Basically, the fossil record. We notice that there are periods of time where the variety of fossils decreases drastically. We can date how old the rock is so we can tie together global observations to the same time period. A large drop in global biodiversity makes it a very likely candidate for a mass extinction.
We will often find other evidence that suggests a huge event occurred at the same time which adds more evidence in support of a mass extinction. Things like major climate shifts (caused by asteroids or volcanic activity), major shifts in atmospheric composition (the great oxygenation event), or anomalous isotopes (gamma ray burst).
As a side note, it’s just 5 mass extinctions we think we know of. We think there are likely others, we just don’t have the evidence for all of them. And there’s always a chance that we’ve misinterpreted evidence for the known ones.
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