Differences In Evolutionary Rates Research Articles

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.

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.

Dataset complexity impacts both MOTU delimitation and biodiversity estimates in eukaryotic 18S rRNA metabarcoding studies

AbstractHow does the evolution of bioinformatics tools impact the biological interpretation of high‐throughput sequencing datasets? For eukaryotic metabarcoding studies, in particular, researchers often rely on tools originally developed for the analysis of 16S ribosomal RNA (rRNA) datasets. Such tools do not adequately account for the complexity of eukaryotic genomes, the ubiquity of intragenomic variation in eukaryotic metabarcoding loci, or the differential evolutionary rates observed across eukaryotic genes and taxa. Recently, metabarcoding workflows have shifted away from the use of operational taxonomic units (OTUs) toward delimitation of amplicon sequence variants (ASVs). We assessed how the choice of bioinformatics algorithm impacts the downstream biological conclusions that are drawn from eukaryotic 18S rRNA metabarcoding studies. We focused on four workflows including UCLUST and VSearch algorithms for OTU clustering, and DADA2 and Deblur algorithms for ASV delimitation. We used two 18S rRNA datasets to further evaluate whether dataset complexity had a major impact on the statistical trends and ecological metrics: a “high complexity” (HC) environmental dataset generated from community DNA in Arctic marine sediments, and a “low complexity” (LC) dataset representing individually barcoded nematodes. Our results indicate that ASV algorithms produce more biologically realistic metabarcoding outputs, with DADA2 being the most consistent and accurate pipeline regardless of dataset complexity. In contrast, OTU clustering algorithms inflate the metabarcoding‐derived estimates of biodiversity, consistently returning a high proportion of “rare” molecular operational taxonomic units (MOTUs) that appear to represent computational artifacts and sequencing errors. However, species‐specific MOTUs with high relative abundance are often recovered regardless of the bioinformatics approach. We also found high concordance across pipelines for downstream ecological analysis based on beta‐diversity and alpha‐diversity comparisons that utilize taxonomic assignment information. Analyses of LC datasets and rare MOTUs are especially sensitive to the choice of algorithms and better software tools may be needed to address these scenarios.

Trait evolution rates shape continental patterns of species richness in North America's most diverse angiosperm genus (Carex, Cyperaceae)

AbstractEcological opportunity has been associated with increases in diversification rates across the tree of life. Under an ecological diversification model, the emergence of novel environments is hypothesized to promote morpho‐ and ecospace evolution. Whether this model holds at the clade level within the most species‐rich angiosperm genus found in North America (Carex, Cyperaceae) is yet to be tested. Recent works demonstrate a temporal coupling of climate cooling and widespread colonization of Carex in North America, implicating ecological diversification. In addition, research has consistently found asymmetric patterns of lineage‐level diversification in the genus. Why does variation in clade sizes exist in the genus? Is ecological diversification involved? In this study, we tested whether rates of morphological and ecological trait evolution are correlated with clade‐level species richness in Carex of North America north of Mexico. We constructed a phylogeny of 477 species—an almost complete regional sample. We estimated rates of evolution of morphological traits, habitat, and climatic niche and assessed whether differences in rates of evolution correlate with species richness differences in replicate non‐nested sister clades. Our work demonstrates significant positive correlations between climatic niche rates, habitat and reproductive morphological evolution, and species richness. This coupling of trait and niche evolution and species richness in a diverse, continental clade sample strongly suggests that the ability of clades to explore niche and functional space has shaped disparities in richness and functional diversity across the North American flora region. Our findings highlight the importance of the evolutionary history of trait and niche evolution in shaping continental and regional floras.

Drivers and patterns of bite force evolution in liolaemid lizards

Abstract Phenotypic variation is the result of selection on traits that are relevant in a given ecological context. Phylogenetic history, genetic drift, and any developmental or structural constraints may, however, limit variation in trait expression. It has been proposed that organismal performance traits take up a pivotal role in driving variation in morphology due to their central role in survival and reproductive success. However, how strong the links are between morphology and performance, and how the strength of this relationship impacts the rate of evolution of form and function need to be studied across a wider variety of systems to better understand the origin and evolution of biodiversity. Here we used data on the jaw system (muscle architecture and head dimensions) of liolaemid lizards to investigate the drivers of in vivo bite force variation and test for differences in evolutionary rates in morphology and performance. Our results show high rates of evolution for performance traits compared to morphological traits such as external head dimensions. Many-to-one mapping of morphology to performance, that is the possibility that different anatomical trait combinations lead to similar levels of performance, appears to be common in the jaw system of these lizards. Finally, traits showing greater mechanical sensitivity (muscle cross-sectional areas) showed higher rates of evolution compared to traits involved in other functions and that are probably subject to trade-offs (e.g. head width).

Extreme climate shifts pest dominance hierarchy through thermal evolution and transgenerational plasticity

Abstract Dominance hierarchy, the dominance ranking of members in a community, is determined by the relative population fitness of coexisting species. Climate change can shift dominance hierarchies depending on how species respond to changing climate, but ecological mechanisms underlying such shifts remain largely unknown. Specifically, dominance hierarchy shifts under climate change have rarely been linked to eco‐evolutionary responses to thermal extremes, which we consider in this study. We conducted an 8‐year field survey to link extreme high‐temperature events to the shift in dominance hierarchy of two worldwide cereal aphid species (Rhopalosiphum padi and Sitobion avenae), which may respond rapidly through evolutionary or plastic responses to thermal extremes due to their short generation duration, clonal structure and high thermal sensitivity. To further understand the mechanism involved in this change in species' dominance, we characterised aphid heat tolerance and demography of the two species sourced from relatively mild (Xinxiang) and hot (Wuhan) locations in a common garden design and compared the same measures in up‐ and down‐selected lines of the two aphid species. We found that accumulation of extreme high‐temperature events (EHTs) affected per capita growth rate of S. avenae but not R. padi, driving a shift in annual relative dominance of these two common species in wheat fields. Furthermore, evidence from common garden tests and artificial thermal selection revealed that evolutionary and plastic changes in thermal tolerance under EHTs were species‐dependent; R. padi evolved higher heat tolerance without reducing fitness while S. avenae did not evolve heat tolerance but showed detrimental transgenerational plastic changes under thermal extremes. Rhopalosiphum padi may take over the dominant position of S. avenae in a warmer future, due to a higher evolutionary potential of heat tolerance and less detrimental plasticity following selection. Field surveys and laboratory experiments together point to a shift in species dominance related to interspecific differences in species' evolutionary rates and transgenerational plasticity of thermal traits during selection events associated with extreme climatic conditions. This study highlights that eco‐evolutionary dynamics can contribute to community responses to natural thermal extremes. A free Plain Language Summary can be found within the Supporting Information of this article.

Dynamics of Nanoparticle Self-Assembly by Liquid Crystal Sorting in Two Dimensions

We study nonlinear dynamical equations for coupled conserved and non-conserved fields describing nanoparticle concentration and liquid crystal order parameter, respectively, and solve them numerically over bidimensional domains. These equations model the rapid segregation of nanoparticles away from nematic domains, which has been observed experimentally in a suspension of gold nanoparticles in 5CB below the isotropic-nematic transition temperature. We contrast the different behaviors obtained when the LC order parameter is treated as a scalar or a tensor, as well as the different rates of evolution observed with each of these. We find, after an instantaneous quench lowering the temperature below the transition one, an initial linear regime where the ordering of the nematic phase proceeds exponentially with time. Only after a lag period the nanoparticle material couples effectively to the LC order parameter and segregates to regions that are less orientationally ordered (extended domain walls for a scalar order parameter, but point disclinations for a tensor one). The lag period is followed by the onset of nonlinear dynamics and saturation of the order parameter. The choice of a scalar or tensor LC order parameter does not change this sequence but results in a clear overshooting of the nonlinear saturation level for the tensor order parameter case. These results are found to be insensitive to weak anchoring due to coupling of gradients of the conserved and non-conserved variables, for the nanoparticle concentrations and anchoring parameters studied. Our modeling approach can be extended in a straightforward manner to cases where the cooling rate is finite and to other systems where a locally conserved concentration is coupled to a orientation field, such as active Langmuir monolayers, and possibly to other examples of nonlinear dynamics in ecological or excitable media problems.

An Investigation of the Variations in Complete Mitochondrial Genomes of Lingula anatina in the Western Pacific Region.

Simple SummaryLingula anatina has been attracted researchers because its morphological characteristics show limited changes compared to the ancestor. Even though L. anatina is a common brachiopod in the western Pacific region, a few studies were performed to investigate genetic variations of this species. To understand the mitogenomic diversity of L. anatina in the region, the present study conducted comparative analyses of mitogenome sequences from Korea, Vietnam, and Japan. The sequencing results indicated that L. anatina mitogenomes are extraordinarily longer than the typical animal mitogenome. Besides, the gene orders of L. anatina mitogenomes are variable among localities. The calculation based on protein-coding genes revealed relatively low substitution rates among mitogenome sequences from Buan (Korea), Doson (Vietnam) and Yanagawa (Japan). The phylogenetic analyses indicated the divergence of L. anatina in the western Pacific region. This investigation provides new information on the molecular systematics of L. anatina and could be helpful in exploring the diversity and evolution of mitogenomes in brachipod.Lingula anatina is a brachiopod widely distributed in the western Pacific region. Even though L. anatina has been targeted for a number of biological studies, there is still limited information on intraspecific genetic variations of L. anatina. In this study, L. anatina specimens were collected from Korea and Vietnam, and complete mitochondrial genome (mitogenome) sequences were analyzed and compared with previous records. The total mitogenomes of L. anatina were 24,875 bp and 25,305 bp in size for Korean and Vietnamese specimens, respectively. Those mitogenomes are extraordinarily longer than the typical mitogenome size for an animal but shorter than the previous record from Yanagawa (Japan) for this species. The gene orders and the sizes of the protein-coding genes are also different from those for the Japanese specimen. Furthermore, the nonsynonymous (Ka) and synonymous (Ks) substitution rates in protein-coding genes (PCGs) were calculated to test the idea of evolutionary rate differences in mitochondrial genomes. The analyses showed relatively low Ka and Ks for the complete mitogenomes from Buan (Korea), Doson (Vietnam) and Yanagawa (Japan). The Ka/Ks ratio was less than 1 in comparisons of three localities, indicating the existence of purifying selection in this species. The phylogenetic analyses showed that L. anatina diverged among localities in the western Pacific region.

Progress on the origin, function and evolutionary mechanism of RHR transcription factor family.

Transcription factors are a class of proteins that regulate gene transcription and expression by binding to gene-specific sequences and play an essential role in regulating the biological activities of cells. The RHR (Rel-homology region) transcription factor family is the primary member of the IF (immunoglobulin fold) transcription factor superfamily, whose members contain the conserved Rel domain and IPT (immunoglobulin-like fold) domain. As an ancient transcription factor family, the RHR family continues differentiation on gene gain and loss through gene duplication, mutation, and silencing, accompanied with the evolution of diverse species. Natural selection has led to different rates of evolution among members of the family, and some domains of the protein family have shown unique mechanisms of evolution. However, the current reviews about the origin and differentiation of RHR family are rare. In this review, we summarize the research results on the distribution, classification, function, and evolution of the members of the RHR family in order to provide a reference and new idea for studying the evolution mechanism of the whole transcription factor family and the evolutionary relationship among species.