lighter than expected by their seed size. The wild progenitors of crops displayed the same trend, indicating that deviations cannot be solely attributed to artificial selection during or after domestication. The evolution of seeds with small coats in crops likely resulted from a combination of various pressures, including the selection of wild progenitors with coats smaller than other wild plants, further decreases during early evolution under cultivation, and indirect selection due to the seed coat-seed size allometry.

Estimating scale-specific and localized spatial patterns in allele frequency.

Characterizing spatial patterns in allele frequencies is fundamental to evolutionary biology because these patterns contain evidence of underlying processes. However, the spatial scales at which gene flow, changing selection, and drift act are often unknown. Many of these processes can operate inconsistently across space, causing non-stationary patterns. We present a wavelet approach to characterize spatial pattern in allele frequency that helps solve these problems. We show how our approach can characterize spatial patterns in relatedness at multiple spatial scales, i.e. a multi-locus wavelet genetic dissimilarity. We also develop wavelet tests of spatial differentiation in allele frequency and quantitative trait loci (QTL). With simulation we illustrate these methods under different scenarios. We also apply our approach to natural populations of Arabidopsis thaliana to characterize population structure and identify locally-adapted loci across scales. We find, for example, that Arabidopsis flowering time QTL show significantly elevated genetic differentiation at 300 to 1300 km scales. Wavelet transforms of allele frequencies offer a flexible way to reveal geographic patterns and underlying evolutionary processes.

The tightness of the measure-based method to estimate quantum coherence

With the advancement of quantum information science, the understanding of quantum coherence has become increasingly important. In this paper, we investigate the effects of different channels on quantum states and analyze the evolution process of quantum states during channel transmission. Our findings reveal variations in the impact of different channels on quantum coherence. Additionally, we explore the estimation of lower bounds on coherence after passing through these diverse channels. We observe that channel transmission has a certain influence on the tightness of lower bounds on quantum coherence. We conduct a detailed analysis of this influence and propose improvement method to enhance the tightness of the lower bound estimation. Based on our research results, we draw conclusions that unveil the characteristics of quantum coherence under different channel conditions. Furthermore, we provide an effective estimation method and improvement strategies to accurately assess the coherence of quantum states. This research holds significant implications for further advancements in quantum information processing and quantum communication.

Conserved regulatory switches for the transition from natal down to juvenile feather in birds.

The transition from natal downs for heat conservation to juvenile feathers for simple flight is a remarkable environmental adaptation process in avian evolution. However, the underlying epigenetic mechanism for this primary feather transition is mostly unknown. Here we conducted time-ordered gene co-expression network construction, epigenetic analysis, and functional perturbations in developing feather follicles to elucidate four downy-juvenile feather transition events. We report that extracellular matrix reorganization leads to peripheral pulp formation, which mediates epithelial-mesenchymal interactions for branching morphogenesis. α-SMA (ACTA2) compartmentalizes dermal papilla stem cells for feather renewal cycling. LEF1 works as a key hub of Wnt signaling to build rachis and converts radial downy to bilateral symmetry. Novel usage of scale keratins strengthens feather sheath with SOX14 as the epigenetic regulator. We show that this primary feather transition is largely conserved in chicken (precocial) and zebra finch (altricial) and discuss the possibility that this evolutionary adaptation process started in feathered dinosaurs.

Addiction: A Decease Theory with a Definitive Piousness-Spiritual Correlation

This article bear attention to scholars as well as who are working as professionals in the realms of addiction-related paradigms. That is the introduction. The purpose therefore of the article is to bring a way (methodology), how individuals (both those the professionals as well as the addicted individuals), in how should they interpret the Higher Power or Spiritual propositions, and the reason is that it will align the reader's knowledge of the proposed appreciation of a Higher Power/Spiritual (therefore the piousness) concept regarding addiction. Relucted analyses have studied the 12-act paradigms in grasping the Higher Power or Spirituality concept in the groundwork of therapy behaviourism of piousness-religion and Spirituality, although the efforts have been little and too far between. Considering the accepted hindrances towards elevated exhaustion of the addicts and approvals together using reciprocal-abed differentials, further enhanced research must take place to amend and grasp the piousness- Deity or Spirituality propositions among the 12-act research paradigms and realms at work in these intended rehabilitation attempts. The following methods will be used: In a survey concentrating on fixation and piousness, sixty percent of the enclosed articles remain affiliated with this twelve-act doctrine/ideology, pinpointing a percolated theory in addiction research. The results could be either or, for instance yet and notwithstanding IT, is it difficult enough to pass the test, to get sober and to be cleansed. Still, and here is the core message: if not achieved it is still not the end of the world, as it still stays part of an evolutionary process. You did not sober-up yet and therefore not (un) conditionally.

Study on Permeability Evolution Law of Rock Mass under Mining Stress

In order to study the stress–strain–permeability coefficient relationship of overlying strata in a fractured zone after coal mining, taking the Changcun coal mine in the Changzhi basin as an example, the permeability evolution law of coarse sandstone, fine sandstone, siltstone and mudstone during a stress–strain process was analyzed through a triaxial compression permeability test. The generalized model of the rock mass permeability evolution process under mining stress was summarized, and then a coupling model of the stress–water pressure–permeability coefficient of fractured rock was established based on the continuum model of rock mass. The results showed that the maximum permeability coefficient of different coal overburden types was quite different, and the peak strength of the rock mass preceded the maximum permeability coefficient during the rock mass failure process; the permeability coefficient first decreased and then increased, reaching its maximum value after the peak stress, which occurred during the strain-softening stage; the generalized model of rock mass permeability included the compaction stage, elasticity stage, stable fracture stage, unstable fracture stage, macroscopic failure stage and residual strength stage.

Study on the Evaluation of Urban Park Landscape Pattern Index and Its Driving Mechanisms in Nanchang City

Urban planning is often influenced by industrial and construction activities, leading to a lack of attention to the planning and construction of urban parks, which results in prominent spatial layout problems. Urban parks, as an important part of the urban green space system, play a significant role in improving the ecological environment, promoting urban economic development, and enhancing the daily living standards of the people. As a typical representative of China’s second and third-tier cities, Nanchang’s analysis of the evolution process of urban landscape patterns has reference significance for other similar cities in China. This paper is based on the theoretical foundations of landscape ecology, human geography, and urban planning, and analyzes the evolution of the park landscape pattern in the central urban area of Nanchang from 1999 to 2019 from the perspective of urban context, revealing the driving mechanisms. It provides important references and bases for the further optimization and construction development of the park landscape pattern in Nanchang. The results show that the park area and number in the central urban area of Nanchang have significantly increased, with the overall layout evolving from “central aggregation” to “core aggregation in each area”, and from “central scarcity, more on the periphery” to “inward concentration, outward diffusion”. However, the distribution of various types of parks is uneven, and there is a lack of green corridor links between parks. The park landscape pattern is driven by multiple factors such as natural factors of urban context, socio-economic factors, urban construction factors, historical policies, and related planning, which can have positive or negative effects. Incorporating relevant urban factors into the park planning system analysis can promote the benign development of urban context and park landscape layout, thereby achieving the “parkification” of the city.

Analysis of Multi-Stakeholder Behavioral Strategies in the Construction and Demolition Waste Recycling Industry through an Evolutionary Game Theory

Construction and demolition waste (C&DW) recycling products have drawn worldwide attention over the past few decades. There is a general agreement among researchers that C&DW recycling is an important means for curbing the deterioration of the environment. Previous papers mainly focused on the decision-making behavior of dual stakeholders or tripartite stakeholders, as well as the lack of cooperation among multiple stakeholders. This study explored a dynamic evolutionary game model with three different parameter conditions to research the decision-making behaviors and stable strategies of the multi-stakeholders involved in the C&DW recycling product industry, including government departments and some enterprises. This research also investigated how the government’s supervision costs, penalties applied to enterprises, and resource taxes affect the dynamic evolution process of C&DW recycling. This research conducted numerical simulations using Python to analyze stakeholders’ behavioral evolutionarily stable strategy (ESS) and the sensitivity to main factors in each stage of the C&DW recycling process to accelerate the development of construction waste resource utilization. Based on the results of the evolutionary game, this paper proposed that the roles of multi-stakeholders are different at different stages of industry development, and that supervision costs, penalties, and resource tax have their own impacts on the C&DW recycling product industry. The paper suggests a range of discussions and simulation studies to highlight the significance of the government’s refined and moderate adjustments to the regulatory incentive system and the level of government regulation and involvement at different stages of the process. These adjustments are aimed at promoting the sustainable recycling and utilization of construction and demolition waste (C&DW) products within some countries’ construction industry.

Genome reduction and horizontal gene transfer in the evolution of Endomicrobia-rise and fall of an intracellular symbiosis with termite gut flagellates.

Bacterial endosymbionts of eukaryotic hosts typically experience massive genome reduction, but the underlying evolutionary processes are often obscured by the lack of free-living relatives. Endomicrobia, a family-level lineage of host-associated bacteria in the phylum Elusimicrobiota that comprises both free-living representatives and endosymbionts of termite gut flagellates, are an excellent model to study evolution of intracellular symbionts. We reconstructed 67 metagenome-assembled genomes (MAGs) of Endomicrobiaceae among more than 1,700 MAGs from the gut microbiota of a wide range of termites. Phylogenomic analysis confirmed a sister position of representatives from termites and ruminants, and allowed to propose eight new genera in the radiation of Endomicrobiaceae. Comparative genome analysis documented progressive genome erosion in the new genus Endomicrobiellum, which comprises all flagellate endosymbionts characterized to date. Massive gene losses were accompanied by the acquisition of new functions by horizontal gene transfer, which led to a shift from a glucose-based energy metabolism to one based on sugar phosphates. The breakdown of glycolysis and many anabolic pathways for amino acids and cofactors in several subgroups was compensated by the independent acquisition of new uptake systems, including an ATP/ADP antiporter, from other gut microbiota. The putative donors are mostly flagellate endosymbionts from other bacterial phyla, including several, hitherto unknown lineages of uncultured Alphaproteobacteria, documenting the importance of horizontal gene transfer in the convergent evolution of these intracellular symbioses. The loss of almost all biosynthetic capacities in some lineages of Endomicrobiellum suggests that their originally mutualistic relationship with flagellates is on its decline.IMPORTANCEUnicellular eukaryotes are frequently colonized by bacterial and archaeal symbionts. A prominent example are the cellulolytic gut flagellates of termites, which harbor diverse but host-specific bacterial symbionts that occur exclusively in termite guts. One of these lineages, the so-called Endomicrobia, comprises both free-living and endosymbiotic representatives, which offers the unique opportunity to study the evolutionary processes underpinning the transition from a free-living to an intracellular lifestyle. Our results revealed a progressive gene loss in energy metabolism and biosynthetic pathways, compensated by the acquisition of new functions via horizontal gene transfer from other gut bacteria, and suggest the eventual breakdown of an initially mutualistic symbiosis. Evidence for convergent evolution of unrelated endosymbionts reflects adaptations to the intracellular environment of termite gut flagellates.

Can near-to-mid infrared spectral energy distribution quantitatively trace protoplanetary disk evolution?

Abstract Infrared (IR) spectral energy distribution (SED) is the major tracer of protoplanetary disks. It was recently proposed to use the near-to-mid IR (or K-24) SED slope $\alpha$ defined between 2-24$\mu$m as a potential quantitative tracer of disk age. We critically examine the viability of this idea and confront it with additional statistics of IR luminosities and SED shapes. We point out that, because the statistical properties of most of the complicated physical factors involved in disk evolution are still poorly understood in a quantitative sense, the only viable way is to assume them to be random so that an idealized `average disk' can be defined, which allows the $\alpha$ histogram to trace its age. We confirm that the statistics of the zeroth order (luminosity), first order (slope $\alpha$) and second order characteristics (concavity) of the observed K-24 SEDs indeed carry useful information upon the evolutionary processes of the `average disk'. We also stress that intrinsic diversities in K-24 SED shapes and luminosities are always large at the level of individual stars so that the application of the evolutionary path of the `average disk' to individual stars must be done with care. The data of most curves in plots are provided on GitHub.

Wie erlebt man die Evolution? Kulturelle Evolution als Lebenserfahrung

AbstractThe evolution of human culture continues to divide social and biological science. Key issues for both sides are the complexity and variability of culture, the frequency of cultural traits that have no adaptive or functional value, and the apparent exceptionality of human creativity and rationality. This article argues that an examination of how evolution affects the lifetime experience of evolution can reconcile these features of human culture with Darwin’s contention that natural and cultural selection follow the same process of evolution. The article offers a new paradigm that focuses on the relationship between uncertainty and choice in human cultural evolution.

Understanding Evolutionary Rescue and Parallelism in Response to Environmental Stress.

Evolutionary rescue, the process by which populations facing environmental stress avoid extinction through genetic adaptation, is a critical area of study in evolutionary biology. The order in which mutations arise and get established will be relevant to the population's rescue. This study investigates the degree of parallel evolution at the genotypic level between independent populations fac- ing environmental stress and subject to different demographic regimes. Under density regulation, two regimes exist: in the first, the population can restore positive growth rates by adjusting its population size or through adaptive mu- tations, whereas in the second regime, the population is doomed to extinction unless a rescue mutation occurs. Analytical approximations for the likelihood of evolutionary rescue are obtained and contrasted with simulation results. We show that the initial level of maladaptation and the demographic regime signifi- cantly affect the level of parallelism. There is an evident transition between these two regimes. Whereas in the first regime, parallelism decreases with the level of maladaptation, it displays the opposite behavior in the rescue/extinction regime. These findings have important implications for understanding population persis- tence and the degree of parallelism in evolutionary responses as they integrate demographic effects and evolutionary processes.

Design and performance assessment of improved evolutionary computing based LEACH protocol for energy efficient and lifetime extension of wireless sensor network

Abstract The strengths of a Memetic Algorithm and an enhanced Low-Energy Adaptive Clustering Hierarchy (LEACH) protocol are combined in this research study to propose a revolutionary method for improving the energy efficiency and longevity of Wireless Sensor Networks (WSNs). WSNs are widely used for a variety of applications, including industrial automation, healthcare, and environmental monitoring, where extending network lifetime and energy conservation are crucial. Although successful, conventional clustering algorithms like LEACH feature subpar cluster formation and premature cluster head failures. To get over these restrictions, a memetic algorithm is used to maximize cluster formation and reduce energy usage. This algorithm was influenced by natural evolution and cultural learning processes. 
The Memetic Algorithm iteratively improves the LEACH protocol in the proposed technique by enhancing dynamic clustering, energy-aware routing, and cluster head selection. These methods work together to increase energy efficiency and lengthen the life of the network. In compared to conventional LEACH-based WSNs and other cutting-edge algorithms, the paper's study of the simulation results shows how successful the suggested technique is. In light of network longevity, energy use, and data transmission efficiency, the results obtained demonstrate notable improvements.

Evolution and genetic characterization of Seoul virus in wild rats Rattus norvegicus from an urban park in Lyon, France 2020-2022.

Seoul virus (SEOV) is an orthohantavirus primarily carried by rats. In humans, it may cause hemorrhagic fever with renal syndrome (HFRS). Its incidence is likely underestimated and given the expansion of urban areas, a better knowledge of SEOV circulation in rat populations is called for. Beyond the need to improve human case detection, we need to deepen our comprehension of the ecological, epidemiological, and evolutionary processes involved in the transmission of SEOV. We performed a comprehensive serological and molecular characterization of SEOV in Rattus norvegicus in a popular urban park within a large city (Lyon, France) to provide essential information to design surveillance strategies regarding SEOV. We sampled rats within the urban park of 'La Tête d'Or' in Lyon city from 2020 to 2022. We combined rat population genetics, immunofluorescence assays, SEOV high-throughput sequencing (S, M, and L segments), and phylogenetic analyses. We found low structuring of wild rat populations within Lyon city. Only one sampling site within the park (building created in 2021) showed high genetic differentiation and deserves further attention. We confirmed the circulation of SEOV in rats from the park with high seroprevalence (17.2%) and high genetic similarity with the strain previously described in 2011 in Lyon city. This study confirms the continuous circulation of SEOV in a popular urban park where the risk for SEOV transmission to humans is present. Implementing a surveillance of this virus could provide an efficient early warning system and help prepare risk-based interventions. As we reveal high gene flow between rat populations from the park and the rest of the city, we advocate for SEOV surveillance to be conducted at the scale of the entire city.

In situ/Operando Synchrotron Radiation Analytical Techniques for CO2/CO Reduction Reaction: From Atomic Scales to Mesoscales.

Electrocatalytic carbon dioxide/carbon monoxide reduction reaction (CO(2)RR) has emerged as a prospective and appealing strategy to realize carbon neutrality for manufacturing sustainable chemical products. Developing highly active electrocatalysts and stable devices has been demonstrated as effective approach to enhance the conversion efficiency of CO(2)RR. In order to rationally design electrocatalysts and devices, a comprehensive understanding of the intrinsic structure evolution within catalysts and micro-environment change around electrode interface, particularly under operation conditions, is indispensable. Synchrotron radiation has been recognized as a versatile characterization platform, garnering widespread attention owing to its high brightness, elevated flux, excellent directivity, strong polarization and exceptional stability. This review systematically introduces the applications of synchrotron radiation technologies classified by radiation sources with varying wavelengths in CO(2)RR. By virtue of in situ/operando synchrotron radiationanalytical techniques, we also summarize relevant dynamic evolution processes from electronic structure, atomic configuration, molecular adsorption, crystal lattice and devices, spanning scales from the angstrom to the micrometer. The merits and limitations of diverse synchrotron characterization techniques are summarized, and their applicable scenarios in CO(2)RR are further presented. On the basis of the state-of-the-art fourth-generation synchrotron facilities, a perspective for further deeper understanding of the CO(2)RR process using synchrotron radiation analytical techniques is proposed.

In situ/Operando Synchrotron Radiation Analytical Techniques for CO2/CO Reduction Reaction: From Atomic Scales to Mesoscales

AbstractElectrocatalytic carbon dioxide/carbon monoxide reduction reaction (CO(2)RR) has emerged as a prospective and appealing strategy to realize carbon neutrality for manufacturing sustainable chemical products. Developing highly active electrocatalysts and stable devices has been demonstrated as effective approach to enhance the conversion efficiency of CO(2)RR. In order to rationally design electrocatalysts and devices, a comprehensive understanding of the intrinsic structure evolution within catalysts and micro‐environment change around electrode interface, particularly under operation conditions, is indispensable. Synchrotron radiation has been recognized as a versatile characterization platform, garnering widespread attention owing to its high brightness, elevated flux, excellent directivity, strong polarization and exceptional stability. This review systematically introduces the applications of synchrotron radiation technologies classified by radiation sources with varying wavelengths in CO(2)RR. By virtue of in situ/operando synchrotron radiationanalytical techniques, we also summarize relevant dynamic evolution processes from electronic structure, atomic configuration, molecular adsorption, crystal lattice and devices, spanning scales from the angstrom to the micrometer. The merits and limitations of diverse synchrotron characterization techniques are summarized, and their applicable scenarios in CO(2)RR are further presented. On the basis of the state‐of‐the‐art fourth‐generation synchrotron facilities, a perspective for further deeper understanding of the CO(2)RR process using synchrotron radiation analytical techniques is proposed.

Study of the Dynamic Recrystallization Behavior of Mg-Gd-Y-Zn-Zr Alloy Based on Experiments and Cellular Automaton Simulation

The exploration of the relationship between process parameters and grain evolution during the thermal deformation of rare-earth magnesium alloys using simulation software has significant implications for enhancing research and development efficiency and advancing the large-scale engineering application of high-performance rare-earth magnesium alloys. Through single-pass hot compression experiments, this study obtained high-temperature flow stress curves for rare-earth magnesium alloys, analyzing the variation patterns of these curves and the softening mechanism of the materials. Drawing on physical metallurgical theories, such as the evolution of dislocation density during dynamic recrystallization, recrystallization nucleation, and grain growth, the authors of this paper establish a cellular automaton model to simulate the dynamic recrystallization process by tracking the sole internal variable—the evolution of dislocation density within cells. This model was developed through the secondary development of the DEFORM-3D finite element software. The results indicate that the model established in this study accurately simulates the evolution process of grain growth during heat treatment and the dynamic recrystallization microstructure during the thermal deformation of rare-earth magnesium alloys. The simulated results align well with relevant theories and metallographic experimental results, enabling the simulation of the dynamic recrystallization microstructure and grain size prediction during the deformation process of rare-earth magnesium alloys.