Mitochondria:

• Functions and replicates separately from the rest of the cell (it doesn't take orders from the nucleus).
• Houses mtDNA, which is maternal only.

Nuclear vs. mtDNA:

• Nuclear DNA is linear and less easily preserved in comparison to the smaller, compact, circular mtDNA.

• The nuclear genome is divided unequally into a number of chromosomes, each composed of a DNA molecule whereas the mitochondrial genome is represented by a single molecule of mtDNA. This implies that you need only find one molecule of mtDNA to compare mt-genomes as opposed to requiring all nuclear chromosomes to compare nuclear genomes.