Is segregation natural ?

India is a country which has practiced segregation and anti-miscegenation (caste system) religiously much as other countries of the world including South Africa (apartheid), the US (separate but equal), etc., and almost every society of the past. This was practiced for religious reason and to maintain the moral order in different countries. If segregation and anti-miscegenation was universal for thousands years and supported not only by the state but by the majority of yogis, pastors, biblical prophets, saints and spiritual masters, then is it not logical to think they considered segregation and anti-miscegenation as something natural? Only recently public opinion started to go away from traditional social values as with other subjects like abortion, homosexuality, masturbation, pornography, drugs, seen as unnatural in much of recorded history.