In butterfly mtDNA, the composition bias is extreme toward A-T (80 to 90%
depending on gene and codon position).
It seems also unlikely that every kind of substitution has equal probability
Furthermore a selection against substitutions providing G and C, which has
been demonstrated in Dloop of mammalians (A-T rich), is not correctly
represented by ML models. At least for what I know about Maximum Likelihood
and PAUP* options, it is impossible to use a non reversible model. Even if
it was possible, what kind of weighting sheme could fit to the actual (not
the observed) substitution pattern?