Variation in mitochondrial DNA (mtDNA) is extremely useful in studying genetic diversity. There are a number of reasons for this:
mtDNA is maternally inherited with no recombination and, all markers in this genome are effectively linked as a single haplotype. Hence the number of nucleotide differences between mitochondrial genomes is a direct reflection of the genetic distance that separates them,
each cell has thousands of copies of mtDNA and,
regions of mtDNA mutate 5-10 times more than nuclear DNA making it ideal for studying the divergence between wild and domestic populations under the relative short timescale of domestication (<10,000 years).
The usual way to analyse mtDNA is the sequencing of the cytochrome b gene and of the control region that shows greater variation than the other parts of the mtDNA molecule.