Hunter-gatherers show highest genetic diversity with Khoisan exceeding Pygmies. Genetic diversity correlates strongly with geographic distance across Africa. Khoisan, Pygmies, sub-Saharan agriculturalists, and North Africans form four major genetic clusters. North Africans cluster closely with Eurasians due to massive Eurasian admixture up to 85%. Sub-Saharan agriculturalists admixed with nearby hunter-gatherers like Khoisan and Pygmies. Khoisan ancestors maintained largest effective population sizes throughout history. Pygmy ancestors also sustained larger Ne than non-hunter-gatherers post-split. No Neanderthal or Denisovan introgression in sub-Saharan Africans. Best model shows ghost archaic XAf splits from AMH lineage 528kya then introgresses into Africans. Khoisan receive 4.0% archaic ghost DNA. Mbuti Pygmies receive 4.3% archaic ghost DNA. Mandenka/West Africans receive 5.8% archaic ghost DNA. Sahara acts as major genetic barrier splitting North and sub-Saharan Africans. Hunter-gatherers more differentiated with higher runs of homozygosity indicating isolation. Bantu expansion homogenized sub-Saharan agriculturalist genetics. Basal human split places Khoisan at root with larger Ne due to southern African climate. Ghost archaic related directly to AMH lineage not Neanderthals.