scholarly journals The unique evolutionary dynamics of the SARS-CoV-2 Delta variant

2021 ◽  
Author(s):  
Adi Stern ◽  
Shay Fleishon ◽  
Talia Kustin ◽  
Michal Mandelboim ◽  
Oran Erster ◽  
...  
Keyword(s):  
Genetic Drift ◽  
Evolutionary Dynamics ◽  
Evolutionary Process ◽  
Random Genetic Drift ◽  
Evolutionary Patterns ◽  
Nucleocapsid Proteins ◽  
Synonymous Substitutions ◽  
Synonymous Mutations ◽  
Second Year ◽  
Compare And Contrast

The SARS-Coronavirus-2 (SARS-CoV-2) driven pandemic was first recognized in late 2019, and the first few months of its evolution were relatively clock-like, dominated mostly by neutral substitutions. In contrast, the second year of the pandemic was punctuated by the emergence of several variants that bore evidence of dramatic evolution. Here, we compare and contrast evolutionary patterns of various variants, with a focus on the recent Delta variant. Most variants are characterized by long branches leading to their emergence, with an excess of non-synonymous substitutions occurring particularly in the Spike and Nucleocapsid proteins. In contrast, the Delta variant that is now becoming globally dominant, lacks the signature long branch, and is characterized by a step-wise evolutionary process that is ongoing. Contrary to the star-like topologies of other variants, we note the formation of several distinct clades within Delta that we denote as clades A-E. We find that sequences from the Delta D clade are dramatically increasing in frequency across different regions of the globe. Delta D is characterized by an excess of non-synonymous mutations, mostly occurring in ORF1a/b, and also T140I in ORF7b, and G215C in Nucleocapsid. We conclude that the Delta surge these days is composed almost exclusively of Delta D, and discuss whether selection or random genetic drift has driven the emergence of Delta D.

scholarly journals Emergence of evolutionary driving forces in pattern-forming microbial populations

2018 ◽  
Vol 373 (1747) ◽  
pp. 20170106 ◽  
Author(s):  
Jona Kayser ◽  
Carl F. Schreck ◽  
QinQin Yu ◽  
Matti Gralka ◽  
Oskar Hallatschek
Keyword(s):  
Natural Selection ◽  
Pattern Formation ◽  
Genetic Drift ◽  
Cell Biology ◽  
Evolutionary Dynamics ◽  
Driving Forces ◽  
Population Level ◽  
Microbial Populations ◽  
Random Genetic Drift ◽  
Pattern Forming

Evolutionary dynamics are controlled by a number of driving forces, such as natural selection, random genetic drift and dispersal. In this perspective article, we aim to emphasize that these forces act at the population level, and that it is a challenge to understand how they emerge from the stochastic and deterministic behaviour of individual cells. Even the most basic steric interactions between neighbouring cells can couple evolutionary outcomes of otherwise unrelated individuals, thereby weakening natural selection and enhancing random genetic drift. Using microbial examples of varying degrees of complexity, we demonstrate how strongly cell–cell interactions influence evolutionary dynamics, especially in pattern-forming systems. As pattern formation itself is subject to evolution, we propose to study the feedback between pattern formation and evolutionary dynamics, which could be key to predicting and potentially steering evolutionary processes. Such an effort requires extending the systems biology approach from the cellular to the population scale. This article is part of the theme issue ‘Self-organization in cell biology’.

CYTO-NUCLEAR EPISTASIS: TWO-LOCUS RANDOM GENETIC DRIFT IN HERMAPHRODITIC AND DIOECIOUS SPECIES

Evolution ◽  
2006 ◽  
Vol 60 (4) ◽  
pp. 643 ◽  
Author(s):  
Michael J. Wade ◽  
Charles J. Goodnight
Keyword(s):  
Genetic Drift ◽  
Random Genetic Drift ◽  
Dioecious Species

scholarly journals Influence of Random Genetic Drift on Human Immunodeficiency Virus Type 1envEvolution During Chronic Infection

Genetics ◽  
2004 ◽  
Vol 166 (3) ◽  
pp. 1155-1164 ◽  
Author(s):  
Daniel Shriner ◽  
Raj Shankarappa ◽  
Mark A. Jensen ◽  
David C. Nickle ◽  
John E. Mittler ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Genetic Drift ◽  
Chronic Infection ◽  
Random Genetic Drift ◽  
Immunodeficiency Virus

scholarly journals A General Solution of the Wright–Fisher Model of Random Genetic Drift

2016 ◽  
Vol 27 (4) ◽  
pp. 467-492 ◽  
Author(s):  
Tat Dat Tran ◽  
Julian Hofrichter ◽  
Jürgen Jost
Keyword(s):  
General Solution ◽  
Genetic Drift ◽  
Random Genetic Drift ◽  
Fisher Model

scholarly journals Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers

Animals ◽  
2022 ◽  
Vol 12 (2) ◽  
pp. 148
Author(s):  
Watcharaporn Thapana ◽  
Nattakan Ariyaraphong ◽  
Parinya Wongtienchai ◽  
Nararat Laopichienpong ◽  
Worapong Singchat ◽  
...  
Keyword(s):  
Evolutionary Process ◽  
Mitochondrial Genomes ◽  
Sequence Analyses ◽  
Evolutionary Patterns ◽  
Evolutionary Pattern ◽  
Independent Evolution ◽  
Substitution Saturation ◽  
Varanus Salvator ◽  
Monitor Lizards ◽  
Control Regions

Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage.

scholarly journals Evolution of correlated complexity in the radically different courtship signals of birds-of-paradise

2018 ◽  
Author(s):  
Russell A. Ligon ◽  
Christopher D. Diaz ◽  
Janelle L. Morano ◽  
Jolyon Troscianko ◽  
Martin Stevens ◽  
...  
Keyword(s):  
Sexual Selection ◽  
Natural Selection ◽  
Evolutionary Biology ◽  
Evolutionary Dynamics ◽  
Functional Integration ◽  
Empirical Support ◽  
Evolutionary Patterns ◽  
Evolutionary Innovation ◽  
Birds Of Paradise ◽  
Analytical Approaches

Ornaments used in courtship often vary wildly among species, reflecting the evolutionary interplay between mate preference functions and the constraints imposed by natural selection. Consequently, understanding the evolutionary dynamics responsible for ornament diversification has been a longstanding challenge in evolutionary biology. However, comparing radically different ornaments across species, as well as different classes of ornaments within species, is a profound challenge to understanding diversification of sexual signals. Using novel methods and a unique natural history dataset, we explore evolutionary patterns of ornament evolution in a group - the birds-of-paradise - exhibiting dramatic phenotypic diversification widely assumed to be driven by sexual selection. Rather than the tradeoff between ornament types originally envisioned by Darwin and Wallace, we found positive correlations among cross-modal (visual/acoustic) signals indicating functional integration of ornamental traits into a composite unit - the courtship phenotype. Furthermore, given the broad theoretical and empirical support for the idea that systemic robustness - functional overlap and interdependency - promotes evolutionary innovation, we posit that birds-of-paradise have radiated extensively through ornamental phenotype space as a consequence of the robustness in the courtship phenotype that we document at a phylogenetic scale. We suggest that the degree of robustness in courtship phenotypes among taxa can provide new insights into the relative influence of sexual and natural selection on phenotypic radiations.Author SummaryAnimals frequently vary widely in ornamentation, even among closely related species. Understanding the patterns that underlie this variation is a significant challenge, requiring comparisons among drastically different traits - like comparing apples to oranges. Here, we use novel analytical approaches to quantify variation in ornamental diversity and richness across the wildly divergent birds-of-paradise, a textbook example of how sexual selection can profoundly shape organismal phenotypes. We find that color and acoustic complexity, along with behavior and acoustic complexity, are positively correlated across evolutionary time-scales. Positive covariation among ornament classes suggests that selection is acting on correlated suites of traits - a composite courtship phenotype - and that this integration may be partially responsible for the extreme variation we see in birds-of-paradise.

scholarly journals Sequence diversity and evolution of an iflavirus family associated with ticks

2020 ◽  
Author(s):  
Romain Daveu ◽  
Caroline Hervet ◽  
Louane Sigrist ◽  
Davide Sassera ◽  
Aaron Jex ◽  
...  
Keyword(s):  
Cell Line ◽  
Complete Genome ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Rna Viruses ◽  
Ixodes Scapularis ◽  
Fine Scale ◽  
Rna Seq ◽  
Strong Positive Selection ◽  
Synonymous Mutations

AbstractWe studied a family of iflaviruses, a group of RNA viruses frequently found in arthropods, focusing on viruses associated with ticks. Our aim was to bring insight on the evolutionary dynamics of this group of viruses, which may interact with the biology of ticks. We explored systematically de novo RNA-Seq assemblies available for species of ticks which allowed to identify nine new genomes of iflaviruses. The phylogeny of virus sequences was not congruent with that of the tick hosts, suggesting recurrent host changes across tick genera along evolution. We identified five different variants with a complete or near-complete genome in Ixodes ricinus. These sequences were closely related, which allowed a fine-scale estimation of patterns of substitutions: we detected a strong excess of synonymous mutations suggesting evolution under strong positive selection. ISIV, a sequence found in the ISE6 cell line of Ixodes scapularis, was unexpectedly nearidentical with I. ricinus variants, suggesting a contamination of this cell line by I. ricinus material. Overall, our work constitutes a step in the understanding of the interactions between this family of viruses and ticks.

scholarly journals Evolution of gene regulatory networks by means of selection and random genetic drift

2018 ◽  
Author(s):  
Antonios Kioukis ◽  
Pavlos Pavlidis
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Genetic Drift ◽  
Regulatory Networks ◽  
Fitness Landscape ◽  
Random Genetic Drift ◽  
Maturation Period ◽  
Evolutionary Forces ◽  
Gene Regulatory

The evolution of a population by means of genetic drift and natural selection operating on a gene regulatory network (GRN) of an individual has not been scrutinized in depth. Thus, the relative importance of various evolutionary forces and processes on shaping genetic variability in GRNs is understudied. Furthermore, it is not known if existing tools that identify recent and strong positive selection from genomic sequences, in simple models of evolution, can detect recent positive selection when it operates on GRNs. Here, we propose a simulation framework, called EvoNET, that simulates forward-in-time the evolution of GRNs in a population. Since the population size is finite, random genetic drift is explicitly applied. The fitness of a mutation is not constant, but we evaluate the fitness of each individual by measuring its genetic distance from an optimal genotype. Mutations and recombination may take place from generation to generation, modifying the genotypic composition of the population. Each individual goes through a maturation period, where its GRN reaches equilibrium. At the next step, individuals compete to produce the next generation. As time progresses, the beneficial genotypes push the population higher in the fitness landscape. We examine properties of the GRN evolution such as robustness against the deleterious effect of mutations and the role of genetic drift. We confirm classical results from Andreas Wagner’s work that GRNs show robustness against mutations and we provide new results regarding the interplay between random genetic drift and natural selection.

scholarly journals The Dynamics of Influenza A H3N2 Defective Viral Genomes from a Human Challenge Study

2019 ◽  
Author(s):  
Michael A. Martin ◽  
Drishti Kaul ◽  
Gene S. Tan ◽  
Christopher W. Woods ◽  
Katia Koelle
Keyword(s):  
Genetic Drift ◽  
Influenza A ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Gene Segment ◽  
Influenza Viruses ◽  
Genomic Variation ◽  
Wild Type Virus ◽  
Single Nucleotide Variants ◽  
Viral Genomes

AbstractThe rapid evolution of influenza is an important contributing factor to its high worldwide incidence. The emergence and spread of genetic point mutations has been thoroughly studied both within populations and within individual hosts. In addition, influenza viruses are also known to generate genomic variation during their replication in the form of defective viral genomes (DVGs). These DVGs are formed by internal deletions in at least one gene segment that render them incapable of replication without the presence of wild-type virus. DVGs have previously been identified in natural human infections and may be associated with less severe clinical outcomes. These studies have not been able to address how DVG populations evolve in vivo in individual infections due to their cross-sectional design. Here we present an analysis of DVGs present in samples from two longitudinal influenza A H3N2 human challenge studies. We observe the generation of DVGs in almost all subjects. Although the genetic composition of DVG populations was highly variable, identical DVGs were observed both between multiple samples within single hosts as well as between hosts. Most likely due to stochastic effects, we did not observe clear instances of selection for specific DVGs or for shorter DVGs over the course of infection. Furthermore, DVG presence was not found to be associated with peak viral titer or peak symptom scores. Our analyses highlight the diversity of DVG populations within a host over the course of infection and the apparent role that genetic drift plays in their population dynamics.ImportanceThe evolution of influenza virus, in terms of single nucleotide variants and the reassortment of gene segments, has been studied in detail. However, influenza is known to generate defective viral genomes (DVGs) during replication, and little is known about how these genomes evolve both within hosts and at the population level. Studies in animal models have indicated that prophylactically or therapeutically administered DVGs can impact patterns of disease progression. However, the formation of naturally-occurring DVGs, their evolutionary dynamics, and their contribution to disease severity in human hosts is not well understood. Here, we identify the formation of de novo DVGs in samples from human challenge studies throughout the course of infection. We analyze their evolutionary trajectories, revealing the important role of genetic drift in shaping DVG populations during acute infections with well-adapted viral strains.

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