Natural Selection Research Articles

Quantum logic automata generalizing the edge of chaos in complex systems

BackgroundHistorically, although researchers in the science of complex systems proposed the idea of the edge of chaos and/or self-organized criticality as the essential feature of complex organization, they were not able to generalize this concept. Complex organization is regarded at the edge of chaos between the order phase and the chaos phase and a very rare case. Additionally, in cellular automata, the critical property is class IV, which is also rarely found. Therefore, there can be overestimation for natural selection. More recently, developments in cognitive and brain science have led to the free energy principle based on Bayesian inference, while quantum cognition has been established to explain various cognitive phenomena. Since Bayesian inference results in the perspective of a steady state, it can be described in Boolean logic. Considering that quantum logic consists of multiple Boolean logic in terms of lattice theory, the perspective of the free energy principle is the perspective of order, and the perspective of quantum logic might be the perspective of multiple worlds, which is strongly relevant for the edge of chaos.ProblemThe next question arises whether the perspective derived from quantum logic can be generalized for the complex behavior consisting of both order and chaos, instead of the edge of chaos or self-organized criticality, to reveal the property of critical behavior such as a power-law distribution.SolutionIn this study, we define quantum logic automata, which entail quantum logic (orthomodular lattice) in terms of lattice theory and have the features of a dynamical system. Because quantum logic automata are applied to a binary sequence, one can estimate the behavior of those automata with respect to patterns and a time series. Here, we show that most of a group of quantum logic automata display class IV-like behavior, in which oscillatory traveling waves collide with each other, leading to complex behavior; moreover, a time series of binary sequences displays 1/f noise. Therefore, one can see that quantum logic automata generalize and expand the idea of the edge of chaos.

Unification, T-theoreticity, and Testing: The Case of Fitness in Natural Selection

AbstractTheoreticity and unification are two main issues discussed in philosophy of science. The first attempts to clarify the different roles of concepts used in a scientific theory. The second concerns the role of unification in scientific explanation and scientific progress. Both discussions have followed separate, independent paths. In this paper, we examine the interrelatedness of these two notions by focusing on classical particle mechanics and the theory of natural selection. We claim that they are interconnected in two distinct ways. On the one hand, a theory’s unifying power relies on the presence of some theoretical concepts that apply to heterogeneous phenomena through the assumption of a (sometimes unstated) general principle. On the other hand, a sensible application of the theoreticity criterion to these integrating concepts requires the unification not being spurious. We conclude that a correct determination of the theoreticty status requires analyzing how specific applications of different parts of a theory interact with each other.

Evolution of Phytophthora infestans on its potato host since the Irish potato famine

Phytophthora infestans is a major oomycete plant pathogen, responsible for potato late blight, which led to the Irish Potato Famine from 1845–1852. Since then, potatoes resistant to this disease have been bred and deployed worldwide. Their resistance (R) genes recognize pathogen effectors responsible for virulence and then induce a plant response stopping disease progression. However, most deployed R genes are quickly overcome by the pathogen. We use targeted sequencing of effector and R genes on herbarium specimens to examine the joint evolution in both P. infestans and potato from 1845–1954. Currently relevant effectors are historically present in P. infestans, but with alternative alleles compared to modern reference genomes. The historic FAM-1 lineage has the virulent Avr1 allele and the ability to break the R1 resistance gene before breeders deployed it in potato. The FAM-1 lineage is diploid, but later, triploid US-1 lineages appear. We show that pathogen virulence genes and host resistance genes have undergone significant changes since the Famine, from both natural and artificial selection.

Moderate Genetic Diversity of MHC Genes in an Isolated Small Population of Black-and-White Snub-Nosed Monkeys (Rhinopithecus bieti).

Genetic diversity is an essential indicator that echoes the natural selection and environmental adaptation of a species. Isolated small populations are vulnerable to genetic drift, inbreeding, and limited gene flow; thus, assessing their genetic diversity is critical in conservation. In this study, we studied the genetic diversity of black-and-white snub-nosed monkeys (Rhinopithecus bieti) using neutral microsatellites and five adaptive major histocompatibility complex (MHC) genes. Two DQA1 alleles, two DQB1 alleles, two DRB1 alleles, two DRB5 alleles, and three DPB1 alleles were isolated from a population. The results indicate that neutral microsatellites demonstrate a high degree of heterozygosity and polymorphism, while adaptive MHC genes display a high degree of heterozygosity and moderate polymorphism. The results also show that balancing selection has prominently influenced the MHC diversity of the species during evolution: (1) significant positive selection is identified at several amino acid sites (primarily at and near antigen-binding sites) of the DRB1, DRB5, and DQB1 genes; (2) phylogenetic analyses display the patterns of trans-species evolution for all MHC loci. This study provides valuable genetic diversity insights into black-and-white snub-nosed monkeys, which dwell at the highest altitude and have experienced the harshest environmental selection of all primates globally since the Pleistocene. Such results provide valuable scientific evidence and a reference for making or amending conservation strategies for this endangered primate species.

Exploring Codon Usage Patterns and Influencing Factors in Ranavirus DNA Polymerase Genes.

Ranaviruses, members of the genus Ranavirus within the family Iridoviridae, have become a significant concern for amphibian populations globally, along with other cold-blooded vertebrates, due to their emergence as a significant threat. We employed bioinformatics tools to examine the codon usage patterns in 61 DNA pol genes from Ranavirus, Lymphocystivirus, Megalocytivirus, and two unclassified ranaviruses, as no prior studies had been conducted on this topic. The results showed a slight or low level of codon usage bias (CUB) in the DNA pol genes of Ranavirus. Relative synonymous codon usage (RSCU) analysis indicated that the predominant codons favored in Ranavirus DNA pol genes terminate with C or G. Correlation analysis examining nucleotide content, third codon position, effective number of codons (ENC), correspondence analysis (COA), Aroma values, and GRAVY values indicated that the CUB across DNA pol genes could be influenced by both mutation pressure and natural selection. The neutrality plot indicated that natural selection is the primary factor driving codon usage. Furthermore, the analysis of the codon adaptation index (CAI) illustrated the robust adaptability of Ranavirus DNA pol genes to their hosts. Analysis of the relative codon deoptimization index (RCDI) suggested that Ranavirus DNA pol genes underwent greater selection pressure from their hosts. These findings will aid in comprehending the factors influencing the evolution and adaptation of Ranavirus to its hosts.

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.

Evolutionary analysis of ZAP and its cofactors identifies intrinsically disordered regions as central elements in host-pathogen interactions

The zinc-finger antiviral protein (ZAP) is an innate immunity sensor of non-self nucleic acids. Its antiviral activity is exerted through the physical interaction with different cofactors, including TRIM25, Riplet and KHNYN. Cellular proteins that interact with infectious agents are expected to be engaged in genetic conflicts that often result in their rapid evolution. To test this possibility and to identify the regions most strongly targeted by natural selection, we applied in silico molecular evolution tools to analyze the evolutionary history of ZAP and cofactors in four mammalian groups. We report evidence of positive selection in all genes and in most mammalian groups. On average, the intrinsically disordered regions (IDRs) embedded in the four proteins evolve significantly faster than folded domains and most positively selected sites fall within IDRs. In ZAP, the PARP domain also shows abundant signals of selection, and independent evolution in different mammalian groups suggests modulation of its ADP-ribose binding ability. Detailed analyses of the biophysical properties of IDRs revealed that chain compaction and conformational entropy are conserved across mammals. The IDRs in ZAP and KHNYN are particularly compact, indicating that they may promote phase separation (PS). In line with this hypothesis, we predicted several PS-promoting regions in ZAP and KHNYN, as well as in TRIM25. Positively selected sites are abundant in these regions, suggesting that PS may be important for the antiviral functions of these proteins and the evolutionary arms race with viruses. Our data shed light into the evolution of ZAP and cofactors and indicate that IDRs represent central elements in host-pathogen interactions.

Beyond head and wings: Unveiling influence of diet, body size, and phylogeny on the evolution of the femur in phyllostomid bats.

Phyllostomidae, the most diverse family of Neotropical bats, encompass 230 species with varied dietary habits and food acquisition methods. Their feeding niche diversification has shaped skull and wing morphologies through natural selection, reflecting food processing and flight strategies. Yet, evolution of bat hindlimbs, especially in phyllostomids, remains little understood. Previous studies highlighted the femur's morphology as a key to understanding the evolution of quadrupedalism in yangochiropteran bats, including the adept walking observed in vampire bats (Desmodontinae). Here, we aimed to describe the femoral morphological variation in Phyllostomidae, correlating this with body size and assessing the effects of phylogenetic history, dietary habits, and hindlimb usage. Analyzing 15 femoral traits from 45 species across 9 subfamilies through phylogenetically informed methods, we discovered a significant phylogenetic structure in femoral morphology. Allometric analysis indicated that body mass accounts for about 85% of the variance in phyllostomid femoral size and about 11% in femoral shape. Relatively smaller femurs showed to be typical in Stenodermatinae, Lonchophyllinae, and Glossophaginae, in contrast to the larger femurs of Phyllostominae, Desmodontinae, Micronycterinae, and Lonchorrhininae. Furthermore, extensive femur shape variation was detected, with the most distinct morphologies in vampire bats, followed by frugivorous species. Adaptive evolutionary models related to diet more effectively explained variations in femoral relative size and shape than stochastic models. Contrary to the conventional belief of limited functional demand on bat femurs, our findings suggest that femoral morphology is significantly influenced by functional demands associated with diet and food capture, in addition to being partially structured by body size and shared evolutionary history.

Unveiling Resistance and Virulence Mechanisms under Darwinian Positive Selection for Novel Drug Discovery for Gardnerella vaginalis

Gardnerella vaginalis is a Gram-variable bacillus capable of causing bacterial vaginosis, a condition prevalent in reproductive-age women, this bacterium is present in almost 100% of cases and is also considered a gateway to various sexually transmitted infections. This organism exhibits high pathogenicity linked to virulence and resistance genes acquired throughout evolution, showcasing elevated resistance to a broad spectrum of drug classes. This study conducted comparative genomic analyses to identify these genes and correlate their presence with positive Darwinian selection. Additionally, new drug targets were selected through docking and molecular modeling, guided by the heightened antimicrobial resistance exhibited by this microbial species. The available genomes of G. vaginalis were analyzed, and the orthologous genes were delineated and positively selected, whereby 29 groups were found. Of these genes, one of great importance was predicted, Mef(A), which is related to resistance to the macrolide group of antibiotics, which are one of the main choices for the treatment of sexually transmitted infections. Additionally, two potential protein candidates were selected as drug targets. These proteins were linked with a natural compound each and are considered good potential drug targets. The analyses in this study contribute to analyzing the evolution of the species and how resistance genes are related to their permanence as a potential pathogen.

The evolution of morphological castes under decoupled control.

Eusociality, where units that previously reproduced independently function as one entity, is of major interest in evolutionary biology. Obligate eusociality is characterized by morphologically differentiated castes and reduced conflict. We explore conditions under which morphological castes may arise in the Hymenoptera and factors constraining their evolution. Control over offspring morphology and behaviour seems likely to be decoupled. Provisioners (queens and workers) can influence offspring morphology directly through the nutrition they provide, while adult offspring control their own behaviour. Provisioners may, however, influence worker behaviour indirectly if offspring modify their behaviour in response to their morphology. If manipulation underlies helping, we should not see helping evolve before specialized worker morphology, yet empirical observations suggest that behavioural castes precede morphological castes. We use evolutionary invasion analyses to show how the evolution of a morphologically differentiated worker caste depends on the prior presence of a behavioural caste: specialist worker morphology will be mismatched with behaviour unless some offspring already choose to work. A mother's certainty about her offspring's behaviour is also critical-less certainty results in greater mismatch. We show how baseline worker productivity can affect the likelihood of a morphological trait being favoured by natural selection. We then show how under a decoupled control scenario, morphologically differentiated castes should be less and less likely to be lost as they become more specialized. We also suggest that for eusociality to be evolutionarily irreversible, workers must be unable to functionally replace reproductives and reproductives must be unable to reproduce without help from workers.

Variability in thermal tolerance of clutches from different mothers indicates adaptation potential to climate warming in sea turtles.

The current climate warming is a challenge to biodiversity that could surpass the adaptation capacity of some species. Hence, understanding the means by which populations undergo an increase in their thermal tolerance is critical to assess how they could adapt to climate warming. Specifically, sea turtle populations could respond to increasing temperatures by (1) colonizing new nesting areas, (2) nesting during cooler times of the year, and/or (3) by increasing their thermal tolerance. Differences in thermal tolerance of clutches laid by different females would indicate that populations have the potential to adapt by natural selection. Here, we used exhaustive information on nest temperatures and hatching success of leatherback turtle (Dermochelys coriacea) clutches over 14 years to assess the occurrence of individual variability in thermal tolerance among females. We found an effect of temperature, year, and the interaction between female identity and nest temperature on hatching success, indicating that clutches laid by different females exhibited different levels of vulnerability to high temperatures. If thermal tolerance is a heritable trait, individuals with higher thermal tolerances could have greater chances of passing their genes to following generations, increasing their frequency in the population. However, the high rate of failure of clutches at temperatures above 32°C suggests that leatherback turtles are already experiencing extreme heat stress. A proper understanding of mechanisms of adaptation in populations to counteract changes in climate could greatly contribute to future conservation of endangered populations in a rapidly changing world.

Natural selection requires no teleology in addition to heritable variation in fitness

According to the standard formulation, natural selection requires variation, differential fitness, and heritability. I argue that this formulation is inadequate because it fails to distinguish natural selection from artificial selection, intelligent design, forward-looking orthogenetic selection, and adaptation via the selection of nonrandom variation. I suggest adding a no teleology condition. The no teleology condition says that the evolutionary process is not guided toward an endpoint represented in the mind of an agent, variation is produced randomly with respect to adaptation, and selection pressures are not forward looking.

Selection against domestication alleles in introduced rabbit populations.

Humans have moved domestic animals around the globe for thousands of years. These have occasionally established feral populations in nature, often with devastating ecological consequences. To understand how natural selection shapes re-adaptation into the wild, we investigated one of the most successful colonizers in history, the European rabbit. By sequencing the genomes of 297 rabbits across three continents, we show that introduced populations exhibit a mixed wild-domestic ancestry. We show that alleles that increased in frequency during domestication were preferentially selected against in novel natural environments. Interestingly, causative mutations for common domestication traits sometimes segregate at considerable frequencies if associated with less drastic phenotypes (for example, coat colour dilution), whereas mutations that are probably strongly maladaptive in nature are absent. Whereas natural selection largely targeted different genomic regions in each introduced population, some of the strongest signals of parallelism overlap genes associated with neuronal or brain function. This limited parallelism is probably explained by extensive standing genetic variation resulting from domestication together with the complex mixed ancestry of introduced populations. Our findings shed light on the selective and molecular mechanisms that enable domestic animals to re-adapt to the wild and provide important insights for the mitigation and management of invasive populations.

Genetic structure of apical membrane antigen-1 in Plasmodium falciparum isolates from Pakistan.

Plasmodium falciparum apical membrane antigen-1 (PfAMA-1) is a major candidate for the blood-stage malaria vaccine. Genetic polymorphisms of global pfama-1suggest that the genetic diversity of the gene can disturb effective vaccine development targeting this antigen. This study was conducted to explore the genetic diversity and gene structure of pfama-1 among P. falciparum isolates collected in the Khyber Pakhtunkhwa (KP) province of Pakistan. A total of 19 full-length pfama-1 sequences were obtained from KP-Pakistan P. falciparum isolates, and genetic polymorphism and natural selection were investigated. KP-Pakistan pfama-1 exhibited genetic diversity, wherein 58 amino acid changes were identified, most of which were located in ectodomains, and domains I, II, and III. The amino acid changes commonly found in the ectodomain of global pfama-1 were also detected in KP-Pakistan pfama-1. Interestingly, 13 novel amino acid changes not reported in the global population were identified in KP-Pakistan pfama-1. KP-Pakistan pfama-1 shared similar levels of genetic diversity with global pfama-1. Evidence of natural selection and recombination events were also detected in KP-Pakistan pfama-1.

Recent secondary contact, genome-wide admixture, and asymmetric introgression of neo-sex chromosomes between two Pacific island bird species.

Secondary contact between closely related taxa represents a "moment of truth" for speciation-an opportunity to test the efficacy of reproductive isolation that evolved in allopatry and to identify the genetic, behavioral, and/or ecological barriers that separate species in sympatry. Sex chromosomes are known to rapidly accumulate differences between species, an effect that may be exacerbated for neo-sex chromosomes that are transitioning from autosomal to sex-specific inheritance. Here we report that, in the Solomon Islands, two closely related bird species in the honeyeater family-Myzomela cardinalis and Myzomela tristrami-carry neo-sex chromosomes and have come into recent secondary contact after ~1.1 my of geographic isolation. Hybrids of the two species were first observed in sympatry ~100 years ago. To determine the genetic consequences of hybridization, we use population genomic analyses of individuals sampled in allopatry and in sympatry to characterize gene flow in the contact zone. Using genome-wide estimates of diversity, differentiation, and divergence, we find that the degree and direction of introgression varies dramatically across the genome. For sympatric birds, autosomal introgression is bidirectional, with phenotypic hybrids and phenotypic parentals of both species showing admixed ancestry. In other regions of the genome, however, the story is different. While introgression on the Z/neo-Z-linked sequence is limited, introgression of W/neo-W regions and mitochondrial sequence (mtDNA) is highly asymmetric, moving only from the invading M. cardinalis to the resident M. tristrami. The recent hybridization between these species has thus enabled gene flow in some genomic regions but the interaction of admixture, asymmetric mate choice, and/or natural selection has led to the variation in the amount and direction of gene flow at sex-linked regions of the genome.

Population genetic structure in a self-compatible hermaphroditic snail is driven by drift independently of its contemporary mating system.

Genetic drift, gene flow, and natural selection commonly influence population genetic diversity. In populations of self-compatible hermaphrodites, the mating system (e.g., self-fertilization) further reduces individual heterozygosity. Furthermore, selfing, as a form of inbreeding, significantly impacts genetic drift by reducing effective population size (N e). This can potentially accelerate genetic drift, particularly in small populations where self-fertilization is likely during founder events. To investigate the roles of genetic drift and contemporary mating system in populations of the freshwater snail Lymnaea stagnalis, we examined their effective population sizes (N e) and Tajima's D values, which reflect genetic drift over extended time periods, as well as estimates of within-population selfing rates and pairwise relatedness reflecting contemporary mating system. We used 4054 SNP markers obtained using restriction site associated DNA (RAD) sequencing from individuals in five snail populations originating from geographically closely located ponds. We found strong population genetic structure and differences in genetic diversity among populations. Covariation between genetic diversity and N e estimates and Tajima's D values suggested drift being an important determinant of genetic diversity and structure in these populations. However, this effect was independent of the contemporary mating system, as indicated by the similarity of selfing rates and relatedness estimates among populations. Thus, founder events (possibly including historical inbreeding) and/or drift due to small sizes of L. stagnalis populations are likely to explain their genetic structure and limit within-population genetic diversity.

Hybrid model for sentiment analysis combination of PSO, genetic algorithm and voting classification

As social network services like Weibo and Twitter have grown in popularity, natural language processing (NLP) has seen a great deal of interest in sentiment analysis of social media messages and Information mining. Social media users, whose numbers are always increasing, have the ability to exchange information on their platforms. The study of sentiment, domains and themes are closely related. Manually collecting enough labelled data from the vast array of subjects covered by large-scale social media to train sentiment classifiers across several domains would be extremely difficult. The literature review conducted concludes that models already proposed in the previous researches are not able to achieve good accuracy. This work suggests a unique model that combines of genetic algorithm and particle swarm optimization to effectively extract the features and then the voting technique is applied for the classification. Model proposed is compared with 4 ensemble datasets achieving a consistent accuracy of more than 90% for three different diversified database owing to natural selection of sequences by GA and at the same time achieves a fast convergence with PSO, the model may be employed for highly accurate recommenders demanding precision and accuracy.

Information Dynamics in Evolving Networks Based on the Birth-Death Process: Random Drift and Natural Selection Perspective

Information Dynamics in Evolving Networks Based on the Birth-Death Process: Random Drift and Natural Selection Perspective

Selective and non-selective evolutionary signatures found in the simplest replicative biological entities.

Mitoviruses, which are considered evolutionary relics of extinct alpha-proteobacteria RNA phages, represent one of the simplest self-replicating biological systems. This study aims to quantitatively describe genomes and identify potential genomic signatures that support the protein phylogenetic-based classification criterion. Genomic variables, such as mononucleotide and dinucleotide composition, codon usage bias, and minimal free energy derived from optimized predicted RNA secondary structure, were analyzed. From the values obtained, the main evolutionary pressures were discussed, indicating that natural selection plays a significant role in shaping mitovirus genomes. However, neutral evolution also makes a significant contribution. This study reveals a significant discovery of structural divergence in Kvaramitovirus. The energy minimization approach employed to study 2D folding in this study reveals a distinct spatial organization of their genomes, providing evidence for the hypothesis of a single evolutionary event of circularization in the most recent common ancestor of the lineage. This hypothesis was discussed in light of recent discoveries by other researchers that partially support the existence of mitoviruses with circular genomes. Finally, this study represents a significant advancement in the understanding of mitoviruses, as it quantitatively describes the nucleotide sequence at the family and genus taxonomic levels. Additionally, we provide hypotheses that can be experimentally validated to inspire new research and address the gaps in knowledge of this fascinating, basally divergent RNA virus lineage.

Annual temperature, body size, and sexual size dimorphism in the evolution of Pyrgomorphidae.

In many animal species, larger body size is positively correlated with male mating success and female fecundity. However, in the case of insects, in high seasonality environments, natural selection favors a faster maturation that decreases the risk of pre-reproductive death. However, this advantageous adaptation comes at a tradeoff, resulting in a reduction in body size. Maturation time is influenced by environmental factors, such as temperature, season length, and food availability during the rains. The geographic variation in these parameters provides an opportunity to study their impact on the adaptive evolution of body size in Pyrgomorphidae grasshoppers. These grasshoppers exhibit remarkable variation in body size and wing development and can be found in diverse plant communities across Africa, Asia, Australia, and tropical America. In this study, we utilized a phylogenetic approach to examine the evolution of body size, considering climatic factors, and the influence of sexual selection on size differences between males and females. We found a positive correlation between mean annual temperature and sexual size dimorphism (SSD). Remarkably, species exhibiting a strong bias toward larger females were found to be adapted to regions with higher temperatures. In the Pyrgomorphidae family, an intermediate body size was identified as the ancestral trait. Additionally, winged male and female grasshoppers were observed to be larger than their wingless counterparts. Despite the potential conflicting pressures on body size in males and females, these grasshoppers adhere to Rench's Rule, suggesting that sexual selection on males' body size may explain the evolution of SSD.