The continuing prevalence of a highly heritable and hypo-reproductive extreme tail of a human neurobehavioral quantitative diversity suggests the reproductive majority retains the genetic mechanisms for extremes. From the perspective of stochastic epistasis, the effect of an epistatic modifier variant can randomly vary in both phenotypic value and effect direction among carriers depending on the genetic identity and the modifier carriers are ubiquitous in the population. The neutrality of the mean genetic effect in carriers ensures the survival of the variant under selection pressures. Functionally or metabolically related modifier variants make an epistatic network module and dozens of modules may be involved in the phenotype. To assess the significance of stochastic epistasis, a simplified module-based model was simulated. The individual repertoire of the modifier variants in a module also contributes in genetic identity, which determines the genetic contribution of each carrier modifier. Because the entire contribution of a module to phenotypic outcome is unpredictable in the model, the module effect represents the total contribution of related modifiers as a stochastic unit in simulations. As a result, the intrinsic compatibility between distributional robustness and quantitative changeability could mathematically be simulated using the model. The artificial normal distribution shape in large-sized simulations was preserved in each generation even if the lowest fitness tail was non-reproductive. The robustness of normality across generations is analogous to the real situation of complex human diversity, including neurodevelopmental conditions. The repeated regeneration of a non-reproductive extreme tail may be essential for survival and change of the reproductive majority, implying extremes for others. Further simulation to illustrate how the fitness of extreme individuals can be low across generations may be necessary to increase the plausibility of this stochastic epistasis model.
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Heredity (Edinb)
July 2024
Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark.
Stochastic simulation software is commonly used to aid breeders designing cost-effective breeding programs and to validate statistical models used in genetic evaluation. An essential feature of the software is the ability to simulate populations with desired genetic and non-genetic parameters. However, this feature often fails when non-additive effects due to dominance or epistasis are modeled, as the desired properties of simulated populations are estimated from classical quantitative genetic statistical models formulated at the population level.
View Article and Find Full Text PDFBMC Genomics
April 2024
Zhejiang Sci-Tech University, Second Street 928, Hangzhou, Zhejiang, 310018, China.
Background: Single-cell clustering has played an important role in exploring the molecular mechanisms about cell differentiation and human diseases. Due to highly-stochastic transcriptomics data, accurate detection of cell types is still challenged, especially for RNA-sequencing data from human beings. In this case, deep neural networks have been increasingly employed to mine cell type specific patterns and have outperformed statistic approaches in cell clustering.
View Article and Find Full Text PDFGenetics
December 2023
Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France.
Quantitative genetics models have shown that long-term selection responses depend on initial variance and mutational influx. Understanding limits of selection requires quantifying the role of mutational variance. However, correlative responses to selection on nonfocal traits can perturb the selection response on the focal trait; and generations are often confounded with selection environments so that genotype by environment (G×E) interactions are ignored.
View Article and Find Full Text PDFNat Struct Mol Biol
May 2023
Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands.
Transcriptional bursting has been linked to the stochastic positioning of nucleosomes. However, how bursting is regulated by the remodeling of promoter nucleosomes is unknown. Here, we use single-molecule live-cell imaging of GAL10 transcription in Saccharomyces cerevisiae to measure how bursting changes upon combined perturbations of chromatin remodelers, the transcription factor Gal4 and preinitiation complex components.
View Article and Find Full Text PDFPhilos Trans R Soc Lond B Biol Sci
May 2023
Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
Owing to stochastic fluctuations arising from finite population size, known as genetic drift, the ability of a population to explore a rugged fitness landscape depends on its size. In the weak mutation regime, while the mean steady-state fitness increases with population size, we find that the height of the first fitness peak encountered when starting from a random genotype displays various behaviours versus population size, even among small and simple rugged landscapes. We show that the accessibility of the different fitness peaks is key to determining whether this height overall increases or decreases with population size.
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