scholarly journals Dynamics of adaptation in an anisotropic phenotype-fitness landscape

2019 ◽  
Author(s):  
F. Hamel ◽  
F. Lavigne ◽  
G. Martin ◽  
L. Roques
Keyword(s):  
Experimental Evolution ◽  
Fitness Landscape ◽  
Empirical Studies ◽  
Stem Form ◽  
Asexual Population ◽  
Nonlocal Parabolic Equation ◽  
Long Time ◽  
Evolution Experiment ◽  
Phenotype Distribution ◽  
Mean Fitness

AbstractWe study the dynamics of adaptation of a large asexual population in a n-dimensional phenotypic space, under anisotropic mutation and selection effects. When n = 1 or under isotropy assumptions, the ‘replicator-mutator’ equation is a standard model to describe these dynamics. However, the n-dimensional anisotropic case remained largely unexplored.We prove here that the equation admits a unique solution, which is interpreted as the phenotype distribution, and we propose a new and general framework to the study of the quantitative behavior of this solution. Our method builds upon a degenerate nonlocal parabolic equation satisfied by the distribution of the ‘fitness components’, and a nonlocal transport equation satisfied by the cumulant generating function of the joint distribution of these components. This last equation can be solved analytically and we then get a general formula for the trajectory of the mean fitness and all higher cumulants of the fitness distribution, over time. Such mean fitness trajectory is the typical outcome of empirical studies of adaptation by experimental evolution, and can thus be compared to empirical data.In sharp contrast with the known results based on isotropic models, our results show that the trajectory of mean fitness may exhibit (n − 1) plateaus before it converges. It may thus appear ‘non-saturating’ for a transient but possibly long time, even though a phenotypic optimum exists. To illustrate the empirical relevance of these results, we show that the anisotropic model leads to a very good fit of Escherichia coli long-term evolution experiment, one of the most famous experimental dataset in experimental evolution. The two ‘evolutionary epochs’ that have been observed in this experiment have long puzzled the community: we propose that the pattern may simply stem form a climbing hill process, but in an anisotropic fitness landscape.

Experimental Evolution of Adaptive Diversification in Microbes

2011 ◽  
Author(s):  
Michael Doebeli
Keyword(s):  
Escherichia Coli ◽  
Experimental Evolution ◽  
Empirical Studies ◽  
Attractive Alternative ◽  
Frequency Dependent Selection ◽  
Adaptive Diversification ◽  
Long Time ◽  
Ecological Mechanism ◽  
Time Periods

This concluding chapter argues that experimental evolution with microbes has emerged as a very attractive alternative to overcome the problem of long time scales in empirical studies of evolution. This is exemplified by the long-term evolution experiments of Richard Lenski, whose experimental Escherichia coli lines have evolved for more than 40,000 generations to date. Lenski and his many collaborators convincingly argued that the diversified strains have coexisted over long time periods, and hence that this diversification represents a case of asexual speciation. The ecological mechanism for diversification in this case appears to be related to crossfeeding, a scenario in which one strain or species persists by scavenging on nutrients that accumulate in the environment as metabolic byproducts of the coexisting strain. With crossfeeding, polymorphisms can be maintained even in simple environments with a single limiting resource such as glucose. This is an excellent example of frequency-dependent selection, as the fitness of the crossfeeder depends on the presence or absence of the glucose specialist.

scholarly journals Long-Term Experimental Evolution in Escherichia coli. VI. Environmental Constraints on Adaptation and Divergence

Genetics ◽  
1997 ◽  
Vol 146 (2) ◽  
pp. 471-479 ◽  
Author(s):  
Michael Travisano
Keyword(s):  
Escherichia Coli ◽  
Genetic Variation ◽  
Experimental Evolution ◽  
Population Genetic ◽  
Environmental Constraints ◽  
Asymmetric Pattern ◽  
Nutrient Environment ◽  
Mean Fitness ◽  
Population Genetic Variation

The effect of environment on adaptation and divergence was examined in two sets of populations of Escherichia coli selected for 1000 generations in either maltose- or glucose-limited media. Twelve replicate populations selected in maltose-limited medium improved in fitness in the selected environment, by an average of 22.5%. Statistically significant among-population genetic variation for fitness was observed during the course of the propagation, but this variation was small relative to the fitness improvement. Mean fitness in a novel nutrient environment, glucose-limited medium, improved to the same extent as in the selected environment, with no statistically significant among-population genetic variation. In contrast, 12 replicate populations previously selected for 1000 generations in glucose-limited medium showed no improvement, as a group, in fitness in maltose-limited medium and substantial genetic variation. This asymmetric pattern of correlated responses suggests that small changes in the environment can have profound effects on adaptation and divergence.

scholarly journals Segregation and the Evolution of Sex Under Overdominant Selection

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 1119-1128 ◽  
Author(s):  
Elie S Dolgin ◽  
Sarah P Otto
Keyword(s):  
Correlated Response ◽  
Heterozygote Advantage ◽  
Genetic Associations ◽  
Asexual Population ◽  
Modifier Locus ◽  
Sexual And Asexual Reproduction ◽  
Overdominant Selection ◽  
Mean Fitness ◽  
Changes Over Time ◽  
Inbred Populations

AbstractThe segregation of alleles disrupts genetic associations at overdominant loci, causing a sexual population to experience a lower mean fitness compared to an asexual population. To investigate whether circumstances promoting increased sex exist within a population with heterozygote advantage, a model is constructed that monitors the frequency of alleles at a modifier locus that changes the relative allocation to sexual and asexual reproduction. The frequency of these modifier alleles changes over time as a correlated response to the dynamics at a fitness locus under overdominant selection. Increased sex can be favored in partially sexual populations that inbreed to some extent. This surprising finding results from the fact that inbred populations have an excess of homozygous individuals, for whom sex is always favorable. The conditions promoting increased levels of sex depend on the selection pressure against the homozygotes, the extent of sex and inbreeding in the population, and the dominance of the invading modifier allele.

scholarly journals Narrative Frames as a Course Evaluation Instrument

2018 ◽  
Vol 42 (1) ◽  
pp. 3
Author(s):  
Takaaki Hiratsuka
Keyword(s):  
University Students ◽  
Teaching Methods ◽  
Empirical Studies ◽  
Course Evaluation ◽  
Student Feedback ◽  
Methods Course ◽  
Written Feedback ◽  
Evaluation Instrument ◽  
Japanese University ◽  
Long Time

Although getting student feedback on courses via questionnaires has been practiced for a long time, empirical studies on the topic are not substantial enough, nor are alternatives adequately considered. This study introduces and evaluates an alternative qualitative instrument known as narrative frames, which uses prompts to stimulate written feedback. In order to investigate its feasibility, I collected data from 26 Japanese university students in an English Teaching Methods course. Findings suggest that these narrative frames served as a useful tool for eliciting the students’ experiences in the course, their impressions of it, and its impact on them. These findings led me, as the instructor of the course, to be able to critically reflect on its content. Pedagogical and research implications for the future use of narrative frames are provided. 学生による授業評価アンケートは教育改善のために必要な手段として長年定着しているが、それらに関する研究、またそれに取って代わる手段の議論は不十分である。本論では、質的研究手法の1つで、書き手の文章作成を助長するとされているナラティブフレーム（物語枠組み）を授業評価の手段として用い、その評価を行った。データは英語科教育法を受講した26人の大学生から収集した。結果、ナラティブフレームは授業評価手段としての機能を十分に果たし、学生の授業への印象や彼らが授業から受けた影響の詳細を明らかにできることが分かった。また、これらの結果内容は担当教員が授業を批判的に精査し、振り返り活動を行うことに役立った。本論では最後に、ナラティブフレームの使用、研究に関する提言を行う。

The Effectiveness of Multiple Media Tools in L2 Listening

2019 ◽  
pp. 585-616 ◽  
Author(s):  
Tingting Kang
Keyword(s):  
Second Language ◽  
Listening Comprehension ◽  
Empirical Studies ◽  
First Language ◽  
Future Research ◽  
Source Language ◽  
Moderator Analysis ◽  
Long Time ◽  
Multiple Media ◽  
L2 Listening

Due to the nature of listening, multiple media tools (e.g., audiocassette players, radio, video, multimedia, and language laboratory) have been utilized in second language (L2) listening instruction for a long time. This chapter recruited the most recently published empirical studies and meta-analyzed available evidence on the effects of different multiple media tools on L2 listening comprehension. The results revealed a medium-to-large effect of multiple media tools on listening comprehension in between-group designs (Cohen's d = .69). The effects of individual multiple media tools have also been statistically synthesized. Further, moderator analysis could help L2 educators and test developers make decisions on applying different multiple media tools in the fields of L2 instruction and assessment. Specifically, subtitles (in the first language/L1) /captions (in the source language/L2), as well as self-regulated listening and slow speed, are recommended to teachers and test developers as a means to improve learners' listening comprehension. In the end, this chapter concludes by identifying potential areas for future research.

scholarly journals Adaptive fitness landscape for replicator systems: to maximize or not to maximize

2018 ◽  
Vol 13 (3) ◽  
pp. 25 ◽  
Author(s):  
Alexander S. Bratus ◽  
Yuri S. Semenov ◽  
Artem S. Novozhilov
Keyword(s):  
Natural Selection ◽  
Fitness Landscape ◽  
Evolutionary Process ◽  
Hill Climbing ◽  
Adaptive Landscape ◽  
Basic Model ◽  
Mean Fitness ◽  
The Mean ◽  
The Hill ◽  
Fisher’S Fundamental Theorem

Sewall Wright’s adaptive landscape metaphor penetrates a significant part of evolutionary thinking. Supplemented with Fisher’s fundamental theorem of natural selection and Kimura’s maximum principle, it provides a unifying and intuitive representation of the evolutionary process under the influence of natural selection as the hill climbing on the surface of mean population fitness. On the other hand, it is also well known that for many more or less realistic mathematical models this picture is a severe misrepresentation of what actually occurs. Therefore, we are faced with two questions. First, it is important to identify the cases in which adaptive landscape metaphor actually holds exactly in the models, that is, to identify the conditions under which system’s dynamics coincides with the process of searching for a (local) fitness maximum. Second, even if the mean fitness is not maximized in the process of evolution, it is still important to understand the structure of the mean fitness manifold and see the implications of this structure on the system’s dynamics. Using as a basic model the classical replicator equation, in this note we attempt to answer these two questions and illustrate our results with simple well studied systems.

scholarly journals Distinct Patterns of Selective Sweep and Polygenic Adaptation in Evolve and Resequence Studies

2020 ◽  
Vol 12 (6) ◽  
pp. 890-904 ◽  
Author(s):  
Neda Barghi ◽  
Christian Schlötterer
Keyword(s):  
Experimental Evolution ◽  
Selective Sweep ◽  
Time Series Data ◽  
Empirical Studies ◽  
Series Data ◽  
Stabilizing Selection ◽  
Selection Signatures ◽  
Polygenic Adaptation ◽  
Frequency Changes ◽  
Optimum Model

Abstract In molecular population genetics, adaptation is typically thought to occur via selective sweeps, where targets of selection have independent effects on the phenotype and rise to fixation, whereas in quantitative genetics, many loci contribute to the phenotype and subtle frequency changes occur at many loci during polygenic adaptation. The sweep model makes specific predictions about frequency changes of beneficial alleles and many test statistics have been developed to detect such selection signatures. Despite polygenic adaptation is probably the prevalent mode of adaptation, because of the traditional focus on the phenotype, we are lacking a solid understanding of the similarities and differences of selection signatures under the two models. Recent theoretical and empirical studies have shown that both selective sweep and polygenic adaptation models could result in a sweep-like genomic signature; therefore, additional criteria are needed to distinguish the two models. With replicated populations and time series data, experimental evolution studies have the potential to identify the underlying model of adaptation. Using the framework of experimental evolution, we performed computer simulations to study the pattern of selected alleles for two models: 1) adaptation of a trait via independent beneficial mutations that are conditioned for fixation, that is, selective sweep model and 2) trait optimum model (polygenic adaptation), that is adaptation of a quantitative trait under stabilizing selection after a sudden shift in trait optimum. We identify several distinct patterns of selective sweep and trait optimum models in populations of different sizes. These features could provide the foundation for development of quantitative approaches to differentiate the two models.

scholarly journals Experimental Evolution Reveals a Genetic Basis for Membrane-Associated Virus Release

2020 ◽  
Author(s):  
Juan-Vicente Bou ◽  
Rafael Sanjuán
Keyword(s):  
Experimental Evolution ◽  
Genetic Basis ◽  
Close Association ◽  
Site Directed Mutagenesis ◽  
Full Genome ◽  
Virus Release ◽  
Viral Shedding ◽  
Free Virion ◽  
Viral Particles ◽  
Evolution Experiment

Abstract Many animal viruses replicate and are released from cells in close association to membranes. However, whether this is a passive process or is controlled by the virus remains poorly understood. Importantly, the genetic basis and evolvability of membrane-associated viral shedding have not been investigated. To address this, we performed a directed evolution experiment using coxsackievirus B3, a model enterovirus, in which we repeatedly selected the free-virion or the fast-sedimenting membrane-associated viral subpopulations. The virus responded to this selection regime by reproducibly fixing a series of mutations that altered the extent of membrane-associated viral shedding, as revealed by full-genome ultra-deep sequencing. Specifically, using site-directed mutagenesis, we showed that substitution N63H in the viral capsid protein VP3 reduced the ratio of membrane-associated to free viral particles by 2 orders of magnitude. These findings open new avenues for understanding the mechanisms and implications of membrane-associated viral transmission.

scholarly journals Replaying the tape of life in the twenty-first century

2015 ◽  
Vol 5 (6) ◽  
pp. 20150057 ◽  
Author(s):  
Virginie Orgogozo
Keyword(s):  
Experimental Evolution ◽  
First Century ◽  
Phenotypic Evolution ◽  
Phenotypic Differences ◽  
Diverse Species ◽  
Evolution Of Life ◽  
Long Time ◽  
Time Periods ◽  
Living Organisms ◽  
Life On Earth

Should the tape of life be replayed, would it produce similar living beings? A classical answer has long been ‘no’, but accumulating data are now challenging this view. Repeatability in experimental evolution, in phenotypic evolution of diverse species and in the genes underlying phenotypic evolution indicates that despite unpredictability at the level of basic evolutionary processes (such as apparition of mutations), a certain kind of predictability can emerge at higher levels over long time periods. For instance, a survey of the alleles described in the literature that cause non-deleterious phenotypic differences among animals, plants and yeasts indicates that similar phenotypes have often evolved in distinct taxa through independent mutations in the same genes. Does this mean that the range of possibilities for evolution is limited? Does this mean that we can predict the outcomes of a replayed tape of life? Imagining other possible paths for evolution runs into four important issues: (i) resolving the influence of contingency, (ii) imagining living organisms that are different from the ones we know, (iii) finding the relevant concepts for predicting evolution, and (iv) estimating the probability of occurrence for complex evolutionary events that occurred only once during the evolution of life on earth.

Assessing the Likelihood of Recurrence during RNA Evolution in Vitro

2004 ◽  
Vol 10 (1) ◽  
pp. 1-22 ◽  
Author(s):  
Niles Lehman
Keyword(s):  
Fitness Landscape ◽  
Initial Point ◽  
Living System ◽  
Test Tube ◽  
Adaptive Landscape ◽  
Local Optimum ◽  
Evolution Experiment ◽  
Efficient Selection ◽  
Insight Into

Recurrence is the possibility of resulting in the same endpoint multiple times when a living system is allowed to evolve repeatedly starting from a given initial point. This concept is of concern to both evolutionary theoreticians and molecular biologists who use nucleic acid selection techniques to mimic biotic and computorial processes in the test tube. Using the continuous in vitro evolution methodology, many replicate experimental evolutionary lineages with populations of catalytic RNA were performed to gain insight into the parameters that could affect recurrence. The likelihood that the same genotype will result in parallel trials of an evolution experiment in vitro depends on several factors, including the phenotype under selection, the size and composition of the initial diverse pool of nucleic acids used in the experiment, the degree of mutation possible during the experiment, the shape of the fitness landscape through which the population evolves, and the strategies used to invoke selection and to search the landscape, among others. By considering these factors, it can be predicted that recurrence is more likely when a small, wild-type-based starting pool is used with efficient selection and search strategies involving little online mutagenesis within a rugged adaptive landscape with a strong local optimum. The recurrence experiments performed here on the 150-nucleotide ligase ribozyme demonstrate that it repeatedly jumps from one peak in a fitness landscape to another, apparently hurdling a deep fitness valley. These predictions can and should be tested by additional multiple replicates of actual evolution experiments in the laboratory.

Sign in / Sign up

Export Citation Format

Share Document