Neanderthals have contributed approximately 1-4% of the genomes of non-African modern humans, although a modern human who lived about 40,000 years ago has been found to have between 6-9% Neanderthal DNA (Fu et al 2015). The evidence we have of Neanderthal-modern human interbreeding sheds light on the expansion of modern humans out of Africa. These new discoveries refute many previous hypotheses in which anatomically modern humans replaced archaic hominins, like Neanderthals, without any interbreeding. However, even with some interbreeding between modern humans and now-extinct hominins, most of our genome still derives from Africa. Neanderthals could not have contributed to modern African peoples genomes because Neanderthals evolved and lived exclusively in Eurasia and therefore could not have bred with the humans living in Africa at that time.

For many years, the only evidence of human-Neanderthal hybridization existed within modern human genes. However, in 2016 researchers published a new set of Neanderthal DNA sequences from Altai Cave in Siberia, as well as from Spain and Croatia, that show evidence of human-Neanderthal interbreeding as far back as 100,000 years ago -- farther back than many previous estimates of humans migration out of Africa (Kuhlwilm et al 2016). Their findings are the first to show human gene flow into the Neanderthal genome as opposed to Neanderthal DNA into the human genome. This data tells us that not only were human-Neanderthal interbreeding events more frequent than previously thought, but also that an early migration of humans did in fact leave Africa before the population that survived and gave rise to all contemporary non-African modern humans.

We previously mentioned the lack of genetic contributions by Neanderthals into the modern human mtDNA gene pool. As we have shown that Neanderthal-human interbreeding did occur, why wouldnt we find their DNA in our mtDNA as well as our nuclear DNA? There are several potential explanations for this. It is possible that there were at one point modern humans who possessed the Neanderthal mtDNA, but that their lineages died out. It is also highly possible that Neanderthals did not contribute to the mtDNA genome by virtue of the nature of human-Neanderthal admixture. While we know that humans and Neanderthals bred, we have no way of knowing what the possible social or cultural contexts for such breeding would have been.

Because mtDNA is passed down exclusively from mother to offspring, if Neanderthal males were the only ones contributing to the human genome, their contributions would not be present in the mtDNA line. It is also possible that while interbreeding between Neanderthal males and human females could have produced fertile offspring, interbreeding between Neanderthal females and modern human males might not have produced fertile offspring, which would mean that the Neanderthal mtDNA could not be passed down. Finally, it is possible that modern humans do carry at least one mtDNA lineage that Neanderthals contributed to our genome, but that we have not yet sequenced that lineage in either modern humans or in Neanderthals. Any of these explanations could underlie the lack of Neanderthal mtDNA in modern human populations.

Fast Facts:

Neanderthals have contributed between 1-4% of the DNA of humans of Eurasian descent

Neanderthals have not contributed to the genome of African modern human populations because they never lived there and could not have interbred with the ancestors of those populations

While we dont have evidence of Neanderthal mtDNA in the modern human gene pool, there are several possible explanations for this

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Ancient DNA and Neanderthals | The Smithsonian Institution ...