Some time between 300 – 600,000 years ago humans diverged from the Neanderthals. However, this wasn’t the end of our genetic interaction. Some of us have a few percent Neanderthal DNA, suggesting out two species interbred at some point after the divergence. But is this necessarily the case? This weeks question comes from Art, who asks

suppose (a) this DNA is a holdover from the common ancestor of humans and Neandertals; and (b) it had nearly disappeared from the human lineage when a splinter group of humans left Africa, but that splinter group happened to retain it. It seems this would explain the commonality of DNA, even if no interbreeding took place. Adam, do you think humans and Neandertals interbred? What is your reasoning?

Although human and Neandertal interbreeding is talked about so frequently this is actually a viable alternative. What Art is talking about is the idea that our Neanderthal DNA is a result of ancient population structure, sometimes referred to as “incomplete lineage sorting” (ILS). It is a real biological phenomenon that could explain how we got Neanderthal DNA without any interbreeding occurring; and was actually considered by many scientists for a while. By chance some human populations might share more alleles with Neanderthals than others. This increased similarity is then confused for evidence of interbreeding by sex-obsessed scientists.

ILS is a surprisingly common occurrence and happened when the human branch split from gorillas and orang-utans. In other words a small amount of your DNA appears more similar to gorilla DNA than chimp, despite the fact we’re more closely related to chimps. The amount of DNA “confused” by ILS is small, typically between 1 – 3%. But then we only have about 4% Neanderthal DNA.

One way to test whether ILS has occurred is with linkage disequilibrium. This is when two or more alleles are more likely to be inherited together than would be expected due to random chance. However, sexual reproduction jumbles up the genome, “breaking” linked genes. This means that over time the number of linked genes decreases.

This is useful because under the ILS model we got Neanderthal DNA before our species split 300 – 600,000 years ago. Under the interbreeding model we got it much more recently, within the last 100,000 years. So we can then look at the number of linked alleles shared by us and Neanderthals (which means that they were inherited from a common ancestor). The ILS model predicts we should see fewer linked alleles in this shared DNA, since more time has passed.

Last year a team of scientists investigated whether the amount of linkage disequilibrium was consistent with the ILS model and they found it was not. Instead it indicated that we gained the Neanderthal DNA at some point within the last 100,000 years. This almost certainly suggests that we interbred with Neanderthals after all.

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