Ghost populations are fragments of human DNA which belong to unknown humanoid ancestors. DNA and genome studies into 300,000 years of humanity has shown a rich and complicated picture of archaic and modern elements spread over a wide range of areas and times. Some of these are known to us, but those that remain a mystery are referred to as ghost populations.

Over half of the known human ancestor species so far discovered have been found in the last 10 to 20 years. However, the development of DNA sequencing has shown us something new – that some of us, and at different levels, are related to hitherto unknown species of humanoids. 

This is extremely exciting for those of us trying to unpick the human evolution puzzle. It also helps to prove that our evolutionary tree is not a simple set of splits, but rather a series of populations splitting then interbreeding again later on.

How did DNA revolutionize the study of human evolution?

Prior to the discovery, mapping, and analysis of DNA, archaeologists relied upon bones to differentiate different humanoid populations. To a certain extent this was supplemented by material culture finds ranging from clothing to stone tools. Much of the analysis was rudimentary and led to a proliferation of human ancestors.

The problem with treating each individual find as a new species is that it forgets humans vary greatly in size and shape. We are uncertain if an ancestor is just a different race within the same species or is of the same species but a particularly big or small individual, or if they are part of a new evolution or a separate species. 

DNA revolutionized the study of human evolution by allowing scientists to analyze the exact genetic makeup of bones and teeth. This has had many functions from tracking population movements to working out where an individual was born. Eventually we learned if an individual was a modern human, an ancestor, or from a different species based on their DNA. 

What are the known DNA mixes?

However, we also began to understand our own DNA more and this led to finding interspecies hybrids. This is where we can prove our ancestors came from more than one proto-human species.

The amount of DNA from our ancestors varies from individual to individual, but also region to region. It proves a very varied human history of interbreeding. As someone who is not a scientist, I wonder if the DNA two species share, is the remnant of a common ancestor rather than a sign of interbreeding. Would it show up differently if it was inherited rather than from breeding?

Known human-other species mixes include:

  • Human-Neanderthals: Found worldwide with the exception of African populations with highest mixes in Europe. Top mix at around 4-6% in Tuscany though it mostly averages as 2%. Recent studies into tooth DNA suggests we split as a species 800,000 years ago.
  • Human-Denisovans: Mostly found in Polynesia and SE Asia incl. Some Aboriginals. The largest percentage of Denisovan DNA found in modern humans so far is 2%.
  • Homo Erectus: Evidence found in DNA.
  • Homo Habilis: Evidence found in DNA

As far as we can tell, there is no evidence that the Neanderthals or the Denisovans ever lived in Africa. From what’s known we see Neanderthals across Eurasia and possibly into the Americas with the Denisovans east of the Urals in Asia alone; especially southeast Asia.

Examples of human-ghost populations in modern humans

Of course human-ghost populations are difficult to spot because they leave behind no physical traces. We do not have bones and if they left behind a material culture, then it is indistinguishable from other humans and hominids. Let’s look at some examples.

An Asia-Oceania ghost population

In early 2019, a computational study of eight evolutionary models determined there to be an ancient ghost population of archaic humans who interbred with modern humans. This is the latest in a small, but growing list of ghost populations.

The traces are small and fragmentary, so little is known so far. This DNA evidence seems to match paleoanthropological theories which have Neanderthals and Denisovans interbreeding in southeast Asia and then mixing with modern humans. Bear in mind this is a model based on models, and so is not relying on hardcore data just yet. While it included DNA databases, I’d wait to see if there’s more evidence of this ghost population (though it seems likely), and the proposed date of 180,000 years ago.

Are there ghost populations in Africa?

So far only 30 genomes have been found from African DNA dating between 300 and 15,000 years old with none found older than that. Current research suggests that between 2 and 7% of modern African DNA comes from a ghost population thought to have originated in central Africa.

Studies of the Khoe-san (Khoisan?) people – who are thought to be the oldest human population, including a 2,000 year old boy’s bones, suggest the population developed around 260,000 years ago. Meanwhile the Jebel Irhoud skulls found in Morocco suggest human development dating to 250,000-380,000 years ago. The Moroccan skulls were not modern humans, but Jean-Jacques Hublin suggests they were instead part of a single, African stem population along with the ancestors of the Khoe-san.

Genetic studies are suggesting that there was a Neanderthal-type population of archaic humans living in Africa as recently as 20,000 years ago. They were not Neanderthals, but were an old species which co-existed and interbred. Interestingly, new studies suggest that Homo Naledi dates from around the same time – 200,000 to 350,000 years ago.  

Will ghost populations change the ‘Out of Africa’ model?

Human evolution is controversial. As with any study of human differences whether the intent was benign or not, much can be read into and many can play the results off to suit their agenda. The same is true for studying human evolution; especially if there are differences between African and non-African evolution.

So we come to the study of the MUC7 saliva protein. This protein shows signs of archaic admixture across the world. However there are significant differences between African and non-African admixtures.

It appears that Neanderthals and Denisovans contributed to the protein’s admixtures for Eurasians and therefore also for native American populations. The protein for African populations is different – this shows a ghost population of archaic DNA. 

The potential cause for this is the original split in the homo erectus population somewhere between 1.5 million and 2 million years ago. The non-African branch led to the Neanderthals and the Denisovans while the African branch evolved into Homo Ergaster. 

However, there is a problem. The calculated date for when the non-human DNA admixture for MUC7 in Africans is 150,000 years ago. This is about 100,000 years prior to the accepted out of Africa model. It seems unlikely that the population which would eventually become non-African did not interbreed with this ghost population for 100,000 years leaving zero evidence of it in modern non-Africans.

As you might expect, this ghost DNA has led many to switch to an ‘Into Africa’ theory where humans evolved in Asia and modern Africans moved into Africa 150,000 years ago where they mixed with the ghost population.

Middle Eastern ghost population – Basal Eurasians

A more recent ghost population has been found in the Middle East. Dubbed the Basal Eurasians, this population dates from around 45,000 years ago. This makes them contemporaries of the Denisovans, but far removed from them and genetically different.

Curiously for non-African humans, the Basal Eurasians show now signs of interbreeding with Neanderthals. What seems to have happened is that a small population of humans moved out of Africa around 60,000 years ago and formed their own, isolated community in the Middle East. This allowed, over time, for their DNA to become distinct enough to create its own ghost population.

From Papua New Guinea to the Americas

DNA analysis of two tribes in the Amazon – the Surui and the Karitiana, suggests a second wave of migration to the Americas. However, this one might not have gone via Beringia as the Eurasians did around 15,000 years ago. 

The study found that the closest population genetically to the Surui and the Karitiana were from Papua New Guinea and Australian aboriginals. This astounded many but builds on some evidence of common myths and legends between the two populations.

This has led to thoughts of a ghost population in the region which was once more dominant than it is now. There is much to say for this theory as polynesian migration into Oceania is much more recent than other migrations. Plus the later Beringia migration may have overwritten the earlier trans-Pacific migration.

What is the ghost population found within Denisovan DNA?

While the only Denisovan finds were dug up in a cave in Siberia, humans with Denisovan DNA in them are predominantly from the Polynesia area; specifically Papua New Guinea and some nearby Australasian populations. 

However, within the DNA of the Denisovans ghost DNA has been found alongside evidence of some Neanderthal-Denisovan interbreeding. The latter dates from over 50,000 years ago, while the former may be much older.

So far this remains a total ghost population. The current theory is that multiple populations left Africa a million years ago. This included the ghost population. It is possible therefore that the DNA belongs to an unfound ancestor of Homo Floresiensis or it’s Filipino cousins, or to an unknown Asian branch of the Homo Erectus family.

If you’d like some more Denisovan excitement – DNA studies are continuing and they suggest two Denisovan populations. This means that the Denisovans who are almost a ghost population themselves also had their own ghost population. Time will tell where this goes.

How have ghost populations been found?

Ghost populations within human genomes have been found thanks to more advanced testing techniques combined new finds. However, the biggest contributor to these startling developments has been the increased computational power of modern computers and programmes.

These developments are only going to increase though there is no doubt a limit to what even the most powerful computers of the future can do. DNA corrupts and only lasts for so long after all. What these programmes are able to do, however, is peer deep into the past.

They are also able to calculate not just genome and DNA patterns then compare them to other species, but are able to determine likely speciation points. That is to say where one species begins to divide into two. It is through complex calculations that scientists estimated the divergence of humans and Neanderthals to have begun as long ago as 800,000 years.

The complicated calculations take into account patterns, familiar genomes, mutations, and so on. This allows them to shake out small pockets of differentiation, which could be a local mutation or signs of an unknown archaic human.

How can we account for ghost populations?

The appearance of known and unknown DNA suggests humans have a complicated past. Some studies are positing the idea that humans evolved in a haphazard manner across multiple regions of central Africa. This would have included all kinds of population movements and cross-breeding.

An alternative theory would have it that this haphazard crossbreeding took place for hundreds of thousands of years across the whole world. This is certainly possible because the great ape ancestors of humans evolved in southeast Asia and not in Africa. Plus we know about humans interbreeding with both Neanderthals and Denisovans even though with the former the DNA differences were getting to a point where it would be impossible.

We should also bear in mind that climate changes paid a big role in human evolution. The last 10,000 years have been unusually benign with warm periods (including many warmer than now) and some mini ice ages. However the story prior to 9,000 BC was much more variable.

In the deep past there were great ice ages and warmer periods. We have big volcanoes that could have killed huge portions of humans or their ancestors, plus rising and falling sea levels. Bear in mind the sea level is 400 meters above what it was during the last ice age. 

And all that is not to mention the deadly plagues often linked to colder periods (think Justinian plague and the Black Death as two examples). These changes would have pushed humans around the world, bumping them into distant relatives, rekindling connections, and adding to the human evolution story.

Why can’t we find these ghost populations?

When exploring the past it is vital to understand the science of material survival. Within a span of 10,000 years all of humanity you see today would disappear with the possible exceptions of the great pyramids and Mount Rushmore. Even all the plastic would go.

Furthermore, DNA degrades at a fast rate when it does survive. The oldest African genomes, for example, are only 15,000 years old. This makes it difficult to find truly old genetic material which we can test against other species. This leads to most of the results being built on less than reliable computer models.

Therefore, the vast majority of ancient human remains have long since disappeared. There may be hope in long abandoned caves, remote deserts where bone may have turned to stone, or in the Siberian permafrosts. The simple fact is that most of it has gone and so we have a very tatty picture of human evolution.

Now tell me what you think, will we find these ghost populations? Is it just a matter of time or will it always be a mystery to us?


Texts Consulted:

Alex, Bridget, 2019, With ancient human DNA, Africa’s deep history is coming to light, Discover Magazine online

Barras, Colin, 2017, Ancient Humans: What we know and still don’t know about them, The New Scientist online.

Bower, Bruce, 2019, Fossil teeth push human-neanderthal split back to about 1 million years ago,

Brahic, Catherine, 2018, Traces of mystery ancient humans found lurking in our genomes, The New Scientist, online

Callaway, Ewen, 2015, Ghost population’ hints at long-lost migration to the Americas,

Callaway, Ewen, 2016, Evidence mounts for interbreeding bonanza in ancient human species,

Capelewicz, Jordana, 2019, Fossil DNA Reveals New Twists in Modern Human Origins, Quanta Magazine

Fenton, Bruche, 2017, Gene Study Suggests Migration of Homo sapiens Into Africa & Interbreeding with Local Hominins 150,000 Years Ago, Ancient News

Hsu, Charlotte, 2017, The evolutionary history of a salivary protein may point to interbreeding between humans and an enigmatic ancient relative,

Scerri, Eleanor et al., 2018, Humans did not stem from a single ancestral population in one region of Africa, Max Planck Institute via