Nat Geo Mar 06, on page 62, right column, 1/4 way down; it says that "Similarly, most of the Y chromosome ,which determines maleness, travels intact from father to son."
HMmmm... 'most' (emphasis mine)
Further down it say...
"Scientists now calculate that all living humans are related to a single woman who lived roughly 150,000 years ago in Africa..." (emphasis mine)
[I gotta be ELSIE, so...
How does they know she was single? And how does they know she had a rough life?]
I think a little shuffling can occur between the X and the Y, but only in certain, well defined loci of the Y chromosome. The studies which traced the human migration patterns over the Earth looked at polymorphisms outside this area which never undergo recombination.
This book does a great job of explaining how those studies were conducted. There was a special on TV along with the book.