Whether interaction between genes is better represented by synergistic or antagonistic epistasis has been a focus of experimental research in bacterial population genetics. Our previous research on evolution of modifiers of epistasis in diploid systems has indicated that the strength of positive or negative epistasis should increase provided linkage disequilibrium is maintained. Here we study a modifier of epistasis in fitness between two loci in a haploid system. Epistasis is modified in the neighborhood of a mutation-selection balance. We show that when linkage in the three-locus system is tight, an increase in the frequency of a modifier allele that induces either more negative or more positive epistasis is possible. Epistasis here can be measured on either an additive or multiplicative scale.
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http://dx.doi.org/10.1016/j.tpb.2007.11.010 | DOI Listing |
Plant Physiol
December 2024
Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain.
The number and distribution of trichomes, i.e., the trichome pattern, in different plant organs shows a conspicuous inter- and intraspecific diversity across Angiosperms that is presumably involved in adaptation to numerous environmental factors.
View Article and Find Full Text PDFProtein Sci
January 2025
Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
There is strong interest in accurate methods for predicting changes in protein stability resulting from amino acid mutations to the protein sequence. Recombinant proteins must often be stabilized to be used as therapeutics or reagents, and destabilizing mutations are implicated in a variety of diseases. Due to increased data availability and improved modeling techniques, recent studies have shown advancements in predicting changes in protein stability when a single-point mutation is made.
View Article and Find Full Text PDFPhys Rev E
November 2024
Université Grenoble Alpes, CEA List, 38000 Grenoble, France.
Models for viral populations with high replication error rates (such as RNA viruses) rely on the quasispecies concept, in which mutational pressure beyond the so-called "error threshold" leads to a loss of essential genetic information and population collapse, an effect known as the "error catastrophe." We explain how crossing this threshold, as a result of increasing mutation rates, can be understood as a second-order phase transition, even in the presence of lethal mutations. In particular, we show that, in fitness landscapes with a single peak, this collapse is equivalent to a ferroparamagnetic transition, where the back-mutation rate plays the role of the external magnetic field.
View Article and Find Full Text PDFbioRxiv
December 2024
Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
We recently reanalyzed 20 combinatorial mutagenesis datasets using a novel reference-free analysis (RFA) method and showed that high-order epistasis contributes negligibly to protein sequence-function relationships in every case. Dupic, Phillips, and Desai (DPD) commented on a preprint of our work. In our published paper, we addressed all the major issues they raised, but we respond directly to them here.
View Article and Find Full Text PDFBrain
December 2024
Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia 30100, Spain.
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