Four years ago, the story of modern human origins seemed fairly simple. Modern humans originated in Africa sometime around 200,000 years ago. Some modern people spread into other parts of the world sometime after 100,000 years ago, mixing a bit with archaic human groups they met along the way.

New discoveries have shown just how oversimplified this picture was. The common ancestors of today’s modern humans lived a lot earlier than we thought, and we can’t connect them to the fossil record. They were far from alone: Africa was full of other groups, now extinct, and some of them mixed Neanderthal-like into living populations.

The last month has seen more shake-ups to the modern human origins story than any time I can remember. Here’s what we have learned in the last few weeks about this key time period in Africa.

The deepest split

Modern humans share a lot with each other. We’re 99.9% genetically the same, and that impressive genetic similarity comes from inbreeding.

When geneticists first started measuring genetic differences between people, they realized that the population must have once been a lot smaller. They came up with the idea of a genetic “bottleneck”, a period in which the human population might have been very small.

But the last few years have added a lot of complications to this simple picture.

A result from PSMC studies of human genomes from different populations (indicated). The French underwent a clear bottleneck, starting between 100,000 and 50,000 years ago, which was actually shared by all other people outside Africa. But the African populations here had no strong bottleneck. The Khoe-San people in this chart have no sign of a bottleneck at all. From Mallick et al., 2016, doi:10.1038/nature18964

One problem is that the “bottleneck” concept applies mostly to people outside of Africa. They have inherited most of their genes from a small population that grew and dispersed throughout the world. That dispersal carried that signal of a “founder effect” along with it. Those people further mixed a small fraction with archaic humans, the Neanderthals and, for a few, the Denisovans. That founder effect unfolded within the last 100,000 years.

The story of the rest of the world during the last 100,000 years is not the story of Africa. Most humans continued to live in Africa and didn’t share the bottleneck. They preserve a pattern of diversity that goes much earlier back in time, meaning that today they are much more diverse in their genes.

In all the world, genetic diversity is greatest today among the Khoe-San peoples of southern Africa. Until this week, geneticists have thought that their ancestral lineage has existed for as long as 200,000 years. That origin, the deepest split between human populations that still exist, points to the stem population of all living people. It doesn’t divide Africans from non-Africans, it reflects a deep history of diversity among African populations — the founder effect leading to non-African peoples was much later.

That stem population, in genetic terms, is the origin of modern humans.

This week, Carina Schlebusch and colleagues posted a preprint that reports on the ancient genome of a boy who lived at Ballito Bay, South Africa, around 2000 years ago. His genome connects him to the Khoe-San peoples of today. But there’s an important difference. By comparing his genome with the genes of living people, Schlebusch and her coworkers found that today’s Khoe-San have received a lot of genetic mixture from other populations during the last 2000 years.

That’s not a surprise. Humans mix with each other, and that mixture has increased in recent times. Very ancient peoples mixed too, but migration and mixing were less in the distant past than in recent history.

What this means is that today’s Khoe-San people share many genes with people in other parts of Africa, and with people in Eurasia, from recent mixing. If we use today’s genetic diversity to try to work out the original ancestors of modern humans, we’re going to come up with an answer that is too recent, because of these recently shared genes.

Schlebusch and her team used the 2000-year-old genome to come up with a better estimate of when the stem population of modern humans lived. The answer was a lot older, around 260,000 years ago. Modern populations, the ancestors of living people, have been diversifying from each other within Africa for at least that long.

It’s a good reminder that within humans, a genetic “split” is not really a split. Populations of humans mix. That’s what we do. So when we look back into the past, we are looking at populations that reticulated with each other.

Who were these early modern humans?

Selenge River delta (Landsat)

Genetics tells us that the ancestry of African groups is like a river delta, spreading from some 260,000 years ago up to the present. But anthropologists really disagree about how to identify “modern humans” in the fossil record. A fossil that shares some human traits might be part of that delta network leading to some living populations. But just as easily, it might instead be off on its own branch, flowing until it disappears into the desert sands.

Archaic people in Africa — all the humans who were not part of that river delta — were not Neanderthals. So they didn’t share the features of Neanderthals, certainly not all of them. Many of them would have shared features with modern people. So how can we recognize them? And how many groups of them were there?

One big clue has been published just this week, by Jean-Jacques Hublin and his colleagues. They conducted new excavations at a site in Morocco called Jebel Irhoud. Old excavations carried out in the 1960s had produced parts of three skulls and some other human bones. Previous scholars had tried to work out the geological age of these remains, ultimately deciding they were around 150,000 years old.

Jebel Irhoud 1. Credit: John Hawks CC-BY

The new excavations, coupled with renewed geological dating, have yielded a new range of ages. These fossils and the archaeological layer they come from are somewhere between 220,000 and 380,000 years old. That overlaps with the time range of the first modern humans.

That seems like convenient timing. Do these fossils fit into the origin of modern humans somehow? Anthropologists are unanimous that the braincases of the Jebel Irhoud skulls don’t look much like modern humans. They are elongated, with an angled cranial rear. They aren’t Neanderthals, but it would be a big stretch to connect them to living people.

La Ferrassie 1 Neanderthal skull (top) compared to Jebel Irhoud 1 skull (bottom). The face of Jebel Irhoud is shorter than the Neanderthal, but it has a clear and continuous browridge, and its braincase is not very much like modern humans. Photo courtesy of Milford Wolpoff.

On the other hand, the faces and mandibles preserved in this collection are a bit more like those of modern humans. The faces of Jebel Irhoud 1, and the newly-discovered Jebel Irhoud 10, are a bit shorter, with cheeks are shaped more like modern humans than like Neanderthals. The brows of Jebel Irhoud 2 are reduced, like robust modern humans in their form, although Jebel Irhoud 1 has a stout and continuous browridge. The jaws from the site are robust and have big teeth, but they are taller in the front than in the back, and the midline of the jawbones are vertical.

Still, these human features are not the majority, and it’s not clear that they’re special. The jaws lack that most modern mandibular feature, the chin. Many of the humanlike aspects of the face can also be found in some much older fossil remains, such as the Homo antecessor fossils from Spain.

Hublin and his coworkers have drawn attention to the humanlike features, but they agree with other anthropologists that the Jebel Irhoud skulls are not modern humans themselves.

However, Hublin is proposing a big idea: These skulls, together with the whole population of Africa at the time they lived, was on the road to modern human origins. The paper describing this idea mentions another old fossil with a combination of archaic and modern features, a partial skull from Florisbad, South Africa, also clearly not modern human, but with a few humanlike features.

The partial skull from Florisbad might be in this time range, but the date depends on a tooth that may not be the same context or individual.

In Hublin and colleagues’ “pan-African” hypothesis, every African fossil that had parted ways with Neanderthals is part of a single lineage, a stem population for modern humans. They connect the evolution of these early H. sapiens people to a new form of technology, the Middle Stone Age, which was found in various regions of Africa by 300,000 years ago.

So how many other archaic groups were in Africa? Under the Hublin model, there may have been none. Every fossil sharing some modern human traits may have a place within the “pan-African” evolutionary pattern. These were not river channels flowing into the desert, every channel was part of the mainstream.

But there may be a problem. Geneticists think there were others.

Ghosts haunting our origins

So far, nobody has recovered ancient DNA from archaic human skeletal remains in Africa. The 2000-year-old Ballito Bay boy is not the oldest, but there are no DNA results from truly archaic specimens, like the Kabwe skull from Zambia. As a result, we don’t have the kind of record within Africa that geneticists have built for Neanderthals and Denisovans in Eurasia.

But a series of genetic studies on living Africans have succeeded in identifying signs of mixture from ancient people. This work, led by Michael Hammer, Jeff Wall, Joe Lachance, and others, is built upon a close examination of the genomes from living people. What they are finding is genetic ghosts.

The breakthrough of the Neanderthal and Denisovan genomes may not have led to the recovery of equally old African genomes, at least not yet, but having ancient DNA from those Eurasian fossils did give rise to some statistical clues about how to identify genetic mixture from ancient peoples. Using those clues, researchers are now able to identify “ghost populations”, ancient groups whose mixture with modern humans helps to explain some aspects of diversity in African genomes today.

These ghosts were the African equivalent of Neanderthals. They were ancient lineages with long histories, starting from long before any modern humans existed, and they were mixing with modern populations as recently as 20,000 years ago.

Skull from Iwo Eleru, Nigeria. Photo credit: Katerina Harvati and colleagues CC-BY

We don’t know what fossils might represent these ghosts. Some anthropologists have suggested possible candidates. One archaic-looking human skull, found from Iwo Eleru, Nigeria, even existed during this latest part of the Pleistocene when the last signs of mixture have been identified.

What we know is that such genetically divergent lineages, now gone, existed during the entire time modern humans were evolving, from well before their first appearance 200,000 years ago.

Our species was never alone. As the modern human delta was spreading toward the sea, it took in a few streams from the branches that were heading into the desert.

What this means for fossils like Jebel Irhoud is that we don’t know where they fit. There was a river delta, leading from a common ancestor population to the diverse groups of living people today. But the river leading to that delta was not one big channel; it was a braided series of streams.

The streams were not equal — some of them only contributed a small amount to modern humans, while one was dominant, contributing more than 90% of the ancestry of all living groups. That dominant stream, that special population of human ancestors, lived sometime before 260,000 years ago. Jebel Irhoud might have been on the mainstream, or it might have been part of one of the more minor contributing archaic groups, making up a percent or two of the genomes of living people. Or it might belong to a still more distant extinct branch, its facial features inherited from very ancient ancestors like H. antecessor and marking no special relationship with any modern humans.

The thing is, the fossils we have today are not enough. They cannot answer this question because they cover such a tiny fraction of the African continent.

The wild card

That brings us to the other major discovery of the last month: Homo naledi lived at the same time these events were unfolding.

“Neo” skull (left) compared to DH1 skull of Homo naledi (right). Photo credit: John Hawks CC-BY

Four years ago, I was part of a team working under Lee Berger in the Rising Star cave system in South Africa, where we recovered the first specimens of a new species, Homo naledi. Last month, our team published the first scientific assessment of the age of this new species, between 236,000 and 335,000 years old.

H. naledi existed at the same time that the modern human delta was emerging from the braided stream.

This species, which has a small brain and many primitive features, seems to have originated more than a million years ago. It was there when Neanderthals and Denisovans went first into Eurasia, and it was there at the dawn of our own species. It lived during the time that hominins were making Acheulean handaxes, and it lived as Middle Stone Age techniques began to proliferate in southern Africa. We cannot assume that H. naledi wasn’t the species that made these tools where it lived.

We don’t know what the interactions between H. naledi and other populations may have been. The fossil record isn’t good enough to say whether they existed in the same place as any other modern or archaic humans.

“Neo” skull of H. naledi (left), Omo 2 skull usually attributed to modern humans (right). Photo credit: John Hawks CC-BY

But we can’t rule out the idea that H. naledi may have even mixed with modern humans.

The problem is that we don’t know if these populations ever met. In part, this is because we only have a handful of fossils from tiny parts of the continent. In part, our lack of knowledge comes from a lack of good context. Many of the important fossils, like the Florisbad skull, and the Kabwe skull from Zambia, were recovered at a time when fossil contexts were not recorded with the level of precision as today. Methods of direct dating such fossils have improved, but each advance means that old dates may not be trustworthy. That is, after all, why we are talking about new dates for Jebel Irhoud right now.

The next frontier

This time is exhilarating for researchers like me, facing so many new and unexpected questions. The answer is to make more discoveries.

Morphology does not tell the story of modern human origins. The handful of fossils that exist in Africa in the later Middle Pleistocene share different features with modern humans. Even H. naledi shares some modern human features that are not present in the Jebel Irhoud skulls.

Did short faces and rounded braincases really make a difference to the survival and success of modern humans? Maybe they were chance legacies of the population that gave rise to our gene pool. We don’t know.

As many archaeologists have noted, the behaviors of living people around the world are hugely varied, and most of them are paralleled within the record of Neanderthals and other archaic people. One thing that H. naledi reminds us is that the development of technology is a broader issue than the origin of modern humans.

In Eurasia, Middle Paleolithic tool assemblages were made by Neanderthals, Denisovans, and modern humans when they arrived. In Africa, we have to assume that Middle Stone Age was also a product of multiple populations, at least archaic and early modern humans, and likely H. naledi.

Modern humans arose from a complex process. The answers to these questions are not simple. Our evolution may have encompassed many parts of Africa, but it certainly was not uniform, and right now it looks like the subequatorial part of the story was especially complex and interesting.

We have to discover more fossils. That’s the way that we will start to solve these new problems and shed light on old mysteries.

Like the article? You may want to check out our book, Almost Human: The Astonishing Tale of Homo naledi.