Independent civilizations

Independent civilizations, or minor civilizations, occupy a single planet in a given system and do not have the technology or ambition to expand beyond their homeworld. They cannot be conquered, but it is possible to destroy them with orbital bombing and then send a colony ship to claim their planet; or you can settle on a different planet in their homeworld and turn them into a protectorate of your empire.

Protectorate status
As a protectorate, a minor civilization will provide each turn all your colonies in their system with bonus resources: food,  research, or  credits, depending on their class. You can invest in them to provide a greater yield (400 to reach level 2, and 800  more to reach level 3), which can be interesting if you have more than one colonies in their system.

They will also vote for their protector at the Galactic council. If several major civilizations have settled their system, they will ally which whichever has the greatest influence over them. There are three structures that bring influence points: the space port, the capitol, and the military outpost. One of each is enough (having two colonies with a starport each in their system will still only bring a single point), and building a capitol is only possible in your own home system. (Since the interplanetary administration is referenced in game code as the "system capitol", cf.    IsSystemCapitol function in Colony.cs, it is possible that capitol point was meant to come from this structure instead.)

Unimplemented features
It was planned for minor civilizations to have "quests" where they would demand things of their protector and provide a reward a few turns after completion of their requests. Traces of this can be found in Globals.yaml, where rewards in the form of credits, research points, and marines are listed. Civilization.cs also contains dead code if you disassemble MasterOfOrion_Data\Managed\Assembly-CSharp.dll.

Independent races can also provide production points to colonies, instead of credits, food, or research points, though none of them are set to do so.

Leaders from the minor races were also planned, and they have portraits and biographies (with some discrepancies) but they were not finished and are not enabled.

A banner and some placeholder values for a tenth race can also be found in the game data, but again they were not finished and added to the game.

Trivia
Some of the portraits are likely mismatched. For example, the Nyunyu are described as "furry", a description that only matches the banner given to the Degonite instead. The description and portraits for independent leaders also show that Akirian, Thersonian, and Glis were rotated at some point.