Joshua L. Payne – SIB Group Leader at the Institute of Integrative Biology of the Department of Environmental Systems Science (ETH Zurich) – begins his fascinating talk on the underlying mechanics of evolution, how these mechanics themselves evolve and the notion of evolutionary landscapes. Landscapes? During the course of the 20th Century, the American population geneticist Sewall Wright was the first to depict evolution as landscapes – where coordinates in physical space correspond to genotypes in an abstract genotype space, and the elevation at each coordinate corresponds to fitness or a related phenotype. Visually, these landscapes are similar to geological maps.

the hills and valleys of evolution payne virtualFigure adapted from Payne & Wagner (2018) “The causes of evolvability and their evolution.” Nature Reviews Genetics
“Rugged adaptive landscapes can hinder evolvability, because a population’s location within such a landscape determines the amount of phenotypic variation that mutation can bring forth. For example, the mutational path indicated by the black circles leads to a local, suboptimal peak that is separated from the global peak by an adaptive valley. In contrast, the mutational path indicated by the white circles leads to the global peak.”

“What’s exciting, says Payne, is that until now the study of landscapes had been largely theoretical, but thanks to the huge advances in biotechnologies, we now have data we can use to develop models and build empirical landscapes.” For their research, Payne and his team chose to study gene regulation, more specifically the interactions between regulatory proteins and their nucleic acid sequence ligands – interactions that drive fundamental biological process in development, behavior, and physiology. In particular, the regulatory proteins Payne studies are transcription factors and RNA-binding proteins in both Drosophila and humans.

“To begin with, we established the mutational robustness and evolvability of the genotypes of both the transcription factors and the RNA-binding proteins,” explains Payne. Whether a mutation has an effect on a phenotype is related to what has been coined ‘mutational robustness’. The less weight a given mutation has on a phenotype, the more robust that phenotype is to mutation. This means that genes, and their phenotypes, are endowed with a sort of plasticity, i.e. space within which they can wriggle. “What we want to find out is whether a system can be both robust and evolvable,” continues Payne, “and evolutionary landscapes help us see this.”

“Once the robustness and evolvability of the proteins’ genotypes were established, we then went on to build their evolutionary landscapes.” Payne moves his finger along the edge of one landscape, from its base to its peak, explaining how mutations can increase binding strength, until you reach the hill’s summit, or peak, of maximum binding strength. “The contour I have just outlined represents a path that leads you from a state of low binding strength to one of high binding strength, which we consider mutationally accessible, because binding strength only increases along this path.”

“We have been able to develop landscape models at unprecedented resolution,” says Payne who then briefly introduces the Genonets Server that his team has developed. “The input form is super simple, he adds, and researchers can carry out on their own data, all the tests I have just described with it.”

 

Joshua Payne is currently Assistant Professor of Computational Biology and SIB Group Leader at the Institute of Integrative Biology of the Department of Environmental Systems Science (ETH Zurich).
Following an undergrad in mathematics and computer science at Regis University in Denver, Colorado, and a masters in operations research at Rensselaer Polytechnic Institute in Troy, New York, Payne earned his Ph.D. in computer science in 2009 at the University of Vermont. From 2009 to 2011, he was a postdoctoral researcher in the Computational Genetics Laboratory at Dartmouth College before moving to the Department of Evolutionary Biology and Environmental Studies at the University of Zurich. In 2017, he joined the ETH Zurich and became an SIB Group Leader in 2018.