If I understand where you want to go with this; yes what goes for our DNA also to a greater extent goes for our ancestors. However, humans became humans as a group, not as an individual. We can trace our Y chromosome to our most recent common ancestor but this does not mean that there existed at that time (the time of our MRCA) only one man. It means that of all the men alive at the time, only one is an ancestor of all human males in our current population.
Nor does this mean that the Y chromosome does not change, just that it changes in trackable ways.
Huh?
How does we KNOW this?
How can a 'mutation' take place in a group and not in an individual?