There’s now little doubt that modern day humans, homo sapiens, are partly Neanderthal. From skin disorders to the immune system, sex with archaic species changed Homo sapiens reports Nature:
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Our ancestors were not a picky bunch. Overwhelming genetic evidence shows that Homo sapiens had sex with Neanderthals, Denisovans and other archaic relatives. Now researchers are using large genomics studies to unravel the decidedly mixed contributions that these ancient romps made to human biology — from the ability of H. sapiens to cope with environments outside Africa, to the tendency of modern humans to get asthma, skin diseases and maybe even depression.
The proportion of the human genome that comes from archaic relatives is small. The genomes of most Europeans and Asians are 2–4% Neanderthal1, with Denisovan DNA making up about 5% of the genomes of Melanesians2 and Aboriginal Australians3. DNA slivers from other distant relatives probably pepper a variety of human genomes4.