Reconstructed skull gives surprising clues to our enigmatic Ancestor X

The origins of our species may lie much further back in time than we thought, and the same may be true of our extinct Neanderthal and Denisovan cousins. According to a new analysis of fossil remains, the shared ancestor of the three groups lived over a million years ago – more than twice as old as previously believed.

“It does mean that we are missing a huge bit of the early story of these lineages, if we’re correct about these ancient branching points,” says Chris Stringer at the Natural History Museum in London.

The results could potentially help settle the search for Ancestor X: the population that gave rise to modern humans, Neanderthals and Denisovans. They could also mean that the Denisovans were our closest relatives – even closer than the Neanderthals, though not everyone is convinced on this last point.

Stringer and his colleagues, including Xijun Ni at the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing, China, re-examined a fossil hominin from Yunxian in central China.

Two partial skulls were uncovered in a terrace above the Han River in 1989 and 1990, and described in 1992. Both skulls had been squashed during their time in the ground. However, the second, Yunxian 2, was less badly damaged.

Stringer, Ni and their colleagues used the latest methods to reconstruct Yunxian 2, including a technique that can use CT scans to digitally separate individual fragments of bone from the surrounding “matrix” of rock and sediment. “It’s long and low, with a big brow ridge,” says Stringer. It also has “a bit of a beaky nose”, and while the teeth are large, the third molars are small.

The Yunxian 2 cranium is 940,000 to 1.1 million years old. Hominins of that age are often thought to belong to Homo erectus, which emerged in Africa around 2 million years ago before spreading to southern Asia, including Indonesia, where it survived until perhaps 108,000 years ago. However, Stringer says it doesn’t fit the profile. Many of its features are typical of later groups, like the Neanderthals.

To figure out what Yunxian 2 is, the team compared it to 56 other hominin fossils. Based on the shapes of the remains, they drew a family tree, with similar fossils being closely related. On this basis, they identified three major groups, which include most of the fossils from the past million years.

The first was modern humans (Homo sapiens). The second was Neanderthals (Homo neanderthalensis), who lived in Europe and Asia during the past few hundred thousand years, vanishing around 40,000 years ago. The third was Denisovans, from eastern Asia.

Denisovans were originally discovered in 2010 using DNA from a bone fragment, and it has taken 15 years to identify larger fossils. Stringer was involved in the description of a skull from Harbin in China, dubbed Homo longi, which was identified as a Denisovan using molecular evidence in June. Yunxian 2 appears to be an early Denisovan, as do several other Asian fossils.

It is helpful to tie all these fossils into the Denisovan lineage, says geneticist Aylwyn Scally at the University of Cambridge. “We can get a better idea about where the Denisovans were, how they lived, and what kind of species they were.”

The finding that Yunxian 2 is Denisovan rewrites the story of recent human evolution in two ways. First, it appears to change how the three populations emerged. The conventional story, as revealed by genetics, is that an ancestral population – Ancestor X – split into two: one half became modern humans, and the other half became Neanderthals and Denisovans, who split from each other a bit later. However, in this reconstruction, it was the Neanderthals who broke away first, 1.38 million years ago, with modern humans and the Denisovans separating 1.32 million years ago.

If that is correct, Denisovans were our closest relatives, instead of being equally close to us as Neanderthals were, as the genetics indicates. However, Scally is dubious. That is partly because the history of these populations seems to be complex. “It isn’t actually well described by a simple tree,” which is the model the researchers used, but rather by a “tangled network”, he says. Furthermore, Scally says genetics is a better guide to such relationships than morphology – especially when you have only partial skeletons – and the genetics tells a clear story.

The second change is bigger: all three groups are much older than we thought. Genetics has suggested that the ancestors of modern humans split from the progenitors of Neanderthals and Denisovans around 500,000-700,000 years ago. But Yunxian 2 indicates that the Denisovan group was already separate over a million years ago.

It may be that there isn’t a single date for any of these splits, says Scally. They could have been protracted, with groups sometimes separating and sometimes coming together. In that case, Stringer and his colleagues could be correct that the divergence began over a million years ago, but it took hundreds of thousands of years to play out.

This longer timeline opens new questions. The oldest known fossils of our species are about 300,000 years old. So, where are all the older ancestors dating back a million years ago? “Either we don’t have them, or they’re there and they haven’t been recognised,” says Stringer.

We also don’t know what Ancestor X was like, or where it lived. “Ten years ago, I would have said probably Africa is the ancestry of most of these groups,” says Stringer. “It looks more likely that the ancestor was outside of Africa, perhaps in Western Asia,” he says. “That would imply that the ancient sapiens ancestor must have gone into Africa and then evolved in Africa for most of the rest of that 1 million years.”

Stringer points out that there are few known fossils from western Asia dating to a million years ago, and India has yielded only one hominin fossil. “There’s many, many places where we really don’t have the evidence,” he says.

One source of data may be the Yunxian site. In 2022, a third skull was found there, apparently in better condition, but it hasn’t yet been described.

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