scholarly journals Implications of Two Opposing Variations of Neutral Theory

2018 ◽  
Vol 1 (1) ◽  
pp. 51-52
Author(s):  
Jonathan Bartlett
Keyword(s):  
Prior Information ◽  
Evolutionary Dynamics ◽  
Neutral Theory ◽  
Neutral Evolution ◽  
Theory Of Evolution ◽  
Comprehensive Theory ◽  
The Difference

This letter discusses the difference between neutral theory as an observation of present evolutionary dynamics compared to neutral theory as a more-or-less comprehensive theory of evolution.  The letter suggests that prior information, not neutral evolution itself, creates the patterns in the genome in ways that make the dynamics described by neutral theory possible in modern organisms.

scholarly journals Neutral evolution test of the spike protein of SARS-CoV-2 and its implications in the binding to ACE2

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Georgina I. López-Cortés ◽  
Miryam Palacios-Pérez ◽  
Gabriel S. Zamudio ◽  
Hannya F. Veledíaz ◽  
Enrique Ortega ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Neutral Theory ◽  
Purifying Selection ◽  
Spike Protein ◽  
Health Concern ◽  
Neutral Evolution ◽  
Evolutionary Mechanisms ◽  
Theory Of Evolution ◽  
Selective Pressures

AbstractAs the SARS-CoV-2 has spread and the pandemic has dragged on, the virus continued to evolve rapidly resulting in the emergence of new highly transmissible variants that can be of public health concern. The evolutionary mechanisms that drove this rapid diversity are not well understood but neutral evolution should open the first insight. The neutral theory of evolution states that most mutations in the nucleic acid sequences are random and they can be fixed or disappear by purifying selection. Herein, we performed a neutrality test to better understand the selective pressures exerted over SARS-CoV-2 spike protein from homologue proteins of Betacoronavirus, as well as to the spikes from human clinical isolates of the virus. Specifically, Tyr and Asn have higher occurrence rates on the Receptor Binding Domain (RBD) and in the overall sequence of spike proteins of Betacoronavirus, whereas His and Arg have lower occurrence rates. The in vivo evolutionary phenomenon of SARS-CoV-2 shows that Glu, Lys, Phe, and Val have the highest probability of occurrence in the emergent viral particles. Amino acids that have higher occurrence than the expected by the neutral control, are favorable and are fixed in the sequence while the ones that have lower occurrence than expected, influence the stability and/or functionality of the protein. Our results show that most unique mutations either for SARS-CoV-2 or its variants of health concern are under selective pressures, which could be related either to the evasion of the immune system, increasing the virus’ fitness or altering protein – protein interactions with host proteins. We explored the consequences of those selected mutations in the structure and protein – protein interaction with the receptor. Altogether all these forces have shaped the spike protein and the continually evolving variants.

scholarly journals Pairwise Interact-and-Imitate Dynamics

2021 ◽  
Author(s):  
Ennio Bilancini ◽  
Leonardo Boncinelli ◽  
Nicola Campigotto
Keyword(s):  
Evolutionary Dynamics ◽  
Social Dilemmas ◽  
Asymptotically Stable ◽  
Globally Asymptotically Stable ◽  
Symmetric Game ◽  
Dominated Strategies ◽  
The Difference ◽  
Payoff Uncertainty

Abstract This paper introduces and studies a class of evolutionary dynamics --- Pairwise Interact-and-Imitate Dynamics (PIID) --- in which agents are matched in pairs, engage in a symmetric game, and imitate the opponent with a probability that depends on the difference in their payoffs. We provide a condition on the underlying game, named supremacy, and show that the population state in which all agents play the supreme strategy is globally asymptotically stable. We extend the framework to allow for payoff uncertainty, and check the robustness of our results to the introduction of some heterogeneity in the revision protocol followed by agents. Finally, we show that PIID can allow the survival of strictly dominated strategies, leads to the emergence of inefficient conventions in social dilemmas, and makes assortment ineffective in promoting cooperation.

scholarly journals Divergent and convergent evolution of housekeeping genes in human–pig lineage

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4840 ◽  
Author(s):  
Kai Wei ◽  
Tingting Zhang ◽  
Lei Ma
Keyword(s):  
Active Sites ◽  
Evolutionary Dynamics ◽  
Purifying Selection ◽  
Housekeeping Genes ◽  
Neutral Evolution ◽  
Structure Evolution ◽  
Tissue Cell ◽  
Sequencing Data ◽  
Cellular Functions ◽  
Species Specific

Housekeeping genes are ubiquitously expressed and maintain basic cellular functions across tissue/cell type conditions. The present study aimed to develop a set of pig housekeeping genes and compare the structure, evolution and function of housekeeping genes in the human–pig lineage. By using RNA sequencing data, we identified 3,136 pig housekeeping genes. Compared with human housekeeping genes, we found that pig housekeeping genes were longer and subjected to slightly weaker purifying selection pressure and faster neutral evolution. Common housekeeping genes, shared by the two species, achieve stronger purifying selection than species-specific genes. However, pig- and human-specific housekeeping genes have similar functions. Some species-specific housekeeping genes have evolved independently to form similar protein active sites or structure, such as the classical catalytic serine–histidine–aspartate triad, implying that they have converged for maintaining the basic cellular function, which allows them to adapt to the environment. Human and pig housekeeping genes have varied structures and gene lists, but they have converged to maintain basic cellular functions essential for the existence of a cell, regardless of its specific role in the species. The results of our study shed light on the evolutionary dynamics of housekeeping genes.

GENETIC REPRESENTATION AND GENETIC NEUTRALITY IN GENE EXPRESSION PROGRAMMING

2002 ◽  
Vol 05 (04) ◽  
pp. 389-408 ◽  
Author(s):  
CÂNDIDA FERREIRA
Keyword(s):  
Gene Expression ◽  
Molecular Evolution ◽  
Gene Expression Programming ◽  
Neutral Theory ◽  
Artificial System ◽  
Evolutionary Systems ◽  
Theory Of Evolution ◽  
Coding Regions ◽  
Neutral Mutations

The neutral theory of molecular evolution states that the accumulation of neutral mutations in the genome is fundamental for evolution to occur. The genetic representation of gene expression programming, an artificial genotype/phenotype system, not only allows the existence of non-coding regions in the genome where neutral mutations can accumulate but also allows the controlled manipulation of both the number and the extent of these non-coding regions. Therefore, gene expression programming is an ideal artificial system where the neutral theory of evolution can be tested in order to gain some insights into the workings of artificial evolutionary systems. The results presented in this work show beyond any doubt that the existence of neutral regions in the genome is fundamental for evolution to occur efficiently.

Opposing Evolutionary Pressures Drive Clonal Evolution and Health Outcomes in the Aging Blood System

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 37-37
Author(s):  
Kimberly Skead ◽  
Armande Ang Houle ◽  
Sagi Abelson ◽  
Marie-Julie Fave ◽  
Boxi Lin ◽  
...  
Keyword(s):  
Gene Disruption ◽  
Large Scale ◽  
Evolutionary Dynamics ◽  
Clonal Evolution ◽  
Neutral Evolution ◽  
Driver Mutations ◽  
Cancer Evolution ◽  
Sequencing Data ◽  
High Coverage ◽  
Passenger Mutations

The age-associated accumulation of somatic mutations and large-scale structural variants (SVs) in the early hematopoietic hierarchy have been linked to premalignant stages for cancer and cardiovascular disease (CVD). However, only a small proportion of individuals harboring these mutations progress to disease, and mechanisms driving the transformation to malignancy remains unclear. Hematopoietic evolution, and cancer evolution more broadly, has largely been studied through a lens of adaptive evolution and the contribution of functionally neutral or mildly damaging mutations to early disease-associated clonal expansions has not been well characterised despite comprising the majority of the mutational burden in healthy or tumoural tissues. Through combining deep learning with population genetics, we interrogate the hematopoietic system to capture signatures of selection acting in healthy and pre-cancerous blood populations. Here, we leverage high-coverage sequencing data from healthy and pre-cancerous individuals from the European Prospective Investigation into Cancer and Nutrition Study (n=477) and dense genotyping from the Canadian Partnership for Tomorrow's Health (n=5,000) to show that blood rejects the paradigm of strictly adaptive or neutral evolution and is subject to pervasive negative selection. We observe clear age associations across hematopoietic populations and the dominant class of selection driving evolutionary dynamics acting at an individual level. We find that both the location and ratio of passenger to driver mutations are critical in determining if positive selection acting on driver mutations is able to overwhelm regulated hematopoiesis and allow clones harbouring disease-predisposing mutations to rise to dominance. Certain genes are enriched for passenger mutations in healthy individuals fitting purifying models of evolution, suggesting that the presence of passenger mutations in a subset of genes might confer a protective role against disease-predisposing clonal expansions. Finally, we find that the density of gene disruption events with known pathogenic associations in somatic SVs impacts the frequency at which the SV segregates in the population with variants displaying higher gene disruption density segregating at lower frequencies. Understanding how blood evolves towards malignancy will allow us to capture cancer in its earliest stages and identify events initiating departures from healthy blood evolution. Further, as the majority of mutations are passengers, studying their contribution to tumorigenesis, will unveil novel therapeutic targets thus enabling us to better understand patterns of clonal evolution in order to diagnose and treat disease in its infancy. Disclosures Dick: Bristol-Myers Squibb/Celgene: Research Funding.

Combinatorics of Genotype-Phenotype Maps: An RNA Case Study

2005 ◽  
Author(s):  
Christian M. Reidys
Keyword(s):  
Natural Selection ◽  
Genetic Drift ◽  
Optimization Problem ◽  
Neutral Theory ◽  
Biological Evolution ◽  
Neutral Evolution ◽  
Evolutionary Search ◽  
Random Drift ◽  
Molecular Change ◽  
Biological Phenomena

The fundamental mechanisms of biological evolution have fascinated generations of researchers and remain popular to this day. The formulation of such a theory goes back to Darwin (1859), who in the The Origin of Species presented two fundamental principles: genetic variability caused by mutation, and natural selection. The first principle leads to diversity and the second one to the concept of survival of the fittest, where fitness is an inherited characteristic property of an individual and can basically be identified with its reproduction rate. Wright [530, 531] first recognized the importance of genetic drift in evolution in improving the evolutionary search capacity of the whole population. He viewed genetic drift merely as a process that could improve evolutionary search. About a decade later, Kimura proposed [317] that the majority of changes that are observed in evolution at the molecular level are the results of random drift of genotypes. The neutral theory of Kimura does not deny that selection plays a role, but claims that no appreciable fraction of observable molecular change can be caused by selective forces: mutations are either a disadvantage or, at best, neutral in present day organisms. Only negative selection plays a major role in the neutral evolution, in that deleterious mutants die out due to their lower fitness. Over the last few decades, there has been a shift of emphasis in the study of evolution. Instead of focusing on the differences in the selective value of mutants and on population genetics, interest has moved to evolution through natural selection as an abstract optimization problem. Given the tremendous opportunities that computer science and the physical sciences now have for contributing to the study of biological phenomena, it is fitting to study the evolutionary optimization problem in the present volume. In this chapter, we adopt the following framework: assuming that selection acts exclusively upon isolated phenotypes, we introduce the following compositum of mappings . . . Genotypes→ Phenotypes →Fitness . . . . We will refer to the first map as to the genotype-phenotype map and call the preimage of a given phenotype its neutral network. Clearly, the main ingredients here are the phenotypes and genotypes and their respective organization. In the following we will study various combinatorial properties of phenotypes and genotypes for RNA folding maps.

scholarly journals Transcriptional Mutagenesis Prevents Ribosomal DNA Deterioration: The Role of Duplications and Deletions

2019 ◽  
Vol 11 (11) ◽  
pp. 3207-3217
Author(s):  
Enrico Sandro Colizzi ◽  
Paulien Hogeweg
Keyword(s):  
Genome Stability ◽  
Evolutionary Dynamics ◽  
Point Mutations ◽  
Gene Duplications ◽  
Genetic Operators ◽  
Theory Of Evolution ◽  
Long Term Stability ◽  
Number Variation

Abstract Clashes between transcription and replication complexes can cause point mutations and chromosome rearrangements on heavily transcribed genes. In eukaryotic ribosomal RNA genes, the system that prevents transcription–replication conflicts also causes frequent copy number variation. Such fast mutational dynamics do not alter growth rates in yeast and are thus selectively near neutral. It was recently found that yeast regulates these mutations by means of a signaling cascade that depends on the availability of nutrients. Here, we investigate the long-term evolutionary effect of the mutational dynamics observed in yeast. We developed an in silico model of single-cell organisms whose genomes mutate more frequently when transcriptional load is larger. We show that mutations induced by high transcriptional load are beneficial when biased toward gene duplications and deletions: they decrease mutational load even though they increase the overall mutation rates. In contrast, genome stability is compromised when mutations are not biased toward gene duplications and deletions, even when mutations occur much less frequently. Taken together, our results show that the mutational dynamics observed in yeast are beneficial for the long-term stability of the genome and pave the way for a theory of evolution where genetic operators are themselves cause and outcome of the evolutionary dynamics.

The Anamneses and Institution Narrative in the Liturgy of Apostolic Constitutions Book VIII

1958 ◽  
Vol 9 (1) ◽  
pp. 1-7
Author(s):  
W. E. Pitt
Keyword(s):  
Holy Spirit ◽  
Comprehensive Theory ◽  
Book Viii ◽  
The Holy Spirit ◽  
Christian Worship ◽  
True Description ◽  
The Difference ◽  
Eucharistic Prayer ◽  
The Church

More than one comprehensive theory of liturgical history has made much of the difference between the eucharistic prayer in the Apostolic Tradition of St. Hippolytus and that described in the Catecheses of St. Cyril of Jerusalem. The former consists of a thanksgiving for creation and redemption through Christ, leading to an institution narrative, and followed by an anamnesis and an epiclesis, in which, however, the descent of the Holy Spirit upon the oblation is asked for, not to convert it, but to join the Church in one. The latter consists of a ‘preface’ (which is not a thanksgiving, although the opening dialogue suggests that it will be) and sanctus, followed at once by a fully consecratory epiclesis, and intercessions. It is true that scholars of former generations thought that the prayer described by St. Cyril was, in fact, a fully developed prayer of the Syro-Byzantine type, and that St. Cyril only commented on certain paragraphs of it. It was natural to think so when it was believed that the liturgy of Apostolic Constitutions VIII, which contains the oldest known prayer of this type, was the work of St. Clement of Rome and a true description of apostolic practice; but it will hardly do to-day, when we know that Apostolic Constitutions was written several years later than St. Cyril's Catecheses. Besides, St. Cyril describes the prayer in considerable verbal detail, a procedure which is not easy to reconcile with the omission of whole paragraphs. Nor will it do to say that he comments upon the institution narrative elsewhere; he could scarcely explain the Eucharist to catechumens without doing so, but that hardly explains how, after mentioning and explaining the various choirs of angels who sing the sanctus, he could pass over the thanksgiving for creation and redemption, institution narrative, and anamnesis without a word, and expect an audience of people who were new to Christian worship to be able to follow the prayer as a result. And it would be a strange coincidence if the parts omitted by St. Cyril were just those which are in the Apostolic Tradition.

scholarly journals Cognitive niche

2020 ◽  
Vol 11 (1) ◽  
pp. 64-70
Author(s):  
Đorđe Petronić ◽  
Igor Vujović
Keyword(s):  
Charles Darwin ◽  
Life Forms ◽  
Human Intelligence ◽  
Theory Of Evolution ◽  
Cognitive Niche ◽  
Human Habitat ◽  
Science Philosophy ◽  
The Origin Of Life ◽  
The Difference ◽  
Survival Mode

In a joint publication with Alfred Russell Wallace, Charles Darwin presented the theory which stated that all life forms were developed by natural selection in which the fight for survival had the effect similar to artificial intelligence applied to selective breeding. Despite a coincidence of views concerning the origin of life, these two scientists had their disagreements. Wallace argued that intelligence could have never arisen through the process of natural adaptation, but rather as a consequence of intelligent design. On the other hand, Darwin insisted that human intelligence could only be explained by the theory of evolution. This difference in point of views on the matter is a manifestation of the difference in the efforts to answer the question: "Why are people so intelligent?" In this context, the main aim of the study is to present a literature review concerning evolutionary psychology and to provide an explanation of the evolution of human intelligence. In other words, the study seeks to explain why people are able to accomplish such intellectual exploits as the ones found in mathematics, science, philosophy, law, etc., bearing in mind that such abilities or talents cannot be found in the original human habitat. The results have showed that evolutionary psychologists consider humans to be so intelligent due to the fact that they have evolved to fill the "cognitive niche". The cognitive niche is a survival mode characterized by managing the environment through mediating cognition and social cooperation.

scholarly journals The maintenance of single-locus polymorphism. IV. Models with mutation from existing alleles.

Genetics ◽  
1992 ◽  
Vol 130 (1) ◽  
pp. 211-221 ◽  
Author(s):  
H G Spencer ◽  
R W Marks
Keyword(s):  
Neutral Theory ◽  
Allele Frequencies ◽  
Allelic Polymorphism ◽  
High Frequencies ◽  
Viability Selection ◽  
Theory Of Evolution ◽  
Population Comparisons ◽  
Constructionist Approach ◽  
Very High ◽  
Joint Evolution

Abstract The ability of viability selection to maintain allelic polymorphism is investigated using a constructionist approach. In extensions to the models we have previously proposed, a population is bombarded with a series of mutations whose fitnesses in conjunction with other alleles are functions of the corresponding fitnesses with a particular allele, the parent allele, already in the population. Allele frequencies are iterated simultaneously, thus allowing alleles to be driven to extinction by selection. Such models allow very high levels of polymorphism to evolve: up to 38 alleles in one case. Alleles that are lethal as homozygotes can evolve to surprisingly high frequencies. The joint evolution of allele frequencies and viabilities highlights the necessity to consider more than the current morphology of a population. Comparisons are made with the neutral theory of evolution and it is suggested that failure to reject neutrality using the Ewens-Watterson test cannot be regarded as evidence for the neutral theory.

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