Few things that pop up in my head:
- disease
- nuclear (or comparable) war
- depletion of natural resources
- natural disaster
- extra terrestrial influence: asteroid or alien invasion
- artificial intelligence
- anarchy / disruption of social security
hmm...anything else?
Doesn't have to robots and test tubes, just separate groups that drift apart far enough that they can't interbreed (definition of species) and one species wipes out the other as often happens, and if the species that got wiped out got to hold the legacy "human race" species, well then...
You have a definition problem where evolution is obviously quite natural, just like comets striking the earth is natural (although very rare), so those are natural disasters, although thats probably not what you meant.
From history, it usually takes a couple things to wipe out "apocalypse" a civilization although it often only takes one thing to get the ball rolling.
My money is on something like "peak phosphorous for fertilizer production for cereal grains causes supply chain shock leading to self destruction"
"Things have happened quickly. It took us millions of years to evolve into what we are, but in the last sixty years, with atomic weaponry, we've created the potential to extinguish ourselves. And if it's not us, it will inevitably be something else. If not a meteorite in the relative short term, then the expansion of the Sun's corona. It will happen."
He has also said that there are a number of other threats with the ability to extinct life on Earth. They include an engineered virus unleashed by terrorists, an inadvertent creation of a micro black hole, or a yet unknown technology.
The keywords are: existential risks.
also on the extra terrestrial influence side, there's direct hits by gamma rays that could wipe out Earth in an instant.
The inversion of magnetic pole could have some impact on how we are shielded from space radiation.
AI is the only thing listed with the capability to literally destroy the planet. While something might still exist afterwards, it will likely be totally meaningless and worthless: http://lesswrong.com/lw/y3/value_is_fragile/