in·dig·e·nous
/inˈdijənəs/
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adjective
adjective: indigenous
originating or occurring naturally in a particular place; native.
That’s what Native Americans are, indigenous. They are a genetic population that evolved in the New World. As far as populations worldwide go, they are very distinct and ancient.
In anthropology indigenous means first people to inhabit an area. It has nothing to do with how long they’ve been there.