Adaptive molecular convergence is pervasive across deep time and largely decoupled from phenotypic convergence

Researchers often infer evolutionary repeatability when selection scans implicate homologous genes in repeatedly evolved traits or ecologies. However, the causes and frequency of genome-scale molecular convergence remain unresolved, particularly over deep time. We show that adaptive molecular convergence— excess convergence of nonsynonymous substitutions, consistent with positive selection—is pervasive across Medusozoa. Molecular convergence declines over time but persists among lineages separated by > 600 million years, exceeding null expectations based on random overlap. However, lineages sharing repeatedly evolved phenotypes (eyes, medusa loss, upright colonies) do not exhibit elevated molecular convergence relative to other comparisons. Instead, convergence is non-randomly distributed across genes and enriched for environment-facing functions, including metabolism, immunity, and xenobiotic processing, suggesting that widespread reuse of genes reflects multifaceted organism-environment interactions.