Re: Y chromosomes:
Okay, if I am reading that right we have as little in common with our closest cousin (on the Y line) as we do with a chicken? That just sounds nuts. IIRC, Otzi's the Ice Man's Y chromosome was different from modern humans. Perhaps these differences are somehow related? You gave some options but what is your read on this (assuming they are right)? Is there a chance they are wrong or misinterpreted the data?
If that is true what does it say for evolution of other species than primates? Why would we be so different from our closest cousin when coyotes, dogs, wolves, and jackals can all interbreed successfully? Even horses and donkeys produce mules. It just seems like it is a much bigger deal than people are making it out to be. We ought to be hearing it on every news cast.
On the other hand, perhaps the Onion-Worth Mr Sitchin is right and the reason we are so different is because the Nibelungs or whatever swapped a bunch of our regular genes for super spaceman genes. We should therefore be looking for our mothership before too long.
I for one welcome our Nephilim overlords!
To be fair, we don't know what a chicken's Y looks like. The comparison is that the divergence rate of the Y has given us a level of difference for the Y that would be equivalent to the amount of difference between us and chickens on the other chromosomes. Apples and oranges in that sense, but it gives an impression of how extreme the Y is compared to the others.
Re: interbreeding: The Y is less than one percent of the genome, and it is quite possible to survive without it -- as most women do. So we might consider it "special" in the sense that the rest of the genome can tolerate the lack of Y genes, possibly leaving them freer to be deleted. The chimpanzee seems to have undergone a lot of gene deletions compared to humans.
Two knowledgeable people independently told me we should wait for the gorilla. We'll see if it's equally weird in some third way, or if chimps are the odd ones out.