How did people figure out that the distant "father" of 1 in 200 males alive today lived 800-1200 years ago? Or that the father of all humans ("Adam") was alive 40-50,000 years ago? These estimates come from looking at differences in the Y chromosome over time.
But wait a minute you might be saying. You just said that we can use the Y chromosome for historical studies because it can't recombine and so stays constant.
Notice I said earlier that the Y chromosome passes from generation to generation virtually unchanged. It does change a little over time because of random mutations (nothing is perfect including copying DNA). It is these rare mutations that let scientists date when things have happened in the past.
Scientists use DNA to estimate when things have happened in the past by assuming a certain rate of mutations over time. Let's say that the Y chromosome gets 1 new mutation/generation (much higher than the actual rate). If this is the case, then if two people have 10 differences between them, then they are 10 generations apart.
The mutation rate scientists have used in the past was based on circumstantial evidence because there was just too much DNA to sequence. Until now.
For the first time, groups in Indiana and New Hampshire have figured out a mutation rate based on sequencing huge amounts of DNA from lots of the roundworm, C. elegans. How much DNA? An astonishing 4 million base pairs -- an impossible number just a few years ago.
What the researchers found was that the mutation rate was 10 times higher than previously believed or around 2 mutations/generation for C. elegans. There are possible reasons that given the way the experiment was done, the mutation rate might have been artificially high. But, if the new number is true, it calls into question all sorts of things.
For example, partly based on DNA evidence, scientists believed that chimps and humans separated about 5 million years ago. Was it actually 500,000 years ago? Humans began their migration out of Africa 100,000 years ago. Or was it 10,000? Did "Adam" live 50,000 or 5000 years ago?
Some of these new numbers are obviously wrong. From archeological digs, we know there were people in Europe, Asia, and even the Americas more than 10,000 years ago. From fossil evidence we know that chimps and humans separated more than 500,000 years ago.
Obviously, then, more work needs to be done to get at this critical number. And if the mutation rate isn't constant over time, we may never be able to get a good number. In the meantime, the work done here will need to be repeated lots more times before we begin rewriting history. With the advent of new sequencing technologies, we are now able to do experiments undreamed of just a few years ago.