scholarly journals Inferring the distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii

PLoS Biology ◽  
2019 ◽  
Vol 17 (6) ◽  
pp. e3000192 ◽  
Author(s):  
Katharina B. Böndel ◽  
Susanne A. Kraemer ◽  
Toby Samuels ◽  
Deirdre McClean ◽  
Josianne Lachapelle ◽  
...  
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Spontaneous Mutations ◽  
Fitness Effects

scholarly journals The distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii inferred using frequency changes under experimental evolution

2021 ◽  
Author(s):  
Katharina B. Böndel ◽  
Toby Samuels ◽  
Rory J. Craig ◽  
Rob W. Ness ◽  
Nick Colegrave ◽  
...  
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Experimental Evolution ◽  
Spontaneous Mutations ◽  
Negative Effects ◽  
Serial Transfer ◽  
Fitness Effects ◽  
Markov Chain Method ◽  
Bayesian Monte Carlo ◽  
High Fraction ◽  
Frequency Changes

The distribution of fitness effects (DFE) for new mutations is fundamental for many aspects of population and quantitative genetics. In this study, we have inferred the DFE in the single-celled alga Chlamydomonas reinhardtii by estimating changes in the frequencies of 254 spontaneous mutations under experimental evolution and equating the frequency changes of linked mutations with their selection coefficients. We generated seven populations of recombinant haplotypes by crossing seven independently derived mutation accumulation lines carrying an average of 36 mutations in the homozygous state to a mutation-free strain of the same genotype. We then allowed the populations to evolve under natural selection in the laboratory by serial transfer in liquid culture. We observed substantial and repeatable changes in the frequencies of many groups of linked mutations, and, surprisingly, as many mutations were observed to increase as decrease in frequency. We developed a Bayesian Monte Carlo Markov Chain method to infer the DFE. This computes the likelihood of the observed distribution of changes of frequency, and obtains the posterior distribution of the selective effects of individual mutations, while assuming a two-sided gamma distribution of effects. We infer that the DFE is a highly leptokurtic distribution, and that approximately equal proportions of mutations have positive and negative effects on fitness. This result is consistent with what we have observed in previous work on a different C. reinhardtii strain, and suggests that a high fraction of new spontaneously arisen mutations are advantageous in a simple laboratory environment.

scholarly journals Direct inference of the distribution of fitness effects of spontaneous mutations in Chlamydomonas reinhardtii

2019 ◽  
Author(s):  
Katharina B. Böndel ◽  
Susanne A. Kraemer ◽  
Tobias S. Samuels ◽  
Deirdre McClean ◽  
Josianne Lachapelle ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Chlamydomonas Reinhardtii ◽  
Spontaneous Mutation ◽  
Evolutionary Process ◽  
Cumulative Effect ◽  
Neutral Evolution ◽  
Spontaneous Mutations ◽  
Effective Population ◽  
Fitness Effects ◽  
Bayesian Mixture

AbstractSpontaneous mutations are the source of new genetic variation and are thus central to the evolutionary process. In molecular evolution and quantitative genetics, the nature of genetic variation depends critically on the distribution of fitness effects (DFE) of mutations. Spontaneous mutation accumulation (MA) experiments have been the principal approach for investigating the overall rate of occurrence and cumulative effect of mutations, but have not allowed the effects of individual mutations to be studied directly. Here, we crossed MA lines of the green alga Chlamydomonas reinhardtii with its unmutated ancestral strain to create haploid recombinant lines, each carrying an average of 50% of the accumulated mutations in a variety of combinations. With the aid of the genome sequences of the MA lines, we inferred the genotypes of the mutations, assayed their growth rate as a measure of fitness, and inferred the DFE using a novel Bayesian mixture model that allows the effects of individual mutations to be estimated. We infer that the DFE is highly leptokurtic (L-shaped), and that a high proportion of mutations increase fitness in the laboratory environment. The inferred distribution of effects for deleterious mutations is consistent with a strong role for nearly neutral evolution. Specifically, such a distribution predicts that nucleotide variation and genetic variation for quantitative traits will be insensitive to change in the effective population size.

scholarly journals Fitness Effects of Spontaneous Mutations in Picoeukaryotic Marine Green Algae

2016 ◽  
Vol 6 (7) ◽  
pp. 2063-2071 ◽  
Author(s):  
Marc Krasovec ◽  
Adam Eyre-Walker ◽  
Nigel Grimsley ◽  
Christophe Salmeron ◽  
David Pecqueur ◽  
...  
Keyword(s):  
Green Algae ◽  
Spontaneous Mutations ◽  
Fitness Effects

MALE-BIASED FITNESS EFFECTS OF SPONTANEOUS MUTATIONS INDROSOPHILA MELANOGASTER

Evolution ◽  
2012 ◽  
Vol 67 (4) ◽  
pp. 1189-1195 ◽  
Author(s):  
Nathaniel P. Sharp ◽  
Aneil F. Agrawal
Keyword(s):  
Spontaneous Mutations ◽  
Fitness Effects

scholarly journals Fitness effects of new mutations in Chlamydomonas reinhardtii across two stress gradients

2015 ◽  
Author(s):  
Susanne A Kraemer ◽  
Andrew D Morgan ◽  
Robert W Ness ◽  
Peter D Keightley ◽  
Nick Colegrave
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Genetic Load ◽  
Relative Fitness ◽  
Stress Gradients ◽  
Population Extinction ◽  
Fitness Effects ◽  
Generation Times ◽  
Fitness Measures ◽  
Detection Of Stress ◽  
Stress Dependent

Most spontaneous mutations affecting fitness are likely to be deleterious, but the strength of selection acting on them might be impacted by environmental stress. Such stress-dependent selection could expose hidden genetic variation, which in turn might increase the adaptive potential of stressed populations. On the other hand, this variation might represent a genetic load and thus lead to population extinction under stress. Previous studies to determine the link between stress and mutational effects on fitness, however, have produced inconsistent results. Here, we determined the net change in fitness in 29 genotypes of the green algae Chlamydomonas reinhardtii that accumulated mutations in the near absence of selection for approximately 1,000 generations across two stress gradients, increasing NaCl and decreasing phosphate. We found mutational effects to be magnified under extremely stressful conditions, but such effects were specific both to the type of stress as well as to the genetic background. The detection of stress-dependent fitness effects of mutations depended on accurately scaling relative fitness measures by generation times, thus offering an explanation for the inconsistencies among previous studies.

scholarly journals The fitness effects of spontaneous mutations nearly unseen by selection in a bacterium with multiple chromosomes

2016 ◽  
Author(s):  
Marcus M. Dillon ◽  
Vaughn S. Cooper
Keyword(s):  
Genome Sequencing ◽  
Common Ancestor ◽  
Burkholderia Cenocepacia ◽  
Missense Mutations ◽  
Spontaneous Mutations ◽  
Nonsense Mutations ◽  
Deletion Mutations ◽  
Fitness Effects ◽  
Quantitative Understanding ◽  
Mutational Processes

ABSTRACTMutation accumulation (MA) experiments employ the strategy of minimizing the population size of evolving lineages to greatly reduce effects of selection on newly arising mutations. Thus, most mutations fix within MA lines independently of their fitness effects. This approach, more recently combined with genome sequencing, has detailed the rates, spectra, and biases of different mutational processes. However, a quantitative understanding of the fitness effects of mutations virtually unseen by selection has remained an untapped opportunity. Here, we analyzed the fitness of 43 sequenced MA lines of the multi-chromosome bacterium Burkholderia cenocepacia that had each undergone 5554 generations of MA and accumulated an average of 6.73 spontaneous mutations. Most lineages exhibited either neutral or deleterious fitness in three different environments in comparison with their common ancestor. The only mutational class that was significantly overrepresented in lineages with reduced fitness was the loss of the plasmid, though nonsense mutations, missense mutations, and coding insertion-deletion mutations were also overrepresented in MA lineages whose fitness had significantly declined. Although the overall distribution of fitness effects was similar between the three environments, the magnitude and even the sign of the fitness of a number of lineages changed with the environment, demonstrating that the fitness of some genotypes was environmentally dependent. These results present an unprecedented picture of the fitness effects of spontaneous mutations in a bacterium with multiple chromosomes and provide greater quantitative support of the theory that the vast majority of spontaneous mutations are neutral or deleterious.

scholarly journals Programmed death in a unicellular organism has species-specific fitness effects

2014 ◽  
Vol 10 (2) ◽  
pp. 20131088 ◽  
Author(s):  
Pierre M. Durand ◽  
Rajdeep Choudhury ◽  
Armin Rashidi ◽  
Richard E. Michod
Keyword(s):  
Cell Death ◽  
Programmed Cell Death ◽  
Chlamydomonas Reinhardtii ◽  
Genetic Relatedness ◽  
Model Organism ◽  
Inhibitory Effect ◽  
Unicellular Organism ◽  
Fitness Effects ◽  
Programmed Death ◽  
Species Specific

Programmed cell death (PCD) is an ancient phenomenon and its origin and maintenance in unicellular life is unclear. We report that programmed death provides differential fitness effects that are species specific in the model organism Chlamydomonas reinhardtii . Remarkably, PCD in this organism not only benefits others of the same species, but also has an inhibitory effect on the growth of other species. These data reveal that the fitness effects of PCD can depend upon genetic relatedness.

THE FITNESS EFFECTS OF SPONTANEOUS MUTATIONS IN CAENORHABDITIS ELEGANS

Evolution ◽  
2000 ◽  
Vol 54 (4) ◽  
pp. 1234 ◽  
Author(s):  
Larissa L. Vassilieva ◽  
Aaron M. Hook ◽  
Michael Lynch
Keyword(s):  
Caenorhabditis Elegans ◽  
Spontaneous Mutations ◽  
Fitness Effects

scholarly journals Fitness effects of spontaneous mutations in a warming world

Evolution ◽  
2021 ◽  
Author(s):  
Elizabeth S. Davenport ◽  
Trenton C. Agrelius ◽  
Krista B. Harmon ◽  
Jeffry L. Dudycha
Keyword(s):  
Spontaneous Mutations ◽  
Fitness Effects ◽  
Warming World
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