Question

No fossils of Homo neanderthalensis have been found in Africa, but many African populations have traces of Neanderthal DNA. If Neanderthals were never in Africa (which is a possibility, though fossils may yet be found), how can the presence of Neanderthal DNA be explained?

Answer 1

A modern human who lived 40,000 years ago had 6-9% of Neanderthal DNA. Non-African modern humans have 1-4% of Neanderthal DNA. There are studies that give evidence of interbreeding between Neanderthals and modern humans. These pieces of evidence shed light on the expansion of humans out of Africa.

Neanderthals evolved and lived mostly in Eurasia and could not have interbred with humans living in Africa at that time. A very recent (2016) study has shown pieces of evidence of Neanderthal and human interbreeding as far as 100,000 years ago when humans didn't even migrate out of Africa. This evidence shows the human gene flow into Neanderthal genome as opposed to the Neanderthal DNA into the human genome. This also suggests that interbreeding was more frequent than previously thought and early migration of humans left Africa before the population that survived and gave rise to non-African modern humans.

There are sufficient pieces of evidence of Neanderthal-human interbreeding but there DNA is not present in our mitochondrial or nuclear DNA. One possible explanation could be that some lineages had Neanderthal DNA in their mtDNA but they died out subsequently leaving no evidence.  Another possible explanation could be that since mtDNA is passed on from mother to offspring, only Neanderthal males could have been taking part in the interbreeding. It could also be possible that interbreeding between Neanderthal females and human males did occur nut fertile offspring were not produced. Or, lastly, it could also be possible that our reasearchers have still not sequenced one mtDNA lineage that Neanderthals contributed to human genome.