(1) The different markers can be useful for different degrees of relatedness, look into the overviews for mtDNA:

Simon C., Frati F., Beckenbach A., Crespi B., Liu H. and Flook

P. 1994 Evolution, weighting, and phylogenetic utility of mitochondrial

gene sequences and a compilation of conserved polymerase

chain reaction primers. Ann. Entomol. Soc. Am. 87,

651–701.

Simon C., Buckley T. R., Frati F., Stewart J. B. and Beckenbach

A. T. 2006 Incorporating molecular evolution into phylogenetic

analysis, and a new compilation of conserved polymerase chain

reaction primers for animal mitochondrial DNA. Ann. Rev. Ecol.

Evol. Syst. 37, 545–579.

For species proposed to be closely related, the mtDNA COI and COII or the ND2, ND5 might be useful. An alternative might be the internal spacer ITS 2.

(2) If you expect some degree of hybridization, this will be better observed by comparison between the maternal heredited mtDNA and the nucDNA.

(3) For a good resolution the right sample design might be as important as choosing the right DNA. You will need an appropriate outgroup, the honeybee might be woth to be included, and I suggest a nested design, with two further bee species added, which belong not to your species under study.

Good luck!

(1) The different markers can be useful for different degrees of relatedness, look into the overviews for mtDNA:

Simon C., Frati F., Beckenbach A., Crespi B., Liu H. and Flook

P. 1994 Evolution, weighting, and phylogenetic utility of mitochondrial

gene sequences and a compilation of conserved polymerase

chain reaction primers. Ann. Entomol. Soc. Am. 87,

651–701.

Simon C., Buckley T. R., Frati F., Stewart J. B. and Beckenbach

A. T. 2006 Incorporating molecular evolution into phylogenetic

analysis, and a new compilation of conserved polymerase chain

reaction primers for animal mitochondrial DNA. Ann. Rev. Ecol.

Evol. Syst. 37, 545–579.

For species proposed to be closely related, the mtDNA COI and COII or the ND2, ND5 might be useful. An alternative might be the internal spacer ITS 2.

(2) If you expect some degree of hybridization, this will be better observed by comparison between the maternal heredited mtDNA and the nucDNA.

(3) For a good resolution the right sample design might be as important as choosing the right DNA. You will need an appropriate outgroup, the honeybee might be woth to be included, and I suggest a nested design, with two further bee species added, which belong not to your species under study.

Good luck!

I agree Gerlind Lehmann' view mentioned above,. Gerenal speaking, the mtDNA (eg, COI, COII) maybe is suitable marker for constructuring phylogenetic tree of intraspecific level in insect, to constructure genus-level phylogenetic relationship can using the combined nuclear or mitochondrial genes as molecular marker!