Neutral mutations are usually the most important evolutive reservoirs of potential advantages that may come in handy at a given moment if the environment changes. They are more likely to reach higher frequencies at a faster rate than mutations that may affect adversely the health of their carriers.
I think the neutral mutations are certainly - from a relations pouint of view - for us here the most important.
What one seeks to know, studying relations between species, is wheter A or B is more distinct from C - and that quite a few times, or whther A splitted away from C before or after B did.
Should one be looking at a characteristic which is important for the fish, he will have to take care not te mess relatedness up with adaptation.
Chuco and Paraneetroplus fishes life in a similar environment, thus they will have to look similar, and the genes which produce theis shape will, most likely, be similar too.
However, lost of a fishes DNA does not produce any protein, thus any change wil be a neutral change, unless the change wil result in the production of a protein.
As I'm a chemist myself, I always feld genes were much more clear than morophology, untill I read about the problem with genes: they consist of very long strand of DNA, which code in for letters: ACGT. If a letter is changed into another, this is quite esily detected, but its meaning might be harder to find. However, the problem is, if I see an A, I can not say whether this A has recently been a C or not.
To say it differently, I can not say whether de diffenrence I see is recently acquired or not. Therefore, I can not determins fout of this change whether A splitted away from C before or after B did.
This is solved by using the systen - the easies way to solve a problem is the most likely, but it is know some genes change much faster than others.
Therefore, I think DNA itself can not serve to solve the queries, but it can certainly help - foir instance to raise questions
Bas
on the subject ......... 
Me too!!!!!!!!