Horizontal Evolution Research Articles

Dimensions of Level-1 Group-Based Phylogenetic Networks

Phylogenetic networks represent evolutionary histories of sets of taxa where horizontal evolution or hybridization has occurred. Placing a Markov model of evolution on a phylogenetic network gives a model that is particularly amenable to algebraic study by representing it as an algebraic variety. In this paper, we give a formula for the dimension of the variety corresponding to a triangle-free level-1 phylogenetic network under a group-based evolutionary model. On our way to this, we give a dimension formula for codimension zero toric fiber products. We conclude by illustrating applications to identifiability.

Investigation on the size effect of compacted clay mode I fracture based on NDB specimens

The size effect is closely related to the cracking resistance of compacted clay, which is crucial in engineering applications, but little attention has been given to it in previous studies. This study investigated the size effect on mode I fracture behaviors of compacted clay using single-edge notched deep beam (NDB) specimens. Through the digital image correlation (DIC) method, the crack initiation mechanism of compacted clay was analyzed. The results showed that the specimen size and dimensionless crack length did not change the failure pattern, while peak load, peak displacement, and fracture energy gradually increased with the increase of specimen size. Based on the load–displacement curves and the horizontal strain evolution laws, the three horizontal strain stages at the crack tip crack initiation point were defined, i.e., the steady strain growth stage, the nonlinear strain growth stage, and the nonlinear strain intensification stage. Through the Bažant size effect model (SEM), the fracture process zone length Cf and mode I fracture toughness KIC of compacted clay without the size effect were inferred. The separated form of SEM was applied, and the contribution ratios of the strength criterion and linear elastic fracture mechanics were quantitatively analyzed. Combing the characteristics of the NDB specimens, a prediction model considering the support spacing, specimen structure parameters, and fracture toughness was established.

Incongruence in the phylogenomics era.

Genome-scale data and the development of novel statistical phylogenetic approaches have greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its branches. However, incongruence - the inference of conflicting evolutionary histories - remains pervasive in phylogenomic data, hampering our ability to reconstruct and interpret the tree of life. Biological factors, such as incomplete lineage sorting, horizontal gene transfer, hybridization, introgression, recombination and convergent molecular evolution, can lead to gene phylogenies that differ from the species tree. In addition, analytical factors, including stochastic, systematic and treatment errors, can drive incongruence. Here, we review these factors, discuss methodological advances to identify and handle incongruence, and highlight avenues for future research.

Concrete-filled cold-formed steel (CF-CFS) built-up columns subjected to elevated temperatures: Test and design

This paper evaluates the behaviour of an innovative type of lightweight concrete-filled cold-formed steel (CF-CFS) built-up composite long column in the fire. Twelve fire resistance tests were performed on CF-CFS columns. The experimental results were discussed, including test observations, buckling modes characterization, vertical and horizontal deformations, temperature evolution, and fire resistance in terms of load-bearing capacity. A finite element modelling approach was developed and validated against the test results. Then, the experimental data were compared against analytical predictions following EN1994-1-2, assessing the suitability of existing design methodologies. For this purpose, two analytical approaches available in EN1994-1-2 were used, including Annex-H and the general method (Clause 4.3.5.1). The results showed that the fire resistance prediction according to EN1994-1-2, Annex H, was remarkably conservative. However, the general method of EN1994-1-2 (Clause 4.3.5.1) provided unsafe predictions. Therefore, a modification to the analytical prediction of EN1994-1-2 (Clause 4.3.5.1) was applied to account for the CFS effective cross-sectional area, buckling curve d, and experimental degradation of CFS mechanical properties at elevated temperatures, resulting in an excellent agreement with the test results. Reliability analysis and safety evaluation criteria proposed by Kruppa were also carried out to assess the suitability of the design methodologies.

Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing

The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01–2.5–50–100 mg L−1). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L−1). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.

Precise Empirical Determination of Metallicity Dependence of Near-infrared Period–Luminosity Relations for RR Lyrae Variables

RR Lyrae variables are excellent Population II distance indicators thanks to their well-defined period–luminosity relations (PLRs) at infrared wavelengths. We present results of near-infrared (NIR) monitoring of Galactic globular clusters to empirically quantify the metallicity dependence of NIR PLRs for RR Lyrae variables. Our sample includes homogeneous, accurate, and precise photometric data for 964 RR Lyrae variables in 11 globular clusters covering a large metallicity range (Δ[Fe/H] ∼ 2 dex). We derive JHK s -band period–luminosity–metallicity (PLZ) and period–Wesenheit–metallicity (PWZ) relations anchored using 346 Milky Way field RR Lyrae stars with Gaia parallaxes, and simultaneously solved for independent distances to globular clusters. We find a significant metallicity dependence of ∼0.2 mag dex−1 in the JHK s -band PLZ and PWZ relations for RR Lyrae stars independent of the adopted metallicity scale. The metallicity coefficients and the zero-points of the empirical PLZ and PWZ relations are in excellent agreement with the predictions from the horizontal branch evolution and pulsation models. Furthermore, RR Lyrae–based distances to our sample of globular clusters are also statistically consistent with other independent measurements in the literature. Our recommended empirical JHK s -band PLZ relations for RR Lyrae stars with periods of fundamental mode pulsation (P f) are: MJ=−0.44(±0.03)−1.83(±0.02)log(Pf)+0.20(±0.02)[Fe/H](σ=0.05mag)MH=−0.74(±0.02)−2.29(±0.02)log(Pf)+0.19(±0.01)[Fe/H](σ=0.05mag)MKs=−0.80(±0.02)−2.37(±0.02)log(Pf)+0.18(±0.01)[Fe/H](σ=0.05mag).

Period–Luminosity–Metallicity relations for Classical Pulsators at Near-infrared Wavelengths

AbstractClassical pulsating stars such as Cepheid and RR Lyrae variables exhibit well-defined Period–Luminosity relations at near-infrared wavelengths. Despite their extensive use as stellar standard candles, the effects of metallicity on Period–Luminosity relations for these pulsating variables, and in turn, on possible biases in distance determinations, are not well understood. We present ongoing efforts in determining accurate and precise metallicity coefficients of Period–Luminosity-Metallicity relations for classical pulsators at near-infrared wavelengths. For Cepheids, it is crucial to obtain a homogeneous sample of photometric light curves and high-resolution spectra for a wide range of metallicities to empirically determine metallicity coefficient and reconcile differences with the predictions of the theoretical models. For RR Lyrae variables, using their host globular clusters covering a wide range of metallicities, we determined the most precise metallicity coefficient at near-infrared wavelengths, which is in excellent agreement with the predictions of the horizontal branch evolution and stellar pulsation models.

Temporal and Spatial Evolution of Precipitation under the Summer Sprite Parent Mesoscale Convective Systems in Japan

Transient luminous events (TLEs) are electrical discharges in the upper atmosphere caused by vigorous thunderstorms. Six sprites, which are part of TLEs, were observed on 22 July 2013 from Mt. Fuji (3776 m above sea level), Japan. All the six sprites were associated with intense positive cloud-to-ground strikes (+CGs), whose causative positive charges can reside in the stratiform region. Consequently, we assumed that the main sprites causative charges could generate an in situ charging mechanism, accompanied by precipitation growth in the extensive stratiform region. Thus, we supposed that there can be a relationship between the time sequence of surface precipitation intensity and the sprite emissions. In this study, we conclude that time sequences and horizontal evolution of Mesoscale Convective Systems (MCSs) precipitation are associated with sprites. As the result, prior to sprites 1–5, the areal amount of strong precipitation (≥8 mm/h) increased considerably, and only a small increase occurred during sprite 6. Analyzing the time sequence of the percentage of strong and weak precipitation with respect to the total precipitation, it was found that sprites 1–6 occurred within 20 min after the local peaks with respect to strong precipitation compared to total precipitation. In particular, sprites 2–5 occurred very close to local peaks. The rise time to the first peak of the strong precipitation rate associated with the first sprite was 80 min, while the rise time to the last peak associated with sprite 6 was 30 min. The temporal differences until the peaks suggest that the charging speeds, or mechanisms, related to precipitation differ between sprites 1–5 and sprite 6 in parent MCSs.

Physical modelling of EPB TBM in dry sand and greenfield conditions

This paper presents the results obtained during the first stage of a large experimental project based on the so-called ‘Earth Pressure Balanced Shield’ (EPBS) method adapted to tunnelling in soft ground. In the first part, the details of a 1 g laboratory model of EPBS specially improved within the framework of this project are presented. In particular, the new elements of the experimental setup, its instrumentations, the machine control, the preparation of the soil mass model are detailed. In the second part, the results obtained from this new EPBS model for two excavation tests, carried out in purely frictional soil mass (dry fine silica sand) and greenfield conditions (without neighbouring structures), are presented. The analysis concerns both soil surface and subsurface displacements, vertical and horizontal stress evolution in the ground when the Tunnel Boring Machine (TBM) progresses. It confirms that the highly sophisticated design of the machine allows to simulate the 3D excavation process closely, and to reproduce kinematic phenomena in the ground being in good agreement with those observed in the practice. In the case of the steady state excavation imposed during the tests, the extension of the TBM impact zone could also be identified based on the measured stress and strain variations of the ground.

Phage Therapy: Challenges and Opportunities

The development of antibiotic resistance in bacteria is a growing concern. This situation demands a search for antibiotic alternatives. Bacteriophages—natural viral predators of bacteria—are viewed as a possible alternative to treat bacterial infections. Many clinical trials today have not found phages effective as therapeutics. Some of the major challenges regarding usage of bacteriophage as a therapeutic have been: horizontal evolution of bacteria, limited host range of bacteriophage, removal of endotoxins in preparations, the technical feasibility of isolation, mode of administration, rapid clearance and immune rejection.These issues have been addressed in this review. Applications of genetic engineered phages and other remarkable non-human applications are also discussed.

Morphological evolution of creek networks in 10 restored coastal wetlands in the UK

Coastal wetlands provide crucial ecosystem services including flood protection and carbon storage, but are being lost rapidly worldwide to the combined effects of sea-level rise, erosion and coastal urbanisation. Managed Realignment (MR) aims to mitigate for these losses by restoring reclaimed land to tidal influence. Data of creek evolution is critical to assess the performance of design strategies and improve design and implementation practices. This data descriptor provides a dataset of the horizontal morphological evolution of creek systems from various initial conditions in 10 MR schemes across the UK. Using a semi-automated workflow, morphological creek parameters were extracted from 52 lidar datasets at 1 m horizontal resolution spanning 2 to 20 years post-breach. This constitutes the most comprehensive systematic monitoring of MR creek morphology to date. The dataset will assist future MR design and provide baseline morphological information for ecological and biogeochemical surveying.

Horizontal transfer and evolution of the biosynthetic gene cluster for benzoxazinoids in plants

Benzoxazinoids are a class of protective and allelopathic plant secondary metabolites that have been identified in multiple grass species and are encoded by the Bx biosynthetic gene cluster (BGC) in maize. Data mining of 41 high-quality grass genomes identified complete Bx clusters (containing genes Bx1–Bx5 and Bx8) in three genera (Zea, Echinochloa, and Dichanthelium) of Panicoideae and partial clusters in Triticeae. The Bx cluster probably originated from gene duplication and chromosomal translocation of native homologs of Bx genes. An ancient Bx cluster that included additional Bx genes (e.g., Bx6) is presumed to have been present in ancestral Panicoideae. The ancient Bx cluster was putatively gained by the Triticeae ancestor via horizontal transfer (HT) from the ancestral Panicoideae and later separated into multiple segments on different chromosomes. Bx6 appears to have been under less constrained selection compared with the Bx cluster during the evolution of Panicoideae, as evidenced by the fact that it was translocated away from the Bx cluster in Zea mays, moved to other chromosomes in Echinochloa, and even lost in Dichanthelium. Further investigations indicate that purifying selection and polyploidization have shaped the evolutionary trajectory of Bx clusters in the grass family. This study provides the first candidate case of HT of a BGC between plants and sheds new light on the evolution of BGCs.

Horizontal vs Vertical Evolution of the Compositional and Morphological Profiles in Nanostructured Titania Thin-Films for Photocatalytic Application

Horizontal vs Vertical Evolution of the Compositional and Morphological Profiles in Nanostructured Titania Thin-Films for Photocatalytic Application

EU Expert Bodies in Light of the Glyphosate Saga and the Dieselgate Scandal

Several scandals shed light on the eroding capacity and legitimacy of the Single Market’s scientific decision-making in the current era of constant economic, environmental and societal challenges when the need for solid science has never been greater. A sector-specific nature still characterises the EU law and the Single Market competencies. Yet, the emerging relevance of the EU law’s horizontal evolution inevitably leads us to the cross-sectoral elements of EU expert bodies and scientific decision-making. The purposes of this paper are 1. to describe the evolution of EU expert bodies with the comparison of two relatively diverse policy areas of the EU’s food sector and transportation, which are similarly characterised by the scandals of the glyphosate saga and the Dieselgate scandal; 2. to explore the sector-specific elements of the scientific decision-making of these

Observations of bay-breeze and ozone events over a marine site during the OWLETS-2 campaign

Land-sea recirculation such as bay and sea-breezes are important local circulations that facilitate pollution events. Measurements over a marine site in the Chesapeake Bay revealed the evolution of two bay-breeze events and associated ozone vertical structure. The horizontal and vertical structure of the bay-breeze was detailed using scanning Doppler wind lidar measurements and a ground-based ozone lidar was used to characterize the vertical distribution of ozone. The two bay-breeze events on 29–30 June 2018 observed during the Ozone Water-Land Environmental Transition Study Phase 2 (OWLETS-2) campaign showed distinct differences in the horizontal and vertical evolution of wind as well as the accompanying vertical structure of ozone. The analysis of the wind circulation showed that the intensity of the offshore flow plays an important role in the initiation time, development, and strength of the bay-breeze on both days. Results showed increased surface ozone concentrations during times of relatively low or decreasing bay-breeze height and weak upwards vertical motion. Upwards vertical motions were significantly enhanced on 30 June 2018 and presented with a decrease in surface ozone concentrations, yet enhanced ozone values were lofted above the surface near the lofted offshore flow. This study shows that both the vertical structure and evolution of pollutants can be impacted by the bay-breeze events through dilution and transport.

Is Global Microbial Biodiversity Increasing, Decreasing, or Staying the Same?

Animal and plant biodiversity is decreasing. In contrast, the global direction and the pace of change in microbial, including viral, biodiversity is unknown. Important niches for microbial diversity occur in highly specific associations with plants and animals, and these niches are lost as hosts become extinct. The taxonomic diversity of human gut bacteria is reported to be decreasing. On the other hand, SARS-CoV-2 variation is increasing. Where microbes are concerned, Darwin’s “tangled bank” of interdependent organisms may be composed mostly of other microbes. There is the likelihood that as some classes of microbes become extinct, others evolve and diversify. A better handle on all processes that affect microbial biodiversity and their net balance is needed. Lack of insight into the dynamics of evolution of microbial biodiversity is arguably the single most profound and consequential unknown with regard to human knowledge of the biosphere. If some or all parts of microbial diversity are relentlessly increasing, then survey approaches may be too slow to ever catch up. New approaches, including single-molecule or single-cell sequencing in populations, as well as focused attention on modulators and vectors of vertical and horizontal evolution may offer more direct insights into some aspects of the pace of microbial evolution.

Genetic Variation in the Glycoprotein B Sequence of Equid Herpesvirus 5 among Horses of Various Breeds at Polish National Studs.

Equid herpesvirus 5 (EHV-5) is one of two γ-herpesviruses that commonly infect horses worldwide. The objective of the study was to estimate the genetic variability within EHV-5 viruses circulating among horses in Poland. Partial glycoprotein B (gB) sequences from 92 Polish horses from 13 studs throughout Poland were compared to each other and to three EHV-5 sequences from other countries. Despite the overall high level of conservation, considerable variability was observed around the putative furin cleavage site. Based on phylogenetic analysis, the viruses clustered within two major lineages (A and B), with further sub-clustering within group A. The clustering of EHV-5 sequences was independent of age or geographical origin of the sampled horses. Recombination was identified as one of the factors contributing to the genomic heterogeneity. Viruses from unweaned foals were more similar to viruses from other foals at the same stud than to viruses form their dams, suggesting the horizontal transfer and/or evolution of EHV-5 within individual hosts. Our data indicate that the gB sequence is not suitable for tracking the source of EHV-5 infection. Further research is needed to elucidate the importance of the sequence variability around the EHV-5 gB furin cleavage site on the biology of the virus.

The role of sorption-induced coal matrix shrinkage on permeability and stress evolutions under replicated in situ condition for CBM reservoirs

Matrix shrinkage is a unique property of coal which dictates the sorption induced strain in the constitutive relation. Both permeability and stress profiles are passively modified with continuous depletion and they are intrinsically controlled by both poroelastic and matrix shrinkage properties. The models for quantifying matrix shrinkage related effects including horizontal stress loss, vertical strain variation and permeability evolution were proposed. The matrix shrinkage property was also coupled into the poroelastic relationships to study the potential possibility of local failure. Experimental study was performed to measure the permeability and its dynamic applied horizontal stress under replicated in situ uniaxial strain condition. The effects of sorption induced horizontal stress evolution varies with gas types depending on the sorption intensity. The vertical strain of coal bulk under uniaxial strain condition consists of the sorption induced matrix shrinkage/swelling strain, cleat volume strain and matrix mechanical strain due to changes of pore pressure and external stresses, which was validated against with the experiment data. As gas depletion from 4.14 MPa to 0.55 MPa, matrix shrinkage effects can lead to the permeability ratio nonlinearly increases from 1 to 2.27 (~127%) for methane and from 1 to 4.58 (~358%) for carbon dioxide, respectively. Additionally, the magnitude of the vertical effective stress always increases with continuous gas depletion, but the horizontal effective stress may increase or decrease depending on the intensity of sorption-induced matrix shrinkage. The local deviatoric effective stress tends to increase by considering matrix shrinkage effect, which potentially increase the possibility of local coal failure.

Mechanism and Prevention and Control of Mine Earthquake in Thick and Hard Rock Strata considering the Horizontal Stress Evolution of Stope

This study investigated the mechanism, prevention measures, and control methods for earthquake disasters typically occurring in mines with thick and hard rock strata. A mine stope with large faults and thick hard rock strata in Hebei Province was taken as the background study object. Then, theoretical analysis and numerical simulation methods were adopted in conjunction with field monitoring to explore how horizontal stress evolves in the thick and hard hanging roofs of such mines, potentially leading to mining earthquakes. Then, based on the obtained results, a mining design method was proposed to reduce the horizontal stress levels of earthquake mitigation. The results showed that, under the control of large faults, semiopen and semiclosed stopes with thick hard rock strata are formed, which cause influentially pressurized and depressurized zones during the evolution of the overburden movements and horizontal stress. It was determined that the stress concentrations mainly originated from the release and transfer of horizontal stress during the rock fractures and movements in the roof areas, which were calculated using a theoretical estimation model. The horizontal stress concentrations formed “counter torques” at both ends of the thick and hard strata, which prevented the support ending due to tensile failures. As a result, the limit spans were increased. This study proposed a mining strategy of using narrow working faces, strip mining processes, and reasonable mining speeds, which could effectively reduce horizontal stress concentrations and consequently prevent and control mining earthquakes. This study’s research results were successfully applied to the mining practices in working face 16103.

Numerical modeling of soil liquefaction and lateral spreading using the SANISAND-Sf model in the LEAP experiments

Laboratory element and centrifuge tests from LEAP-UCD-2017 and LEAP-Asia-2019 were used for model calibration and evaluation in a dynamic coupled analysis of a saturated and gently sloped deposit of sand subjected to base excitation. The paper focuses on using a recently proposed novel constitutive ingredient for modeling the post-liquefaction large cyclic shear strains in sands. An existing critical state compatible, bounding surface plasticity reference model is used, with and without this new constitutive ingredient, to explore its improved modeling capabilities. The constitutive model was first calibrated based on available laboratory element tests on Ottawa-F65 sand, and compared to the reference model showed significantly improved performance in capturing the strain-based liquefaction strength curve of a series of undrained hollow cylinder cyclic torsional shear tests. The calibrated models were used in Class-C prediction of the slope surface deformation in five centrifuge tests on a mildly sloping liquefiable ground of the same soil subjected to dynamic loading, in the three-dimensional finite difference program FLAC3D. The simulation results were compared with experiments in terms of acceleration history, spectral response, excess pore water pressure development, and horizontal displacement evolution at specified control points. The vectors and contours of displacements at the end of shaking also revealed a pattern of slope deformation consistent with that of a gently sloped liquefiable ground. Following the insights from the performance of the models in simulation of the slope response, the calibration was adjusted to more realistically account for the impact of initial static shear stress on the development of post-liquefaction shear strains. The models were again used for Class-C1 prediction of the slope deformation of the same centrifuge tests. The overall assessment revealed the capabilities and limitations of the models in simulating the soil liquefaction strength and its post-liquefaction response.