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

2016 ◽  
Vol 29 (3) ◽  
pp. 583-593 ◽  
Author(s):  
S. A. Kraemer ◽  
A. D. Morgan ◽  
R. W. Ness ◽  
P. D. Keightley ◽  
N. Colegrave
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Stress Gradients ◽  
Fitness Effects ◽  
New Mutations

scholarly journals LI Detector: a framework for sensitive colony-based screens regardless of the distribution of fitness effects

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Saurin Bipin Parikh ◽  
Nelson Castilho Coelho ◽  
Anne-Ruxandra Carvunis
Keyword(s):  
Linear Interpolation ◽  
Colony Growth ◽  
Relative Fitness ◽  
Environment Interaction ◽  
Nutrient Distribution ◽  
Underlying Distribution ◽  
Fitness Effects ◽  
Fitness Value ◽  
Genetic Perturbations ◽  
Surface Irregularities

Abstract Microbial growth characteristics have long been used to investigate fundamental questions of biology. Colony-based high-throughput screens enable parallel fitness estimation of thousands of individual strains using colony growth as a proxy for fitness. However, fitness estimation is complicated by spatial biases affecting colony growth, including uneven nutrient distribution, agar surface irregularities, and batch effects. Analytical methods that have been developed to correct for these spatial biases rely on the following assumptions: (1) that fitness effects are normally distributed, and (2) that most genetic perturbations lead to minor changes in fitness. Although reasonable for many applications, these assumptions are not always warranted and can limit the ability to detect small fitness effects. Beneficial fitness effects, in particular, are notoriously difficult to detect under these assumptions. Here, we developed the linear interpolation-based detector (LI Detector) framework to enable sensitive colony-based screening without making prior assumptions about the underlying distribution of fitness effects. The LI Detector uses a grid of reference colonies to assign a relative fitness value to every colony on the plate. We show that the LI Detector is effective in correcting for spatial biases and equally sensitive toward increase and decrease in fitness. LI Detector offers a tunable system that allows the user to identify small fitness effects with unprecedented sensitivity and specificity. LI Detector can be utilized to develop and refine gene–gene and gene–environment interaction networks of colony-forming organisms, including yeast, by increasing the range of fitness effects that can be reliably detected.

scholarly journals Increase in Zucchini yellow mosaic virus Symptom Severity in Tolerant Zucchini Cultivars Is Related to a Point Mutation in P3 Protein and Is Associated with a Loss of Relative Fitness on Susceptible Plants

2003 ◽  
Vol 93 (12) ◽  
pp. 1478-1484 ◽  
Author(s):  
C. Desbiez ◽  
A. Gal-On ◽  
M. Girard ◽  
C. Wipf-Scheibel ◽  
H. Lecoq
Keyword(s):  
Mosaic Virus ◽  
Point Mutation ◽  
Zucchini Yellow Mosaic Virus ◽  
Genetic Load ◽  
Yellow Mosaic Virus ◽  
Relative Fitness ◽  
Interspecific Crosses ◽  
Mixed Infections ◽  
Wild Type ◽  
Sequence Comparisons

Zucchini yellow mosaic virus (ZYMV, Potyvirus) is a very damaging cucurbit virus worldwide. Interspecific crosses with resistant Cucurbita moschata have led to the release of “resistant” zucchini squash (C. pepo) F1 hybrids. However, although the resistance is almost complete in C. moschata, the commercial C. pepo hybrids are only tolerant. ZYMV evolution toward increased aggressiveness on tolerant hybrids was observed in the field and was obtained experimentally. Sequence comparisons and recombination experiments revealed that a point mutation in the P3 protein of ZYMV was enough to induce tolerance breaking. Competition experiments were performed between quasi-isogenic wild-type, and aggressive variants of ZYMV distinguished by monoclonal antibodies. The aggressive mutants were more fit than wild-type strains in mixed infections of tolerant zucchini, but they presented a drastic fitness loss in mixed infections of susceptible zucchini or melon. Thus, the ability to induce severe symptoms in tolerant zucchini is related to a genetic load in susceptible zucchini, but also on other susceptible hosts. This represents the first quantitative study of the fitness cost associated with tolerance breaking for a plant virus. Thus, although easily broken, the tolerance might prove durable in some conditions if the aggressive variants are counterselected in susceptible crops.

scholarly journals Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation

2020 ◽  
Author(s):  
Dimitra Aggeli ◽  
Yuping Li ◽  
Gavin Sherlock
Keyword(s):  
Evolutionary Dynamics ◽  
Common Ancestor ◽  
Single Point ◽  
Relative Fitness ◽  
Single Point Mutation ◽  
Historical Contingency ◽  
Mutational Spectra ◽  
Fitness Effects ◽  
Mutational Step ◽  
Diminishing Returns

AbstractThe fitness effects of random mutations are contingent upon the genetic and environmental contexts in which they occur, and this contributes to the unpredictability of evolutionary outcomes at the molecular level. Despite this unpredictability, the rate of adaptation in homogeneous environments tends to decrease over evolutionary time, due to diminishing returns epistasis, causing relative fitness gains to be predictable over the long term. Here, we studied the extent of diminishing returns epistasis and the changes in the adaptive mutational spectra after yeast populations have already taken their first adaptive mutational step. We used three distinct adaptive clones that arose under identical conditions from a common ancestor, from which they diverge by a single point mutation, to found populations that we further evolved. We followed the evolutionary dynamics of these populations by lineage tracking and determined adaptive outcomes using fitness assays and whole genome sequencing. We found compelling evidence for diminishing returns: fitness gains during the 2nd step of adaptation are smaller than those of the 1st step, due to a compressed distribution of fitness effects in the 2nd step. We also found strong evidence for historical contingency at the genic level: the beneficial mutational spectra of the 2nd-step adapted genotypes differ with respect to their ancestor and to each other, despite the fact that the three founders’ 1st-step mutations provided their fitness gains due to similar phenotypic improvements. While some targets of selection in the second step are shared with those seen in the common ancestor, other targets appear to be contingent on the specific first step mutation, with more phenotypically similar founding clones having more similar adaptive mutational spectra. Finally, we found that disruptive mutations, such as nonsense and frameshift, were much more common in the first step of adaptation, contributing an additional way that both diminishing returns and historical contingency are evident during 2nd step adaptation.

scholarly journals Fitness Effects of Replichore Imbalance in Salmonella enterica

2010 ◽  
Vol 192 (22) ◽  
pp. 6086-6088 ◽  
Author(s):  
T. David Matthews ◽  
Stanley Maloy
Keyword(s):  
Salmonella Enterica ◽  
Fitness Cost ◽  
Chromosome Rearrangements ◽  
Relative Fitness ◽  
Fitness Effects ◽  
The Impact

ABSTRACT A fitness cost due to imbalanced replichores has been proposed to provoke chromosome rearrangements in Salmonella enterica serovars. To determine the impact of replichore imbalance on fitness, the relative fitness of isogenic Salmonella strains containing transposon-held duplications of various sizes and at various chromosomal locations was determined. Although duplication of certain genes influenced fitness, a replichore imbalance of up to 16° did not affect fitness.

scholarly journals Are elder siblings helpers or competitors? Antagonistic fitness effects of sibling interactions in humans

2013 ◽  
Vol 280 (1750) ◽  
pp. 20122313 ◽  
Author(s):  
Aïda Nitsch ◽  
Charlotte Faurie ◽  
Virpi Lummaa
Keyword(s):  
Life History ◽  
Sexual Maturity ◽  
Life History Stage ◽  
Same Sex ◽  
Fitness Effects ◽  
Sibling Interactions ◽  
Fitness Consequences ◽  
Opposite Sex ◽  
Fitness Measures

Determining the fitness consequences of sibling interactions is pivotal for understanding the evolution of family living, but studies investigating them across lifetime are lacking. We used a large demographic dataset on preindustrial humans from Finland to study the effect of elder siblings on key life-history traits. The presence of elder siblings improved the chances of younger siblings surviving to sexual maturity, suggesting that despite a competition for parental resources, they may help rearing their younger siblings. After reaching sexual maturity however, same-sex elder siblings' presence was associated with reduced reproductive success in the focal individual, indicating the existence of competition among same-sex siblings. Overall, lifetime fitness was reduced by same-sex elder siblings' presence and increased by opposite-sex elder siblings' presence. Our study shows opposite effects of sibling interactions depending on the life-history stage, and highlights the need for using long-term fitness measures to understand the selection pressures acting on sibling interactions.

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 The Sheltered Genetic Load Linked to the S Locus in Plants: New Insights From Theoretical and Empirical Approaches in Sporophytic Self-Incompatibility

Genetics ◽  
2009 ◽  
Vol 183 (3) ◽  
pp. 1105-1118 ◽  
Author(s):  
Violaine Llaurens ◽  
Lucy Gonthier ◽  
Sylvain Billiard
Keyword(s):  
Inbreeding Depression ◽  
Balancing Selection ◽  
Genetic Load ◽  
Relative Fitness ◽  
Self Incompatibility ◽  
Deleterious Mutations ◽  
Gas Treatment ◽  
Genomic Inbreeding ◽  
Genomic Regions ◽  
Empirical Approaches

Inbreeding depression and mating systems evolution are closely linked, because the purging of deleterious mutations and the fitness of individuals may depend on outcrossing vs. selfing rates. Further, the accumulation of deleterious mutations may vary among genomic regions, especially for genes closely linked to loci under balancing selection. Sporophytic self-incompatibility (SSI) is a common genetic mechanism in angiosperm that enables hermaphrodite plants to avoid selfing and promote outcrossing. The SSI phenotype is determined by the S locus and may depend on dominance relationships among alleles. Since most individuals are heterozygous at the S locus and recombination is suppressed in the S-locus region, it has been suggested that deleterious mutations could accumulate at genes linked to the S locus, generating a “sheltered load.” In this article, we first theoretically investigate the conditions generating sheltered load in SSI. We show that deleterious mutations can accumulate in linkage with specific S alleles, and particularly if those S alleles are dominant. Second, we looked for the presence of sheltered load in Arabidopsis halleri using CO2 gas treatment to overcome self-incompatibility. By examining the segregation of S alleles and measuring the relative fitness of progeny, we found significant sheltered load associated with the most dominant S allele (S15) of three S alleles tested. This sheltered load seems to be expressed at several stages of the life cycle and to have a larger effect than genomic inbreeding depression.

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