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Effects of ploidy and recombination on evolution of robustness in a model of the segment polarity network.

Kim KJ, Fernandes VM - PLoS Comput. Biol. (2009)

Bottom Line: Robustness was measured by simulating a mutation in the network and measuring the effect on the engrailed and wingless patterns; higher robustness corresponded to insensitivity of this pattern to perturbation.We compared robustness in diploid and haploid populations, with either asexual or sexual reproduction.In all cases, robustness increased, and the greatest increase was in diploid sexual populations; diploidy and sex synergized to evolve greater robustness than either acting alone.

View Article: PubMed Central - PubMed

Affiliation: Center for Cell Dynamics, Friday Harbor Labs, University of Washington, Friday Harbor, Washington, USA. kjkim@u.washington.edu

ABSTRACT
Many genetic networks are astonishingly robust to quantitative variation, allowing these networks to continue functioning in the face of mutation and environmental perturbation. However, the evolution of such robustness remains poorly understood for real genetic networks. Here we explore whether and how ploidy and recombination affect the evolution of robustness in a detailed computational model of the segment polarity network. We introduce a novel computational method that predicts the quantitative values of biochemical parameters from bit sequences representing genotype, allowing our model to bridge genotype to phenotype. Using this, we simulate 2,000 generations of evolution in a population of individuals under stabilizing and truncation selection, selecting for individuals that could sharpen the initial pattern of engrailed and wingless expression. Robustness was measured by simulating a mutation in the network and measuring the effect on the engrailed and wingless patterns; higher robustness corresponded to insensitivity of this pattern to perturbation. We compared robustness in diploid and haploid populations, with either asexual or sexual reproduction. In all cases, robustness increased, and the greatest increase was in diploid sexual populations; diploidy and sex synergized to evolve greater robustness than either acting alone. Diploidy conferred increased robustness by allowing most deleterious mutations to be rescued by a working allele. Sex (recombination) conferred a robustness advantage through "survival of the compatible": those alleles that can work with a wide variety of genetically diverse partners persist, and this selects for robust alleles.

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Distinguishing effects of mutation from recombination.(A) Fraction of mutated individuals that were viable during evolutionary                            simulation. (B) Fraction of dead individuals during the simulation that                            did not have a mutation. A dramatically higher fraction of deaths were                            caused by recombination in sexual diploid populations than sexual                            haploid. (C) Fitness load calculated from Equation 16. Plots show                            average of 40 simulations, smoothed with a sliding window over 50                            generations.
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pcbi-1000296-g006: Distinguishing effects of mutation from recombination.(A) Fraction of mutated individuals that were viable during evolutionary simulation. (B) Fraction of dead individuals during the simulation that did not have a mutation. A dramatically higher fraction of deaths were caused by recombination in sexual diploid populations than sexual haploid. (C) Fitness load calculated from Equation 16. Plots show average of 40 simulations, smoothed with a sliding window over 50 generations.

Mentions: Why does sex produce more robust populations? In our simulations, individuals have reduced fitness/survivorship if they fail to sharpen the correct en and wg patterns sufficiently. Fitness/survivorship can be reduced by two sources: a new mutation or, in sexual populations, recombination of alleles that do not function properly together. Figure 6 shows the relative effect of recombination and mutation on survival. During the simulation, we recorded the number of dead individuals and their genotypes, and whether they had a new mutation. Figure 6A shows the fraction of individuals with a new mutation that were viable. This data is qualitatively consistent with Figure 5A, but includes mutations that could alter multiple genes and bit-sequences during evolution. To determine how often recombination produced incompatible allele combinations, we measured the fraction of deaths where individuals did not have a new mutation (i.e. the fraction of the dead due to recombination). Figure 6B shows diploid sexual populations showed a near doubling of this fraction compared to the haploid sexual populations. Thus, diploid sexual populations experience a greater pressure to maintain alleles that both produce the correct phenotype and that are also highly compatible with the other alleles in the population. Recombination constantly produces new allele combinations that cause quantitative variation; thus sexual populations (especially diploid sexual populations) more strongly select for genotypes (and alleles) that are robust to quantitative variation.


Effects of ploidy and recombination on evolution of robustness in a model of the segment polarity network.

Kim KJ, Fernandes VM - PLoS Comput. Biol. (2009)

Distinguishing effects of mutation from recombination.(A) Fraction of mutated individuals that were viable during evolutionary                            simulation. (B) Fraction of dead individuals during the simulation that                            did not have a mutation. A dramatically higher fraction of deaths were                            caused by recombination in sexual diploid populations than sexual                            haploid. (C) Fitness load calculated from Equation 16. Plots show                            average of 40 simulations, smoothed with a sliding window over 50                            generations.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2637435&req=5

pcbi-1000296-g006: Distinguishing effects of mutation from recombination.(A) Fraction of mutated individuals that were viable during evolutionary simulation. (B) Fraction of dead individuals during the simulation that did not have a mutation. A dramatically higher fraction of deaths were caused by recombination in sexual diploid populations than sexual haploid. (C) Fitness load calculated from Equation 16. Plots show average of 40 simulations, smoothed with a sliding window over 50 generations.
Mentions: Why does sex produce more robust populations? In our simulations, individuals have reduced fitness/survivorship if they fail to sharpen the correct en and wg patterns sufficiently. Fitness/survivorship can be reduced by two sources: a new mutation or, in sexual populations, recombination of alleles that do not function properly together. Figure 6 shows the relative effect of recombination and mutation on survival. During the simulation, we recorded the number of dead individuals and their genotypes, and whether they had a new mutation. Figure 6A shows the fraction of individuals with a new mutation that were viable. This data is qualitatively consistent with Figure 5A, but includes mutations that could alter multiple genes and bit-sequences during evolution. To determine how often recombination produced incompatible allele combinations, we measured the fraction of deaths where individuals did not have a new mutation (i.e. the fraction of the dead due to recombination). Figure 6B shows diploid sexual populations showed a near doubling of this fraction compared to the haploid sexual populations. Thus, diploid sexual populations experience a greater pressure to maintain alleles that both produce the correct phenotype and that are also highly compatible with the other alleles in the population. Recombination constantly produces new allele combinations that cause quantitative variation; thus sexual populations (especially diploid sexual populations) more strongly select for genotypes (and alleles) that are robust to quantitative variation.

Bottom Line: Robustness was measured by simulating a mutation in the network and measuring the effect on the engrailed and wingless patterns; higher robustness corresponded to insensitivity of this pattern to perturbation.We compared robustness in diploid and haploid populations, with either asexual or sexual reproduction.In all cases, robustness increased, and the greatest increase was in diploid sexual populations; diploidy and sex synergized to evolve greater robustness than either acting alone.

View Article: PubMed Central - PubMed

Affiliation: Center for Cell Dynamics, Friday Harbor Labs, University of Washington, Friday Harbor, Washington, USA. kjkim@u.washington.edu

ABSTRACT
Many genetic networks are astonishingly robust to quantitative variation, allowing these networks to continue functioning in the face of mutation and environmental perturbation. However, the evolution of such robustness remains poorly understood for real genetic networks. Here we explore whether and how ploidy and recombination affect the evolution of robustness in a detailed computational model of the segment polarity network. We introduce a novel computational method that predicts the quantitative values of biochemical parameters from bit sequences representing genotype, allowing our model to bridge genotype to phenotype. Using this, we simulate 2,000 generations of evolution in a population of individuals under stabilizing and truncation selection, selecting for individuals that could sharpen the initial pattern of engrailed and wingless expression. Robustness was measured by simulating a mutation in the network and measuring the effect on the engrailed and wingless patterns; higher robustness corresponded to insensitivity of this pattern to perturbation. We compared robustness in diploid and haploid populations, with either asexual or sexual reproduction. In all cases, robustness increased, and the greatest increase was in diploid sexual populations; diploidy and sex synergized to evolve greater robustness than either acting alone. Diploidy conferred increased robustness by allowing most deleterious mutations to be rescued by a working allele. Sex (recombination) conferred a robustness advantage through "survival of the compatible": those alleles that can work with a wide variety of genetically diverse partners persist, and this selects for robust alleles.

Show MeSH