Combining nuclear and chloroplast data in Structure

[CB]

Are there any major problems with combining haploid plastid DNA data
(or
mtDNA for that matter) with diploid nuclear data in a STRUCTURE
analysis under an admixture model?

I have run both a nuclear-only dataset and a combined nuclear-
plastid (haploid) data. In the latter case, I have coded the "other"
plastid copy as missing data. Am I introducing any bias into the
analysis by applying unjustified weight to the plastid data relative
to the nuclear data? If I understand this correctly, I am basically
forcing STRUCTURE to treat haploid data as if it were diploid. How
serious of a violation is this, and is there a way to circumvent it
while still combining haploid and diploid DNA?

Lastly, can anyone refer me to a study where this or something
similar
has been done (e.g. mtDNA + microsats, etc.)?


Thanks!
CB