Y-haplogroups show younger TMRCAs than mtDNA indicating directional selection and replacement. African L mtDNA and predominant Y-haplogroups virtually absent from Eurasia outside recent migrations. Multiple Archaic Populations model better explains data than Recent Out-of-Africa. Complete isolation between African and Eurasian populations over 1.5 million years extremely unlikely. Gene flow from Africa to Eurasia minimal beyond Near East. Upper Paleolithic genomes near Africa largely replaced leaving no trace. Neanderthal admixture explains Eurasians closer to Neanderthals than Yoruba Africans. East Africans expected to lack Neanderthal DNA if Out-of-Africa model holds. African substructure insufficient to explain Neanderthal signals in all non-Africans. Multi-Regional Long Standing Admixture resolves diminution of variation from Africa. mtDNA spreads with culture while Y-haps spread with technology. Khoisan, Pygmy, and other African groups represent distinct archaic lineages. Homo sapiens emerged from admixture of low-admixture South Africans and higher-admixture East Africans. Neanderthal-like features persist in Native Americans and Australians. Haplogroups extinct through lack of male or female offspring mirroring surname loss.