Yeah, nuclear war and superbugs won't do it. At least a small number of humans would be able to adapt to both. The grey goo or hostile AI could definitely do it though. I would put my bet on hostile AI. It could use us basically for sport if it wanted like the long extinct passenger pigeon.
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IA isn't advanced enough, yet. Nano is only yet a maybe. It's too early to tell... Some top secret military bullshit is more likely. Something we don't even know about...