[HTML][HTML] From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics

S Manrubia, JA Cuesta, J Aguirre, SE Ahnert… - Physics of Life …, 2021 - Elsevier
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is
arguably the next major missing piece in a fully predictive theory of evolution. We refer to this …

Multi-locus interactions and the build-up of reproductive isolation

I Satokangas, SH Martin… - … of the Royal …, 2020 - royalsocietypublishing.org
All genes interact with other genes, and their additive effects and epistatic interactions affect
an organism's phenotype and fitness. Recent theoretical and empirical work has advanced …

Sequence entropy of folding and the absolute rate of amino acid substitutions

RA Goldstein, DD Pollock - Nature ecology & evolution, 2017 - nature.com
Adequate representations of protein evolution should consider how the acceptance of
mutations depends on the sequence context in which they arise. However, epistatic …

Biophysics and population size constrains speciation in an evolutionary model of developmental system drift

BS Khatri, RA Goldstein - PLoS computational biology, 2019 - journals.plos.org
Developmental system drift is a likely mechanism for the origin of hybrid incompatibilities
between closely related species. We examine here the detailed mechanistic basis of hybrid …

Neighboring genes for DNA-binding proteins rescue male sterility in Drosophila hybrids

MA Liénard, LO Araripe… - Proceedings of the …, 2016 - National Acad Sciences
Crosses between closely related animal species often result in male hybrids that are sterile,
and the molecular and functional basis of genetic factors for hybrid male sterility is of great …

Simple biophysical model predicts faster accumulation of hybrid incompatibilities in small populations under stabilizing selection

BS Khatri, RA Goldstein - Genetics, 2015 - academic.oup.com
Speciation is fundamental to the process of generating the huge diversity of life on Earth.
However, we are yet to have a clear understanding of its molecular-genetic basis. Here, we …

A new mechanism for mendelian dominance in regulatory genetic pathways: competitive binding by transcription factors

AH Porter, NA Johnson, AY Tulchinsky - Genetics, 2017 - academic.oup.com
We report a new mechanism for allelic dominance in regulatory genetic interactions that we
call binding dominance. We investigated a biophysical model of gene regulation, where the …

Both Binding Strength and Evolutionary Accessibility Affect the Population Frequency of Transcription Factor Binding Sequences in Arabidopsis thaliana

G Schweizer, A Wagner - Genome Biology and Evolution, 2021 - academic.oup.com
Mutations in DNA sequences that bind transcription factors and thus modulate gene
expression are a source of adaptive variation in gene expression. To understand how …

Genetic drift promotes and recombination hinders speciation on holey fitness landscapes

A Kalirad, CL Burch, RBR Azevedo - PLoS Genetics, 2024 - journals.plos.org
Dobzhansky and Muller proposed a general mechanism through which microevolution, the
substitution of alleles within populations, can cause the evolution of reproductive isolation …

[HTML][HTML] Redundancy-selection trade-off in phenotype-structured populations

L Miele, RML Evans, S Azaele - Journal of Theoretical Biology, 2021 - Elsevier
Realistic fitness landscapes generally display a redundancy-fitness trade-off: highly fit trait
configurations are inevitably rare, while less fit trait configurations are expected to be more …