Taxes are collected from all the colonists in your bases. Colonists on ships and in pods are not taxed. Troops, crew and high guard rangers do not pay taxes.
Natives are also taxed. Natives grow unhappy if over taxed and prefer the ultra conservative tax rate.
The tax setting is universal it applies to all your bases at the same time and can be changed at any time.
You will collect the most money the fastest using enslavement, however enslavement can cause unhappiness slowing down growth rate.
April 1, 2004