Eugenics rejects the idea that all are created equal. Equality is supported by both Judeo-Christian theology and secular enlightenment philosophy.

I can think of little modern philosophy more regressive than the idea that a self-appointed superior can determine that another is inferior to the point that they (or their offspring) should be culled from existence. Eugenics and racism have been intertwined since the beginning and with a modern twist continue to target vulnerable populations.

For the most part they come out of emotions that evolution found useful for procreation (love, fear, anger), then extrapolated to people living in small groups, then to larger societies after the invention of agriculture via the "iterated prisoners dilemma".

I think that in this context it's more useful to pose the question in there other direction: which moral systems declare that the slave trade and the disenfranchisement of persons on the basis of skin colour is not ok?

Ethics is a field of study. I know some on this site loathe the humanities, but those same often don’t mind using language, psychology, and sociology to make a buck.