Indigenous
Indigenous was a term that meant that something was native to or naturally occurring in a place. The word also applied to groups of people that were native to a particular place.

People
The North, Central, and South American regions of Earth were home to a number of indigenous Human ethnic groups. () Those areas were heavily colonized by more technologically advanced Humans from other continents after the 15th century, leading to the destruction of many of these indigenous cultures. ()

In 2268, Kirk and the  encountered a number of indigenous peoples from Earth, including people from the Delaware, Navajo, and Mohican tribes, on a planet where they had been transported by the Preservers several centuries earlier, so that they could live undisturbed. ()

General terminology
In July 2151,  encountered a humanoid species on their homeworld homeworld. While scanning the planet, Archer asked T'Pol to scan for non-indigenous biosigns. While there, the Enterprise crew discovered that Garos, a newcomer to the planet, claimed that a mysterious disease affecting the locals was indigenous, when it was actually caused by Garos' antimatter reactor. ()

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Science