Don't know if your numbers are right but the basic theory is based on the fact that DNA will tend to mutate very slowly over a long period of time. The number of variations between two samples of DNA will give an estimate of how long it is since the two people shared a common ancestor. There are two types of DNA in question - nuclear DNA which we get 50% from each parent and mitochondrial DNA which we get entirely from our mothers because the mitochondria are passed down in the structure of the egg cell.
By looking at the relatively small differences between key areas in the mitochondrial DNA geneticists have found evidence to support the "out of Africa" theory of human evolution. There would appear to be clear linkages between all modern European and Near East populations which all stem from around 8 female lines. There are similarly low numbers of female ancestors to explain other human populations around the world. The largest variation is in Africa itself which is logical if we assume a radiating pattern of evolution from a source somewhere in Africa but with only one strand of this crossing into Sinai and then giving rise to all non-African populations around the world. The only part of the nuclear DNA which can be traced in this way is the Y chromosome which is uniquely transmitted from father to son. Plotting variations in this chromosomal DNA allows a similar conclusion to that reached in the mitochondrial DNA analysis. Relatively low variation and a small original gene pool.
The uniform nature of human mitochondrial DNA is one of the main arguments against any interbreeding between Neanderthal and Cro-Magnon populations.