[maitaman]

The problem (as I see it) with DNA classification is that the position of dominant characteristics is sometimes as important as the having or lack of the specific gene. A weak marker in a dominant position will have far more effect on the plant than a strong marker in a low influence position.
I personally think many so-called species are merely varieties of the same thing, with strong argument in Epidendrums, catasetums, etc. Most divergent catasetum "species" found here are really sub-species (varieties) of integerinium (IMHO) as many Epidendrum are sub-species of diforme, and almost all anacheilum are sub-species of the old radians (now radiatum?) or fragrans. The supposed differences are in dominant/non-dominant positioning on the chains.
A lot of the problems could be solved by calling a sub-species a sub-species - but that has its own bewares.