I have recently been examining several different protein sequences
(URA3, ADH, CYC) in yeasts and comparing the resulting trees to trees
derived through comparison of ribosomal sequences.
In general, ribosomal sequences are appropriate for determining
relationships over rather long distances, but are less reliable in
distinguishing closer species.
Although not an exact relationship, whre data are available, trees
generated by URA3, ADH and CYC separate related yeasts in similar ways.
Also, contrary to popular opinion, unicellular ascomycetous yeasts form
a monophyletic group.