The molecular clock basically is the simple concept that mutations accumulate in a piece of DNA at a roughly constant rate because they occur by chance. Therefore if you have a individual who then has children who have children who have children, over that time as generations move outward, there is a certain probability with each generation that a new mutation will occur, in that piece of DNA. So if you know the rough rate that those mutations occur by chance, then at some later time you can look at the DNA of the descendant from individual of line A and the descendant of line B, and examine the number of changes in their mitochondrial DNAs, or nuclear DNAs, compare them, and the number of changes will be roughly proportional to the time that they shared a common ancestor. So in fact than, by sequencing the mitochondrial DNA of a large number of people around the world, what we've been able to do is exactly determine the relative amount of time that it's been since each of them shared a common mother because we're using mitochondrial DNA. So you can then reconstruct the maternal ancestry of all the people around the world by simply comparing the number of ticks on the molecular clock, that is the number of mutations between any two pieces of mitochondrial DNA.

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