Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins

By Daniel M. Weinreich, N. F. Delaney, Mark A. DePristo, Daniel L. Hartl. 2006

1,383 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Molecular Medicine

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Citations in the corpus

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1 (2015, background): “…in evolutionary and medical biology: It has a key role in our understanding of mutational pathways accessible in the course of evolution [2–4], it can lead to the identification of genetic determinants of complex diseases based on rare variants [5], and it can guide towards the…”
A biophysical protein folding model accounts for most mutational fitness effects in viruses (2011, background): “Such tradeoffs often result from mutations to an enzyme’s active site (16-18) when evolving a new function, i.”
Should evolutionary geneticists worry about higher-order epistasis? (2013, neutral): “coli β-lactamase mutant resistance [27,37]”
Stability-mediated epistasis constrains the evolution of an influenza protein (2013, background): “, 2006), bacterial (Wang et al., 2002; Bershtein et al., 2006; Weinreich et al., 2006) and viral (Chang and Torbett, 2011) drug resistance, and H5N1 transmissibility (Imai et al.”
Evolutionary velocity with protein language models (2021, background): “The robustness of evo-velocity 278 pseudotime to language model implementation may be because, in our framework, language 279 models only need to consider natural sequence changes [11], rather than the artificial mutations 280 introduced in deep mutational scanning (DMS) experiments; evo-velocity th”
A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape (2014, background): “Among point mutants, only 6% of the alleles completely lost the ability to provide any Amp resistance and 33% of those were nonsense mutations (fig.”
Global Epistasis Makes Adaptation Predictable Despite Sequence-Level Stochasticity (2014, background): “However, recent work in microbial and viral systems shows that epistasis is often pervasive, leading to a rugged fitness landscape where adaptability depends strongly and without any apparent regularity on genotype (13-18).”
A model of substitution trajectories in sequence space and long-term protein evolution. (2015, background): “Two types of approaches are being used to reveal the type and amount of epistasis in protein evolution: First, studies aiming to reconstruct recent evolutionary trajectories revealing potential epistatic interactions among substitutions that occurred recently (Weinreich et al. 2006; Bridgham et al. ”
Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins (2011, neutral): “various pathogens [35,43–46] including influenza [16,32].”
Capturing the mutational landscape of the beta-lactamase TEM-1 (2013, background): “Particularly in the case of TEM-1, the stabilizing mutation M182T has been shown to be beneficial in the hydrolysis spectrum extension of the enzyme, only when some destabilizing mutations in the active site were present (25, 26).”