Functional bottlenecks can emerge from non-epistatic underlying traits

TL;DR

This paper shows that functional bottlenecks in protein fitness landscapes can emerge from simple global epistasis models with additive traits, highlighting the importance of mutation balance in their formation.

Contribution

It introduces a stylized model demonstrating how global epistasis with additive traits can produce functional bottlenecks, emphasizing the role of mutation balance.

Findings

Functional bottlenecks arise with high probability in the model.

Proper calibration of the model is crucial for bottleneck emergence.

A balance between neutral and non-neutral mutations is necessary.

Abstract

Protein fitness landscapes frequently exhibit epistasis, where the effect of a mutation depends on the genetic context in which it occurs, i.e., the rest of the protein sequence. Epistasis increases landscape complexity, often resulting in multiple fitness peaks. In its simplest form, known as global epistasis, fitness is modeled as a non-linear function of an underlying additive trait. In contrast, more complex epistasis arises from a network of (pairwise or many-body) interactions between residues, which cannot be removed by a single non-linear transformation. Recent studies have explored how global and network epistasis contribute to the emergence of functional bottlenecks - fitness landscape topologies where two broad high-fitness basins, representing distinct phenotypes, are separated by a bottleneck that can only be crossed via one or a few mutational paths. Here, we introduce and analyze a stylized model of global epistasis with an additive underlying trait. We demonstrate that functional bottlenecks arise with high probability if the model is properly calibrated. Furthermore, our results underscore that a proper balance between neutral and non-neutral mutations is needed for the emergence of functional bottlenecks.