Differences In Evolutionary Rates Research Articles

Two methods to analyze radial diffusion ensembles: The perils of space- and time-dependent diffusion

Particle dynamics in Earth's outer radiation belt can be modeled using a diffusion framework, where large-scale electron movements are captured by a diffusion equation across a single adiabatic invariant, L*(L). While ensemble models are promoted to represent physical uncertainty, as yet there is no validated method to analyze radiation belt ensembles. Comparisons are complicated by the domain dependent diffusion, since diffusion coefficient DLL is dependent on L. We derive two tools to analyze ensemble members: time to monotonicity tm and mass/energy moment quantities N,E. We find that the Jacobian (1/L2) is necessary for radiation belt error metrics. Components of ∂E/∂t are explicitly calculated to compare the effects of outer and inner boundary conditions, and loss, on the ongoing diffusion. Using tm, N, and E, we find that: (a) different physically motivated choices of outer boundary condition and location result in different final states and different rates of evolution; (b) the gradients of the particle distribution affect evolution more significantly than DLL; (c) the enhancement location, and the amount of initial background particles, are both significant factors determining system evolution; (d) loss from pitch-angle scattering is generally dominant; it mitigates but does not remove the influence of both initial conditions and outer boundary settings, which are due to the L-dependence of DLL. We anticipate that this study will promote renewed focus on the distribution gradients, on the location and nature of the outer boundary in radiation belt modeling, and provide a foundation for systematic ensemble modeling.

Absence of heterosis for hypoxia tolerance in F1 hybrids of Tigriopus californicus.

Hybridization produces a range of outcomes from advantageous to disadvantageous, and a goal of genetic research is to understand the gene interactions that generate these outcomes. Interactions between cytoplasmic elements, such as mitochondria, and the nucleus may be particularly vulnerable to accruing disadvantageous combinations as a result of their different rates of evolution. However, mitonuclear incompatibilities often do not have an observable effect until the F2 and later generations. We used Tigriopus californicus, a model system for mitonuclear incompatibilities that is also known for exhibiting heterosis in the F1 generation, to test whether hypoxia was more stressful for mitonuclear interactions than other environmental stressors. We generated 284 parental and 436 F1 hybrids from four population crosses (720 total) and compared parental and F1 populations for hypoxia tolerance. We observed that, on average, F1 hybrids were less likely to survive a hypoxia stress test than parental populations (Parental:F1 coefficients ranged from -0.04 to 0.14 with none significantly different from 0). This suggests that hypoxia may be a particularly intense stressor for mitonuclear coordination, and that hybridization outcomes vary by trait.

Rapid evolution of mitochondrion-related genes in haplodiploid arthropods

BackgroundMitochondrial genes and nuclear genes cooperate closely to maintain the functions of mitochondria, especially in the oxidative phosphorylation (OXPHOS) pathway. However, mitochondrial genes among arthropod lineages have dramatic evolutionary rate differences. Haplodiploid arthropods often show fast-evolving mitochondrial genes. One hypothesis predicts that the small effective population size of haplodiploid species could enhance the effect of genetic drift leading to higher substitution rates in mitochondrial and nuclear genes. Alternatively, positive selection or compensatory changes in nuclear OXPHOS genes could lead to the fast-evolving mitochondrial genes. However, due to the limited number of arthropod genomes, the rates of evolution for nuclear genes in haplodiploid species, besides hymenopterans, are largely unknown. To test these hypotheses, we used data from 76 arthropod genomes, including 5 independently evolved haplodiploid lineages, to estimate the evolutionary rates and patterns of gene family turnover of mitochondrial and nuclear genes.ResultsWe show that five haplodiploid lineages tested here have fast-evolving mitochondrial genes and fast-evolving nuclear genes related to mitochondrial functions, while nuclear genes not related to mitochondrion showed no significant evolutionary rate differences. Among hymenopterans, bees and ants show faster rates of molecular evolution in mitochondrial genes and mitochondrion-related nuclear genes than sawflies and wasps. With genome data, we also find gene family expansions and contractions in mitochondrion-related genes of bees and ants.ConclusionsOur results reject the small population size hypothesis in haplodiploid species. A combination of positive selection and compensatory changes could lead to the observed patterns in haplodiploid species. The elevated evolutionary rates in OXPHOS complex 2 genes of bees and ants suggest a unique evolutionary history of social hymenopterans.

Molecular characterization, genetic divergence, expression of encapsidiation and synergism by a bipartite begomovirus; Tomato leaf curl Palampur virus (ToLCPMV) infecting bitter gourd (Momordica charantia)

The Tomato leaf curl Palampur virus (ToLCPMV) is a bipartite begomovirus that poses a substantial risk to agriculture by infecting a variety of crops, including cucurbitaceous group. This study examines the manifestation of encapsidation and synergism by ToLCPMV in bitter gourd (Momordica charantia) and focuses on its epidemiological approaches and implications of managing this virus in tomatoes growing areas. Through the utilization of molecular and biological techniques, we have successfully ascertained the epidemiology of this highly destructive virus, highlighting the vital roles played by its two genetic components. An analysis was conducted to identify the mechanism by which the virus clusters its DNA into virions, known as the encapsidation process. Additionally, the impact of synergism with other viral or environmental factors over the degree of infection was examined. The evolutionary rate differences among sites were modeled deploying a discrete Gamma distribution with 5 categories and a [+G] parameter. The results of this study provide important and unique information about synergism, encapsidiation and host-virus interactions. Sequencing study revealed that the bipartite ToLCPMV is linked to the occurrence of leaf curl disease in bitter gourd. The DNA-A and DNA-B of the ToLCPMV isolates infecting bitter gourd (SP1-4) showed 89 %, 93 %, 95 %, and 98 % similarity respectively. Mean evolutionary rates in these categories were 0.19, 0.47, 0.79, 1.24, 2.31 substitutions per site. Unexpectedly, the DNA-A sequences of ToLCPMV that infect this particular host seemed to be an amalgamation of sequences that are closely associated with tomato leaf curl New Delhi virus (ToLCNDV). Additionally, reiterate cropping of tomatoes with vegetables expanded the virus's host geographic region. This understanding will create some specific ways to regulate the dissemination of ToLCPMV and minimize its adverse impacts in tomato growing regions. Through the implementation of these strategies, the ability of crops to withstand and recover from adverse conditions can be enhanced, so encouraging the adoption of sustainable farming practices in affected regions.

Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole-genome duplications.

Identification of allelic or corresponding genes (pan-genes) within a species or genus is important for discovery of biologically significant genetic conservation and variation. Similarly, identification of orthologs (gene families) across wider evolutionary distances is important for understanding the genetic basis for similar or differing traits. Especially in plants, several complications make identification of pan-genes and gene families challenging, including whole-genome duplications, evolutionary rate differences among lineages, and varying qualities of assemblies and annotations. Here, we document and distribute a set of workflows that we have used to address these problems. Pandagma is a set of configurable workflows for identifying and comparing pan-gene sets and gene families for annotation sets from eukaryotic genomes, using a combination of homology, synteny, and expected rates of synonymous change in coding sequence. The Pandagma workflows, example configurations, implementation details, and scripts for retrieving public datasets, are available at https://github.com/legumeinfo/pandagma.

A general principle governing neuronal evolution reveals a human-accelerated neuron type potentially underlying the high prevalence of autism in humans.

The remarkable ability of a single genome sequence to encode a diverse collection of distinct cell types, including the thousands of cell types found in the mammalian brain, is a key characteristic of multicellular life. While it has been observed that some cell types are far more evolutionarily conserved than others, the factors driving these differences in evolutionary rate remain unknown. Here, we hypothesized that highly abundant neuronal cell types may be under greater selective constraint than rarer neuronal types, leading to variation in their rates of evolution. To test this, we leveraged recently published cross-species single-nucleus RNA-sequencing datasets from three distinct regions of the mammalian neocortex. We found a strikingly consistent relationship where more abundant neuronal subtypes show greater gene expression conservation between species, which replicated across three independent datasets covering >106 neurons from six species. Based on this principle, we discovered that the most abundant type of neocortical neurons-layer 2/3 intratelencephalic excitatory neurons-has evolved exceptionally quickly in the human lineage compared to other apes. Surprisingly, this accelerated evolution was accompanied by the dramatic down-regulation of autism-associated genes, which was likely driven by polygenic positive selection specific to the human lineage. In sum, we introduce a general principle governing neuronal evolution and suggest that the exceptionally high prevalence of autism in humans may be a direct result of natural selection for lower expression of a suite of genes that conferred a fitness benefit to our ancestors while also rendering an abundant class of neurons more sensitive to perturbation.

Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation.

The role of interspecific hybridization has recently seen increasing attention, especially in the context of diversification dynamics. Genomic research has now made it abundantly clear that both hybridization and introgression-the exchange of genetic material through hybridization and backcrossing-are far more common than previously thought. Besides cases of ongoing or recent genetic exchange between taxa, an increasing number of studies report "ancient introgression"- referring to results of hybridization that took place in the distant past. However, it is not clear whether commonly used methods for the detection of introgression are applicable to such old systems, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species, affected by recent or ongoing genetic exchange. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violated as evolutionary divergence increases. To test the limitations of introgression detection methods when being applied to old systems, we simulated thousands of genomic datasets under a wide range of settings, with varying degrees of among-species rate variation and introgression. Using these simulated datasets, we showed that some commonly applied statistical methods, including the D-statistic and certain tests based on sets of local phylogenetic trees, can produce false-positive signals of introgression between divergent taxa that have different rates of evolution. These misleading signals are caused by the presence of homoplasies occurring at different rates in different lineages. To distinguish between the patterns caused by rate variation and genuine introgression, we developed a new test that is based on the expected clustering of introgressed sites along the genome and implemented this test in the program Dsuite.

Dynamics of star clusters with tangentially anisotropic velocity distribution

Recent high-precision observations with HST and Gaia enabled new investigations of the internal kinematics of star clusters (SCs) and the dependence of kinematic properties on the stellar mass. These studies raised new questions about the dynamical evolution of self-gravitating stellar systems. We aim to develop a more complete theoretical understanding of how the various kinematical properties of stars affect the global dynamical development of their host SCs. We perform $N$-body simulations of globular clusters with isotropic, radially anisotropic, and tangentially anisotropic initial velocity distributions. We also study the effect of an external Galactic tidal field. We obtain three main results. First, compared to the conventional, isotropic case, the relaxation processes are accelerated in the tangentially anisotropic models and, in agreement with our previous investigations, are slower in the radially anisotropic ones. This leads to, for example, more rapid mass segregation in the central regions of the tangential models or their earlier core collapse. Second, although all SCs become isotropic in the inner regions after several relaxation times, we observe differences in the anisotropy profile evolution in the outer cluster regions --- all tidally filling models gain tangential anisotropy there, while the underfilling models become radially anisotropic. Third, we observe different rates of evolution towards energy equipartition (EEP). While all SCs evolve towards EEP in their inner regions (regardless of the filling factor), the outer regions of the tangentially anisotropic and isotropic models are evolving to an `inverted' EEP (i.e.\ with the high-mass stars having higher velocity dispersion than the low-mass ones). The extent (both spatial and temporal) of this inversion can be attributed to the initial velocity anisotropy --- it grows with increasing tangential anisotropy and decreases as the radial anisotropy rises.

The macroevolution of sexual size dimorphism in birds

Abstract There is considerable variation of sexual size dimorphism (SSD) in body mass among animal groups, yet the drivers of interspecific variation in SSD are still poorly understood. Possible mechanisms have been suggested, including sexual selection, selection for fecundity in females, niche divergence between sexes, and allometry, yet their relative importance is still poorly understood. Here, we tested predictions of these four hypotheses in different avian groups using a large-scale dataset on SSD of body mass for 4761 species. Specifically, we estimated the probability of transition between male- and female-biased SSD, tested for differences in evolutionary rates of body mass evolution for males and females, and assessed the potential ecological and spatial correlates of SSD. Our results were consistent with the sexual selection, fecundity, and niche divergence hypotheses, but their support varied considerably among avian orders. In addition, we found little evidence that the direction of SSD affected the evolution of male or female body mass, and no relationship was detected between SSD and environmental predictors (i.e. temperature and precipitation seasonality, productivity, species richness, and absolute latitude). These results suggest that avian evolution of SSD is likely to be multifactorial, with sexual selection, fecundity, and niche divergence playing important roles in different avian orders.

Elevated evolutionary rates of biting biomechanics reveal patterns of extraordinary craniodental adaptations in some herbivorous dinosaurs

AbstractAdaptation to specialist ecological niches is a key innovation that has contributed to the evolutionary success of many vertebrate clades, underpinning the acquisition of diverse skull morphologies. Dinosaurs, which dominated Mesozoic terrestrial faunas, acquired herbivory multiple times, and evolution of these herbivorous adaptations is linked to drastic changes in dental and craniomandibular functional morphology, yet whether changes in functionally relevant phenotypic traits occurred more rapidly in herbivorous lineages compared to in carnivorous lineages remains largely untested in a statistical phylogenetic framework. Here, we infer rates of phenotypic evolution using phylogenetic variable‐rate models on relative biting edge (tooth row) lengths of 107 dinosaur taxa to test the hypothesis that the acquisition of herbivory is associated with rapid changes in mandibular biomechanics. We find elevated rates of biomechanical evolution in theropods with foreshortened and beaked skulls (Oviraptorosauria, Limusaurus), as well as in ceratopsians and Diplodocus. The presence and position of a reduced tooth row and increased jaw efficiency unite these high‐rate lineages, indicating selection for greater efficiency in biting biomechanics. Large departures from the isometric scaling of these mandibular characteristics helps explain the differences in evolutionary rates in these clades and those of other herbivorous theropods (Therizinosauria, Ornithomimosauria). Additionally, we hypothesize that extreme ontogenetic changes within species lifetimes may be behind some instances of branch‐wise elevated rates. Thus, we show how exceptional rates of biomechanical evolution can reveal signatures of ecological adaptations within dinosaur lineages as well as within‐species ontogenetic sequences.

Nematode histone H2A variant evolution reveals diverse histories of retention and loss and evidence for conserved core-like variant histone genes.

Histone variants are paralogs that replace canonical histones in nucleosomes, often imparting novel functions. However, how histone variants arise and evolve is poorly understood. Reconstruction of histone protein evolution is challenging due to large differences in evolutionary rates across gene lineages and sites. Here we used intron position data from 108 nematode genomes in combination with amino acid sequence data to find disparate evolutionary histories of the three H2A variants found in Caenorhabditis elegans: the ancient H2A.ZHTZ-1, the sperm-specific HTAS-1, and HIS-35, which differs from the canonical S-phase H2A by a single glycine-to-alanine C-terminal change. Although the H2A.ZHTZ-1 protein sequence is highly conserved, its gene exhibits recurrent intron gain and loss. This pattern suggests that specific intron sequences or positions may not be important to H2A.Z functionality. For HTAS-1 and HIS-35, we find variant-specific intron positions that are conserved across species. Patterns of intron position conservation indicate that the sperm-specific variant HTAS-1 arose more recently in the ancestor of a subset of Caenorhabditis species, while HIS-35 arose in the ancestor of Caenorhabditis and its sister group, including the genus Diploscapter. HIS-35 exhibits gene retention in some descendent lineages but gene loss in others, suggesting that histone variant use or functionality can be highly flexible. Surprisingly, we find the single amino acid differentiating HIS-35 from core H2A is ancestral and common across canonical Caenorhabditis H2A sequences. Thus, we speculate that the role of HIS-35 lies not in encoding a functionally distinct protein, but instead in enabling H2A expression across the cell cycle or in distinct tissues. This work illustrates how genes encoding such partially-redundant functions may be advantageous yet relatively replaceable over evolutionary timescales, consistent with the patchwork pattern of retention and loss of both genes. Our study shows the utility of intron positions for reconstructing evolutionary histories of gene families, particularly those undergoing idiosyncratic sequence evolution.

Sequencing, assembly, and genomic annotation of Leucoagaricus gongylophorus LEU18496, a dikarya mutualistic species.

The basidiomycete fungus Leucoagaricus gongylophorus is able to grow in the fungus garden of leaf-cutter ants. This mutualistic interaction has driven the evolutionary adaptation of L. gongylophorus, shaping its metabolism to produce enzymes adept at lignocellulosic biomass degradation. In this study, we undertook the comprehensive sequencing, assembly, and functional annotation of the genome of L. gongylophorus strain LEU18496, mutualistic fungus of the Atta mexicana. Our genomic analyses revealed a distinctive bimodal nature to the genome: a predominant region characterized by AT enrichment and low genetic density, alongside a smaller region exhibiting higher GC content and higher genetic density. The presence of transposable elements (TEs) within the AT-enriched region suggests genomic compartmentalization, facilitating differential evolutionary rates. With a gene count of 6748, the assembled genome of L. gongylophorus LEU18496 surpasses previous reports for this fungal species. Inspection of genes associated with central metabolism unveiled a remarkable abundance of carbohydrate-active enzymes (CAZymes) and fungal oxidative lignin enzymes (FOLymes), underscoring their pivotal roles in the life cycle of this fungus.

The contribution of evolvability to the eco-evolutionary dynamics of competing species.

Evolvability is the capacity of a population to generate heritable variation that can be acted upon by natural selection. This ability influences the adaptations and fitness of individual organisms. By viewing this capacity as a trait, evolvability is subject to natural selection and thus plays a critical role in eco-evolutionary dynamics. Understanding this role provides insight into how species respond to changes in their environment and how species coexistence can arise and be maintained. Here, we create a G-function model of competing species, each with a different evolvability. We analyze population and strategy (= heritable phenotype) dynamics of the two populations under clade initiation (when species are introduced into a population), evolutionary tracking (constant, small changes in the environment), adaptive radiation (availability of multiple ecological niches), and evolutionary rescue (extreme environmental disturbances). We find that when species are far from an eco-evolutionary equilibrium, faster-evolving species reach higher population sizes, and when species are close to an equilibrium, slower-evolving species are more successful. Frequent, minor environmental changes promote the extinction of species with small population sizes, regardless of their evolvability. When several niches are available for a species to occupy, coexistence is possible, though slower-evolving species perform slightly better than faster-evolving ones due to the well-recognized inherent cost of evolvability. Finally, disrupting the environment at intermediate frequencies can result in coexistence with cyclical population dynamics of species with different rates of evolution.

Evolution and distribution of rabies viruses from a panorama view.

Rabies kills more than 59,000 people annually, mainly in developing countries. Previous studies on the evolution and distribution of rabies viruses (RABVs) were scattered. Here, we explore the evolution and distribution of this deadly virus from a novel panorama view. Multiple bioinformatic software tools were employed to analyze the phylogenetic diversity, evolution, spatiotemporal, and distribution of RABVs. The analyses were based on 1,202 qualified full-length genomes of RABVs and numerous literatures. Of the 10 distinct phylogenetic clades of RABV that we identified, more frequent intra- and inter-clade recombination occurs in the sequences of Asian-SEA, Arctic, and Cosmopolitan clades isolated from China, while according to existing sequence information, RABV might originate from bats (posterior probability, PP = 0.75, PP = 0.60 inferred from N and L genes, separately) in North America (PP = 0.57, PP = 0.62 inferred from N and L genes, separately). Due to the difference in evolutionary rate of N (2.22 × 10-4 subs/site/year, 95% HPD 1.99-2.47 × 10-4 subs/site/year) and L genes (1.67 × 10-4 subs/site/year, 95% HPD 1.59-1.74 × 10-4 subs/site/year), the root age was 1,406.6 (95% HPD 1,291.2-1,518.2) and 1,122.7 (95% HPD 1,052.4-1,193.9) inferred from N and L genes, separately. Among other findings, Mephitidae plays an important role in the interspecific transmission and communication of RABV, which we found tends to spread to populations genetically proximate to the host. We also identified amino acids under positive selection in different genes of different clades as well as single nucleotide variation sites important for different lineages. IMPORTANCE Rabies virus is widely distributed all over the world, and wild animals are its largest potential reservoir. Our study offers a panorama view about evolution and distribution of rabies viruses and emphasizes the need to monitor the transmission dynamics of animal rabies.

A pioneering riparian community dominated by Nystroemiaceae gymnosperms from the Guadalupian (middle Permian) of China

A new fossil plant community is documented from the Upper Shihhotse Formation on the North China Block with an extremely unusual composition and diversity. Zircon U–Pb dating yields an age of 268.3 ± 2.3 Ma during the mid-Roadian to early Wordian stages of the Guadalupian. The community occurs in two beds and is dominated by fossils of the gymnosperm family Nystroemiaceae, which account for up to 99% of specimens recovered and comprise stems, branches, roots, ovuliferous complexes of Nystroemia pectiniformis and N. sp., and leaves of Chiropteris reniformis. The two different species of Nystroemia are distinguished on size and apical features of ovules, with N. pectiniformis having two apical bicornuate horns, whereas N. sp. has apical auricular extensions. Leaves of C. reniformis are megaphyllous and possess a long petiole and net venation. In the Cathaysian flora, different species of Nystroemiaceae are distinguished by features of their ovules and habit, but all bear leaves of C. reniformis which suggests evolutionary modularity and different rates of evolution between the ovules and leaves. Both N. pectiniformis and N. sp. are shown to have been short, uptight trees. Sedimentary evidence shows the community grew in a meandering fluvial setting with repeated river channel changes. Compared with contemporaneously diverse Cathaysian floral communities in the Upper Shihhotse Formation, the vegetation has a very restricted diversity and is a rare occurrence of a gymnosperm-dominated community. The Nystroemiaceae demonstrates an r-selective ecological strategy as pioneering plants adapted to living in unstable habitats and newly opened gaps in the riparian zone.

Finite‐time synchronization of network systems with linear and nonlinear couplings via quantized intermittent‐adaptive control

AbstractThis paper investigates the synchronization problem of network systems (NSs) via finite‐time (FIT) control techniques. First, the network systems include two complex networks with linear couplings, nonlinear couplings and different rates of evolution. In order to realize the goal of synchronization, intermittent‐adaptive control schemes with quantizer are designed. Then, several FIT synchronization criteria are established by using the designed controllers whose parameters could be adjusted automatically according to the adaptive laws. At the rest of this article, the numerical simulations are provided to illustrate our results.

The binding pocket properties were fundamental to functional diversification of the GDSL-type esterases/lipases gene family in cotton.

Cotton is one of the most important crops in the world. GDSL-type esterases/lipases (GELPs) are widely present in all kingdoms and play an essential role in regulating plant growth, development, and responses to abiotic and biotic stresses. However, the molecular mechanisms underlying this functional diversity remain unclear. Here, based on the identification of the GELP gene family, we applied genetic evolution and molecular simulation techniques to explore molecular mechanisms in cotton species. A total of 1502 GELP genes were identified in 10 cotton species. Segmental duplication and differences in evolutionary rates are the leading causes of the increase in the number and diversity of GELP genes during evolution for ecological adaptation. Structural analysis revealed that the GELP family has high structural diversity. Moreover, molecular simulation studies have demonstrated significant differences in the properties of the binding pockets among cotton GELPs. In the process of adapting to the environment, GELPs not only have segmental duplication but also have different evolutionary rates, resulting in gene diversity. This diversity leads to significant differences in the 3D structure and binding pocket properties and, finally, to functional diversity. These findings provide a reference for further functional analyses of plant GELPs.

Extensive non-coding sequence divergence between the major human pathogen Aspergillus fumigatus and its relatives.

Invasive aspergillosis is a deadly fungal disease; more than 400,000 patients are infected worldwide each year and the mortality rate can be as high as 50-95%. Of the ~450 species in the genus Aspergillus only a few are known to be clinically relevant, with the major pathogen Aspergillus fumigatus being responsible for ~50% of all invasive mold infections. Genomic comparisons between A. fumigatus and other Aspergillus species have historically focused on protein-coding regions. However, most A. fumigatus genes, including those that modulate its virulence, are also present in other pathogenic and non-pathogenic closely related species. Our hypothesis is that differential gene regulation - mediated through the non-coding regions upstream of genes' first codon - contributes to A. fumigatus pathogenicity. To begin testing this, we compared non-coding regions upstream of the first codon of single-copy orthologous genes from the two A. fumigatus reference strains Af293 and A1163 and eight closely related Aspergillus section Fumigati species. We found that these non-coding regions showed extensive sequence variation and lack of homology across species. By examining the evolutionary rates of both protein-coding and non-coding regions in a subset of orthologous genes with highly conserved non-coding regions across the phylogeny, we identified 418 genes, including 25 genes known to modulate A. fumigatus virulence, whose non-coding regions exhibit a different rate of evolution in A. fumigatus. Examination of sequence alignments of these non-coding regions revealed numerous instances of insertions, deletions, and other types of mutations of at least a few nucleotides in A. fumigatus compared to its close relatives. These results show that closely related Aspergillus species that vary greatly in their pathogenicity exhibit extensive non-coding sequence variation and identify numerous changes in non-coding regions of A. fumigatus genes known to contribute to virulence.

A Review on Equine Influenza from a Human Influenza Perspective.

Influenza A viruses (IAVs) have a main natural reservoir in wild birds. IAVs are highly contagious, continually evolve, and have a wide host range that includes various mammalian species including horses, pigs, and humans. Furthering our understanding of host-pathogen interactions and cross-species transmissions is therefore essential. This review focuses on what is known regarding equine influenza virus (EIV) virology, pathogenesis, immune responses, clinical aspects, epidemiology (including factors contributing to local, national, and international transmission), surveillance, and preventive measures such as vaccines. We compare EIV and human influenza viruses and discuss parallels that can be drawn between them. We highlight differences in evolutionary rates between EIV and human IAVs, their impact on antigenic drift, and vaccine strain updates. We also describe the approaches used for the control of equine influenza (EI), which originated from those used in the human field, including surveillance networks and virological analysis methods. Finally, as vaccination in both species remains the cornerstone of disease mitigation, vaccine technologies and vaccination strategies against influenza in horses and humans are compared and discussed.

Rates of evolutionary change of resident Escherichia coli O157:H7 differ within the same ecological niche

BackgroundShiga toxin-producing Escherichia coli (STEC) O157:H7 is a pathogen known to reside in cattle feedlots. This retrospective study examined 181 STEC O157:H7 strains collected over 23 years from a closed-system feedlot. All strains were subjected to short-read sequencing, with a subset of 36 also subjected to long-read sequencing.ResultsOver 96% of the strains fell into four phylogenetically distinct clades. Clade membership was associated with multiple factors including stx composition and the alleles of a well-characterized polymorphism (tir 255 T > A). Small plasmids (2.7 to 40 kb) were found to be primarily clade specific. Within each clade, chromosomal rearrangements were observed along with a core phageome and clade specific phages. Across both core and mobile elements of the genome, multiple SNP alleles were in complete linkage disequilibrium across all strains within specific clades. Clade evolutionary rates varied between 0.9 and 2.8 SNP/genome/year with two tir A allele clades having the lowest evolutionary rates. Investigation into possible causes of the differing rates was not conclusive but revealed a synonymous based mutation in the DNA polymerase III of the fastest evolving clade. Phylogenetic trees generated through our bioinformatic pipeline versus the NCBI’s pathogen detection project were similar, with the two tir A allele clades matching individual NCBI SNP clusters, and the two tir T allele clades assigned to multiple closely-related SNP clusters.ConclusionsIn one ecological niche, a diverse STEC O157:H7 population exhibited different rates of evolution that associated with SNP alleles in linkage disequilibrium in the core genome and mobile elements, including tir 255 T > A.