[rngfnby]

Well, ya. Of course it was rape. And in retaliation we genocided them, hence the lack of Y and mRNA.

[treyd]

> and mRNA

This might be seen as a bit of a nitpick but I believe you mean mtDNA (mitochondrial).

[jyscao]

>And in retaliation we genocided them

This is far from being the only or even main explanation to their extinction.

The Neanderthal populations were extremely inbred, so I'd guess that was a bigger factor to their decline.