Free energy perturbations in enzyme kinetic models reveal cryptic epistasis. [PDF]
PLoS Computational BiologyEpistasis-the context-dependence of mutational effects-is a key driver of protein evolution, influencing adaptive pathways and functional diversity.
Karol Buda, Nobuhiko Tokuriki
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Resolving discrepancies between chimeric and multiplicative measures of higher-order epistasis [PDF]
Nature CommunicationsEpistasis - the interaction between alleles at different genetic loci - plays a fundamental role in biology. However, several recent approaches quantify epistasis using a chimeric formula that measures deviations from a multiplicative fitness model on an
Uthsav Chitra +2 more
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Epistasis mediates the role of negative frequency-dependent selection in bacterial strain structure. [PDF]
PLoS Computational BiologyStrain structure is a well-documented phenomenon in many pathogenic and commensal bacterial species, where distinct strains persist over time exhibiting stable associations between genetic or phenotypic traits.
Martin Guillemet, Sonja Lehtinen
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Initial mutations direct alternative pathways of protein evolution. [PDF]
PLoS Genetics, 2011 Whether evolution is erratic due to random historical details, or is repeatedly directed along similar paths by certain constraints, remains unclear. Epistasis (i.e.
Merijn L M Salverda +7 more
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Multiple peaks and reciprocal sign epistasis in an empirically determined genotype-phenotype landscape [PDF]
Chaos: An Interdisciplinary Journal of Nonlinear Science, 2010 Insight into the ruggedness of adaptive landscapes is central to understanding the mechanisms and constraints that shape the course of evolution. While empirical data on adaptive landscapes remain scarce, a handful of recent investigations have revealed genotype-phenotype and genotype-fitness landscapes that appeared smooth and single peaked.
Dawid, Alexandre +4 more
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On the incongruence of genotype-phenotype and fitness landscapes.
PLoS Computational Biology, 2022 The mapping from genotype to phenotype to fitness typically involves multiple nonlinearities that can transform the effects of mutations. For example, mutations may contribute additively to a phenotype, but their effects on fitness may combine non ...
Malvika Srivastava, Joshua L Payne
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Fitness ranking of individual mutants drives patterns of epistatic interactions in HIV-1. [PDF]
PLoS ONE, 2011 Fitness interactions between mutations, referred to as epistasis, can strongly impact evolution. For RNA viruses and retroviruses with their high mutation rates, epistasis may be particularly important to overcome fitness losses due to the accumulation ...
Javier P Martínez +6 more
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The consistency of beneficial fitness effects of mutations across diverse genetic backgrounds. [PDF]
PLoS ONE, 2012 Parallel and convergent evolution have been remarkably common observations in molecular adaptation but primarily in the context of the same genotype adapting to the same conditions.
Victoria M Pearson +2 more
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Rank orders and signed interactions in evolutionary biology
eLife, 2020 Rank orders have been studied in evolutionary biology for almost a hundred years. Constraints on the order in which mutations accumulate are known from cancer drug treatment, and order constraints for species invasions are important in ecology.
Kristina Crona
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Coordinated Interaction: A model and test for globally signed epistasis in complex traits [PDF]
, 2020 AbstractInteractions between genetic variants – epistasis – is pervasive in model systems and can profoundly impact evolutionary adaption, population disease dynamics, genetic mapping, and precision medicine efforts. In this work we develop a model for structured polygenic epistasis, calledCoordinated Interaction(CI), and prove that several recent ...
Sheppard, Brooke +5 more
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