Limits of homologization for phylogenetic analysis

[H Douglas]

I am coding morphology, mainly in two subfamilies of one beetle family.
The bursae copulatrix of both groups have sclerites, which appear
informative. I am confident about homologizing sclerites within each
subfamily, but not between them. So, I expect these characters to be
informative only for within subfamily relationships.

I would like to write an independent nomenclature and set of characters
for the sclerites of each subfamily. I would code the second subfamily
as "?" for the unhomologized characters of the first group.

Are there perils here of which I should be aware? Could you suggest a
reference on this subject?

Thanks,

Hume Douglas

Department of Biology, Carleton University, Ottawa ON, CANADA