Evolutionary Process Research Articles

Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification.

The acquisition of microbial symbionts enables animals to rapidly adapt to and exploit novel ecological niches, thus significantly enhancing the evolutionary fitness and success of their hosts. However, the dynamics of host-microbe interactions and their evolutionary implications remain largely underexplored in marine invertebrates. Crabs of the family Sesarmidae (Crustacea: Brachyura) are dominant inhabitants of mangrove forests and are considered keystone species there. Their rapid diversification, particularly after adopting a plant-feeding lifestyle, is believed to have been facilitated by symbiotic gut microbes, enabling successful colonization of intertidal and terrestrial environments. To investigate the patterns and mechanisms shaping the microbial communities and the role of microbes in the evolution of Sesarmidae, we characterized and compared the gut microbiome compositions across 43 crab species from Sesarmidae and other mangrove-associated families using 16S metabarcoding. We found that the gut microbiome assemblages in crabs are primarily determined by host identity, with a secondary influence from environmental factors such as microhabitat and sampling location, and to a lesser extent influenced by biological factors such as sex and gut region. While patterns of phylosymbiosis (i.e. when microbial community relationships recapitulate the phylogeny of their hosts) were consistently observed in all beta-diversity metrics analysed, the strength of phylosymbiosis varied across crab families. This suggests that the bacterial assemblages in each family were differentially shaped by different degrees of host filtering and/or other evolutionary processes. Notably, Sesarmidae displayed signals of cophylogeny with its core gut bacterial genera, which likely play crucial functional roles in their hosts by providing lignocellulolytic enzymes, essential amino acids, and fatty acids supplementation. Our results support the hypothesis of microbial contribution to herbivory and terrestrialization in mangrove crabs, highlighting the tight association and codiversification of the crab holobiont.

Comparative analysis of POD genes and their expression under multiple hormones in Pyrus bretschenedri

BackgroundClass III peroxidase (POD) enzymes play vital roles in plant development, hormone signaling, and stress responses. Despite extensive research on POD families in various plant species, the knowledge regarding the POD family in Chinese pear (Pyrus bretschenedri) is notably limited.ResultsWe systematically characterized 113 POD family genes, designated as PbPOD1 to PbPOD113 based on their chromosomal locations. Phylogenetic analysis categorized these genes into seven distinct subfamilies (I to VII). The segmental duplication events were identified as a prevalent mechanism driving the expansion of the POD gene family. Microsynteny analysis, involving comparisons with Pyrus bretschenedri, Fragaria vesca, Prunus avium, Prunus mume and Prunus persica, highlighted the conservation of duplicated POD regions and their persistence through purifying selection during the evolutionary process. The expression patterns of PbPOD genes were performed across various plant organs and diverse fruit development stages using transcriptomic data. Furthermore, we identified stress-related cis-acting elements within the promoters of PbPOD genes, underscoring their involvement in hormonal and environmental stress responses. Notably, qRT-PCR analyses revealed distinctive expression patterns of PbPOD genes in response to melatonin (MEL), salicylic acid (SA), abscisic acid (ABA), and methyl jasmonate (MeJA), reflecting their responsiveness to abiotic stress and their role in fruit growth and development.ConclusionsIn this study, we investigated the potential functions and evolutionary dynamics of PbPOD genes in Pyrus bretschenedri, positioning them as promising candidates for further research and valuable indicators for enhancing fruit quality through molecular breeding strategies.

Brain-to-brain interface technology: A brief history, current state, and future goals.

A brain-to-brain interface (BBI), defined as a combination of neuroimaging and neurostimulation methods to extract and deliver information between brains directly without the need for the peripheral nervous system, is a budding communication technique. A BBI system is made up of two parts known as the brain-computer interface part, which reads a sender's brain activity and digitalizes it, and the computer-brain interface part, which writes the delivered brain activity to a receiving brain. As with other technologies, BBI systems have gone through an evolutionary process since they first appeared. The BBI systems have been employed for numerous purposes, including rehabilitation for post-stroke patients, communicating with patients suffering from amyotrophic lateral sclerosis, locked-in syndrome and speech problems following stroke. Also, it has been proposed that a BBI system could play an important role on future battlefields. This technology was not only employed for communicating between two human brains but also for making a direct communication path among different species through which motor or sensory commands could be sent and received. However, the application of BBI systems has provoked significant challenges to human rights principles due to their ability to access and manipulate human brain information. In this study, we aimed to review the brain-computer interface and computer-brain interface technologies as components of BBI systems, the development of BBI systems, applications of this technology, arising ethical issues and expectations for future use.

RuSe2 and CoSe2 Nanoparticles Incorporated Nitrogen-Doped Carbon as Efficient Trifunctional Electrocatalyst for Zinc-Air Batteries and Water Splitting.

The development of affordable, highly active, and stable trifunctional electrocatalysts is imperative for sustainable energy applications such as overall water splitting and rechargeable Zn-air battery. Herein, we report a composite electrocatalyst with RuSe2 and CoSe2 hybrid nanoparticles embedded in nitrogen-doped carbon (RuSe2CoSe2/NC) synthesized through a carbonization-adsorption-selenylation strategy. This electrocatalyst is a trifunctional electrocatalyst with excellent hydrogen evolution reaction (HER), oxygen evolution reaction (OER), and oxygen reduction reaction (ORR) activities. An in-depth study of the effect of Se on the electrocatalytic process was conducted. Notably, the incorporation of Se moderately adjusted electronic structure of Ru and Co, enhancing all three types of catalytic performance (HER, η10 = 31 mV; OER, η10 = 248 mV; ORR, E1/2 = 0.834 V) under alkaline condition with accelerated kinetics and improved stability. Density functional theory (DFT) calculation reveals that the (210) crystal facet of RuSe2 is the dominant HER active site as it exhibited the lowest ΔGH* value. The in situ Raman spectra unravel the evolution process of the local electronic environment of Co-Se and Ru-Se bonds, which synergistically promotes the formation of CoOOH as the active intermediate during the OER. The superior catalytic efficiency and remarkable durability of RuSe2CoSe2/NC as an electrode for water splitting and zinc-air battery devices demonstrate its great potential for energy storage and conversion devices.

In Situ Constructed Spinel Layer Stabilized Upcycled LiCoO2 for High Performance Lithium-Ion Batteries.

With ever-increasing requirements for cathodes in the lithium-ion batteries market, an efficiency and eco-friendly upcycling regeneration strategy is imperative to meet the demand for high-performance cathode materials. Herein, a facile, direct and upcycling regeneration strategy is proposed to restore the failed LiCoO2 and enhance the stability at 4.6 V. Double effects combination of relithiation and outside surface reconstruction are simultaneously achieved via a facile solid-phase sintering method. The evolution process of the Li-supplement and grain-recrystallization is systematically investigated, and the high performance of the upcycled materials at high voltage is comprehensively demonstrated. Thanks to the favorable spinel LiCoxMn2-xO4 surface coating, the upcycled sample displays outstanding electrochemical performance, superior to the pristine cathode materials. Notably, the 1% surface-coated LiCoO2 achieves a high discharge-specific capacity of 207.9 mA h g-1 at 0.1 C and delivers excellent cyclability with 77.0% capacity retention after 300 cycles. Significantly, this in situ created spinel coating layer can be potentially utilized for recycling spent LiCoO2, thus providing a viable, promising recycling strategy insights into the upcycling of degraded cathodes.

A backlash against the high‐speed modernity of gastronomy tourism: An analysis of the evolution of Macanese cuisine

In structuration theory, Giddens emphasises the importance of social practices in shaping and reproducing social structures, believing that the constitution of agents and structures represents a duality and advocating that structure is both a medium and outcome of the reproduction of practices. The traditional culture and customs embodied in Macanese cuisine can be considered as a structured process. Macanese cuisine reflects the unique food culture and customs of Macao society, presenting an irreplaceable way of life and cultural value. Macanese cuisine has developed based on the traditional customs and practices of the Macanese. It is recognised as an important intangible cultural heritage, receiving protection and promotion from the government. However, high‐speed modernity challenges the guarantee for continuity of Macanese traditional customs. Debates continue regarding how to promote the sustainability of Macanese cuisine. This study adopts Giddens' structuration theory to understand the evolutionary process of Macanese cuisine. It reveals the significance of individual agents' initiatives in promoting the rebirth of Macanese cuisine, and preserving the distinctiveness and self‐assertion of the Macanese community. Furthermore, the fusion culture that underlies Macanese cuisine can moderate the high‐speed modernity of gastronomy tourism and promote this cuisine's sustainability.

Trans-Atlantic genomic differentiation and parallel environmental and allelic variation in Lumpfish (Cyclopterus lumpus )

Abstract In marine species with large populations and high dispersal potential, large-scale genetic differences and clinal trends in allele frequency can provide insight into the evolutionary processes that shape diversity. Lumpfish, Cyclopterus lumpus, is found throughout the North Atlantic and has traditionally been harvested for roe and more recently used as a cleaner fish in salmon aquaculture. We used a 70 K SNP array to evaluate trans-Atlantic differentiation, genetic structuring, and clinal variation across the North Atlantic. Basin-scale structuring between the Northeast and Northwest Atlantic was significant, with enrichment for loci associated with developmental/mitochondrial function. We identified a putative structural variant on chromosome 2, likely contributing to differentiation between Northeast and Northwest Atlantic Lumpfish, and consistent with post-glacial trans-Atlantic secondary contact. Redundancy analysis identified climate associations both in the Northeast (N = 1269 loci) and Northwest (N = 1637 loci), with 103 shared loci between them. Clinal patterns in allele frequencies were observed in some loci (15%—Northwest and 5%—Northeast) of which 708 loci were shared and involved with growth, developmental processes, and locomotion. The combined evidence of trans-Atlantic differentiation, environmental associations, and clinal loci, suggests that both regional and large-scale potentially-adaptive population structuring is present across the North Atlantic.

Mitochondrial genome fragmentation is correlated with increased rates of molecular evolution.

While mitochondrial genome content and organization is quite diverse across all Eukaryotes, most bilaterian animal mitochondrial genomes (mitogenomes) exhibit highly conserved gene content and organisation, with genes typically encoded on a single circular chromosome. However, many species of parasitic lice (Insecta: Phthiraptera) are among the notable exceptions, having mitogenomes fragmented into multiple circular chromosomes. To better understand the process of mitogenome fragmentation, we conducted a large-scale genomic study of a major group of lice, Amblycera, with extensive taxon sampling. Analyses of the evolution of mitogenome structure across a phylogenomic tree of 90 samples from 53 genera revealed evidence for multiple independent origins of mitogenome fragmentation, some inferred to have occurred less than five million years ago. We leveraged these many independent origins of fragmentation to compare the rates of DNA substitution and gene rearrangement, specifically contrasting branches with fragmented and non-fragmented mitogenomes. We found that lineages with fragmented mitochondrial genomes had significantly higher rates of mitochondrial sequence evolution. In addition, lineages with fragmented mitochondrial genomes were more likely to have mitogenome gene rearrangements than those with single-chromosome mitochondrial genomes. By combining phylogenomics and mitochondrial genomics we provide a detailed portrait of mitogenome evolution across this group of insects with a remarkably unstable mitogenome structure, identifying processes of molecular evolution that are correlated with mitogenome fragmentation.

Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus).

Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera Crotalus and Sistrurus), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species.

Bioinspired Genetic-Algorithm Optimized Ground-Effect Wing Design: Flight Performance Benefits and Aircraft Stability Effects

This paper presents a bioinspired, genetic-algorithm evolutionary process for Ground-Effect vehicle wing design. The study made use of a rapid aerodynamic model generation and results evaluation computational fluid dynamics vortex lattice method software, supervised by a genetic algorithm optimization Python script. The design space for the aircraft wing parametric features drew inspiration from seabirds, under the assumption of their wings being naturally evolved and partially optimized for proximity flight over water surfaces. A case study was based on the A-90 Orlyonok Russian Ekranoplan, where alternative bioinspired wing variations were proposed. The study objective was to investigate the possible increased flight aircraft performance when using bioinspired wings, as well as verify the static and dynamic aircraft stability compliance for Ground-Effect flight. The methodology presented herein along with the study results, provided an incremental step towards advancing Ground-Effect aircraft conceptual designs using computational fluid dynamics.

Non-Poissonian bursts in the arrival of phenotypic variation can strongly affect the dynamics of adaptation.

Modelling the rate at which adaptive phenotypes appear in a population is a key to predicting evolutionary processes. Given random mutations, should this rate be modelled by a simple Poisson process, or is a more complex dynamics needed? Here we use analytic calculations and simulations of evolving populations on explicit genotype-phenotype maps to show that the introduction of novel phenotypes can be 'bursty' or overdispersed. In other words, a novel phenotype either appears multiple times in quick succession, or not at all for many generations. These bursts are fundamentally caused by statistical fluctuations and other structure in the map from genotypes to phenotypes. Their strength depends on population parameters, being highest for 'monomorphic' populations with low mutation rates. They can also be enhanced by additional inhomogeneities in the mapping from genotypes to phenotypes. We mainly investigate the effect of bursts using the well-studied genotype-phenotype map for RNA secondary structure, but find similar behaviour in a lattice protein model and in Richard Dawkins's biomorphs model of morphological development. Bursts can profoundly affect adaptive dynamics. Most notably, they imply that fitness differences play a smaller role in determining which phenotype fixes than would be the case for a Poisson process without bursts.

Hypothesized life cycle of the snow algae Chlainomonas sp. (Chlamydomonadales, Chlorophyta) from the Cascade Mountains, USA.

Chlainomonas (Chlamydomonadales, Chlorophyta) is one of the four genera of snow algae known to produce annual pink or red blooms in alpine snow. No Chlainomonas species have been successfully cultured in the laboratory, but diverse cell types have been observed from many field-collected samples, from multiple species. The diversity of morphologies suggests these algae have complex life cycles with changes in ploidy. Over 7 years (2017-2023), we observed seasonal blooms dominated by a Chlainomonas species from late spring through the summer months on a snow-on-lake habitat in an alpine basin in the North Cascade Mountains of Washington, USA. The Bagley Lake Chlainomonas is distinct from previously reported species based on morphology and sequence data. We observed a similar collection of cell types observed in other Chlainomonas species, with the addition of swarming biflagellate cells that emerged from sporangia. We present a life cycle hypothesis for this species that links cell morphologies observed in the field to seasonally available habitat. The progression of cell types suggests cells are undergoing both meiosis and fertilization in the life cycle. Since the life cycle is the most fundamental biological feature of an organism, with direct consequences for evolutionary processes, it is critical to understand how snow algal life cycles will influence their responses to changes in their habitat driven by climate warming. For microbial taxa that live in extreme environments and are difficult to culture, temporal field studies, such as we report here, may be key to creating testable hypotheses for life cycles.

The evolution of crystal‐poor rhyolite in the middle Okinawa Trough and its implications for the state of magma chamber

The crystal‐poor rhyolitic pumice is the product of extreme magma differentiation and is characterized by highly vesicular, honeycomb‐like structure. However, little is known about the evolutionary history and the time of volatile saturation of the pumice‐forming melt. A crystal‐poor rhyolitic pumice (TVG7‐1) has been collected from the Yoron Hole hydrothermal field in the middle Okinawa Trough, a young continental margin back‐arc basin in the western Pacific. This study conducted a detailed analysis on the texture and in situ chemical composition of plagioclase, orthopyroxene and Fe‐Ti oxides to reveal the evolution process, storage state and eruption triggers of eruptible silicic melt. Texture and zoning of specific minerals and mineral populations suggest a magmatic evolution history of open system. Additionally, the hollow reentrant texture, as well as results from plagioclase‐liquid hygrometers, confirm a water‐rich melt pocket. The exsolution of volatiles (H2O, etc.), in this melt pocket, will contribute to local oxidation conditions, which may have been recorded by the concordant behaviour of FeO and An in plagioclase. Then, the overpressure caused by volatile exsolution would destabilize the magma chamber, which will eventually be broken by magma mixing/recharge, and lead to violent melt evacuation. Consequently, crystal size distribution (CSD) provides a new perspective on understanding the kinetic effect of magma mixing/recharge in the Okinawa Trough, especially on the mineral populations. Our study reveals the petrogenesis of crystal‐poor rhyolite within the framework of the mush model, refines the magma evolution history and demonstrates that pumice magma reaches volatile saturation before the eruption.

Effect of Force and Heat Coupling on Machined Surface Integrity and Fatigue Performance of Superalloy GH4169 Specimens

GH4169 is one of the key materials used to manufacture high-temperature load-bearing parts for aero-engines, and the surface integrity of these parts in service conditions significantly affects their high-temperature fatigue performance. Under a coupling effect of high temperature and alternating load, the evolution process of the machined surface integrity index of superalloy GH4169 specimens was studied, and fatigue performance tests at 20 °C, 450 °C, and 650 °C were carried out to analyze the primary factors affecting the high-temperature fatigue performance of specimens. The results indicated that the surface roughness of specimens remained essentially unchanged. However, the value of surface residual stress decreased significantly, with a release of more than 60% at the highest temperature. At 650 °C, the surface microhardness increased, while the degree of surface plastic deformation decreased under alternating loads. Simultaneously, when the surface roughness was less than Ra 0.4 μm, surface microhardness was the main factor affecting the high-temperature fatigue performance of specimens. The influence of surface microhardness on low-cycle fatigue performance was not consistent with that on high-cycle fatigue performance. The latter increased monotonically, whereas the former initially increased and then decreased with increasing surface microhardness.

Development of a CoFe2O4-MnO Electrocatalyst for an Improved Oxygen Evolution Process in Alkaline Media

Development of a CoFe2O4-MnO Electrocatalyst for an Improved Oxygen Evolution Process in Alkaline Media

PCR amplification, sequencing, and in silico analysis of holandric genes TSPYand SRY in Nili Ravi buffalo

PCR amplification, sequencing, and in silico analysis of holandric genes TSPYand SRY in Nili Ravi buffalo

The exploration of relationship between the evolution of Cu to Cu2O/CuO and photocatalytic efficiency toward water oxidation reaction

This paper introduces a facile method to develop core-shell nanocomposite Cu/(Cu2O/CuO) through gradually oxidation on Cu nanocomposite precursors. As-prepared catalyst exhibited excellent catalytic activity in the reaction of water oxidation reaction (WOR). Comparing with the reported catalyst, Cu/(Cu2O/CuO) posed one of the highest O2 evolution around 7700 μmol g-1·h-1. By analyzing the composition of catalysts in each reaction stages, the evolution pathway of Cu towards Cu2O/CuO and the different roles of each component in catalytic water oxidation reactions were deeply studied. In presence of high conductive Cu element and excellent light absorption Cu2O, the photo generated electron and holes can be effectively separated and greatly improve the efficiency of the catalyst. The evolution process and synergistic effects of the three components play a crucial role in improving photocatalytic efficiency, which promoting the nanocomposite to be a highly efficient core-shell catalyst for WOR.

Reinforcement learning-based differential evolution algorithm for constrained multi-objective optimization problems

Many real-world problems can be established as Constrained Multi-objective Optimization Problems (CMOPs). It is still challenging to automatically set efficient parameters for Constrained Multi-Objective Evolutionary Algorithms (CMOEAs) to solve these CMOPs. A Reinforcement Learning-based Multi-Objective Differential Evolution (RLMODE) algorithm is proposed, in which the main parameters are dynamically adjusted. During the evolution process, the offspring generated is evaluated and compared with its corresponding parents, the relationship between the offspring and parent can adjust the parameters of RLMODE by the Reinforcement Learning (RL) technique. The feedback mechanism can produce the most appropriate parameters for RLMODE, which pushes the population towards feasible regions. The proposed RLMODE is evaluated on thirty functions and compared with some popular CMOEAs. The performance indicator IGD has revealed that the proposed RLMODE is competitive. Then, they are applied to solve the UAV path planning problem with three objectives and a constraint. The real application has further demonstrated the superiority of the proposed RLMODE.

Functional similarity affects similarity in partner composition in flea-mammal networks

Functional signal in an interaction network is a phenomenon in which species resembling each other in their traits interact with similar partners. We tested the functional signal concept in realm-specific and regional flea-host networks from four biogeographic realms and asked whether the species composition of (a) host spectra and (b) flea assemblages is similar between functionally similar flea and host species, respectively. Analogously to testing for phylogenetic signal, we applied Mantel tests to investigate the correlation between flea or host functional distances calculated from functional dendrograms and dissimilarities in sets of interacting partners. In all realm-specific networks, functionally similar fleas tended to exploit similar hosts often belonging to the same genus, whereas functionally similar hosts tended to harbour similar fleas, again often belonging to the same genus. The strength of realm-specific functional signals and the frequency of detecting a significant functional signal in the regional networks differed between realms. The frequency of detecting a significant functional signal in the regional networks correlated positively with the network size for fleas and with the number of hosts in a network for hosts. A functional signal in the regional networks was more frequently found for hosts than for fleas. We discuss the mechanisms behind the functional signal in both fleas and their hosts, relate geographic functional signal patterns to the historic biogeography of fleas and conclude that functional signals in the species composition of host spectra for fleas and of flea assemblages for hosts result from the interplay of evolutionary and ecological processes.

Genesis mechanism of laumontite cement and its impact on the reservoir of siliciclastic rock: A case study of Jurassic Shaximiao Formation in Central Sichuan Basin, China

Laumontite cement's genesis and impacts on reservoir quality in sedimentary basins have long been studied in sedimentology and petroleum geology. This study aims to analyze the petrological and geochemical properties of laumontite in the Shaximiao Formation, Sichuan Basin, China, and to determine the evolutionary process behind the formation of laumontite. Approximately 175 million years ago, huge volume of volcanic materials filled the Sichuan Basin. During the burial diagenesis phase, the hydrolysis of volcanic particles and alteration of plagioclase provided the necessary ions—Ca2+, Al3+, Si4+, Fe3+—facilitating the formation of laumontite. Simultaneously, the hydrolysis of volcanic substances released ions like Ca2+, Mg2+, and Na+, elevating the PH of pore fluids, and fostering the requisite alkaline conditions for laumontite. Additionally, the dehydration of smectite to illite in nearby mudstones generated Ca2+-rich fluids, migrating into sandstones. The hydrolysis of volcanic particles combined with the Ca2+-rich fluids migrating into sandstones led to the abundant formation of laumontite within temperatures ranging from 60 to 100°C. During this phase, the formation of laumontite accelerates the densification of the reservoir, leading to a reduction in porosity. In the meso-diagenetic period, organic acids from the underlying formations penetrate the sandstones through fractures, creating secondary pores and dissolution-related grain-edge fractures, significantly enhancing reservoir permeability.