On the networked architecture of genotype spaces and its critical effects on molecular evolution

J Aguirre, P Catalán, JA Cuesta… - Open …, 2018 - royalsocietypublishing.org
Evolutionary dynamics is often viewed as a subtle process of change accumulation that
causes a divergence among organisms and their genomes. However, this interpretation is …

[图书][B] Fundamentals of computational intelligence: neural networks, fuzzy systems, and evolutionary computation

JM Keller, D Liu, DB Fogel - 2016 - books.google.com
Provides an in-depth and even treatment of the three pillars of computational intelligence
and how they relate to one another This book covers the three fundamental topics that form …

Qualities, challenges and future of genetic algorithms: a literature review

A Vie, AM Kleinnijenhuis, DJ Farmer - arXiv preprint arXiv:2011.05277, 2020 - arxiv.org
Genetic algorithms, computer programs that simulate natural evolution, are increasingly
applied across many disciplines. They have been used to solve various optimisation …

The structure of genotype-phenotype maps makes fitness landscapes navigable

SF Greenbury, AA Louis, SE Ahnert - Nature Ecology & Evolution, 2022 - nature.com
Fitness landscapes are often described in terms of 'peaks' and 'valleys', indicating an
intuitive low-dimensional landscape of the kind encountered in everyday experience. The …

Shifts in mutation spectra enhance access to beneficial mutations

M Sane, GD Diwan, BA Bhat… - Proceedings of the …, 2023 - National Acad Sciences
Biased mutation spectra are pervasive, with wide variation in the magnitude of mutational
biases that influence genome evolution and adaptation. How do such diverse biases …

Analysis of adaptive walks on NK fitness landscapes with different interaction schemes

S Nowak, J Krug - Journal of Statistical Mechanics: Theory and …, 2015 - iopscience.iop.org
Fitness landscapes are genotype to fitness mappings commonly used in evolutionary
biology and computer science which are closely related to spin glass models. In this paper …

Quantifying the role of population subdivision in evolution on rugged fitness landscapes

AF Bitbol, DJ Schwab - PLoS computational biology, 2014 - journals.plos.org
Natural selection drives populations towards higher fitness, but crossing fitness valleys or
plateaus may facilitate progress up a rugged fitness landscape involving epistasis. We …

Innovation in viruses: fitness valley crossing, neutral landscapes, or just duplications?

P Banse, SF Elena, G Beslon - Virus Evolution, 2024 - academic.oup.com
Viruses evolve by periods of relative stasis interleaved with sudden, rapid series of mutation
fixations, known as evolutionary bursts. These bursts can be triggered by external factors …

Toy models for macroevolutionary patterns and trends

B Alicea, R Gordon - BioSystems, 2014 - Elsevier
Many models have been used to simplify and operationalize the subtle but complex
mechanisms of biological evolution. Toy models are gross simplifications that nevertheless …

The space of genotypes is a network of networks: implications for evolutionary and extinction dynamics

P Yubero, S Manrubia, J Aguirre - Scientific reports, 2017 - nature.com
The forcing that environmental variation exerts on populations causes continuous changes
with only two possible evolutionary outcomes: adaptation or extinction. Here we address this …