Saturation
Expand: Needs more explanation and a graphic & example or two.
Saturation is a phenomenon where multiple substitutions at a site decrease the amount of information available to infer a phylogeny. Site rate variation, where different sites evolve at different rates, can worsen the effects by making some sites more likely to have received multiple substitutions.
Models ignoring saturation end up suffering from long branch attraction. Jukes Cantor was the first model to account for multiple substitutions.