# Inferring the correlated fitness effects of nonsynonymous mutations at the same site using triallelic population genomics

## TL;DR

This study shows that mutations at the same site in proteins have correlated fitness effects, revealing a new aspect of protein evolution.

## Contribution

A new model and method to infer correlated fitness effects of mutations at the same site using triallelic population genomics.

## Key findings

- Nonsynonymous mutations at the same codon show moderate correlation in fitness effects.
- The correlation is consistent across organisms and not influenced by protein structure features.
- The method agrees strongly with biochemical mutational scanning experiments.

## Abstract

The distribution of mutation fitness effects is central to evolutionary genetics. Typical univariate distributions, however, cannot model the effects of multiple mutations at the same site, so we introduce a model in which mutations at the same site have correlated fitness effects. To infer the strength of that correlation, we developed a diffusion approximation to the triallelic frequency spectrum, which we applied to data from D. melanogaster. We found a moderate correlation between the fitness effects of nonsynonymous mutations at the same codon, suggesting that both mutation identity and location are important for determining fitness effects in proteins. We validated our approach by comparing with biochemical mutational scanning experiments, finding strong quantitative agreement, even between different organisms. We also found that the correlation of mutation fitness effects was not affected by protein solvent exposure or structural disorder. Together, our results suggest that the correlation of fitness effects at the same site is a previously overlooked yet fundamental property of protein evolution.