scholarly journals Intrinsic adaptive value and early fate of gene duplication revealed by a bottom-up approach

2017 ◽  
Author(s):  
Guillermo Rodrigo ◽  
Mario A. Fares
Keyword(s):  
Population Genetics ◽  
Gene Regulation ◽  
Natural Selection ◽  
Gene Duplication ◽  
Genetic Drift ◽  
Evolutionary Process ◽  
Selective Advantage ◽  
Gene Copy ◽  
Adaptive Value ◽  
Trade Offs

ABSTRACTGene duplication is a major source of functional innovations and genome complexity, albeit this evolutionary process requires the preservation of duplicates in the genomes for long time. However, the population genetic mechanisms governing this preservation, especially in the critical very initial phase, have remained largely unknown. Here, we demonstrate that gene duplication confers per se a weak selective advantage in scenarios of fitness trade-offs. Through a precise quantitative description of a model system, we show that a second gene copy enhances the information transfer from the environmental signal to the phenotypic response by reducing gene expression inaccuracies derived from pervasive molecular noise and suboptimal gene regulation. We then reveal that such a phenotypic accuracy yields a selective advantage in the order of 0.1% on average, which would allow the positive selection of gene duplication in populations with moderate or large sizes. This advantage is greater at higher noise levels and intermediate concentrations of the environmental molecule, when fitness trade-offs become more evident. Moreover, we show that the genome rearrangement rates greatly condition the eventual fixation of duplicated genes, either by natural selection or by random genetic drift. Overall, our theoretical results highlight an original adaptive value for cells carrying new-born duplicates, broadly analyze the selective conditions that determine their early fates in different organisms, and reconcile population genetics with evolution by gene duplication.SIGNIFICANCEGene duplication is considered a major driver for the evolution of biological complexity. However, it is still enigmatic to what extent natural selection and genetic drift have governed this evolutionary process. This work uncovers a selective advantage for genotypes carrying duplicates, called phenotypic accuracy, widely characterized thanks to a multi-scale mathematical model coupling gene regulation with population genetics. Importantly, the integrative results presented here provide a detailed mechanistic description for the fixation of duplicates, which allows making predictions about the genome architectures, and which is relevant to understand the origins of complexity.

scholarly journals Intrinsic adaptive value and early fate of gene duplication revealed by a bottom-up approach

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Guillermo Rodrigo ◽  
Mario A Fares
Keyword(s):  
Gene Duplication ◽  
Genome Rearrangement ◽  
Quantitative Description ◽  
Selective Advantage ◽  
Gene Copy ◽  
Adaptive Value ◽  
Trade Offs ◽  
Molecular Noise ◽  
Genetic Mechanisms ◽  
Selection Of

The population genetic mechanisms governing the preservation of gene duplicates, especially in the critical very initial phase, have remained largely unknown. Here, we demonstrate that gene duplication confers per se a weak selective advantage in scenarios of fitness trade-offs. Through a precise quantitative description of a model system, we show that a second gene copy serves to reduce gene expression inaccuracies derived from pervasive molecular noise and suboptimal gene regulation. We then reveal that such an accuracy in the phenotype yields a selective advantage in the order of 0.1% on average, which would allow the positive selection of gene duplication in populations with moderate/large sizes. This advantage is greater at higher noise levels and intermediate concentrations of the environmental molecule, when fitness trade-offs become more evident. Moreover, we discuss how the genome rearrangement rates greatly condition the eventual fixation of duplicates. Overall, our theoretical results highlight an original adaptive value for cells carrying new-born duplicates, broadly analyze the selective conditions that determine their early fates in different organisms, and reconcile population genetics with evolution by gene duplication.

Applications of Supercomputers in Population Genetics

2015 ◽  
pp. 176-200
Author(s):  
Gerard G. Dumancas
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Genetic Drift ◽  
Critical Role ◽  
Allele Frequency Distribution ◽  
Modern Approach ◽  
Mathematical Discipline ◽  
Modern Evolutionary Synthesis ◽  
Changes Over Time ◽  
Over Time

Population genetics is the study of the frequency and interaction of alleles and genes in population and how this allele frequency distribution changes over time as a result of evolutionary processes such as natural selection, genetic drift, and mutation. This field has become essential in the foundation of modern evolutionary synthesis. Traditionally regarded as a highly mathematical discipline, its modern approach comprises more than the theoretical, lab, and fieldwork. Supercomputers play a critical role in the success of this field and are discussed in this chapter.

Evolution: Medicine’s most basic science

2020 ◽  
pp. 39-42
Author(s):  
Randolph M. Nesse ◽  
Richard Dawkins
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Basic Science ◽  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
The Body ◽  
Clinical Implications ◽  
Trade Offs ◽  
The Cost

The role of evolutionary biology as a basic science for medicine is expanding rapidly. Some evolutionary methods are already widely applied in medicine, such as population genetics and methods for analysing phylogenetic trees. Newer applications come from seeking evolutionary as well as proximate explanations for disease. Traditional medical research is restricted to proximate studies of the body’s mechanism, but separate evolutionary explanations are needed for why natural selection has left many aspects of the body vulnerable to disease. There are six main possibilities: mismatch, infection, constraints, trade-offs, reproduction at the cost of health, and adaptive defences. Like other basic sciences, evolutionary biology has limited direct clinical implications, but it provides essential research methods, encourages asking new questions that foster a deeper understanding of disease, and provides a framework that organizes the facts of medicine.

scholarly journals A conditional likelihood is required to estimate the selection coefficient in ancient DNA

2016 ◽  
Author(s):  
Angelo Valleriani
Keyword(s):  
Time Series ◽  
Population Genetics ◽  
Natural Selection ◽  
Genetic Drift ◽  
Ancient Dna ◽  
Fitness Landscape ◽  
Likelihood Function ◽  
Allele Frequencies ◽  
Conditional Likelihood ◽  
Selection Coefficient

AbstractTime-series of allele frequencies are a useful and unique set of data to determine the strength of natural selection on the background of genetic drift. Technically, the selection coefficient is estimated by means of a likelihood function built under the hypothesis that the available trajectory spans a sufficiently large portion of the fitness landscape. Especially for ancient DNA, however, often only one single such trajectories is available and the coverage of the fitness landscape is very limited. In fact, one single trajectory is more representative of a process conditioned both in the initial and in the final condition than of a process free to visit the available fitness landscape. Based on two models of population genetics, here we show how to build a likelihood function for the selection coefficient that takes the statistical peculiarity of single trajectories into account. We show that this conditional likelihood delivers a precise estimate of the selection coefficient also when allele frequencies are close to fixation whereas the unconditioned likelihood fails. Finally, we discuss the fact that the traditional, unconditioned likelihood always delivers an answer, which is often unfalsifiable and appears reasonable also when it is not correct.

scholarly journals Models of the population genetics of transposable elements

2005 ◽  
Vol 85 (3) ◽  
pp. 171-181 ◽  
Author(s):  
ARNAUD LE ROUZIC ◽  
GRÉGORY DECELIERE
Keyword(s):  
Population Genetics ◽  
Drosophila Melanogaster ◽  
Natural Selection ◽  
Transposable Elements ◽  
Genetic Drift ◽  
Self Regulation ◽  
Evolutionary Forces ◽  
Classical Models

Although transposable elements (TEs) have been found in all organisms in which they have been looked for, the ways in which they invade genomes and populations are still a matter of debate. By extending the classical models of population genetics, several approaches have been developed to account for the dynamics of TEs, especially in Drosophila melanogaster. While the formalism of these models is based on simplifications, they enable us to understand better how TEs invade genomes, as a result of multiple evolutionary forces including duplication, deletion, self-regulation, natural selection and genetic drift. The aim of this paper is to review the assumptions and the predictions of these different models by highlighting the importance of the specific characteristics of both the TEs and the hosts, and the host/TE relationships. Then, perspectives in this domain will be discussed.

Applications of Supercomputers in Population Genetics

Biotechnology ◽  
2019 ◽  
pp. 693-719
Author(s):  
Gerard G. Dumancas
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Genetic Drift ◽  
Critical Role ◽  
Allele Frequency Distribution ◽  
Modern Approach ◽  
Mathematical Discipline ◽  
Modern Evolutionary Synthesis ◽  
Changes Over Time ◽  
Over Time

Population genetics is the study of the frequency and interaction of alleles and genes in population and how this allele frequency distribution changes over time as a result of evolutionary processes such as natural selection, genetic drift, and mutation. This field has become essential in the foundation of modern evolutionary synthesis. Traditionally regarded as a highly mathematical discipline, its modern approach comprises more than the theoretical, lab, and fieldwork. Supercomputers play a critical role in the success of this field and are discussed in this chapter.

scholarly journals Allele Based Inference on Evolution and Extinction; A Genetic Drift Approach

2019 ◽  
Vol 1 (4) ◽  
pp. 1-15
Author(s):  
S. Oluwafemi Oyamakin ◽  
Angela U. Chukwu ◽  
Wale-Orojo Oluwaseun A ◽  
Ogunjobi E. O
Keyword(s):  
Natural Selection ◽  
Genetic Drift ◽  
Selective Advantage ◽  
Random Mutation ◽  
Genetic Changes ◽  
Moran Model ◽  
Fitness Advantage ◽  
Model Probability ◽  
Or Gene ◽  
Probability Of Fixation

In other to present a series of stochastic models from population dynamics capable of describing rudimentary aspects of genetic evolution, we studied two-allele Wright–Fisher and the Moran models for evolution of the relative frequencies of two alleles at a diploid locus under random genetic drift in a population of fixed size “simplest form, selection, and random mutation”. Principal results were presented in qualitative terms, illustrated by Monte Carlo simulations from R and http://www.radford.edu/~rsheehy/Gen_flash/popgen. Moran and the Wright-Fisher Models exhibited the same fixation probabilities, only that the Moran model runs twice as fast as the Wright-Fisher Model. A clue that can help us to understand this result is provided by the variance in reproductive success in the two models. Genetic changes due to drift were neither directional nor predictable in any deterministic way. Nonetheless, genetic drift led to evolutionary change in the absence of mutation (P=0.5), natural selection or gene flow. In general, alleles drift to fixation is significantly faster in smaller populations. Probability of fixation of an allele A was approximately equivalent to the initial frequency of that allele. With the inclusion of selection in our model, probability of fixation of a favoured allele due to natural selection increased with increase in fitness advantage and population size. The time taken to reach fixation is much slower, in case of no selective advantage, than a fixation under mutation with selective advantage.

scholarly journals Gene Expression Space Shapes the Bioprocess Trade-Offs among Titer, Yield and Productivity

2021 ◽  
Vol 11 (13) ◽  
pp. 5859
Author(s):  
Fernando N. Santos-Navarro ◽  
Yadira Boada ◽  
Alejandro Vignoni ◽  
Jesús Picó
Keyword(s):  
Gene Expression ◽  
Gene Transcription ◽  
Performance Metrics ◽  
Cell Mass ◽  
Gene Copy ◽  
Substrate Uptake ◽  
Promoter Strength ◽  
Expression Levels ◽  
Trade Offs ◽  
Wide Range

Optimal gene expression is central for the development of both bacterial expression systems for heterologous protein production, and microbial cell factories for industrial metabolite production. Our goal is to fulfill industry-level overproduction demands optimally, as measured by the following key performance metrics: titer, productivity rate, and yield (TRY). Here we use a multiscale model incorporating the dynamics of (i) the cell population in the bioreactor, (ii) the substrate uptake and (iii) the interaction between the cell host and expression of the protein of interest. Our model predicts cell growth rate and cell mass distribution between enzymes of interest and host enzymes as a function of substrate uptake and the following main lab-accessible gene expression-related characteristics: promoter strength, gene copy number and ribosome binding site strength. We evaluated the differential roles of gene transcription and translation in shaping TRY trade-offs for a wide range of expression levels and the sensitivity of the TRY space to variations in substrate availability. Our results show that, at low expression levels, gene transcription mainly defined TRY, and gene translation had a limited effect; whereas, at high expression levels, TRY depended on the product of both, in agreement with experiments in the literature.

scholarly journals Recombination Can Evolve in Large Finite Populations Given Selection on Sufficient Loci

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2249-2258 ◽  
Author(s):  
Mark M Iles ◽  
Kevin Walters ◽  
Chris Cannings
Keyword(s):  
Experimental Evidence ◽  
Genetic Drift ◽  
Finite Population ◽  
Selective Advantage ◽  
Indirect Selection ◽  
Small Populations ◽  
Finite Populations ◽  
Population Sizes ◽  
Population Recombination

AbstractIt is well known that an allele causing increased recombination is expected to proliferate as a result of genetic drift in a finite population undergoing selection, without requiring other mechanisms. This is supported by recent simulations apparently demonstrating that, in small populations, drift is more important than epistasis in increasing recombination, with this effect disappearing in larger finite populations. However, recent experimental evidence finds a greater advantage for recombination in larger populations. These results are reconciled by demonstrating through simulation without epistasis that for m loci recombination has an appreciable selective advantage over a range of population sizes (am, bm). bm increases steadily with m while am remains fairly static. Thus, however large the finite population, if selection acts on sufficiently many loci, an allele that increases recombination is selected for. We show that as selection acts on our finite population, recombination increases the variance in expected log fitness, causing indirect selection on a recombination-modifying locus. This effect is enhanced in those populations with more loci because the variance in phenotypic fitnesses in relation to the possible range will be smaller. Thus fixation of a particular haplotype is less likely to occur, increasing the advantage of recombination.

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