The causes of evolvability and their evolution

JL Payne, A Wagner - Nature Reviews Genetics, 2019 - nature.com
Evolvability is the ability of a biological system to produce phenotypic variation that is both
heritable and adaptive. It has long been the subject of anecdotal observations and …

Recent insights into the genotype–phenotype relationship from massively parallel genetic assays

H Kemble, P Nghe, O Tenaillon - Evolutionary applications, 2019 - Wiley Online Library
With the molecular revolution in Biology, a mechanistic understanding of the genotype–
phenotype relationship became possible. Recently, advances in DNA synthesis and …

Robustness and innovation in synthetic genotype networks

J Santos-Moreno, E Tasiudi… - Nature …, 2023 - nature.com
Genotype networks are sets of genotypes connected by small mutational changes that share
the same phenotype. They facilitate evolutionary innovation by enabling the exploration of …

The highly rugged yet navigable regulatory landscape of the bacterial transcription factor TetR

CA Westmann, L Goldbach, A Wagner - Nature Communications, 2024 - nature.com
Transcription factor binding sites (TFBSs) are important sources of evolutionary innovations.
Understanding how evolution navigates the sequence space of such sites can be achieved …

Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution

Y Schaerli, A Jiménez, JM Duarte… - Molecular Systems …, 2018 - embopress.org
Phenotypic variation is the raw material of adaptive Darwinian evolution. The phenotypic
variation found in organismal development is biased towards certain phenotypes, but the …

Changes in gene expression predictably shift and switch genetic interactions

X Li, J Lalić, P Baeza-Centurion, R Dhar… - Nature …, 2019 - nature.com
Non-additive interactions between mutations occur extensively and also change across
conditions, making genetic prediction a difficult challenge. To better understand the plasticity …

Why and how to study genetic changes with context-dependent effects

Y Eguchi, G Bilolikar, K Geiler-Samerotte - Current Opinion in Genetics & …, 2019 - Elsevier
The phenotypic impacts of a genetic change can depend on genetic background (eg
epistasis), as well as other contexts including environment, developmental stage, cell type …

Experimental determination of evolutionary barriers to horizontal gene transfer

H Acar Kirit, M Lagator, JP Bollback - BMC microbiology, 2020 - Springer
Background Horizontal gene transfer, the acquisition of genes across species boundaries, is
a major source of novel phenotypes that enables microbes to rapidly adapt to new …

Linking molecular mechanisms to their evolutionary consequences: A primer

R Grah, CC Guet, G Tkačik, M Lagator - Genetics, 2024 - academic.oup.com
A major obstacle to predictive understanding of evolution stems from the complexity of
biological systems, which prevents detailed characterization of key evolutionary properties …

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

F Baier, F Gauye, R Perez-Carrasco, JL Payne… - Science …, 2023 - science.org
Mutations to gene regulatory networks can be maladaptive or a source of evolutionary
novelty. Epistasis confounds our understanding of how mutations affect the expression …