2 - 4% of many peoples' DNA comes from the Neanderthals. This is the result of interbreeding between our species before the last ice age; which gave us many genes important for our survival. Despite this importance, these relationships between our ancestors and the Neanderthals appear to have been rare. But what happens when you look at people who aren't our ancestors? After all, not every group of modern humans that lived with the Neanderthals survived until the present day.
Ancient DNA recovered from some of these fossils reveals they were interbreeding with the Neanderthals a lot more often than the lineages which ultimately gave rise to modern populations. In fact, these extinct branches of humanity have more than double the Neanderthal DNA, when compared to the "survivors". Could this closer relationship with the Neanderthals even explain why these groups died out? After all, we know many Neanderthal genes also harmed our ancestors.
Perhaps being prudish and not mating outside our species as often actually gave our ancestors an advantage.
Interbreeding in Romania
The evidence for extra Neanderthal interbreeding comes from a fossil of a modern human from Romania. The individual - labelled "Oase 1" after where they were found - lived in the country more than 37,000 years ago. That would place them shortly after the arrival of modern humans not just in Romania, but in the whole of Europe.
Oase 1 is only a bit of jaw, but it's clearly a modern human bit of jaw. Another, more complete, skull called Oase 2 supports this; also showing modern human characteristics. However, both Oase 1 & 2 also contained a few unusual features. For example, the forehead of Oase 2 is clearly modern; possessing a forehead and lacking a brow ridge, which Neanderthals lack and possess respectively. At the same time, other parts of that forehead falls slap bang in the middle of the Neanderthal average.
There was some debate over why these fossils might have these strange features. Some speculated that it might be a case of regional adaptation. These early migrants were beginning to evolve to suit their new European homes. Others thought that it might be evidence of Neanderthal interbreeding. It looked like this debate could never be resolved... until someone managed to recover DNA from Oase 1.
This genetic material confirmed that Oase 1's family had interbred with Neanderthals very recently. Upwards of 7% of their DNA came from the Neanderthals, more than double what was found in modern humans. When analysed more thoroughly, it indicated that within 4 - 6 previous generations they had a Neanderthal family member. Imagine if your great, great grandparent was a different species! It would certainly make family reunions more interesting.
However, something more interesting about Oase 1 is how much DNA they shared with later modern humans. Or rather, how little they shared. Researchers found that Oase 1 was equally related to all later humans; meaning it wasn't the ancestor of any of them (or it would be more similar to that one lineage).
Siberian interbreeding
The Oase individuals are interesting, but not that notable on their own. Things begin to pick up when you examine the DNA of other early Europeans living around this time. Enter the Ust'-Ishim individual; a modern human fossil femur from Siberia that lived 45,000 years ago. Again, Ust'-Ishim was one of the early modern human migrants into Eurasia and, again, they had more Neanderthal DNA than later modern humans. However, they differ from Oase 1 in several important characteristics.
The first is Ust'-Ishim is related to modern humans. Their lineage didn't disappear from history but went on to become widespread across Eurasia. They seem to have been a basal member of the mtDNA haplogroup R. This emerged in Siberia and went on to become widespread across Central Eurasia and Eastern Europe. Ust'-Ishim was also a male, belonging to the Y-chromosomal haplogroup K; which is now dominant in West Asia (although has been found all over the world).
The second key point is that they interbred with the Neanderthals much longer ago. Similar calculations to those performed on Oase 1 reveal they their Neanderthal ancestor was more than 200 generations ago. Based on human generation times, this would suggest the interbreeding between Ust'Ishim's ancestors and Neanderthals took place closer to 60,000 years ago. At this time, some modern humans were spreading into the Middle East, where they might have encountered Neanderthals. Perhaps this might be where they interbred.
Thus, we're left with two similar - yet crucially different - individuals. Oase 1 who interbred with the Neanderthals recently but ultimately died out, and a Siberian dude whose family interbred with the Neanderthals much longer ago but they survived. In other words, it looks like Neanderthal interbreeding was more common than expected (occurring at least as recently as ~37,000 years ago) but much of this evidence vanished as the individuals engaging in intraspecies sexy time died out.
Neanderthal downsides
So it looks like there was additional interbreeding between Neanderthals and Europeans, but that this happened in European lineages that went extinct; masking these relationships. Interbreeding with the Neanderthals was more common than we thought.
However, Europe is a ruddy big place and it's hard to make inferences about the history of humans on the continent from just 2 individuals. Fortunately, we do have a lot more DNA from living modern humans; which backs up this story. Estimates of when our Neanderthal ancestors entered our family tree place them at some time between 50,000 - 80,000 years ago. This would be consistent with the Siberian DNA, but much too late for the Romanian interbreeding. This would confirm that Oase 1 represents a bit of extra interbreeding, showing it was more common than we thought. Just how common requires more fossils DNA to say.
Could this extra interbreeding explain why Oase 1's lineage ultimately went extinct? We certainly know that Neanderthal genes can be very harmful. In particular, they really muck up our ability to reproduce. As a result of this, the Neanderthal genes associated with reproduction have been purged from our system. If Oase 1 retained them then it would definitely put them at a disadvantage compared to the descendants of the Siberian dude, who could reproduce a lot easier.
But much like the overall history of interbreeding, it's hard to conclude this based on a single sample. With more data we might find more examples of Neanderthal interbreeding, and perhaps get a better idea of how badly it harmed over those Europeans who engaged in additional Neanderthal liaisons. Perhaps they got screwed twice!
Summary
DNA from modern humans who died out reveal there was more interbreeding with Neanderthals than expected. These extinct lineages had extra liaisons with them
References
Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S.M., Bondarev, A.A., Johnson, P.L., Aximu-Petri, A., Prüfer, K., de Filippo, C. and Meyer, M., 2014. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature, 514(7523), pp.445-449.
Fu, Q., Hajdinjak, M., Moldovan, O.T., Constantin, S., Mallick, S., Skoglund, P., Patterson, N., Rohland, N., Lazaridis, I., Nickel, B. and Viola, B., 2015. An early modern human from Romania with a recent Neanderthal ancestor. Nature, 524(7564), pp.216-219.
Rougier, H., Milota, Ş., Rodrigo, R., Gherase, M., Sarcinǎ, L., Moldovan, O., Zilhão, J., Constantin, S., Franciscus, R.G., Zollikofer, C.P. and de León, M.P., 2007. Peştera cu Oase 2 and the cranial morphology of early modern Europeans. Proceedings of the National Academy of Sciences, 104(4), pp.1165-1170.
Sankararaman, S., Patterson, N., Li, H., Pääbo, S. and Reich, D., 2012. The date of interbreeding between Neandertals and modern humans. PLoS Genet, 8(10), p.e1002947.
