The Degeneracy of the Genetic Code

The more changes you make over these long time periods, the chances that not only has there been one substitution. But imagine if there's been five substitutions. And so you'd be underestimating how closely related any two species are. So they try to account for that by actually treating the differences in the amino acids that they see a little bit differently. It's sort of a conservative approach that tries to accounts for that.