There are identifiable characters to match up. Like the Scottish Highlands and the Appalachian mountains in the US have matching characteristics, fit together geographically, and also the current movements are still ongoing. Like for the Himalayans are still growing due to the plates still moving. So being able to work out “X plate moves Y distance, XXX million years ago would place it right next to this other place.”
Hundreds of years of thinking really hard and guessing. Since we know that animals and plants don’t normally appear from nothing, we can “trace” the existence of an animal or plant or fish from one region to the other. We may find a species came from another place or another species, creating a sort of timeline. We can observe the continents as they are moving now, compare that with past observations, and figure out that because these animals/plants had no way to cross the ocean and because we think these two continents used to be connected that they must have been connected around that time (given the current speed and the history of both continent’s animals)
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