AFLP reliable for study of evolution?

[Lai-Lai Teo]

I'm currently working on DNA-typing of plant.  In our laboratory, we use
Amplified Fragment Length Polymorphism (AFLP), published by Vos et al.
(1995).
>From the literature and discussion with some friends, I found that the
reliability of this technique is possibly questionable.  The main problem
is the homology of the bands migrating at the same rate.  If the bands
migrate at the same rate, they are assumed to have the same length and thus
indicate similarity along evolutionary line.  I don't know much about
evolution, but I have a few questions here.  Firstly, is two homologous DNA
fragment necessarily the same product of evolution?  If selective force can
produce homologous structures like the wings of butterfly and the wings of
bird through convergent, I'm sure it can also do the same to DNA
restriction fragment length from different evolutionary line.  Secondly, if
the above question is not the main problem, are the bands that migrate at
the same rate truly homologous?  All we can say for sure is that the first
and last few nucleotides (primer sequence plus 3 selective nucleotides) are
exactly the same.  how about those in the middle?
I hope there's someone out there who can help me to clarify my doubt so
that I can proceed with better condidence.  Your advise and recomendation
will be much appreciated.