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The effects of low-impact mutations in digital organisms.

Nelson CW, Sanford JC - Theor Biol Med Model (2011)

Bottom Line: These results suggest that selection breaks down for low-impact mutations below a certain fitness effect, the selection threshold.Experiments using biologically relevant parameter settings show the tendency for increasing genetic load to lead to loss of biological functionality.An understanding of such genetic deterioration is relevant to human disease, and may be applicable to the control of pathogens by use of lethal mutagenesis.

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Affiliation: Rainbow Technologies, Inc,, 877 Marshall Rd,, Waterloo, NY 13165, USA. cwnelson88@gmail.com

ABSTRACT

Background: Avida is a computer program that performs evolution experiments with digital organisms. Previous work has used the program to study the evolutionary origin of complex features, namely logic operations, but has consistently used extremely large mutational fitness effects. The present study uses Avida to better understand the role of low-impact mutations in evolution.

Results: When mutational fitness effects were approximately 0.075 or less, no new logic operations evolved, and those that had previously evolved were lost. When fitness effects were approximately 0.2, only half of the operations evolved, reflecting a threshold for selection breakdown. In contrast, when Avida's default fitness effects were used, all operations routinely evolved to high frequencies and fitness increased by an average of 20 million in only 10,000 generations.

Conclusions: Avidian organisms evolve new logic operations only when mutations producing them are assigned high-impact fitness effects. Furthermore, purifying selection cannot protect operations with low-impact benefits from mutational deterioration. These results suggest that selection breaks down for low-impact mutations below a certain fitness effect, the selection threshold. Experiments using biologically relevant parameter settings show the tendency for increasing genetic load to lead to loss of biological functionality. An understanding of such genetic deterioration is relevant to human disease, and may be applicable to the control of pathogens by use of lethal mutagenesis.

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Phenotype frequencies in a case study population under default settings. A mutation producing the XOR operation also deactivated NOT and AND around generation 6,580. Clonal interference resulted in the near-extinction of NOT and AND. However, a compensatory mutation restored the NOT operation, and it regained a high frequency.
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Figure 2: Phenotype frequencies in a case study population under default settings. A mutation producing the XOR operation also deactivated NOT and AND around generation 6,580. Clonal interference resulted in the near-extinction of NOT and AND. However, a compensatory mutation restored the NOT operation, and it regained a high frequency.

Mentions: The competition of different beneficial mutations, known as clonal interference in asexual systems [40], was commonly observed in our study. Because they cannot recombine into a single genotype, such mutations can hinder one another's progress toward fixation, with highly beneficial mutations driving more moderate ones to extinction. For example, in one experiment (Figure 2), a mutation appeared to deactivate the NOT and AND operations (fitness effects of 1.0 and 3.0, respectively) to produce the XOR operation (fitness effect of 15.0) around generation 6,580, driving the former operations to near extinction. The success of XOR followed expectation, because the advantage of XOR exceeds the combined fitness bonuses of NOT and AND. However, because NOT arises very commonly in Avida, a compensatory mutation produced it in the XOR genotype within about 100 generations, allowing it to regain a high frequency in the population.


The effects of low-impact mutations in digital organisms.

Nelson CW, Sanford JC - Theor Biol Med Model (2011)

Phenotype frequencies in a case study population under default settings. A mutation producing the XOR operation also deactivated NOT and AND around generation 6,580. Clonal interference resulted in the near-extinction of NOT and AND. However, a compensatory mutation restored the NOT operation, and it regained a high frequency.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3102618&req=5

Figure 2: Phenotype frequencies in a case study population under default settings. A mutation producing the XOR operation also deactivated NOT and AND around generation 6,580. Clonal interference resulted in the near-extinction of NOT and AND. However, a compensatory mutation restored the NOT operation, and it regained a high frequency.
Mentions: The competition of different beneficial mutations, known as clonal interference in asexual systems [40], was commonly observed in our study. Because they cannot recombine into a single genotype, such mutations can hinder one another's progress toward fixation, with highly beneficial mutations driving more moderate ones to extinction. For example, in one experiment (Figure 2), a mutation appeared to deactivate the NOT and AND operations (fitness effects of 1.0 and 3.0, respectively) to produce the XOR operation (fitness effect of 15.0) around generation 6,580, driving the former operations to near extinction. The success of XOR followed expectation, because the advantage of XOR exceeds the combined fitness bonuses of NOT and AND. However, because NOT arises very commonly in Avida, a compensatory mutation produced it in the XOR genotype within about 100 generations, allowing it to regain a high frequency in the population.

Bottom Line: These results suggest that selection breaks down for low-impact mutations below a certain fitness effect, the selection threshold.Experiments using biologically relevant parameter settings show the tendency for increasing genetic load to lead to loss of biological functionality.An understanding of such genetic deterioration is relevant to human disease, and may be applicable to the control of pathogens by use of lethal mutagenesis.

View Article: PubMed Central - HTML - PubMed

Affiliation: Rainbow Technologies, Inc,, 877 Marshall Rd,, Waterloo, NY 13165, USA. cwnelson88@gmail.com

ABSTRACT

Background: Avida is a computer program that performs evolution experiments with digital organisms. Previous work has used the program to study the evolutionary origin of complex features, namely logic operations, but has consistently used extremely large mutational fitness effects. The present study uses Avida to better understand the role of low-impact mutations in evolution.

Results: When mutational fitness effects were approximately 0.075 or less, no new logic operations evolved, and those that had previously evolved were lost. When fitness effects were approximately 0.2, only half of the operations evolved, reflecting a threshold for selection breakdown. In contrast, when Avida's default fitness effects were used, all operations routinely evolved to high frequencies and fitness increased by an average of 20 million in only 10,000 generations.

Conclusions: Avidian organisms evolve new logic operations only when mutations producing them are assigned high-impact fitness effects. Furthermore, purifying selection cannot protect operations with low-impact benefits from mutational deterioration. These results suggest that selection breaks down for low-impact mutations below a certain fitness effect, the selection threshold. Experiments using biologically relevant parameter settings show the tendency for increasing genetic load to lead to loss of biological functionality. An understanding of such genetic deterioration is relevant to human disease, and may be applicable to the control of pathogens by use of lethal mutagenesis.

Show MeSH