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Underlying natural phenomena have been causing extinction on earth since life began. Asteroid collisions can result in mass extinction by causing particulate matter to block out sunlight and disrupt plant life for several years. Super-volcanoes can cause similar harm to agriculture. More exotic cosmological phenomena, like gamma-ray bursts, are conjectured to pose a natural existential risk.

We have a fairly good sense of the frequency of such risks, because of the historical record. As a consequence, we can estimate that they are relatively unlikely to cause human extinction in any given century. For this reason, it is generally believed that anthropogenic existential risks pose a more serious threat than do natural risks.

Further reading

Cotton-Barratt, Owen et al. 2016. Global catastrophic risks.
A report focusing on natural catastrophic risks, as well as other types of global catastrophic risk.