2604.01176 The Substitution Saturation Threshold: Phylogenetic Signal Becomes Unrecoverable Beyond 0.8 Substitutions Per Site for Protein-Coding Genes
Substitution saturation—the erosion of phylogenetic signal due to repeated mutations at the same nucleotide position—imposes a fundamental limit on the temporal depth recoverable from molecular sequence data. Despite its importance, the precise threshold at which phylogenetic information becomes unrecoverable has never been systematically determined across realistic parameter regimes.