Teleost convergence paper published

The update is a bit late on the webite, but the teleost convergence paper was published earlier this year in MBE.

At its core, this study concerns protein evolution. Proteins are chains of amino acids, whose sequences shape their structure and function. When environments change, natural selection can favour amino-acid substitutions that alter a protein in ways that improve their function under new conditions. In some cases, two distantly related species can start out with completely different amino acids at important functional sites in the protein, and yet independently acquire the same substitution at the same site over evolutionary time. This kind of repeated, site-specific change is molecular convergence. These changes cannot be attributed to random chance. Instead, it reflects adaptation acting on the available set amino acids to reach the same molecular “solution” despite different evolutionary histories.
Over the decades, researchers have found that certain classes of genes, such as those encoding for proteins involved in gas transport and sensory perception are frequent targets of adaptive change. In contrast, pleiotropic genes have traditionally been viewed as poor candidates for adaptation. Pleiotropy refers to a single gene influencing multiple biological systems. Because changes to such genes can have widespread effects, a substitution that is beneficial in one context may be harmful in another, leading pleiotropic proteins to be strongly constrained and conserved. But, as with many ideas in biology, the more systems we examine, the more we encounter exceptions.

In this study, we analysed over two million protein-coding genes from 143 teleost fish genomes to search for signatures of molecular convergence. We used a novel unsupervised, data-driven approach to identify convergent signals without relying on a pre-defined set of genes or pathways. This approach yielded 89 gene families with evidence of molecular convergence. Surprisingly, a majority of these genes showed broad expression across tissues and cell types. Moreover, genetic perturbations of these genes were associated with phenotypic effects spanning multiple biological systems. Together, these lines of evidence point to their pleiotropic nature, and suggest that adaptive variation can, under some circumstances, accumulate even in pleiotropic genes.

Using targeted simulations, we further show that in specific evolutionary scenarios, adaptation via pleiotropic genes may not only be possible, but even favoured (see that here). While our study is not the first to raise this possibility, it is the first to demonstrate the pattern at such a broad phylogenetic scale in an exceptionally diverse vertebrate lineage like teleost fishes. As comparative genomics has expanded, similar observations have become increasingly difficult to ignore. Indeed a recent study in jellyfishes found the exact same patterns as we did, across almost double the phylogenetic distance (Berger et al 2026). We are therefore now at a point where the classic view that pleiotropic genes are generally off-limits to adaptation, needs refinement in light of accumulating evidence.