But this is very well understood in phylogenetics. This is the basis of codon models and the “maximum likelihood school” of phylogenetic modelling. You can see this by looking at IQ-TREE (a modern phylogenetic inference tool): https://iqtree.github.io/doc/Substitution-Models
Good point! I guess I was mostly thinking of changes at the trait level, but you are right that now even for species the gene level is used, and that there are much more precise models of mutations at the gene level.
I haven’t explored this in enough detail to figure out if there is anything as subtle as the diffraction process of textual criticism, where the hard reading is not only replaced by simpler ones but lost completely, yet can sometimes be inferred back from the meter of poem and the rhymes and other constraints.
Good point! I guess I was mostly thinking of changes at the trait level, but you are right that now even for species the gene level is used, and that there are much more precise models of mutations at the gene level.
I haven’t explored this in enough detail to figure out if there is anything as subtle as the diffraction process of textual criticism, where the hard reading is not only replaced by simpler ones but lost completely, yet can sometimes be inferred back from the meter of poem and the rhymes and other constraints.