The Alan Rogers paper which includes ideas of “super-archaics”, is finally out, Neanderthal-Denisovan ancestors interbred with a distantly related hominin. It’s open access, so I encourage you to read it. In it, the authors looking at patterns of derived mutations that vary between populations and try and see which models fit the pattern. I’ve added some labels to the figure above for clarity. The raw results in figure 2 are easy enough to understand. But how do they go from that to the model?

I haven’t reread the legofit paper, so honestly, I don’t know the details. Rather, I’m more interested in the discussion:

Our results shed light on the early portion of the middle Pleistocene, about 600 ka ago, when large-brained hominins appear in the fossil record of Europe along with Acheulean stone tools. There is disagreement about how these early Europeans should be interpreted. Some see them as the common ancestors of modern humans and Neanderthals (28), others as an evolutionary dead end, later replaced by immigrants from Africa (29, 30), and others as early representatives of the Neanderthal lineage (6, 7). Our estimates are most consistent with the last of these views. They imply that by 600 ka ago, Neanderthals were already a distinct lineage, separate not only from the modern lineage but also from Denisovans.

These results resolve a discrepancy involving human fossils from Sima de los Huesos (SH). Those fossils had been dated to at least 350 ka ago and perhaps 400 to 500 ka ago (31). Genetic evidence showed that they were from a population ancestral to Neanderthals and therefore more recent than the separation of Neanderthals and Denisovans (9). However, genetic evidence also indicated that this split occurred about 381 ka ago [(2), table S12.2]. This was hard to reconcile with the estimated age of the SH fossils. To make matters worse, improved dating methods later showed that the SH fossils are even older, about 600 ka, and much older than the molecular date of the Neanderthal-Denisovan split (32). Our estimates resolve this conflict because they push the date of the split back well beyond the age of the SH fossils.

Basically, the genetic results have been conflicting with the archaeology in a really strange way for a long time. The geneticists keep saying that the divergence between Neanderthals and Denisovans is relatively recent, and the Neanderthal fossils predate the estimated split. This is a case where I trust the paleoanthropology people, so methods that resolve this problem are welcome.

More broadly, I assume some form of this model is correct, even if not in the details. With what we know today, it seems unlikely that pre-Neanderthal/Denisovan humans did not mix with the newcomers. These results indicate that in fact these earlier archaic groups mixed with the expanding proto-Neanderthal/Denisovan population, the Neandersovans.

Update: A friend who I trust looked closely at the legofit paper. He says “I don’t believe a word of this shit.”