Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

A Currin, N Swainston, PJ Day, DB Kell - Chemical Society Reviews, 2015 - pubs.rsc.org
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …

Should evolutionary geneticists worry about higher-order epistasis?

DM Weinreich, Y Lan, CS Wylie… - Current opinion in …, 2013 - Elsevier
Natural selection drives evolving populations up the fitness landscape, the projection from
nucleotide sequence space to organismal reproductive success. While it has long been …

Adaptation in protein fitness landscapes is facilitated by indirect paths

NC Wu, L Dai, CA Olson, JO Lloyd-Smith, R Sun - Elife, 2016 - elifesciences.org
The structure of fitness landscapes is critical for understanding adaptive protein evolution.
Previous empirical studies on fitness landscapes were confined to either the neighborhood …

Evolutionary game theory using agent-based methods

C Adami, J Schossau, A Hintze - Physics of life reviews, 2016 - Elsevier
Evolutionary game theory is a successful mathematical framework geared towards
understanding the selective pressures that affect the evolution of the strategies of agents …

Detecting high-order epistasis in nonlinear genotype-phenotype maps

ZR Sailer, MJ Harms - Genetics, 2017 - academic.oup.com
High-order epistasis has been observed in many genotype-phenotype maps. These multi-
way interactions between mutations may be useful for dissecting complex traits and could …

Evolutionary instability of zero-determinant strategies demonstrates that winning is not everything

C Adami, A Hintze - Nature communications, 2013 - nature.com
Zero-determinant strategies are a new class of probabilistic and conditional strategies that
are able to unilaterally set the expected payoff of an opponent in iterated plays of the …

Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis arenosa

JD Hollister, BJ Arnold, E Svedin, KS Xue… - PLoS …, 2012 - journals.plos.org
Genome duplication, which results in polyploidy, is disruptive to fundamental biological
processes. Genome duplications occur spontaneously in a range of taxa and problems such …

Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens

AA Gheyas, A Vallejo-Trujillo, A Kebede… - Molecular biology …, 2021 - academic.oup.com
Breeding for climate resilience is currently an important goal for sustainable livestock
production. Local adaptations exhibited by indigenous livestock allow investigating the …

Biophysical principles predict fitness landscapes of drug resistance

JV Rodrigues, S Bershtein, A Li… - Proceedings of the …, 2016 - National Acad Sciences
Fitness landscapes of drug resistance constitute powerful tools to elucidate mutational
pathways of antibiotic escape. Here, we developed a predictive biophysics-based fitness …

Limited evolutionary rescue of locally adapted populations facing climate change

K Schiffers, EC Bourne, S Lavergne… - … of the Royal …, 2013 - royalsocietypublishing.org
Dispersal is a key determinant of a population's evolutionary potential. It facilitates the
propagation of beneficial alleles throughout the distributional range of spatially outspread …