scholarly journals Neutral quasispecies evolution and the maximal entropy random walk

2021 ◽  
Vol 7 (16) ◽  
pp. eabb2376
Author(s):  
M. Smerlak
Keyword(s):  
Random Walk ◽  
Evolutionary Dynamics ◽  
Maximal Entropy ◽  
Eigenvector Centrality ◽  
Mutational Robustness ◽  
Neutral Variant ◽  
Word Game ◽  
Selection For ◽  
Neutral Mutations ◽  
Quasispecies Evolution

Even if they have no impact on phenotype, neutral mutations are not equivalent in the eyes of evolution: A robust neutral variant—one which remains functional after further mutations—is more likely to spread in a large, diverse population than a fragile one. Quasispecies theory shows that the equilibrium frequency of a genotype is proportional to its eigenvector centrality in the neutral network. This paper explores the link between the selection for mutational robustness and the navigability of neutral networks. I show that sequences of neutral mutations follow a “maximal entropy random walk,” a canonical Markov chain on graphs with nonlocal, nondiffusive dynamics. I revisit M. Smith’s word-game model of evolution in this light, finding that the likelihood of certain sequences of substitutions can decrease with the population size. These counterintuitive results underscore the fertility of the interface between evolutionary dynamics, information theory, and physics.

scholarly journals Localization of neutral evolution: selection for mutational robustness and the maximal entropy random walk

2020 ◽  
Author(s):  
Matteo Smerlak
Keyword(s):  
Random Walk ◽  
Sequence Space ◽  
Evolutionary Dynamics ◽  
Selective Advantage ◽  
Neutral Evolution ◽  
Maximal Entropy ◽  
Mutational Robustness ◽  
Population Evolution ◽  
Word Game ◽  
Selection For

AbstractIf many mutations confer no immediate selective advantage, they can pave the way for the discovery of fitter phenotypes and their subsequent positive selection. Understanding the reach of neutral evolution is therefore a key problem linking diversity, robustness and evolvability at the molecular scale. While this process is usually described as a random walk in sequence space with clock-like regularity, new effects can arise in large microbial or viral populations where new mutants arise before old ones can fix. Here I show that the clonal interference of neutral variants shuts off the access to neutral ridges and thus induces localization within the robust cores of neutral networks. As a result, larger populations can be less effective at exploring sequence space than smaller ones—a counterintuitive limitation to evolvability which invalidates analogies between evolution and percolation. I illustrate these effects by revisiting Maynard Smith’s word-game model of protein evolution. Interestingly, the phenomenon of neutral interference connects evolutionary dynamics to a Markov process known in network science as the maximal-entropy random walk; its special properties imply that, when many neutral variants interfere in a population, evolution chooses mutational paths—not individual mutations—uniformly at random.

scholarly journals Selection against expression noise explains the origin of the hourglass pattern of Evo-Devo

2019 ◽  
Author(s):  
Jialin Liu ◽  
Michael Frochaux ◽  
Vincent Gardeux ◽  
Bart Deplancke ◽  
Marc Robinson-Rechavi
Keyword(s):  
Regulatory Elements ◽  
Mutational Robustness ◽  
Expression Variability ◽  
Expression Noise ◽  
Environmental Perturbations ◽  
Phylotypic Stage ◽  
Robustness To Noise ◽  
Selection For ◽  
Hourglass Model ◽  
Evo Devo

The evolution of embryological development has long been characterized by deep conservation. Both morphological and transcriptomic surveys have proposed a “hourglass” model of Evo-Devo1,2. A stage in mid-embryonic development, the phylotypic stage, is highly conserved among species within the same phylum3–7. However, the reason for this phylotypic stage is still elusive. Here we hypothesize that the phylotypic stage might be characterized by selection for robustness to noise and environmental perturbations. This could lead to mutational robustness, thus evolutionary conservation of expression and the hourglass pattern. To test this, we quantified expression variability of single embryo transcriptomes throughout fly Drosophila melanogaster embryogenesis. We found that indeed expression variability is lower at extended germband, the phylotypic stage. We explain this pattern by stronger histone modification mediated transcriptional noise control at this stage. In addition, we find evidence that histone modifications can also contribute to mutational robustness in regulatory elements. Thus, the robustness to noise does indeed contributes to robustness of gene expression to genetic variations, and to the conserved phylotypic stage.

scholarly journals Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection

2019 ◽  
Author(s):  
Caroline B. Turner ◽  
Sean W. Buskirk ◽  
Katrina B. Harris ◽  
Vaughn S. Cooper
Keyword(s):  
Evolutionary Dynamics ◽  
Burkholderia Cenocepacia ◽  
Natural Environments ◽  
Fluctuating Selection ◽  
Frequency Dependent ◽  
Frequency Dependent Selection ◽  
Fluctuating Environment ◽  
Fluctuating Environments ◽  
Negative Frequency Dependent Selection ◽  
Selection For

AbstractNatural environments are rarely static; rather selection can fluctuate on time scales ranging from hours to centuries. However, it is unclear how adaptation to fluctuating environments differs from adaptation to constant environments at the genetic level. For bacteria, one key axis of environmental variation is selection for planktonic or biofilm modes of growth. We conducted an evolution experiment with Burkholderia cenocepacia, comparing the evolutionary dynamics of populations evolving under constant selection for either biofilm formation or planktonic growth with populations in which selection fluctuated between the two environments on a weekly basis. Populations evolved in the fluctuating environment shared many of the same genetic targets of selection as those evolved in constant biofilm selection, but were genetically distinct from the constant planktonic populations. In the fluctuating environment, mutations in the biofilm-regulating genes wspA and rpfR rose to high frequency in all replicate populations. A mutation in wspA first rose rapidly and nearly fixed during the initial biofilm phase but was subsequently displaced by a collection of rpfR mutants upon the shift to the planktonic phase. The wspA and rpfR genotypes coexisted via negative frequency-dependent selection around an equilibrium frequency that shifted between the environments. The maintenance of coexisting genotypes in the fluctuating environment was unexpected. Under temporally fluctuating environments coexistence of two genotypes is only predicted under a narrow range of conditions, but the frequency-dependent interactions we observed provide a mechanism that can increase the likelihood of coexistence in fluctuating environments.

scholarly journals Inbreeding parents should invest more resources in fewer offspring

2016 ◽  
Author(s):  
A. Bradley Duthie ◽  
Aline M. Lee ◽  
Jane M. Reid
Keyword(s):  
General Theory ◽  
Evolutionary Dynamics ◽  
Inbreeding Avoidance ◽  
The Other ◽  
Trade Off ◽  
Offspring Number ◽  
Focal Female ◽  
Special Cases ◽  
Selection For ◽  
Joint Consideration

AbstractInbreeding increases parent-offspring relatedness and commonly reduces offspring viability, shaping selection on reproductive interactions involving relatives and associated parental investment (PI). Nevertheless, theories predicting selection for inbreeding versus inbreeding avoidance and selection for optimal PI have only been considered separately, precluding prediction of optimal PI and associated reproductive strategy given inbreeding. We unify inbreeding and PI theory, demonstrating that optimal PI increases when a female's inbreeding decreases the viability of her offspring. Inbreeding females should therefore produce fewer offspring due to the fundamental trade-off between offspring number and PI. Accordingly, selection for inbreeding versus inbreeding avoidance changes when females can adjust PI with the degree that they inbreed. In contrast, optimal PI does not depend on whether a focal female is herself inbred. However, inbreeding causes optimal PI to increase given strict monogamy and associated biparental investment compared to female-only investment. Our model implies that understanding evolutionary dynamics of inbreeding strategy, inbreeding depression, and PI requires joint consideration of the expression of each in relation to the other. Overall, we demonstrate that existing PI and inbreeding theories represent special cases of a more general theory, implying that intrinsic links between inbreeding and PI affect evolution of behaviour and intra-familial conflict.

scholarly journals Higher-fitness yeast genotypes are less robust to deleterious mutations

Science ◽  
2019 ◽  
Vol 366 (6464) ◽  
pp. 490-493 ◽  
Author(s):  
Milo S. Johnson ◽  
Alena Martsul ◽  
Sergey Kryazhimskiy ◽  
Michael M. Desai
Keyword(s):  
Second Order ◽  
Order Selection ◽  
Deleterious Mutations ◽  
Mutational Robustness ◽  
First Order ◽  
Fitness Effects ◽  
Yeast Strains ◽  
Selection For ◽  
Microbial Systems ◽  
Insertion Mutations

Natural selection drives populations toward higher fitness, but second-order selection for adaptability and mutational robustness can also influence evolution. In many microbial systems, diminishing-returns epistasis contributes to a tendency for more-fit genotypes to be less adaptable, but no analogous patterns for robustness are known. To understand how robustness varies across genotypes, we measure the fitness effects of hundreds of individual insertion mutations in a panel of yeast strains. We find that more-fit strains are less robust: They have distributions of fitness effects with lower mean and higher variance. These differences arise because many mutations have more strongly deleterious effects in faster-growing strains. This negative correlation between fitness and robustness implies that second-order selection for robustness will tend to conflict with first-order selection for fitness.

scholarly journals EMERGENT NETWORK STRUCTURE, EVOLVABLE ROBUSTNESS, AND NONLINEAR EFFECTS OF POINT MUTATIONS IN AN ARTIFICIAL GENOME MODEL

2009 ◽  
Vol 12 (03) ◽  
pp. 293-310 ◽  
Author(s):  
THIMO ROHLF ◽  
CHRISTOPHER R. WINKLER
Keyword(s):  
Evolutionary Dynamics ◽  
Genetic Regulation ◽  
Point Mutations ◽  
Nonlinear Effects ◽  
High Rate ◽  
Stabilizing Selection ◽  
Clear Understanding ◽  
Stochastic Fluctuations ◽  
Neutral Mutations ◽  
Genome Model

Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this paper we investigate these properties within an artificial genome model originally introduced by Reil [Proc. 5th European Conf. Artificial Life (Springer, 1999), pp. 457–466]. We analyze statistical properties of randomly generated genomes both on the sequence and network level, and show that this model correctly predicts the frequency of genes in genomes as found in experimental data. Using an evolutionary algorithm based on stabilizing selection for a phenotype, we show that dynamical robustness against single base mutations, as against random changes in initial states of regulatory dynamics that mimic stochastic fluctuations in environmental conditions, can emerge in parallel. Point mutations at the sequence level can have strongly nonlinear effects on network wiring, including structurally neutral mutations and simultaneous rewiring of multiple connections, which occasionally lead to strong reorganization of the attractor landscape and metastability of evolutionary dynamics. Similar to real genomes, evolved artificial genomes exhibit both highly conserved regions, as well as regions that are characterized by a high rate of accepted base substitutions.

scholarly journals Localization of the Maximal Entropy Random Walk

2009 ◽  
Vol 102 (16) ◽  
Author(s):  
Z. Burda ◽  
J. Duda ◽  
J. M. Luck ◽  
B. Waclaw
Keyword(s):  
Random Walk ◽  
Maximal Entropy

scholarly journals Selection for thermostability can lead to the emergence of mutational robustness in an RNA virus

2010 ◽  
Vol 23 (11) ◽  
pp. 2453-2460 ◽  
Author(s):  
P. DOMINGO-CALAP ◽  
M. PEREIRA-GÓMEZ ◽  
R. SANJUÁN
Keyword(s):  
Rna Virus ◽  
Mutational Robustness ◽  
Selection For

scholarly journals Linking influenza virus evolution within and between human hosts

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Katherine S Xue ◽  
Jesse D Bloom
Keyword(s):  
Influenza Virus ◽  
Evolutionary Dynamics ◽  
Global Scale ◽  
Influenza Viruses ◽  
Global Evolution ◽  
Synonymous Sites ◽  
Selection For ◽  
H3n2 Influenza ◽  
Human Infections ◽  
Individual Human

Abstract Influenza viruses rapidly diversify within individual human infections. Several recent studies have deep-sequenced clinical influenza infections to identify viral variation within hosts, but it remains unclear how within-host mutations fare at the between-host scale. Here, we compare the genetic variation of H3N2 influenza within and between hosts to link viral evolutionary dynamics across scales. Synonymous sites evolve at similar rates at both scales, indicating that global evolution at these putatively neutral sites results from the accumulation of within-host variation. However, nonsynonymous mutations are depleted between hosts compared to within hosts, suggesting that selection purges many of the protein-altering changes that arise within hosts. The exception is at antigenic sites, where selection detectably favors nonsynonymous mutations at the global scale, but not within hosts. These results suggest that selection against deleterious mutations and selection for antigenic change are the main forces that act on within-host variants of influenza virus as they transmit and circulate between hosts.

Study on pedestrian flow evacuation with individual-guidance mechanism

Kybernetes ◽  
2016 ◽  
Vol 45 (5) ◽  
pp. 772-787 ◽  
Author(s):  
Can Zhong Yao ◽  
Xiao Feng Liu ◽  
Ji Nan Lin
Keyword(s):  
Random Walk ◽  
Majority Rule ◽  
Design Methodology ◽  
Pedestrian Flow ◽  
Content Type ◽  
Optimal Ratio ◽  
Selection For

Purpose – The purpose of this paper is to provide the possible and better selection for pedestrian flow evacuation. Design/methodology/approach – Simulation. Findings – First, according to the model with self-decision agents, the paper figures out that the effect of evacuation guided by the random-walk mechanism exceeds that guided by the inertial mechanism, and specifically, the effect of evacuation could significantly improve if random-walk agents restraint the probability of random walk under 0.4. Besides, on neighborhood reference mechanism, individuals who take neighbors’ average direction as reference tend to achieve better effect of evacuation than that of following majority rule. Furthermore, this paper proposes that an optimal ratio of the proportion of clever individuals and system density exists for evacuation effect improvement. Finally, the evacuating effect with barrier locating in different space is also studied in our research. Originality/value – The effect of evacuation could significantly improve if random-walk agents restraint the probability of random walk under 0.4. On neighborhood reference mechanism, individuals who take neighbors’ average direction as reference tend to achieve better effect of evacuation than that of following majority rule.

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