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’.

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 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 Farming and public goods production in Caenorhabditis elegans populations

2017 ◽  
Vol 114 (9) ◽  
pp. 2289-2294 ◽  
Author(s):  
Shashi Thutupalli ◽  
Sravanti Uppaluri ◽  
George W. A. Constable ◽  
Simon A. Levin ◽  
Howard A. Stone ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Public Good ◽  
Foraging Behavior ◽  
Evolutionary Dynamics ◽  
Driving Forces ◽  
Experimental System ◽  
Population Level ◽  
C Elegans ◽  
Exploration Exploitation ◽  
Insight Into

The ecological and evolutionary dynamics of populations are shaped by the strategies they use to produce and use resources. However, our understanding of the interplay between the genetic, behavioral, and environmental factors driving these strategies is limited. Here, we report on a Caenorhabditis elegans–Escherichia coli (worm–bacteria) experimental system in which the worm-foraging behavior leads to a redistribution of the bacterial food source, resulting in a growth advantage for both organisms, similar to that achieved via farming. We show experimentally and theoretically that the increased resource growth represents a public good that can benefit all other consumers, regardless of whether or not they are producers. Mutant worms that cannot farm bacteria benefit from farming by other worms in direct proportion to the fraction of farmers in the worm population. The farming behavior can therefore be exploited if it is associated with either energetic or survival costs. However, when the individuals compete for resources with their own type, these costs can result in an increased population density. Altogether, our findings reveal a previously unrecognized mechanism of public good production resulting from the foraging behavior of C. elegans, which has important population-level consequences. This powerful system may provide broad insight into exploration–exploitation tradeoffs, the resultant ecoevolutionary dynamics, and the underlying genetic and neurobehavioral driving forces of multispecies interactions.

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