Factor In Evolution Research Articles

Ionomic Responses of Local Plant Species to Natural Edaphic Mineral Variations.

Leaf ionome indicates plant phylogenetic evolution and responses to environmental stress, which is a critical influential factor to the structure of species populations in local edaphic sites. However, little is known about leaf ionomic responses of local plant species to natural edaphic mineral variations. In the present study, all plant species and soil samples from a total of 80 soil sites in Shiozuka Highland were collected for multi-elemental analysis. Ioniomic data of species were used for statistical analysis, representing 24 species and 10 families. Specific preferences to ionomic accumulation in plants were obviously affected by the phylogeny, whereas edaphic impacts were also strong but limited within the phylogenetic preset. Correlations among elements resulted from not only elemental synergy and competition but also the adaptive evolution to withstand environmental stresses. Furthermore, ionomic differences of plant families were mainly derived from non-essential elements. The majority of variations in leaf ionome is undoubtedly regulated by evolutionary factors, but externalities, especially environmental stresses also have an important regulating function for landscape formation, determining that the contributions of each factor to ionomic variations of plant species for adaptation to environmental stress provides a new insight for further research on ionomic responses of ecological speciation to environmental perturbations and their corresponding adaptive evolutions.

Detecting dynamic community by fusing network embedding and nonnegative matrix factorization

Many systems in nature and society, ranging from types of cancers to engineering, can be modeled as temporal networks. Identification of dynamic communities is fundamental for investigating the mechanisms of systems. Compared with community detection in static networks, dynamic community detection is challenging because it simultaneously leverages clustering accuracy with clustering drift. Current methods employ the temporal smoothness framework to balance these two items, but the inaccuracy and complexity of these methods have been criticized. To overcome these issues, a novel algorithm called NE2NMF for dynamic community detection is proposed by fusing Network Embedding based Evolutionary Nonnegative Matrix Factorization. Specifically, we use third-order smoothness to characterize clustering drift by fusing snapshots of previous, current, and subsequent time steps, thereby improving the accuracy of the characterization of dynamic communities. Moreover, to reduce time complexity, we decompose the network embedding matrix, rather than the adjacency matrix of each snapshot on the basis of the equivalence between evolutionary non-negative matrix factorization (ENMF) and network embedding. Results demonstrate that NE2NMF outperforms state-of-the-art approaches in terms of accuracy and robustness.

Experiences of Ugliness in Nature and Urban environments

In folk psychology experiences of ugliness are associated with the negation of beauty and disorder, but empirical evidence is remarkably rare. Here, participants (called informed) took 102 photographs of ugly landscapes and urban scenes and reflected on their experiences. Later, participants naïve to the intentional ugliness in the photographs rated landscapes higher than informed participants. The ratings for urban scenes were similar in the two cohorts. Reflective notes revealed that emotional experiences with visual ugliness could overlap (e.g. decay), but ugliness was associated more frequently with fear and death in landscapes, and with sadness and disgust in urban scenes. The findings uncovered a complex layer of associations. Experiences triggered by perceived ugliness were contingent on a composite of socio-cultural, emotional, and evolutionary factors. Rather than being the endpoint on an aesthetic scale culminating with beauty, ugliness seems to be experienced as an independent aesthetic experience with its own processing streams.

Fermented food consumption in wild nonhuman primates and its ecological drivers.

Although fermented food use is ubiquitous in humans, the ecological and evolutionary factors contributing to its emergence are unclear. Here we investigated the ecological contexts surrounding the consumption of fruits in the late stages of fermentation by wild primates to provide insight into its adaptive function. We hypothesized that climate, socioecological traits, and habitat patch size would influence the occurrence of this behavior due to effects on the environmental prevalence of late-stage fermented foods, the ability of primates to detect them, and potential nutritional benefits. We compiled data from field studies lasting at least 9 months to describe the contexts in which primates were observed consuming fruits in the late stages of fermentation. Using generalized linear mixed-effects models, we assessed the effects of 18 predictor variables on the occurrence of fermented food use in primates. Late-stage fermented foods were consumed by a wide taxonomic breadth of primates. However, they generally made up 0.01%-3% of the annual diet and were limited to a subset of fruit species, many of which are reported to have mechanical and chemical defenses against herbivores when not fermented. Additionally, late-stage fermented food consumption was best predicted by climate and habitat patch size. It was more likely to occur in larger habitat patches with lower annual mean rainfall and higher annual mean maximum temperatures. We posit that primates capitalize on the natural fermentation of some fruits as part of a nutritional strategy to maximize periods of fruit exploitation and/or access a wider range of plant species. We speculate that these factors contributed to the evolutionary emergence of the human propensity for fermented foods.

O equilíbrio de Hardy-Weinberg no sistema sanguíneo ABO: um estudo de caso em Engenheiro Coelho – SP

The genetics of human populations is the branch of Genetics that studies the dynamics of genes in natural populations, aiming at the elucidation of mechanisms that alter their genetic composition. Among the fundamentals of this science is the Hardy-Weinberg Equilibrium, which determines that gene frequencies remain unchanged and genotypic proportions reach a stable balance, obtaining the same constant relation with each other over time. To demonstrate this principle, it is necessary to admit that the studied population is not subject to evolutionary factors or to those that alter genotypic frequencies, increasing the homozygosity. More specifically, it is necessary to assume that the population obeys the following premises: random mating, infinite population, non-overlapping generations, in addition to the absence of mutation, selection and migration. More than recalling basic concepts of Genetics and Statistics, this article aims to describe the Bernstein Method for verifying the gene equilibrium for blood types. The research is concluded with a case study in the city of Engenheiro Coelho - SP, where the Hardy-Weinberg Equilibrium for blood types in the population is verified.

Inbreeding depression contributes to the maintenance of habitat segregation between closely related monkeyflower species.

Incompletely reproductively isolated species often segregate into different microhabitats, even when they are able to survive and reproduce in both habitats. Longer term evolutionary factors may contribute to this lack of cross-habitat persistence. When reproductive interference reduces immigrant fitness, assortative mating, including self-fertilization, increases immigrants' fitness in a single generation, but longer term, inbreeding depression may reduce the chance of population persistence. Two California monkeyflower species repeatedly segregate into drier and wetter areas in their zone of sympatry. To test whether inbreeding depression may contribute to the maintenance of this segregation pattern, we transplanted outbred and successively inbred Mimulus guttatus and Mimulus nudatus into their native habitats and heterospecific habitats. We measured germination, survival, and seed set and found that recurrent selfing reduced all aspects of fitness in both species, most strongly in foreign habitats. A simulation model, parameterized from the transplant experiment, found that inbreeding reduced fitness to such an extent that sequentially inbred populations of either species would be unable to persist in heterospecific-occupied habitats in the absence of continued gene flow. These results demonstrate that individual immigrants are unlikely to form persistent populations and thus, inbreeding depression contributes to the absence of fine-scale coexistence in this species pair.

Behavior Evolution of Multi-Group in the Process of Pedestrian Crossing Based on Evolutionary Game Theory

The mixed traffic flow has an increasingly impact on the operation of urban traffic. To study the evolution law of multi-group behaviors in pedestrian crossing, we used the evolutionary game theory to establish a multi-group behavior evolution model for pedestrian crossing. The process of concern started from the risk perception and multi-group behavior choice. The evolutionary stability strategies, evolution trends, and factors affecting the evolutionary path of multi-group behaviors are discussed in this paper. This study found that evolutionary strategy equilibrium of pedestrians, drivers, and traffic managers not only relied on their own earning, but also on those of the other two groups. The factors affecting its behavior included the revenue factor and the limiting factor. Evolutionary game theory was used to analyze the multi-group interaction behavior of pedestrians, vehicle drivers, and traffic managers in the process of pedestrian crossing, as well as to analyze the behavior of traffic subjects in the process of pedestrian crossing. This paper provides a basis for decision-making for the traffic management department to manage road traffic, offering a new idea from the perspective of evolution for solving the conflict of interest at the crosswalk of the road section.

Assessment of assumptions underlying models of prokaryotic pangenome evolution

BackgroundThe genomes of bacteria and archaea evolve by extensive loss and gain of genes which, for any group of related prokaryotic genomes, result in the formation of a pangenome with the universal, asymmetrical U-shaped distribution of gene commonality. However, the evolutionary factors that define the specific shape of this distribution are not thoroughly understood.ResultsWe investigate the fit of simple models of genome evolution to the empirically observed gene commonality distributions and genome intersections for 33 groups of closely related bacterial genomes. A model with an infinite external gene pool available for gene acquisition and constant genome size (IGP-CGS model), and two gene turnover rates, one for slow- and the other one for fast-evolving genes, allows two approaches to estimate the parameters for gene content dynamics. One is by fitting the model prediction to the distribution of the number of genes shared by precisely k genomes (gene commonality distribution) and another by analyzing the distribution of the number of genes common for k genome sets (k-cores). Both approaches produce a comparable overall quality of fit, although the former significantly overestimates the number of the universally conserved genes, while the latter overestimates the number of singletons. We further explore the effect of dropping each of the assumptions of the IGP-CGS model on the fit to the gene commonality distributions and show that models with either a finite gene pool or unequal rates of gene loss and gain (greater gene loss rate) eliminate the overestimate of the number of singletons or the core genome size.ConclusionsWe examine the assumptions that are usually adopted for modeling the evolution of the U-shaped gene commonality distributions in prokaryote genomes, namely, those of infinitely many genes and constant genome size. The combined analysis of genome intersections and gene commonality suggests that at least one of these assumptions is invalid. The violation of both these assumptions reflects the limited ability of prokaryotes to gain new genes. This limitation seems to stem, at least partly, from the horizontal gene transfer barrier, i.e., the cost of accommodation of foreign genes by prokaryotes. Further development of models taking into account the complexity of microbial evolution is necessary for an improved understanding of the evolution of prokaryotes.

Care-giver identity impacts offspring development and performance in an annually social bumble bee

BackgroundThe developmental fates of offspring have the potential to be influenced by the identity of their care-givers and by the nature of the care that they receive. In animals that exhibit both parental and alloparental care, such as the annually eusocial insects, the influence of care-giver identity can be directly assessed to yield mechanistic and evolutionary insights into the origins and elaboration of brood care. Here, we performed a comparative investigation of maternal and worker brood care in bumble bees, a pollinator group where mothers (queens) rear the first offspring in the nest, and then daughters (workers) assume this role upon their emergence. Specifically, we compared the effects of queen and worker brood care on offspring development and also offspring performance, for a set of traits related to sensory biology, learning, and stress resistance.ResultsWe found that queen-reared workers were smaller-bodied than worker-reared offspring, suggesting that bumble bee queens influence body size determination in their offspring. We also found that queen-reared workers were more resistant to starvation, which might be beneficial for early nesting success. These maternal influences could not be explained by feeding rate, given that we detected a similar offspring feeding frequency in both queens and workers.ConclusionBumble bee queens have a unique influence on the development of the first offspring in the nest, which they rear, relative to worker-reared workers. We propose that bumble bee brood care has been shaped by a suite of evolutionary and ecological factors, which might include a maternal influence on traits that promote survival of incipient colonies.

Spatial patterns of genus‐level phylogenetic endemism in the tree flora of Mediterranean Europe

AbstractAimThe Mediterranean Basin is a major hotspot of plant biodiversity, including forest trees. Over the past centuries, Mediterranean forests have been fragmented and over‐exploited, to which the threats of climate change are now added. Our aim is to better understand patterns and processes of tree biodiversity in the Mediterranean and to provide indicators complementing the traditional approaches to biodiversity conservation based on species counts and occurrences, using georeferenced phylogenetic diversity and endemism analyses in a spatial ecological context.LocationMediterranean Europe.MethodsUsing a dated phylogeny of the 64 Euro‐Mediterranean tree genera, we calculated phylogenetic diversity for all 50 × 50 km2 grid cells spanning Mediterranean Europe (n = 643) and compared values with those obtained for genus‐level taxonomic diversity. Then, we tested the relative influence of geography, past and present climate, and soil on tree diversity (phylogenetic or taxonomic) and its geographical turnover. Geographical patterns of phylogenetic endemism were inferred using the Categorical Analyses of Neo‐ and Paleo‐Endemism (CANAPE) methodology.ResultsWe showed that phylogenetic and taxonomic diversity within and among cells are correlated and influenced by soil parameters as well as current, Holocene and Late Glacial Maximum climate. Southern Spain, Cyprus and some Aegean islands contained areas of disproportionately high phylogenetic diversity and a concentration of phylogenetic paleo‐endemics, while phylogenetic neo‐endemism was high in eastern Sicily. Mixed phylogenetic endemism regions were detected in southern Spain and Portugal, in the Balkans and in Crete.Main conclusionsOur phylogenetic approach provides relevant indicators for better protecting forests of the Mediterranean, encompassing past and present evolutionary processes and factors. We consider areas that show a concentration of evolutionary history manifested by high phylogenetic endemism as high priority targets for the conservation of the European tree flora.

Breeding structure and invasiveness in social insects.

Plasticity in life history traits is commonly used to explain the invasion success of social insects. While intraspecific plasticity is often recognized, interspecific variability is easily overlooked, whereby different species exhibit different strategies. The presence of many queens per colony and the collapse of colony boundaries have favored invasiveness for many ant species. However, these strategies are absent from other successful social invaders. Here, we report that various life-history traits may differentially enhance the invasion success in social insects. We suggest that other aspects of their breeding system, like asexual reproduction, intranidal mating and pre-adaptation to inbreeding may enhance their invasion success. Thorough comparative studies between native and introduced populations or studies of closely related species will help identify additional traits favoring the invasion success of social insects, and ultimately provide a more comprehensive picture of the evolutionary factors enhancing invasiveness across this phylogenetically and ecologically diverse group.

Polygenic adaptation of rosette growth in Arabidopsis thaliana

The rate at which plants grow is a major functional trait in plant ecology. However, little is known about its evolution in natural populations. Here, we investigate evolutionary and environmental factors shaping variation in the growth rate of Arabidopsis thaliana. We used plant diameter as a proxy to monitor plant growth over time in environments that mimicked latitudinal differences in the intensity of natural light radiation, across a set of 278 genotypes sampled within four broad regions, including an outgroup set of genotypes from China. A field experiment conducted under natural conditions confirmed the ecological relevance of the observed variation. All genotypes markedly expanded their rosette diameter when the light supply was decreased, demonstrating that environmental plasticity is a predominant source of variation to adapt plant size to prevailing light conditions. Yet, we detected significant levels of genetic variation both in growth rate and growth plasticity. Genome-wide association studies revealed that only 2 single nucleotide polymorphisms associate with genetic variation for growth above Bonferroni confidence levels. However, marginally associated variants were significantly enriched among genes with an annotated role in growth and stress reactions. Polygenic scores computed from marginally associated variants confirmed the polygenic basis of growth variation. For both light regimes, phenotypic divergence between the most distantly related population (China) and the various regions in Europe is smaller than the variation observed within Europe, indicating that the evolution of growth rate is likely to be constrained by stabilizing selection. We observed that Spanish genotypes, however, reach a significantly larger size than Northern European genotypes. Tests of adaptive divergence and analysis of the individual burden of deleterious mutations reveal that adaptive processes have played a more important role in shaping regional differences in rosette growth than maladaptive evolution.

The macroecology and evolution of avian competence forBorrelia burgdorferi

AbstractAimPrediction of novel reservoirs of zoonotic pathogens would be improved by the identification of interspecific drivers of host competence (i.e., the ability to transmit pathogens to new hosts or vectors). Tick‐borne pathogens can provide a useful model system, because larvae become infected only when feeding on a competent host during their first blood meal. For tick‐borne diseases, competence has been studied best forBorrelia burgdorferisensu lato (Bbsl), which causes Lyme borreliosis. Major reservoirs include several small mammal species, but birds might play an under‐recognized role in human risk given their ability to disperse infected ticks across large spatial scales. Here, we provide a global synthesis of the ecological and evolutionary factors that determine the ability of bird species to infect larval ticks withBbsl.LocationGlobal.Time period1983–2019.Major taxa studiedBirds.MethodsWe compiled a dataset ofBbsl competence across 183 bird species and applied meta‐analysis, phylogenetic factorization and boosted regression trees to describe spatial and temporal patterns in competence, characterize its phylogenetic distribution across birds, reconstruct its evolution and evaluate the trait profiles associated with competent avian species.ResultsHalf of the sampled bird species show evidence of competence forBbsl. Competence displays moderate phylogenetic signal, has evolved multiple times across bird species and is pronounced in the genusTurdus. Trait‐based analyses distinguished competent birds with 80% accuracy and showed that such species have low baseline corticosterone, exist on both ends of the pace‐of‐life continuum, breed and winter at high latitudes and have broad migratory movements into their breeding range. We used these trait profiles to predict various likely but unsampled competent species, including novel concentrations of avian reservoirs within the Neotropics.Main conclusionOur results can generate new hypotheses for how birds contribute to the dynamics of tick‐borne pathogens and help to prioritize surveillance of likely but unsampled competent birds. Our findings also emphasize that birds display under‐recognized variation in their contributions to enzootic cycles ofBbsl and the broader need to consider competence in ecological and predictive studies of multi‐host pathogens.

Increasing temperature alters the within-host competition of viral strains and influences virus genetic variability

Environmental conditions can affect viral accumulation, virulence and adaptation, which have implications in the disease outcomes and efficiency of control measures. Concurrently, mixed viral infections are relevant in plants, being their epidemiology shaped by within-host virus–virus interactions. However, the extent in which the combined effect of variations in abiotic components of the plant ecological niche and the prevalence of mixed infections affect the evolutionary dynamics of viral populations is not well understood. Here, we explore the interplay between ecological and evolutionary factors during viral infections and show that isolates of two strains of Pepino mosaic potexvirus coexisted in tomato plants in a temperature-dependent continuum between neutral and antagonistic interactions. After a long-term infection, the mutational analysis of the evolved viral genomes revealed strain-specific single-nucleotide polymorphisms that were modulated by the interaction between the type of infection and temperature. These results suggest that the temperature is an ecological driver of virus-virus interactions, with an effect on the genetic diversity of individual viruses that are co-infecting an individual host. This research provides insights into the effect that changes in host growth temperatures might have on the evolutionary dynamics of viral populations in mixed infections.

Intra-Host Diversity of SARS-Cov-2 Should Not Be Neglected: Case of the State of Victoria, Australia.

Since the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the etiological agent of the current COVID-19 pandemic, a rapid and massive effort has been made to obtain the genomic sequences of this virus to monitor (in near real time) the phylodynamic and diversity of this new pathogen. However, less attention has been given to the assessment of intra-host diversity. RNA viruses such as SARS-CoV-2 inhabit the host as a population of variants called quasispecies. We studied the quasispecies diversity in four of the main SARS-CoV-2 genes (ORF1a, ORF1b, S and N genes), using a dataset consisting of 210 next-generation sequencing (NGS) samples collected between January and early April of 2020 in the State of Victoria, Australia. We found evidence of quasispecies diversity in 68% of the samples, 76% of which was nonsynonymous variants with a higher density in the spike (S) glycoprotein and ORF1a genes. About one-third of the nonsynonymous intra-host variants were shared among the samples, suggesting host-to-host transmission. Quasispecies diversity changed over time. Phylogenetic analysis showed that some of the intra-host single-nucleotide variants (iSNVs) were restricted to specific lineages, highlighting their potential importance in the epidemiology of this virus. A greater effort must be made to determine the magnitude of the genetic bottleneck during transmission and the epidemiological and/or evolutionary factors that may play a role in the changes in the diversity of quasispecies over time.

Genome-Wide Analysis of Transposable Elements and Satellite DNAs in Spinacia Species to Shed Light on Their Roles in Sex Chromosome Evolution.

Sex chromosome evolution has mostly been studied in species with heteromorphic sex chromosomes. The Spinacia genus serves as an ideal model for investigating evolutionary mechanisms underlying the transition from homomorphic to heteromorphic sex chromosomes. Among evolutionary factors, repetitive sequences play multiple roles in sex chromosome evolution while their forces have not been fully explored in Spinacia species. Here, we identified major repetitive sequence classes in male and female genomes of Spinacia species and their ancestral relative sugar beet to elucidate the evolutionary processes of sex chromosome evolution using next-generation sequencing (NGS) data. Comparative analysis revealed that the repeat elements of Spinacia species are considerably higher than of sugar beet, especially the Ty3/Gypsy and Ty1/Copia retrotransposons. The long terminal repeat retroelements (LTR) Angela, Athila, and Ogre may be accounted for the higher proportion of repeats in the spinach genome. Comparison of the repeats proportion between female and male genomes of three Spinacia species indicated the different representation in Spinacia tetrandra samples but not in the S. oleracea or S. turkestanica samples. From these results, we speculated that emergence of repetitive DNA sequences may correlate the formation of sex chromosome and the transition from homomorphic sex chromosomes to heteromorphic sex chromosomes as heteromorphic sex chromosomes exclusively existed in Spinacia tetrandra. Three novel sugar beet-specific satellites were identified and confirmed by fluorescence in situ hybridization (FISH); six out of eight new spinach-specific satellites were mapped to the short arm of sex chromosomes. A total of 141 copies of SolSat01-171-s were found in the sex determination region (SDR). Thus, the accumulation of satellite DNA on the short arm of chromosome 1 may be involved in the sex chromosome evolution in Spinacia species. Our study provides a fundamental resource for understanding repeat sequences in Spinacia species and their roles in sex chromosome evolution.

Evolutionary stability, landscape heterogeneity, and human land-usage shape population genetic connectivity in the Cape Floristic Region biodiversity hotspot.

As human‐induced change eliminates natural habitats, it impacts genetic diversity and population connectivity for local biodiversity. The South African Cape Floristic Region (CFR) is the most diverse extratropical area for plant biodiversity, and much of its habitat is protected as a UNESCO World Heritage site. There has long been great interest in explaining the underlying factors driving this unique diversity, especially as much of the CFR is endangered by urbanization and other anthropogenic activity. Here, we use a population and landscape genetic analysis of SNP data from the CFR endemic plant Leucadendron salignum or “common sunshine conebush” as a model to address the evolutionary and environmental factors shaping the vast CFR diversity. We found that high population structure, along with relatively deeper and older genealogies, is characteristic of the southwestern CFR, whereas low population structure and more recent lineage coalescence depict the eastern CFR. Population network analyses show genetic connectivity is facilitated in areas of lower elevation and higher seasonal precipitation. These population genetic signatures corroborate CFR species‐level patterns consistent with high Pleistocene biome stability and landscape heterogeneity in the southwest, but with coincident instability in the east. Finally, we also find evidence of human land‐usage as a significant gene flow barrier, especially in severely threatened lowlands where genetic connectivity has been historically the highest. These results help identify areas where conservation plans can prioritize protecting high genetic diversity threatened by contemporary human activities within this unique cultural UNESCO site.

Эволюционные предпосылки орудийной деятельности с позиции концепции самоотражения животных и человека

Currently, the subject of the use of tools by animals is avidly explored in comparative psychology and evolution psychology. It is believed that the use of tools, if determined by instincts, is an evidence of complex cognitive processes in the animal, in particular, thinking. The abi­lity to use and make tools was discovered in primates, a number of mammals, birds and even invertebrates. However, the abovementioned animals show an already formed complex ability to use tools. Evolutionary preconditions and factors leading to emergence of the ability to use tools as a part of mental phylogenesis are understudied.
 The author of the paper offers a novel approach to exploring the preconditions for the use of tools based on the concept of self-reflection of animals and human as well as embodied cognition. According to the approach developed, the proto-tool is the body of the animal, which physical characteristics initially serve as an obstacle in achieving the goal of various activities; only afterwards, the animal recognizes its body as an opportunity, a means of affecting the environment.

A Substantial Study on River Basin Governance Formation and Evolutionary Factors

A Substantial Study on River Basin Governance Formation and Evolutionary Factors

Telepsychiatry or Face-to-face Visit, the Near Paradigm Shift in Psychiatry

The Covid-19 pandemic, which has necessitated lockdowns because of the ease of virus spread among the populace, especially the unvaccinated, has forced us to reevaluate and reimagine psychiatric care. Before the pandemic telepsychiatry was one of the major ways outpatient visits were carried out. The other being face to face visits. However, there has been an uptick in the use of telepsychiatry for many reasons. This paper explores telepsychiatry, some of its evolutionary factors, the necessary changes that continue to drive the use of telepsychiatry, and its usefulness in certain vulnerable inpatient populations. The incidence and prevalence of mood disorders and anxiety have increased exponentially during the pandemic, and telepsychiatry may have helped make management easier. The use, techniques, and related legal framework of telepsychiatry continue to evolve with advances in technology. The need for regulatory authorities to continue to reform their oversight to accommodate or ensure the safety of this increasing utility of health delivery is crucial, especially at these times.