The human story begins in Africa, and it is written in our genes. Several hundred thousand years ago, the species Homo sapiens evolved, and its descendants would become all of us alive today. But scientists have recently uncovered evidence that the origins of Homo sapiens might be more varied and complex than we ever imagined, and the story of our evolution might be even more complicated than we previously thought.
Human beings as we know them began in Africa about 300,000 years before the present day. It’s thought that Homo sapiens evolved in a time of climactic upheaval. They weren’t the only human species that existed at the time, and like the others, they were hunter-gatherers who needed to adapt to a difficult environment.
One of the more noticeable differences that could be seen in the modern humans (another name for Homo sapiens) is that they were more lightly built. They also sported big brains, and accommodating these led to changes in their skull shape to look the way we do today: particularly having less prominent brows and jaws that jut less.
Nowadays, the other species of human that once comprised the other parts of the genus Homo are long extinct. But we can see from fossils that there were many other hominins: the name for species that are similar to us. We also know that we lived at the same time as one other human species at the very least: Homo neanderthalensis, better known as the Neanderthals.
As well as hominins, humans have lived alongside other primates. Today, you can see gorillas in Africa, and if you had a time machine, you’d be able to see our ancestors in the same environments as ape-like animals such as Dryopithecus. However, it doesn’t make sense to say humans “descended from the apes,” even if humans and apes share common ancestors.
Now in theory, if you were to trace our lineage back far enough, you’d find an ancestor of both us and the existing apes. However, scientists cannot say for sure which animal that was, and even the more recent relationships between human ancestors are not entirely clear. Scientists may never agree on exactly how we are related to our ancestors, or even which primates they are.
However, scientists do agree about the broader outlines of the progression of human evolution. One thing that seems clear is that the ancestors of humans emerged at some point more than five million but less than seven million years before the present. Creatures somewhat like apes began at that time to walk upright rather than on all fours.
Those ancestors probably evolved from Australopithecus afarensis. This animal is renowned as providing the fossil named “Lucy.” This 3.2-million-year-old specimen was discovered in Ethiopia. It’s older than any Homo designate, which first shows up nearby in the form of a 2.8-million-year-old jawbone. Fossils only become anywhere near common at the two-million-year mark, when several species of Homo ancestors coexisted.
These early humans were able to make tools at about 2.5 million years before the present, and this advance may have helped them survive a drying environment. By two million years ago, the change in climate might well have been responsible for some of these hominins spreading out of Africa.
Homo erectus led the way out of Africa. Its fossils have been found in East Africa, and those are two million years old. A couple of hundred thousand years later, it could be found in what is now the far eastern European country of Georgia. It then radiated into Asia, with the species thriving in Java, for instance, for more than a million years.
The spreading Homo erectus had a string of descendant species, one of which, Homo heidelbergensis, followed it out of Africa. It mostly went west though, and it gave rise eventually to the Neanderthals. At the same time, those Homo heidelbergensis who remained behind eventually led to modern humans, and those in Asia to the Denisovans, another similar species.
So about 130,000 years before now, the world had several species of hominins wandering around it. However, that would change, as Homo sapiens also left Africa. It would eventually push out the other hominins everywhere it went, although this process took time, and, as we’ll see, involved some intermixing of the species.
The first wave of settlers may not have stuck though, having gotten to the Middle East by 100,000 years before now and China 20,000 years later. Scientists have discovered from our genes that we all descend from humans that left Africa in a second wave about 60,000 years ago. These migrants moved quickly to colonize most of the world, although they wouldn’t reach the Americas until perhaps 16,000 years before the present.
When these humans reached Europe, they would have encountered the Neanderthals. Although the latter went extinct by about 40,000 years ago – although remnants in Spain might have lasted a little longer – contact between the species wasn’t entirely hostile. Geneticists confirm that in fact there must have been some romance – because Neanderthal DNA combined with ours.
When in 2010 scientists sequenced the genome of a Neanderthal fossil from Croatia, it became clear that the species had mated. Researchers believe that the first contact was probably 60,000 years before the present in the Middle East. Now all humans, except for Africans, have up to a couple of percent of Neanderthal DNA.
In Asia, humans also mated with Denisovans, a little-known group of hominins. We can only say anything about the Denisovans because of the very few remains of them that have been discovered and the DNA that lay in them. That DNA is reflected by up to 4 percent of the genes in modern indigenous Australians and the related Melanesian peoples.
The spread of their genes suggests that Denisovans might have been more widespread than their few remains would indicate. Fossils that are only about ten millennia old may also be Denisovans. These hominins got around too – they interbred with Neanderthals and another old species that scientists cannot identify accurately but may be the hobbit-like Homo floresiensis.
Interestingly, some Neanderthal DNA does turn up in Africans. This provides the evidence for the two waves theory of human migration. Some of the original migrants of 200,000 years ago likely interbred with Neanderthals before returning to Africa. Before the discovery of Neanderthal ancestors by Princeton scientists in 2020, Africans had been thought not to have any.
All this mixture of species excites some scientists. Richard “Bert” Roberts, a researcher from Australia’s University of Wollongong, told Cosmos magazine in 2018, “I’d have loved to have been on the planet 60,000 years ago. We used to have a fabulous time, with all sorts of other humans running around the planet.”
But the diversity of the past has of course given way to a world in which we’re the only hominins. Roberts remarked, “What a boring state we’re now in with only one human species left on the planet.” For hundreds of thousands of years, we intermingled with Neanderthals and Denisovans; however, Roberts views today’s less diverse state of affairs somewhat dismissively, saying, “What a yawn!”
And in fact those three species of human were not the only ones involved in the intermixing, as research has recently uncovered. We are finding ever more evidence that “ghost populations” of extinct hominins contributed to the human story long before we left Africa. One candidate species for having mated with later modern humans is Homo erectus.
Finding the ghost populations is not an easy task. It requires studying the human genome using complicated models of the intermixing of populations and inheritance. The outcomes are far from certain, particularly when we hope to point the finger at who the ghosts actually were, or even when the mixture of them and modern humans might have happened.
However, the new evidence does make it clear that it wasn’t rare for the varied ancestors of humans to get together and get it on. Murray Cox, a computational biologist at Massey University of New Zealand, Turitea, told Science magazine in February 2020, “It’s now clear that interbreeding between different groups of humans goes all the way back.”
The way that interbreeding is identified with the highest degree of certainty is to sequence DNA that has been extracted from fossils. Then it can be compared with modern genomes to see whether any trace remains. This method revealed the intermingling with Neanderthals and Denisovans, but fossils older than them have not offered up their DNA.
Because of this, scientists working in genetics have developed mathematical tools to examine DNA from today’s humans. By using statistical methods, the researchers hope to identify past mixings of genes. And after a decade of maybes, they have honed in on two stretches of interbreeding from the extremely distant past.
A team working under population geneticist Alan Rogers, who operates out of the University of Utah, Salt Lake City, have found variations at the same place in different genomes. These genomes are from not just Europeans and Asians of today, but also from Neanderthals and Denisovans. They looked at hypothetical outcomes from eight different mathematically modeled cases of mixing to figure out which one best matched what they could see.
Rogers’ team discovered the best fit for the genomes that they were looking at suggested something astonishing. They found that the common precursors of the Neanderthals and Denisovans had mixed with another ancient population two million years before the present. The ghost population whose DNA was there to be seen in the “Neandersovan” genomes may have been Homo erectus and in this case the interbreeding probably happened outside Africa.
Rogers believes that he knows who the culprits are for the interbreeding that he found. He said, “I think the super-archaics were in the first wave of hominids who left Africa. They stayed in Eurasia, largely isolated from Africans, until 700,000 years ago when Neandersovans left Africa and interbred with them.”
This must have been a long time before the modern humans themselves left Africa. Rogers called it “the earliest known interbreeding between ancient human populations and an expansion out of Africa.” So it may be that mixing happened both in Africa and outside of it, although not everyone agrees with that.
Researchers from the University of California Los Angeles (U.C.L.A.) also did similar work on DNA taken from West Africans, comparing it with the genomes of Neanderthals and Denisovans. The idea was that if they shared variations, this should indicate mixing that happened before the ancestors of modern humans ever left Africa. The results were stunning: many populations were involved.
Furthermore, as much as nearly one-fifth of the DNA of modern West Africans might come from the ghost populations. The researchers urged caution though, saying, “While several studies have revealed contributions from deep lineages to the ancestry of present-day Africans, the nature of these contributions remains poorly understood.” This is partly because DNA is hard to come by from Africa’s scarce fossils.
The U.C.L.A. scientists suggested that mixing of species in Africa might be a better explanation for the variations that we see today. This is largely because they discovered outcomes not seen in Neanderthals or Denisovans when they looked at the West African genomes. This implies that ancient populations provided the genes after humans had left Africa for the second time.
Who these candidates might have been is still in question. It could even be a single Homo erectus, Homo heidelbergensis or other related species that survived long enough to mate with the dominant Homo sapiens within the most recent 124,000 years, or it may have been a small group. And although long gone, that one or a few hominins lives on in Africans’ DNA.
For the U.C.L.A. researchers, the matter is complicated because Neanderthal DNA has been discovered in modern African genomes.Lead scientist on the U.C.L.A. team Sriram Sankararaman said a small portion of what he had found might be explained by the back-migration of Neanderthals, but it was most likely to have originated from the archaic ghost hominins.
The U.C.L.A. team is not the only one to have uncovered a ghost population in Africa. University of California San Francisco (U.C.S.F.) scientists found strong echoes in the Khoisan of southern Africa and pygmies of central Africa. However, they could not pinpoint what the ghost population or populations were or when the mixing had happened.
Geneticist Jeff Wall from the U.C.S.F. team had a warning though. It might be that the ghost population was just more modern humans that had lived in separation from the other Homo sapiens for so long that they looked like a different, archaic species. Commenting on this, Princeton University’s Joshua Akey told Science, “Our understanding of African population history, in particular, is so far behind.”
However, whatever the truth of who the ghost population of hominins are, one thing that the scientists agree on is that even hugely separate groups can intermix. Population geneticist Pontus Skoglund, who works at the Francis Crick Institute in London, told Science that this was confirmed by looking at other species that also mix widely separated groups. He said, “We are losing the idea that separation between populations is simple with instant isolation.”
And the intermixture of groups that have been separated from each other for a long time can be very positive. It’s a good way to bring novel genes into a population, which can have benefits when useful traits have evolved. Sankaraman found archaic variations in genes that control hormones and fight tumors, for instance.
Lacking the possibility of a big influx of diversity is not a good thing for modern humans. Now that we’re the only humans, we cannot get a positive influx from other, closely related species. Uppsala University’s Carina Schlebusch told Science, “To have such a large densely-spread species with… so little genetic diversity… is a dangerous situation.”
Still, we may yet find more ghost populations. Bioarchaeologist Joel D. Irish from Liverpool John Moores University said to news network CNN in February 2020, “I think at one time, there’d have been all sorts of populations, with genetics different enough to look a bit different. Everybody tends to mate with everybody. I think we’re going to find more and more of these ‘ghost’ populations coming up.”