JEBEL IRHOUD, Morocco, 1961. In a barium mine in the foothills of the Atlas mountains, a miner makes a ghoulish discovery: a near-complete human skull embedded in the sediment. Archaeologists called in to investigate find that the skull is old, but not that old. It is filed away and largely forgotten.
Hinxton, UK, 2019. Robert Foley, a palaeoanthropologist at the University of Cambridge, is giving the opening address at a three-day conference on human evolution. âWhat Iâm pretty sure of is that, by the end of the first day, something like 20 per cent of what I say will be wrong,â he says to the hall. âBy the end of the second day, something like 50 per cent will be wrong, and at the end of the conference, Iâm hoping that something I said at the beginning still holds true.â
Until recently, the story of our origins was thought to be settled: Homo sapiens evolved in eastern Africa about 150,000 years ago, became capable of modern behaviour some 60,000 years ago and then swept out of Africa to colonise the world, completely replacing any archaic humans they encountered. But new fossils, tools and analyses of ancient and modern genomes are tearing apart that neat tale. The Jebel Irhoud skull has turned out to be a key to a new, slowly emerging paradigm. With the dust yet fully to settle, the question now is how many, if any, of our old assumptions still hold. âShould we be thinking of a completely different model?â asks Foley. âAbandoning out-of-Africa?â Strap in, itâs going to be quite a ride.
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The out-of-Africa paradigm to which Foley refers has become so entrenched that it is easy to forget how new it is. For decades before its emergence, human origins research was dominated by the early characters in the story: Homo erectus, for example, including âPeking Manâ, unearthed in 1929; or Australopithecus afarensis, the famous âLucyâ discovered in Ethiopia in 1974. There was some debate about where modern humans appeared, and ideas were floating around of a recent African origin, but the fossil record seemed to support a model called multiregionalism. This argued that archaic humans were distributed across Africa and Eurasia at least a million years ago and evolved in parallel into modern humans.
Then, in 1987, a bombshell. A team of geneticists at the University of California, Berkeley, sequenced 147 mitochondrial genomes from living people around the world. The mitochondria in cells are inherited from mothers only, and the study indicated that everyone was â dubbed âmitochondrial Eveâ â who probably lived in Africa about 200,000 years ago (see âHow does DNA analysis reveal our prehistory?â).
The result was very influential, says Foley. It was quickly consolidated into what he calls the , the idea that modern humans appeared quite abruptly in eastern or southern Africa some time between 150,000 and 200,000 years ago and went on to conquer the world. The package also introduced the distinction between anatomical and behavioural modernity. Based on archaeological evidence, it looked as though early Homo sapiens had bodies like us but werenât as advanced mentally. Only later, about 50,000 or 60,000 years ago, did the full package evolve â perhaps due to a chance mutation â making dispersal out of Africa possible. This neat, compelling narrative became known as .
For a while, the fossil evidence obligingly supported this story. Although remains from the crucial time of about 150,000 years ago were absent, there were several older human skulls that seemed to fit the idea.
One of the most distinct features of modern humans is the shape of our heads. Compared with our extinct ancestors, we have small, flat, delicate faces, prominent chins and spherical brain cases. A skull with all or most of these features will generally be classified as belonging to our species. Two of the oldest-known complete skulls with hints of this anatomy were discovered by Richard Leakey and his team at Omo-Kibish in southern Ethiopia in 1967. Known as Omo I and Omo II, they are now dated to about 200,000 years old and have a mixture of archaic and modern features â exactly what you would expect of an archaic African human shortly before the evolution of anatomical modernity. Several other specimens from around eastern and southern Africa told a similar story.
âNew fossils, tools and analyses of genomes have thrown everything into disarrayâ
It got even better when, in 1997, palaeontologists in Ethiopiaâs Afar depression unearthed three human skulls, two adults and a juvenile. The so-called are between 154,000 and 160,000 years old, and also have a mixture of archaic and modern facial and cranial features. They were found associated with tools that had elements of both old and new Stone Age technology. The homininsâ age, location and toolkit were neatly in tune with the recent out-of-Africa model and convinced the researchers that they were the .
Done and dusted, you might think. But that turned out to be the high-water mark. Discoveries since then have been difficult, if not impossible, to slot into this neat little box. And the Jebel Irhoud fossils have done more than almost anything else to upend the old order.
Back in 1961, archaeologists noted that the skull had modern facial features â a flat and delicate face, and a prominent chin â together with an archaic, elongated braincase. When dating put it at around 40,000 years old, it was classified as maybe belonging to an African Neanderthal or a relic population of some other archaic hominin, and shunted to the margins of the story. But doubts about the dating persisted and, in 2004, a team led by Jean-Jacques Hublin of the Max Planck Institute for Evolutionary Anthropology in Germany reopened the site. The researchers hoped to get a more accurate date â which they did â but they also got more fossils, including another near-complete skull. It too had a modern face and ancient braincase. When the date came back, it was astounding: 315,000 years old, plus or minus 34,000 years (see âHow to Tell the Age of a Fossilâ).
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Rethinking our roots
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1. Homo antecessorÌę â 900,000 years old. Best candidate for our last direct ancestor
2. Sima hominin â 430,000 years old. Neanderthal, not a direct ancestor as thought
3. Jebel Irhoud human â 315,000 years old. Oldest known remains of a Homo sapiens
4. Florisbad human â 260,000 years old. Surprisingly modern-looking for its age
5. Omo I human â 200,000 years old. Shows a mix of archaic and modern features
6. Herto human â 160,000 years old. Archaic/modern mix, but distinct from Omo I
7. Laetoli human â 120,000 years old. More modern but more archaic-looking
8. Contemporary human â Looks most like Florisbad human
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This was a serious challenge to the out-of-Africa idea. Anatomically, the skull is at least as modern as those found at Herto, which are considered to be right on the cusp of modern humanity. âIt is a creature which is very nearly a modern human, anatomically,â says Foley. And yet it lived at least 130,000 years before H. sapiens was meant to have evolved, at a time when our direct ancestors were still banging rocks together in eastern or southern Africa. It was also on the fringes of the continent, thousands of kilometres from the supposed cradle of humanity.
When the new Jebel Irhoud dates were revealed in 2017, they inspired a major rethink of other fossil skulls from around the same time. It turned out that these told a similar story. The Florisbad specimen from South Africa, for example, is about 260,000 years old, yet has a surprisingly modern face. Ditto some skulls from Laetoli in Tanzania and two locations in Kenya, Guomde and Eliye Springs. All possess a mosaic of modern and archaic features â but, oddly, are also very different from one another.
Another old site with a new story to tell is Olorgesailie in Kenya. Originally excavated in the mid-1980s, Olorgesailie is an ancient lake bed, known for stones rather than bones, specifically an abundance of prehistoric tools. It captures a crucial changing of the guard from one tool-making culture â the Acheulian, with large, crude hand axes â to a more sophisticated one. The site is characterised by a finer and more varied toolkit based on something called the âprepared coreâ: a block of flint or chert worked in such a way that smaller blades and points can be struck from it with a single blow.
Tooling up
Making such a core requires a high level of abstract thought and planning, and so is regarded as a product of modern minds. The Acheulian toolkit, on the other hand, is definitely pre-H. sapiens. It was invented by our distant ancestor H. erectus around 1.2 million years ago. The transition to the prepared core technology was once thought to have been relatively recent, in keeping with the human revolution model, but new dating from Olorgesailie says otherwise. The transition there happened at least 305,000 years ago, and maybe as far back as 320,000 years. Ring any bells?
Olorgesailie isnât the only evidence of earlier-than-expected technological progress. The Jebel Irhoud fossils are also associated with prepared core tools. Whatâs more, Olorgesailie has yielded up tools made of a glassy volcanic rock called obsidian, which doesnât occur locally. The nearest deposits are 25 kilometres away â possible evidence of trade networks.
The site also reveals clear signs of iron-rich rocks being processed into red and black pigments, presumably for artistic purposes, another indication of behavioural and cultural sophistication. It looks as though the transition to modern cognition happened right at the start of the H. sapiens journey, or maybe even before it. So much for the out-of-Africa mainstay, that humanity became physically modern first, but behavioural modernity didnât evolve until much later. âI think the two-step model is dead,â says Foley.
From the stones and bones of Jebel Irhoud, Olorgesailie and elsewhere, a new and increasingly mainstream view of human origins is emerging. âAfrican multiregionalismâ doesnât completely overturn the incumbent model. The continent is still the cradle of humanity â although, as Foley points out, âsaying humans evolved in Africa doesnât mean very much, itâs a vast areaâ â and humanity did disperse out of Africa to eventually inhabit the entire world. But the idea of a recent, localised origin within a discrete population has been buried. In its place is a much deeper origin story beginning at least 300,000 years ago, and perhaps as many as half a million years.
âIf youâre looking for a big framework in which to look at the evolution of modern humans, it is the African Middle Stone Age,â says Foley, referring to the period from about 300,000 to 100,000 years ago. At the start of this span, the whole continent of Africa â possibly even âGreater Africaâ, which includes parts of the Middle East â appears to have been dotted with populations of archaic humans. These were often isolated from one another by geographical or ecological boundaries such as deserts or jungles, and mostly evolved independently, although had sporadic contact and interbreeding, perhaps when and boundaries shifted. This fluid situation persisted for 150,000 years or more, and left behind those now-familiar mosaic skulls.
Genetic studies point in the same direction, says Carina Schlebusch at Uppsala University in Sweden. She and her colleagues analysed a collection of contemporary genomes from all over Africa attempting to home in on the origin of H. sapiens. âIt did not point to any one particular place,â she says. âIt pointed to south Africa, east Africa and west Africa. Basically, it pointed to every place where we had samples from. As I understand it, the transition from archaic to modern happened in different parts of the African continent.â
African multiregionalism represents a major shift in thinking. There was no single ancestral population, but many, spread over a huge area, which merged and split and merged again like a braided stream, evolving at different rates and in distinct directions in different places. The suite of anatomical and behavioural features that define modern humanity didnât appear as one complete package, but gradually coalesced across vast tracts of space and time. âThere was never a single centre of origin,â says Chris Stringer at the Natural History Museum in London. We are a âcompositeâ, he says. âI think it is a really, really important and profound idea,â says Richard Potts at the Smithsonian Institution in Washington DC, who led the Olorgesailie excavations.
The anatomical diversity of these composite humans has inevitably stoked debates about which belong to our species and which donât. Some fossils are widely accepted as being H. sapiens, notably Omo I and the Herto hominins (although they are , and some prefer to categorise the latter as a subspecies). The Jebel Irhoud fossils divide opinion, with some palaeoanthropologists happy to accept them into the immediate family . The rejects are generally categorised, rather vaguely, as âAfrican archaicsâ, which is essentially dodging the issue. Some of these might be separate species. It has been proposed, for example, that the Florisbad fossils be categorised as Homo helmei â however new findings appear to be undermining this idea, as we shall see.
Maybe this is all moot, anyway, hung up on an increasingly outdated concept of what constitutes a species. It is commonly taken to be a group of organisms that can interbreed. But this âbiological speciesâ concept is just one of dozens of competing definitions. Some are based on shared ancestry, others on shared behaviour, genes or anatomy. As Stringer points out, the biological species concept doesnât hold up for many living species of mammals. Coyotes and grey wolves, for example, can , the red wolf. Why not humans too? In this emerging view, early H. sapiens is less a species than a clade: a group of organisms of various taxonomic groups, descended from a common ancestor and sharing many features, but also with a lot of physical variation.
The new model is still a work in progress: everyone accepts it is incomplete and that new discoveries could blow it out of the water. Nevertheless, it is already having some major knock-on effects for other parts of the human origin story. One of these is the search for our last direct ancestor, the species from which H. sapiens evolved. Under the out-of-Africa scenario, this was assumed to be the last ancestor we shared with our sister species the Neanderthals, making it relatively recent. âThe numbers were vague, but people talked in terms of 150,000 to 300,000 years ago,â says Foley. The strong favourite was a species called Homo heidelbergensis, which lived across Africa and Europe from around 700,000 to at least 300,000 years ago. That put it roughly in the right place at the right time. And from an anatomical perspective, H. heidelbergensis looks like a good starting point for both species.
We now know it almost certainly wasnât. First, it has become apparent that there was no common ancestor of humans and Neanderthals. The Denisovans, another lineage of humans, discovered in 2010, are even more closely related to the Neanderthals than we are. That means our last direct ancestor was the species that gave rise to us and the Neanderthal/Denisovan lineage.
Pit of bones
More consequentially, the date of this split has been pushed way back. The latest estimate comes from a remarkable cache of fossils called the Sima hominins, the remains of at least 28 ancient humans found in a cave called Sima de los Huesos (pit of bones) in the Atapuerca mountains of northern Spain. They are 430,000 years old and were long believed to be H. heidelbergensis. But in 2016 their DNA â the oldest ancient human DNA ever sequenced â , and pushed the split between modern humans and Neanderthals/Denisovans back to between 550,000 and 765,000 years ago. That all but rules out H. heidelbergensis and points the finger at an earlier species. âFor about 35 years, Iâve argued that Homo heidelbergensis represents the most reasonable last common ancestor for Neanderthals and modern humans,â says Stringer. âI donât believe that any more.â
So what was? The best candidate is now Homo antecessor, which lived about 900,000 years ago and had a very modern-looking face. However, only a few fossils have ever been found, all in Spain, also in the Atapuerca mountains. Genetics clearly indicates that modern humans evolved in Africa, not Europe, so remains of the same species would need to turn up in Africa or Greater Africa to bolster the homininâs claim to direct ancestry.
Whoâs the daddy?
There are three other candidates in the frame: Homo rhodesiensis, which may just be an African H. heidelbergensis, the Florisbad fossil or perhaps even H. erectus. But nobody can be sure. âIn my view, who that ancestor was, and when and where it lived, are currently unknown,â says Stringer. For now, it is known only as Ancestor X.
Even as it becomes harder to pin down the identity of our direct ancestor, the African multiregionalism model has shifted the spotlight onto a different and, arguably, more interesting ancestor question. If, as the new hypothesis suggests, the African Middle Stone Age was teeming with groups of more-or-less modern humans, evolving semi-independently, which of these actually gave rise to the contemporary human population? âThis is the divergence we should really be thinking about in terms of the shift to modern humans,â says Foley. âAnd when does this occur?â
Unfortunately, at this point the trail goes quite cold. âThe fossil record is very sparse,â says Foley. There are some bones, but they are scrappy and hard to weave into a big picture. The genetics is also quite fuzzy. places the origin of modern humans between 260,000 and 350,000 years ago. This isnât an error bar, but reflects the long process of patchwork evolution across swathes of Africa, says Schlebusch, who led the research.
But there may be another way to pin down the story. Last year, AurĂ©lien Mounier and Marta MirazĂn Lahr, both of the University of Cambridge, created what they called a of all living humans. By mapping the morphological variety of the skulls of ancient and contemporary humans, including Neanderthals but excluding the archaic Africans, they estimated what the skull of a supposed last common ancestor looked like in the early part of the Middle Stone Age. They then compared their virtual skull to the five most complete skulls from that time. The fossil with the greatest similarity to the virtual ancestor was the Florisbad skull from South Africa, followed by two of the East African specimens, Eliye Springs and Omo II. Next came the Laetoli specimen. The North African skull, from Jebel Irhoud, was the least similar, closer to Neanderthals. What this suggests, they say, is that we are descended from archaic Africans in southern and eastern Africa, but not from our friends in the north. In other words, the braided stream eventually coalesced into a main channel, although still with numerous side branches.
Furthermore, fossil finds indicate that those side branches persisted until surprisingly recently. Skulls with a have turned up in Ishango in the Democratic Republic of the Congo, at Lukenya Hill, Kenya, and at Iwo Eleru in Nigeria. They wouldnât look out of place alongside the African archaics, but have all been dated to as little as 14,000 years ago. They may represent final holdouts of those isolated populations that were dotted across Africa at the dawn of our species. It wasnât until about 12,000 years ago, when farming spread around the world, that these last side channels of our braided stream finally ran dry.
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How did humanity conquer Earth?
One central pillar of the out-of-Africa model of human origins is the âoutâ part. This holds that about 60,000 years ago, our species left Africa and, in an epic sweep, filled Eurasia.
Cracks in that paradigm have been growing for a long time. Human skulls discovered at two sites in Israel, for example, are 120,000 years old. These are often seen as evidence that humanity made some brief, failed, forays into western Asia before the mass exodus. But developments in the past few years strongly suggest there was more to it. A 177,000 year-old jawbone from Misliya cave in Israel, for instance, hints there was a much older and longer-lasting human presence in the Middle East.
A real jaw-dropper came last year, when a pair of skulls discovered in Greece in 1978 finally gave up their secrets. They were recovered from a coastal cave called Apidima, stuck together back-to-back in a block of volcanic breccia. Both were assumed to be from Neanderthals and about 150,000 years old, but a reanalysis showed otherwise. One was indeed from a 170,000-year-old Neanderthal. But the other was 210,000 years old and from a Homo sapiens, albeit with a mixture of modern and archaic features. The skulls had somehow ended up in the same part of the cave and became stuck together some time later.
The only conclusion is that modern-ish humans living in Africa more than 200,000 years ago successfully dispersed into southern Europe, a long trek by foot â or possibly raft â around the eastern Mediterranean that probably took millennia. âItâs very surprising,â says Chris Stringer at the Natural History Museum in London, who was part of the team that did the analysis.
Evidence of early dispersals has been found even further from Africa. In 2015, researchers in China announced the discovery of modern human teeth in a cave in the south of the country that dated to at least 80,000 years ago. There are several other tantalising fossils in China dating to about the same time, too. These have conventionally been classified as Homo erectus, the first member of our genus, but it now seems more likely that they are Homo sapiens, says MarĂa MartinĂłn-Torres at he National Research Center of Human Evolution (CENIEH) in Burgos, Spain. âThey were there!â she says. Stringer agrees: âIf they are in Europe than I donât see why they arenât getting into Chinaâ.
These new discoveries of early dispersals are intriguing, but the big picture remains substantially unchanged. The current thinking is that modern humans migrated out of Africa en masse some time after 100,000 years ago, probably via the Arabian Peninsula or the Levant or both. They gradually worked their way into Europe and along the southern coast of Eurasia, most likely in pursuit of high-quality food resources, then âback filledâ into central Asia from what is now China. Around 65,000 years ago some people reached Sahul â an ancient continent that is now Australia and New Guinea â almost certainly by boat. The last great migration then took humanity across the Bering land bridge and into the Americas around 15,000 years ago.
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All change again?
African multiregionalism may be in the ascendancy, but it isnât completely triumphant. A couple of days before the Hinxton conference started, a group of geneticists published . They had analysed mitochondrial DNA from 1217 living people of African ancestry and concluded that they all trace their origin back to a single small population living approximately 200,000 years ago around the Makgadikgadi salt pan in northern Botswana. Now an arid semi-desert, at the time it was the largest wetland in Africa.
If true, it swings the pendulum back towards a recent origin. âThis is something we have to address,â says Schlebusch. But she points to several reasons to doubt the result. For a start, mitochondrial DNA is informative about maternal lineages, but not about entire ancient populations. Just because all Africans are descended from a mitochondrial Eve who lived in Botswana 200,000 years ago doesnât mean that they are only descended from her. They could also have had many other female ancestors whose mitochondrial lineages died out.
Indeed, a similar analysis of Y-chromosomes, passed exclusively down the paternal lineage, points to a . Only by looking at full genomes can the whole picture be inferred, and these point to a pan-African origin, says Schlebusch. In addition, there is all that evidence from tools and fossils. âSingle-place origin is not the best model to describe what actually happened in Africa,â she says. âItâs more like a river delta splitting and merging through time.â
So where do we stand? For now, African multiregionalism looks like the best effort at a coherent new synthesis. Just donât bet on it lasting as long even as the recent out-of-Africa model. Future discoveries will undoubtedly throw more spanners in the works. The study of ancient African genomes is in its infancy. âGenomic data now drives the subject, and it drives it very fast,â says Foley. But there are surely more fossils to find, too. The Middle Stone Age of west Africa is essentially unexplored and, as we have seen, a single skull can bring entire models tumbling down. In addition, there are 25 known taxa of hominins that have yet to be integrated into our tale. âItâs not going to be a simple story,â says Foley. âWe have to think more flexibly and broadly about the processes that are involved.â
Three days might be too short a timescale for almost everything to change. But three years from now, who knows?
Cracks in that paradigm have been growing for a long time. Human skulls discovered at two sites in Israel, for example, are 120,000 years old. These are often seen as evidence that humanity made some brief, failed, forays into western Asia before the mass exodus. But developments in the past few years strongly suggest there was more to it. A 177,000 year-old jawbone from Misliya cave in Israel, for instance, hints there was a much older and longer-lasting human presence in the Middle East.
A real jaw-dropper came last year, when a pair of skulls discovered in Greece in 1978 finally gave up their secrets. They were recovered from a coastal cave called Apidima, stuck together back-to-back in a block of volcanic breccia. Both were assumed to be from Neanderthals and about 150,000 years old, but a reanalysis showed otherwise. One was indeed from a 170,000-year-old Neanderthal. But the other was 210,000 years old and from a Homo sapiens, albeit with a mixture of modern and archaic features. The skulls had somehow ended up in the same part of the cave and became stuck together some time later.
The only conclusion is that modern-ish humans living in Africa more than 200,000 years ago successfully dispersed into southern Europe, a long trek by foot â or possibly raft â around the eastern Mediterranean that probably took millennia. âItâs very surprising,â says Chris Stringer at the Natural History Museum in London, who was part of the team that did the analysis.
Evidence of early dispersals has been found even further from Africa. In 2015, researchers in China in a cave in the south of the country that dated to at least 80,000 years ago. There are several other tantalising , too. These have conventionally been classified as Homo erectus, the first member of our genus, but it now seems more likely that they are Homo sapiens, says MarĂa MartinĂn-Torres at he National Research Center of Human Evolution (CENIEH) in Burgos, Spain. âThey were there!â she says. Stringer agrees: âIf they are in Europe than I donât see why they arenât getting into Chinaâ.
These new discoveries of early dispersals are intriguing, but the big picture remains substantially unchanged. The current thinking is that modern humans migrated out of Africa en masse some time after 100,000 years ago, probably via the Arabian Peninsula or the Levant or both. They gradually worked their way into Europe and along the southern coast of Eurasia, most likely in pursuit of high-quality food resources, then âback filledâ into central Asia from what is now China. Around 65,000 years ago some people reached Sahul â an ancient continent that is now Australia and New Guinea â almost certainly by boat. The last great migration then took humanity across the Bering land bridge and into the Americas around 15,000 years ago.
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What happened to the other species of humans?
According to the standard out-of-Africa model, when our species first spread across Eurasia they completely replaced the more archaic humans they met. Certainly, we are the last hominin standing. But whether Homo sapiens was responsible for the demise of the other species remains a matter of vigorous debate. What has become clear in recent years is that these encounters werenât entirely violent and destructive. At least sometimes, our ancestors made love not war.
Neanderthals and Denisovans, our two closest relatives, both became extinct tens of thousands of years ago. Yet most people around the world have small quantities of DNA inherited from one or both species in their genomes. This is evidence that H. sapiens interbred with them and at least some of these trysts produced fertile offspring. Some people from the Middle East today also carry ghost DNA from another species dubbed hominin X, fossils of which have yet to be found.
Our ancestors may have encountered other hominins as they dispersed around the world, including the enigmatic âhobbitâ, Homo floresiensis, which lived on the Indonesian island of Flores until about 50,000 years ago. Last year, it was discovered that a similar species was living at around the same time 3000 kilometres to the south, on the Philippine island of Luzon. There is, however, no genetic evidence of interbreeding with either of these species, and the role of H. sapiens in their extinction, if any, is unknown.
It was once assumed that interbreeding between early humans and other hominins happened exclusively outside Africa. A small amount of Neanderthal DNA has been found in the genomes of people living in Africa, but as Neanderthals never seem to have lived on that continent it almost certainly arrived as a result of early humans migrating back to Africa from Eurasia. However, more recent analyses suggest that there was interbreeding with other hominins on the continent. In fact, the genomes of some people in Africa are 19 per cent âancientâ, which far exceeds any Neanderthal or Denisovan contribution to Eurasian genomes.
âAt least sometimes, our ancestors made love not war with other homininsâ
The first evidence of this interbreeding came in 2012, when a team led by Sarah Tishkoff at the University of Pennsylvania found ancient DNA in the genomes of modern hunter-gatherers living in Cameroon and Tanzania. It indicated that their ancestors had interbred with an unidentified hominin species no more than 30,000 years ago. Then, in 2018, Arun Durvasula at the University of California, Los Angeles, scanned the whole genomes of people from four sub-Saharan populations and found with another unknown archaic hominin. It seems to have split from our lineage about 625,000 years ago, and then interbred with humans up to 124,000 years ago. This was before the mass exodus out of Africa, which would explain why European genomes carry the same ghost DNA. Earlier this year, analysis of four fossil skeletons from Cameroon saw hints of yet more ghost DNA from an encounter that happened around 250,000 years ago.
Who might these mystery relatives be? One candidate is Homo naledi, a primitive-looking hominin that was discovered in South Africa in 2013 and . Another possibility is Homo antecessor, which lived some 900,000 years ago and is now thought to be our direct ancestor â although we still donât have evidence that it lived in Africa. A more likely possibility is that fossils of the ghost species have yet to be discovered, and maybe never will be. Whatâs more, there seems little doubt that new studies will turn up other ghost ancestors in our DNA.
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How does DNA analysis reveal our prehistory?
Genetics is now at the leading edge of human evolution research and is perhaps even more important than bones and stones. But extracting information about the past from ancient or modern DNA isnât straightforward. The techniques rely on arcane statistics and computational biology. However, the basic principles are easy to grasp.
One key thing that DNA can tell us is how long ago two lineages diverged â for example, when the ancestors of Neanderthals and Homo sapiens split. These analyses are based on mutations, says Carina Schlebusch at the University of Uppsala in Sweden. The simplest method uses mitochondrial DNA, a self-contained mini genome found inside cellsâ mitochondria, which produce energy. This is passed on from mothers to their offspring. âWe sequence different mitochondrial genomes and then compare and count the different mutations between them,â she says. âThen, using the rate at which mutations accumulate, we date how long ago the mitochondria diverged from each other.â
Extracting information from DNA on the Y-chromosome â which is passed from fathers to sons â is also quite straightforward because, like mitochondrial DNA, it is inherited intact. Other chromosomes, however, undergo a process called recombination during the formation of sperm and eggs, in which pieces of DNA are shuffled around. This makes them trickier to analyse. But mitochondrial and Y-chromosome DNA donât tell the whole story, so methods have been developed to estimate divergence times using other chromosomes. There are two approaches. âOne is to take recombination into account, using recombination maps to know where the hotspots are,â says Schlebusch. âAnother is to ignore recombination by using small pieces of DNA randomly sampled across all of the chromosomes.â If these pieces are small enough, researchers assume they have been passed down the generations pretty much intact.
DNA can also reveal when separate populations â or species â interbred. âWhen populations split from each other back in time, they evolve independently and accumulate patterns of mutations that are distinct,â says Arun Durvasula at the University of California, Los Angeles. Then, when interbreeding happens, the resulting genomes will be a mixture of these distinct patterns. âWe can look for these patterns across the thousands of genomes we have sequenced from individuals around the world,â he says.
The time of these interbreeding events can be estimated, too. âWhen [interbreeding] happens, large stretches of DNA come from one population or the other,â says Schlebusch. âThen over generations, because of recombination, these become smaller and smaller. This also happens at a certain rate, and that is what we use to date admixture times.â
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How to tell the age of a fossil
Perhaps the most important date in the new age of human evolution research is 315,000 years ago, give or take 34,000 years. That was the surprise age of a set of Homo sapiens bones found in Jebel Irhoud, Morocco, . The fossils were originally discovered in 1960 and dated to a minimum of 40,000 years old. The new date precipitated a major re-evaluation of our speciesâ origins in Africa. But it almost slipped through the net. At first, the reading had come in at just 160,000 years ago. Luckily, dating guru Rainer GrĂŒn of Griffith University in Queensland, Australia, spotted that something was amiss.
The age of a fossil can be inferred from the age of the sediments in which it is found, and the plants, animals and tools associated with it. But bones may have been buried in a grave or eroded out of older sediments and redeposited. Worse, critical stratigraphic information has been lost for around 90 per cent of the hominin specimens we have found, because they were excavated before rigorous archaeological techniques became the norm in recent decades. âIf you want to know how old fossil hominins are, you have to date them directly,â says GrĂŒn, who has been involved in dating most of the hominin fossils that have rewritten our understanding of human evolution.
55,000 years
Maximum age radio carbon dating can give for a fossil
The original dating of the Jebel Irhoud fossils used radiocarbon analysis, also called carbon-14 dating. Long the only method of dating specimens directly, it relies on the fact that living organisms incorporate the three isotopes of carbon â 12C, 13C and 14C â into their tissues at the relative levels found in the atmosphere. When an organism dies, it no longer incorporates carbon. The unstable 14C gradually decays to nitrogen, reducing the amount of 14C present in the fossil compared with 12C and 13C. It takes 5730 years for half of the 14C in a sample to decay, so measuring the ratio of carbon isotopes gives an estimate of when an organism died, give or take a few hundred years. Unfortunately, the short 14C half-life means that carbon dating can go back only a maximum of 55,000 years and usually no more than 45,000. That limits its usefulness for studying human evolution, and helps explain the original Jebel Irhoud date.
Enter two newer techniques: electron spin resonance (ESR) and uranium series (U-series) dating. ESR is invaluable for dating teeth. It exploits the fact that enamel is full of a mineral called hydroxyapatite, which contains lots of ions that, when zapped by background radiation, form free radicals. These accumulate over time and can be measured by various spectroscopic techniques. This method can indicate the age of a tooth up to 3 million years old, says GrĂŒn.
U-series dating, meanwhile, builds on the observation that living bones contain almost no uranium, thorium or lead. Once buried, however, bones absorb uranyl ions from water in soil or sediments, and the uranium in these then decays to thorium and lead via predictable pathways. So the ratios of the three elements can indicate how long something has been buried. Uraniumâs long half-life (around 245,000 years) means that U-series dating can easily go back 500,000 years or more. This is the technique GrĂŒn was using to date the Jebel Irhoud fossils when he realised he had made an elementary mistake. âI mixed up the thorium and uranium values of the sediment,â he says. On such small details human history can turn.
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What drove the evolution of the modern mind?
Some 320,000 years ago, a technological revolution swept across Africa. The large, flat, leaf-shaped hand axes that had remained largely unchanged for 700,000 years suddenly gave way to a more sophisticated toolkit of smaller, finer points and projectiles.
Palaeoanthropologists increasingly recognise this transition as indicating the dawn of the modern mind, when people who looked like us also began to think like us. It wasnât just a technological revolution but a cognitive one too.
One of the best places to see this on the ground is the Rift valley in Kenya, in particular at a site called , an ancient lake bed rich in stone tools. The transition is stark, says Richard Potts at the Smithsonian Institution in Washington DC. âWe have layer after layer of hand axes then, no more hand axes.â What you see instead is the more sophisticated tools. But, unfortunately, erosion at Olorgesailie means that the sedimentary record has a gap of around 180,000 years between these two technologies. What was happening at this crucial time to drive this epochal change?
A few years ago, Potts and his team drilled a core some 25 kilometres away in an area with a complete sedimentary record. The core is too narrow to capture tools but it tells a story of dynamic environmental upheaval about half a million years ago. âYou have this complex and really interesting combination of faulting, breaking up of the landscape and climate variability,â says Potts. âAll hell breaks loose.â
So far, evidence of cataclysmic change has been seen only at the drill site â a âpinprick in the Rift valleyâ, as Potts describes it. But he says he would expect to see it in other locations too. âWe may be wrong, but at least in the place where weâre working in southern Kenya, this is what the picture shows.â
The region around Olorgesailie also records a major shift in the animals present at this time, with large-bodied grazing animals giving way to smaller and presumably harder-to-catch ones. âItâs an entirely changed ecological setting in which early hominins had to adapt,â says Potts. He thinks this wildly unpredictable environment may have been the selection pressure that drove the evolution of modern behaviour. âFlexibility becomes the new currency of evolution,â he says. We had to think smarter to survive.
