Provided a clean dichotomy. Our analyses by necessity treat "species"
as individuals with zero dimension in space and time. This assumption
is usually accurate enough (at least for nonmolecular datasets), but
there is no guarantee it is correct. And for paleontological
datasets, it is usually not even testable.
Besides, the neontological experience is that nodes as dichotomies
may be more fiction than fact - not always, but often (alternatively:
that nodes as dichotomies are arbitrary and evolutionary quite
meaningless entities).
http://www.genetics.org/content/178/1/427.full
http://sysbio.oxfordjournals.org/content/57/5/719.full It is unlikely
that this is a recent phenomenon.