scholarly journals How does adaptation sweep through the genome? Insights from long-term selection experiments

2012 ◽  
Vol 279 (1749) ◽  
pp. 5029-5038 ◽  
Author(s):  
Molly K. Burke
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Population Biology ◽  
De Novo ◽  
Whole Genome ◽  
Beneficial Mutations ◽  
Adaptive Mutations ◽  
Laboratory Selection ◽  
Standing Variation ◽  
New Mutations

A major goal in evolutionary biology is to understand the origins and fates of adaptive mutations. Natural selection may act to increase the frequency of de novo beneficial mutations, or those already present in the population as standing genetic variation. These beneficial mutations may ultimately reach fixation in a population, or they may stop increasing in frequency once a particular phenotypic state has been achieved. It is not yet well understood how different features of population biology, and/or different environmental circumstances affect these adaptive processes. Experimental evolution is a promising technique for studying the dynamics of beneficial alleles, as populations evolving in the laboratory experience natural selection in a replicated, controlled manner. Whole-genome sequencing, regularly obtained over the course of sustained laboratory selection, could potentially reveal insights into the mutational dynamics that most likely occur in natural populations under similar circumstances. To date, only a few evolution experiments for which whole-genome data are available exist. This review describes results from these resequenced laboratory-selected populations, in systems with and without sexual recombination. In asexual systems, adaptation from new mutations can be studied, and results to date suggest that the complete, unimpeded fixation of these mutations is not always observed. In sexual systems, adaptation from standing genetic variation can be studied, and in the admittedly few examples we have, the complete fixation of standing variants is not always observed. To date, the relative frequency of adaptation from new mutations versus standing variation has not been tested using a single experimental system, but recent studies using Caenorhabditis elegans and Saccharomyces cerevisiae suggest that this a realistic future goal.

scholarly journals Inferring Parameters of the Distribution of Fitness Effects of New Mutations When Beneficial Mutations Are Strongly Advantageous and Rare

2020 ◽  
Vol 10 (7) ◽  
pp. 2317-2326 ◽  
Author(s):  
Tom R. Booker
Keyword(s):  
Evolutionary Genetics ◽  
Molecular Data ◽  
Substantial Contribution ◽  
Beneficial Mutations ◽  
Adaptive Mutations ◽  
Fitness Effects ◽  
Relative Contribution ◽  
Standing Variation ◽  
Accuracy And Precision ◽  
New Mutations

Characterizing the distribution of fitness effects (DFE) for new mutations is central in evolutionary genetics. Analysis of molecular data under the McDonald-Kreitman test has suggested that adaptive substitutions make a substantial contribution to between-species divergence. Methods have been proposed to estimate the parameters of the distribution of fitness effects for positively selected mutations from the unfolded site frequency spectrum (uSFS). Such methods perform well when beneficial mutations are mildly selected and frequent. However, when beneficial mutations are strongly selected and rare, they may make little contribution to standing variation and will thus be difficult to detect from the uSFS. In this study, I analyze uSFS data from simulated populations subject to advantageous mutations with effects on fitness ranging from mildly to strongly beneficial. As expected, frequent, mildly beneficial mutations contribute substantially to standing genetic variation and parameters are accurately recovered from the uSFS. However, when advantageous mutations are strongly selected and rare, there are very few segregating in populations at any one time. Fitting the uSFS in such cases leads to underestimates of the strength of positive selection and may lead researchers to false conclusions regarding the relative contribution adaptive mutations make to molecular evolution. Fortunately, the parameters for the distribution of fitness effects for harmful mutations are estimated with high accuracy and precision. The results from this study suggest that the parameters of positively selected mutations obtained by analysis of the uSFS should be treated with caution and that variability at linked sites should be used in conjunction with standing variability to estimate parameters of the distribution of fitness effects in the future.

scholarly journals Inferring parameters of the distribution of fitness effects of new mutations when beneficial mutations are strongly advantageous and rare

2019 ◽  
Author(s):  
Tom R. Booker
Keyword(s):  
Evolutionary Genetics ◽  
Molecular Data ◽  
Substantial Contribution ◽  
Beneficial Mutations ◽  
Adaptive Mutations ◽  
Fitness Effects ◽  
Relative Contribution ◽  
Standing Variation ◽  
Accuracy And Precision ◽  
New Mutations

AbstractCharacterising the distribution of fitness effects (DFE) for new mutations is central in evolutionary genetics. Analysis of molecular data under the McDonald-Kreitman test has suggested that adaptive substitutions make a substantial contribution to between-species divergence. Methods have been proposed to estimate the parameters of the distribution of fitness effects for positively selected mutations from the unfolded site frequency spectrum (uSFS). However, when beneficial mutations are strongly selected and rare, they may make little contribution to standing variation and will thus be difficult to detect from the uSFS. In this study, I analyse uSFS data from simulated populations subject to advantageous mutations with effects on fitness ranging from mildly to strongly beneficial. When advantageous mutations are strongly selected and rare, there are very few segregating in populations at any one time. Fitting the uSFS in such cases leads to underestimates of the strength of positive selection and may lead researchers to false conclusions regarding the relative contribution adaptive mutations make to molecular evolution. Fortunately, the parameters for the distribution of fitness effects for harmful mutations are estimated with high accuracy and precision. The results from this study suggest that the parameters of positively selected mutations obtained by analysis of the uSFS should be treated with caution and that variability at linked sites should be used in conjunction with standing variability to estimate parameters of the distribution of fitness effects in the future.

scholarly journals Evolutionary stalling and a limit on the power of natural selection to improve a cellular module

2020 ◽  
Vol 117 (31) ◽  
pp. 18582-18590 ◽  
Author(s):  
Sandeep Venkataram ◽  
Ross Monasky ◽  
Shohreh H. Sikaroodi ◽  
Sergey Kryazhimskiy ◽  
Betul Kacar
Keyword(s):  
Escherichia Coli ◽  
Natural Selection ◽  
Adaptive Evolution ◽  
Genetic Load ◽  
Performance Theory ◽  
Biological Functions ◽  
Beneficial Mutations ◽  
Translation Machinery ◽  
Adaptive Mutations ◽  
Organismal Fitness

Cells consist of molecular modules which perform vital biological functions. Cellular modules are key units of adaptive evolution because organismal fitness depends on their performance. Theory shows that in rapidly evolving populations, such as those of many microbes, adaptation is driven primarily by common beneficial mutations with large effects, while other mutations behave as if they are effectively neutral. As a consequence, if a module can be improved only by rare and/or weak beneficial mutations, its adaptive evolution would stall. However, such evolutionary stalling has not been empirically demonstrated, and it is unclear to what extent stalling may limit the power of natural selection to improve modules. Here we empirically characterize how natural selection improves the translation machinery (TM), an essential cellular module. We experimentally evolved populations ofEscherichia coliwith genetically perturbed TMs for 1,000 generations. Populations with severe TM defects initially adapted via mutations in the TM, but TM adaptation stalled within about 300 generations. We estimate that the genetic load in our populations incurred by residual TM defects ranges from 0.5 to 19%. Finally, we found evidence that both epistasis and the depletion of the pool of beneficial mutations contributed to evolutionary stalling. Our results suggest that cellular modules may not be fully optimized by natural selection despite the availability of adaptive mutations.

scholarly journals Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

2021 ◽  
Author(s):  
Sonja Kersten ◽  
Jiyang Chang ◽  
Christian D Huber ◽  
Yoav Voichek ◽  
Christa Lanz ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Herbicide Resistance ◽  
Large Scale ◽  
De Novo ◽  
Bulked Segregant Analysis ◽  
Target Site ◽  
Temperate Climate ◽  
Minor Role ◽  
Standing Variation ◽  
Target Site Resistance

Repeated herbicide applications exert enormous selection on blackgrass (Alopecurus myosuroides), a major weed in cereal crops of the temperate climate zone including Europe. This inadvertent large-scale experiment gives us the opportunity to look into the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much either type of adaptation relies on de novo mutations versus pre-existing standing variation is important for developing strategies to manage herbicide resistance. We generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Bulked-segregant analysis evidenced that non-target-site resistance has a complex genetic architecture. Through empirical data and simulations, we showed that, despite its simple genetics, target-site resistance mainly results from standing genetic variation, with only a minor role for de novo mutations.

scholarly journals Evolutionary dynamics and structural consequences of de novo beneficial mutations and mutant lineages arising in a constant environment

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Margie Kinnersley ◽  
Katja Schwartz ◽  
Dong-Dong Yang ◽  
Gavin Sherlock ◽  
Frank Rosenzweig
Keyword(s):  
High Frequency ◽  
High Throughput Sequencing ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Allelic Diversity ◽  
Microbial Evolution ◽  
De Novo Mutations ◽  
Beneficial Mutations ◽  
Adaptive Mutations ◽  
The Impact

Abstract Background Microbial evolution experiments can be used to study the tempo and dynamics of evolutionary change in asexual populations, founded from single clones and growing into large populations with multiple clonal lineages. High-throughput sequencing can be used to catalog de novo mutations as potential targets of selection, determine in which lineages they arise, and track the fates of those lineages. Here, we describe a long-term experimental evolution study to identify targets of selection and to determine when, where, and how often those targets are hit. Results We experimentally evolved replicate Escherichia coli populations that originated from a mutator/nonsense suppressor ancestor under glucose limitation for between 300 and 500 generations. Whole-genome, whole-population sequencing enabled us to catalog 3346 de novo mutations that reached > 1% frequency. We sequenced the genomes of 96 clones from each population when allelic diversity was greatest in order to establish whether mutations were in the same or different lineages and to depict lineage dynamics. Operon-specific mutations that enhance glucose uptake were the first to rise to high frequency, followed by global regulatory mutations. Mutations related to energy conservation, membrane biogenesis, and mitigating the impact of nonsense mutations, both ancestral and derived, arose later. New alleles were confined to relatively few loci, with many instances of identical mutations arising independently in multiple lineages, among and within replicate populations. However, most never exceeded 10% in frequency and were at a lower frequency at the end of the experiment than at their maxima, indicating clonal interference. Many alleles mapped to key structures within the proteins that they mutated, providing insight into their functional consequences. Conclusions Overall, we find that when mutational input is increased by an ancestral defect in DNA repair, the spectrum of high-frequency beneficial mutations in a simple, constant resource-limited environment is narrow, resulting in extreme parallelism where many adaptive mutations arise but few ever go to fixation.

scholarly journals The neutral rate of whole-genome duplication varies among yeast species and their hybrids

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
S. Marsit ◽  
M. Hénault ◽  
G. Charron ◽  
A. Fijarczyk ◽  
C. R. Landry
Keyword(s):  
Natural Selection ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Yeast Species ◽  
Whole Genome ◽  
Hybrid Speciation ◽  
Relaxed Selection ◽  
Confounding Effect ◽  
Closely Related Species ◽  
Adaptive Mutations

AbstractHybridization and polyploidization are powerful mechanisms of speciation. Hybrid speciation often coincides with whole-genome duplication (WGD) in eukaryotes. This suggests that WGD may allow hybrids to thrive by increasing fitness, restoring fertility and/or increasing access to adaptive mutations. Alternatively, it has been suggested that hybridization itself may trigger WGD. Testing these models requires quantifying the rate of WGD in hybrids without the confounding effect of natural selection. Here we show, by measuring the spontaneous rate of WGD of more than 1300 yeast crosses evolved under relaxed selection, that some genotypes or combinations of genotypes are more prone to WGD, including some hybrids between closely related species. We also find that higher WGD rate correlates with higher genomic instability and that WGD increases fertility and genetic variability. These results provide evidence that hybridization itself can promote WGD, which in turn facilitates the evolution of hybrids.

scholarly journals Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations

2016 ◽  
Author(s):  
Zoe June Assaf ◽  
Susanne Tilk ◽  
Jane Park ◽  
Mark L. Siegal ◽  
Dmitri A. Petrov
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Selection ◽  
De Novo ◽  
Natural Populations ◽  
Gc Content ◽  
Mutation Accumulation ◽  
Sequencing Error ◽  
Low Frequencies ◽  
Nucleotide Mutation ◽  
New Mutations

AbstractMutations provide the raw material of evolution, and thus our ability to study evolution depends fundamentally on whether we have precise measurements of mutational rates and patterns. Here we explore the rates and patterns of mutations using i) de novo mutations from Drosophila melanogaster mutation accumulation lines and ii) polymorphisms segregating at extremely low frequencies. The first, mutation accumulation (MA) lines, are the product of maintaining flies in tiny populations for many generations, therefore rendering natural selection ineffective and allowing new mutations to accrue in the genome. In addition to generating a novel dataset of sequenced MA lines, we perform a meta-analysis of all published MA studies in D. melanogaster, which allows more precise estimates of mutational patterns across the genome. In the second half of this work, we identify polymorphisms segregating at extremely low frequencies using several publicly available population genomic data sets from natural populations of D. melanogaster. Extremely rare polymorphisms are difficult to detect with high confidence due to the problem of distinguishing them from sequencing error, however a dataset of true rare polymorphisms would allow the quantification of mutational patterns. This is due to the fact that rare polymorphisms, much like de novo mutations, are on average younger and also relatively unaffected by the filter of natural selection. We identify a high quality set of ~70,000 rare polymorphisms, fully validated with resequencing, and use this dataset to measure mutational patterns in the genome. This includes identifying a high rate of multi-nucleotide mutation events at both short (~5bp) and long (~1kb) genomic distances, showing that mutation drives GC content lower in already GC-poor regions, and finding that the context-dependency of the mutation spectrum predicts long-term evolutionary patterns at four-fold synonymous sites. We also show that de novo mutations from independent mutation accumulation experiments display similar patterns of single nucleotide mutation, and match well the patterns of mutation found in natural populations.

scholarly journals The rate of whole-genome duplication can be accelerated by hybridization

2020 ◽  
Author(s):  
S. Marsit ◽  
M. Hénault ◽  
G. Charron ◽  
A. Fijarczyk ◽  
C. R Landry
Keyword(s):  
Natural Selection ◽  
Genetic Variability ◽  
Genomic Instability ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Hybrid Speciation ◽  
Relaxed Selection ◽  
Confounding Effect ◽  
Adaptive Mutations

AbstractHybridization and polyploidization are powerful mechanisms of speciation. Hybrid speciation often coincides with whole-genome duplication (WGD) in eukaryotes. This suggests that WGD allows hybrids to thrive by restoring fertility and/or increasing access to adaptive mutations. Alternatively, it has been suggested that hybridization itself may trigger WGD. Testing these models requires quantifying the rate of WGD in hybrids without the confounding effect of natural selection. By measuring the spontaneous rate of WGD of 1304 yeast crosses evolved under relaxed selection, we show that some genotypes are more prone to WGD and WGD can be triggered by hybridization. We also find that higher WGD rate correlates with higher genomic instability and that WGD increases fertility and genetic variability. These results provide evidence that hybridization itself can promote WGD, which in turn facilitates the evolution of hybrids.

scholarly journals Haldane's Sieve and Adaptation From the Standing Genetic Variation

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 875-884 ◽  
Author(s):  
H Allen Orr ◽  
Andrea J Betancourt
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Environmental Change ◽  
Adaptive Evolution ◽  
Sex Expression ◽  
Background Selection ◽  
Beneficial Mutations ◽  
Deleterious Alleles ◽  
Molecular Population Genetics ◽  
New Mutations

Abstract We consider populations that adapt to a sudden environmental change by fixing alleles found at mutation-selection balance. In particular, we calculate probabilities of fixation for previously deleterious alleles, ignoring the input of new mutations. We find that “Haldane's sieve”—the bias against the establishment of recessive beneficial mutations—does not hold under these conditions. Instead probabilities of fixation are generally independent of dominance. We show that this result is robust to patterns of sex expression for both X-linked and autosomal loci. We further show that adaptive evolution is invariably slower at X-linked than autosomal loci when evolution begins from mutation-selection balance. This result differs from that obtained when adaptation uses new mutations, a finding that may have some bearing on recent attempts to distinguish between hitchhiking and background selection by contrasting the molecular population genetics of X-linked vs. autosomal loci. Last, we suggest a test to determine whether adaptation used new mutations or previously deleterious alleles from the standing genetic variation.

scholarly journals Catch me if you can: Adaptation from standing genetic variation to a moving phenotypic optimum

2015 ◽  
Author(s):  
Sebastian Matuszewski ◽  
Joachim Hermisson ◽  
Michael Kopp
Keyword(s):  
Genetic Variation ◽  
De Novo ◽  
Darwinian Evolution ◽  
De Novo Mutations ◽  
Population Means ◽  
Standing Variation ◽  
Analytical Approximations ◽  
Formal Framework ◽  
Phenotype Space ◽  
Effect Size Distribution

Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Out of these, two complementary modelling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation of de-novo mutations only, quantitative genetic models assume that adaptation proceeds exclusively from pre-existing standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. Specifically, we consider the evolution of a quantitative trait to a gradually changing environment. By means of analytical approximations, we derive the distribution of adaptive substitutions from standing genetic variation, that is, the distribution of the phenotypic effects of those alleles from the standing variation that become fixed during adaptation. Our results are checked against individual-based simulations. We find that, compared to adaptation from de-novo mutations, (i) adaptation from standing variation proceeds by the fixation of more alleles of small effect; (ii) populations that adapt from standing genetic variation can traverse larger distances in phenotype space and, thus, have a higher potential for adaptation if the rate of environmental change is fast rather than slow.

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