PLOS Genetics study demonstrates intramolecular epistasis drives clustering of adaptive substitutions in Drosophila Trio protein

A paper published in *PLOS Genetics* on 3 June 2026 by Flora Borne, Andrew M. Taverner, and Peter Andolfatto (Columbia University) addresses a longstanding question in molecular evolution: why do adaptive amino acid substitutions sometimes cluster in particular regions of a protein?

Using a population genetic screen applied to the Trio protein in *Drosophila*, the authors identify lineage-specific adaptive substitutions that occur in spatial proximity within the protein structure. They then provide direct empirical evidence that these clustered substitutions interact epistatically — meaning the fitness effect of one substitution depends on the presence of another at a nearby site. Such intramolecular epistasis has been predicted computationally from genome-wide analyses but has rarely been demonstrated experimentally at the level of specific residues.

The findings suggest that epistatic interactions constrain which evolutionary paths are accessible to a protein: once an initial substitution occurs at a site, it reshapes the fitness landscape for neighbouring residues, making further substitutions at those positions more or less likely. This has implications for understanding the tempo and trajectory of protein evolution and for interpreting patterns of sequence conservation and divergence observed in comparative genomics.

The paper contributes to the theoretical toolkit for evolutionary geneticists and structural biologists seeking to understand adaptive evolution at the protein level.