terça-feira, 21 de maio de 2019

Traces of mystery ancient humans found lurking in our genomes

Prehistoric humans were sexual adventurers, mating with Neanderthals and Denisovans, but DNA studies reveal dalliances with populations we never knew existed
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Humans 10 October 2018
genome artwork
Peter Strain
By Catherine Brahic

WE LEARN about our ancestors in many ways. Bones tell us what they looked like. Teeth reveal their diet. Tools, pots, art and other artefacts hold stories about their culture. Then, a decade ago, the first ancient genome was sequenced, opening a whole new window on our past – one that promised more intimate insights.

The breakthrough famously revealed that Neanderthals got very cosy with humans. Since then, geneticists have been probing more and more fossils for evidence of past cross-species dalliances. The studies haven’t disappointed. But in an intriguing twist, they have started to kick up something unexpected: hidden inside genomes are signs of ancestors that we never knew existed. Geneticists call them “ghosts”.


We have no physical record of these ancient hominins – no bones, no tools, no archaeological remains whatsoever. Yet the genetic code that they left within fossils of other hominins, and in living humans too, is offering profound and unprecedented insights into how our species came to be, and what the world was like at the time.

The idea that each of our cells might contain fragments of genetic code from extinct species has been around for well over a decade. Then, in 2008, Svante Pääbo and his team at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, pulled off the master stroke of teasing DNA out of millennia-old Neanderthal bones in quantities great enough to sequence. This provided an obvious way to find out if Homo sapiens had bred with Neanderthals (Homo neanderthalensis): you could simply look within the genomes of living people for DNA sequences with distinctly Neanderthal patterns of mutations. These comparative studies revealed that early humans had indeed mated with Neanderthals, and not just once. Current estimates are that the genomes of everyone except Africans are between 2 and 4 per cent Neanderthal.

Unexpected dalliances

Here were two clearly distinct species, separated by up to 700,000 years of evolution, yet the remnants of their sexual proclivities are captured in the DNA of the majority of people alive today. What’s more, it soon emerged that our ancestors weren’t only getting it on with Neanderthals.

Just as Pääbo was finishing sequencing the Neanderthal genome, a parcel landed on his desk. It contained a tiny fragment of a finger bone from the Altai mountains in Siberia. The piece was 30,000 to 50,000 years old and was thought to be from another Neanderthal. His team was in for a big surprise. The DNA analysis revealed an entirely new group of archaic humans, now dubbed the Denisovans, which split from a common ancestor with Neanderthals some 500,000 years ago.
Once again, comparisons with modern human genomes showed that the two interbred. Genetic studies reveal this to have happened in Eurasia. They also show that Denisovans ranged from Siberia to South-East Asia, and that at least one of their genes helps modern Tibetans to live at high altitude. The idea that our ancestors hybridised with other hominins was once dismissed. Now it was starting to look as though they would mate with anything vaguely human.

Denisovans are nearly ghosts: we have that one finger bone and a few molars as a physical testament to their existence, but no more. Then in 2016, a true ghost emerged from the genomes of 44 individuals who lived in the Middle East between 14,000 and 3400 years ago. Their DNA held genetic markers indicative of a distinct group of ancient H. sapiens based in the region more than 45,000 years ago. The members of this population are now known as Basal Eurasians, and they present a conundrum. Their DNA, which is still found in modern Europeans, shows none of the telltale signs of interbreeding with Neanderthals. This came as a surprise because ancestral humans mated with Neanderthals very soon after leaving Africa 60,000 years ago in the migration that was to give rise to all people of non-African heritage alive today.
Mystery ancestors
The most-likely explanation is that soon after that migration, a group of humans became isolated while the rest bumped into and mated with Neanderthals. “If you like, it’s a third branch,” says Chris Stringer of the Natural History Museum in London – a branch that is distinct from the humans who had stayed in Africa and the ones who were gradually spreading out across Eurasia, Australia and eventually into the Americas. Because there are no known fossils belonging to Basal Eurasians, it is impossible – for now – to say why they were isolated. Perhaps it was just down to where they settled, far from other groups. Or maybe they developed cultural differences. Either way, these ghosts didn’t mix with the rest of humanity for millennia – long enough to evolve distinct genetic markers.

The Basal Eurasian research showed that rich insights into human history can be gleaned from DNA alone. But, like the Neanderthal and Denisovan studies, it relied on obtaining DNA from fossils, something that remains a huge challenge. DNA degrades with time, so it takes special fossils and special skills to extract it from very old bones, particularly ones that have spent thousands of years buried in hot climates. However, in the mid-2000s, geneticists were already discussing another approach. Among others, Jeffrey Wall, now at the University of California, Los Angeles, and Vincent Plagnol, now at University College London, suggested that it might be possible to spot signs of extinct populations in the DNA of modern humans, simply by using clever statistics.

The broad idea is that all DNA is subject to random mutations that accumulate over millennia and are passed down from generation to generation. By looking at mutation patterns in modern populations, it is possible to spot segments that don’t match the usual H. sapiens pattern. These are presumed to come from populations that evolved separately from our own species for thousands of years before mating with humans. Statistical modelling can then produce estimates of when the two groups mated and how different the other population was from our ancestors.

The past few years have seen several attempts to refine these methods and apply them to Africa – the birthplace of our species and the setting for a slice of our history that we know very little about. This new research has revealed the presence of at least one ancient ghost on the continent.

African Neanderthals?

Josh Akey at the University of Washington in Seattle, Sarah Tishkoff at the University of Pennsylvania and others have spent years sequencing and analysing the genomes of modern Africans who belong to groups with deep ancestral roots, including the Baka hunter-gatherers from Cameroon, and the Hadza and Sandawe from Tanzania. Within these genomes, they have found stretches of DNA that appear to come from another hominin species. Because this DNA is found only in the descendants of African people – not in any Eurasians – the ghost species must have interbred with H. sapiens after the out-of-Africa migration 60,000 years ago. In fact, by the team’s calculations, this probably happened within the past 30,000 years. If true, this is huge. It means that until very recently, there was at least one other species of hominin living alongside us in Africa. According to Akey, soon-to-be published evidence suggests there might have been more than one.
Baka people
A mystery ancestor lives on in the DNA of the Baka people from Cameroon
Mattias Klum/National Geographic creative/Getty
The African ghosts appear as evolutionarily distinct from modern humans as Neanderthals and Denisovans are. “What that means is that they probably came from the same African population that Neanderthals trace their ancestry to,” says Akey. “So the idea is that 700,000 years ago, there’s a population in Africa that splits off from the modern human lineage, goes out of Africa and becomes what we recognise as Neanderthals. At the same time, there’s another split in Africa that becomes sort of like an African Neanderthal.”

Who these “African Neanderthals” were is a mystery. One clue could come from a fossil that Stringer worked on for his PhD back in the 1970s: the Iwo Eleru skull from Nigeria. At around 13,000 years old, this individual was alive just a millennium or so before some humans first started farming, yet it has a strange mix of modern and primitive features. Recently, Stringer and Katarina Harvati at the University of Tübingen in Germany did a fresh analysis of the skull. This confirmed that it is very odd for its age. “It actually resembles early sapiens fossils rather than late ones, and it certainly doesn’t look like any recent Africans,” says Stringer. “We suggested this could be an example of an African whose population had received this archaic introgression.” In other words, it might be a human whose ancestors mated with an African ghost.

As yet, no ancient African hominin has had its genome sequenced, so it is possible that physical remains of this ghost have already been unearthed. One candidate is Homo naledi, a species discovered in 2013 deep inside a narrow cave system in South Africa. The fossils are around 250,000 years old, but no one knows how long the species survived. If pressed, however, Stringer would put his money on another suspect. “My bet is that Homo heidelbergensis is the introgressor,” he says. Recent unpublished evidence suggests that this species was still around less than 300,000 years ago, when humans had already appeared. Alternatively, the ghosts may have been a subpopulation of H. sapiens that, like the Basal Eurasians, was isolated from other populations for long enough that its members’ DNA acquired different markers. “It could be the case that 100,000 years ago or more, there are different populations of anatomically modern humans in different parts of Africa,” says Tishkoff. “And maybe at some point they mix with each other and maybe some populations died out.”

Tishkoff thinks it would be surprising if our ancestors didn’t mate with other ancient hominins in Africa. However, she cautions that the evidence for African ghosts is still tentative: because we know so little about the population history of Africa, she and her colleagues had to make many assumptions to interpret their data. “That doesn’t mean [hybridisation] didn’t occur in Africa,” says Tishkoff. “It’s likely to have occurred. It’s just really challenging to prove.” The clincher will come when someone is able to sequence DNA extracted from an African fossil and compare it with the fragments of ghost DNA found in modern Africans. That is a challenge, but, given the advances in ancient DNA sequencing in the past decade, it is probably only a matter of time before someone meets it.
“There may have been a few hominin species living recently with us in Africa”
“Genetics in general is changing how we understand our species,” says Tomas Marques-Bonet at Pompeu Fabra University in Spain. “To me, everything starts with Denisovans: the first time we lifted DNA from a finger and found neither human nor Neanderthal – something for which we have no face and very little other information – that was the first time genetics illuminated something that had totally escaped palaeontology.”
It now transpires that Denisovans had their own ghosts. People living in Oceania and East and South-East Asia today have inherited about 5 per cent of their DNA from Denisovans. By taking a closer look at these genetic sequences, Akey’s team found that they don’t all relate to the original finger-bone genome in the same way. In fact, the group found signs of two evolutionarily distinct Denisovan populations. “That was really unexpected,” he says. “There’s actually another, ghost, Denisovan lineage.”
What all these studies highlight is that it was the rule, rather than the exception, for hominin populations to split for thousands or even hundreds of thousands of years and then meet again and mate. Neat, bifurcating evolutionary trees must be abandoned. “Take a pen on a piece of paper and start making squiggly lines,” says Akey. “That’s human history.” On a more basic level, it is also causing many in the field to stop using the terms species and subspecies to refer to different hominins, preferring instead to talk about groups or populations. After all, individuals that belong to different species – like H. sapiens and H. neanderthalensis – aren’t meant to be able to produce viable offspring.
Ghosts and nearly-ghosts are making the ancient world a much less lonely place. “If we look around the world today, we are really the only hominin game in town,” says Akey. “People assume that’s the way it must have always been. In fact, the world was a much more interesting place not that long ago.”

Animals have ghosts too

At a conference in China earlier this year, Tomas Marques-Bonet flashed up a slide showing an evolutionary tree of chimpanzees and bonobos. Off to the right of the longest branch was a cartoon Pac-Man-style ghost, with its hands up in the air.
Marques-Bonet and his colleague Martin Kuhlwilm, both at Pompeu Fabra University in Spain, had been looking at the genomes of wild chimps and bonobos in central Africa when they found odd fragments of DNA. The fragments couldn’t be explained by ancient matings with each other, or by random mutations. The DNA, they say, comes from an unknown or “ghost” bonobo population that must have become isolated, evolved independently and later mixed back in with its long-lost relatives.
At the same conference, Greger Larson at the University of Oxford revealed the results of a study of the origins of domesticated dogs in the Americas. Through genetic analyses, his group had traced the ancestry of a mysterious population of dogs that arrived in the New World around 11,000 years ago. The dogs, Larson said, probably accompanied a second wave of human migrations over the land bridge from Siberia and then spread across the continent. They were entirely replaced when European settlers brought their dogs with them.
However, traces of the original American canines live on in a rather strange place. Canine transmissible venereal tumour is described as the world’s worst STD. Genetic analyses of these tumours, found on dog genitals, revealed that they are more closely related to the first American dogs than to any alive today.
Want to know more? Dig deeper into the story with these resources:

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Key research papers

Further reading
The Human Story – The Collection, Volume 1, Issue 4
How to be Human: The ultimate guide to your amazing existence
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