This is a textbook question, I would like to verify my answers. According to the textbook it is possible to construct a phylogeny using nuclear and mitochondrial DNA and these trees to be different, I should give reasons why this might occur.
Here's two that I think might be valid
(1) Mitochondrial DNA is maternal, while nuclear DNA comes from both parents. It is possible to have a (female) hybrid C between species A and B, and if C cross with an individual with genotype (A), the offspring could show some genes from the species B. I consider this to be a phenomenon of introgression, and genic flux would be in these case shown in the nuclear DNA, but not in the mitochondrial.
(2) Mutations might occur. mtDNA has a higher mutation rate than nucDNA. If the phylogeny is constructed looking at a gene, more recent mutation could should in the mtDNA.
This is what I could think of, I would like to know if they sound acceptable, and if there are more possible reason to find different phylogenies using mtDNA and nucDNA.