How do scientists decide which plants are indigenous to a place? Particularly for ancient cities for which there aren’t any records and fossil records?

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How do scientists decide which plants are indigenous to a place? Particularly for ancient cities for which there aren’t any records and fossil records?

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Plants are considered to be indigenous largely because they are not introduced or endangered. As long as scientists don’t have proof that humans had a hand in introducing the plants to the area, the plant (or animal or whatever) is considered indigenous.

So to your point, it can be challenging to find if some plants are truly native to an area, or just the product of early human introduction. This is what an archaeologist or anthropologist would be studying.