Portside

This is an extract from Our Human Story, our newsletter about the revolution in archaeology. Sign up to receive it in your inbox every month.

One of the most vexing unsolved problems in human evolution is its starting point – about which we know almost nothing.

I’m referring to the last common ancestor that we share with chimpanzees and bonobos, our closest living relatives. This mystery ape lived millions of years ago; at some point, the population split into two. One group gave rise to modern-day chimps and bonobos; the other gave rise to us and all our hominin relatives, like Neanderthals and Australopithecus.

It would help to know more about that last common ancestor. Clearly, it was a population of apes, but what were they like? Were they sociable or solitary? How did they communicate? What did they eat? Where did they live? Did they use tools? What was their mating system?

Unfortunately, we don’t know. The fossil record of African apes is pretty poor for the relevant time period, so we don’t even have plausible candidates. When we compare ourselves to chimpanzees and bonobos, we can see all kinds of differences, from face shape and body hair to walking style and spoken language. But we don’t know which of these traits have been inherited from the last common ancestor, and which have evolved more recently.

Genetics can help us with some of these questions, which is one of the reasons why great apes were some of the first large animals to have their DNA read after the sequencing of the human genome. We’re now poised to learn a lot more because, for the first time, the great apes have had their genomes read in full.

No more gaps

Many people don’t appreciate that when the human genome was first “completed” in 2001, it wasn’t actually complete. There are long stretches of repetitive DNA that are extremely hard to read, so they were either left out or only sequenced with low accuracy.

The problem was the way DNA was read back then: in small chunks. Sequencing machines would read a few hundred “letters” of the DNA alphabet, and researchers then used computer programs to stitch all these pieces together. It worked great… except for the highly repetitive sections, which confused the programs in much the same way that humans get confused by jigsaw puzzles with lots of clear blue sky.

Over the last four years, I’ve been following the Telomere-to-Telomere (T2T) consortium, a group of geneticists led by Adam Phillippy at the National Human Genome Research Institute and Karen Miga at the University of California, Santa Cruz. They use more advanced “long read” sequencing, which can read hundreds of thousands of DNA letters in one go.

Hence my first story about them, in 2021, when they produced a much more complete human genome, filling in the 8 per cent that was still either missing or probably wrong. The new genome had 200 million more letters, and more than 2000 new genes.

This rapidly led to new discoveries. For instance, it was now possible to read regions of the genome that are still evolving at speed, like immune system genes. The new genome also enabled researchers to get a closer look at “inversions”, where a chunk of sequence has been flipped end to end, and “segmental duplications”, in which long stretches of DNA have been copied.

The big effort now is to create the human “pangenome”. DNA varies from person to person, so it isn’t possible to obtain a single definitive genome. Instead, the Human Pangenome Reference Consortium wants to obtain genomes from dozens of people from all around the world. This will enable it to create a dataset that tells us which bits of the genome vary from person to person, and how.

That’s all in the works; meanwhile, the team has gone to work on apes.

Rise of the genome of the apes

On 9 April, the scientific journal Nature published a big paper from the T2T team and their colleagues. It describes complete genome sequences for six species of ape: chimpanzees, bonobos, gorillas, Bornean and Sumatran orangutans, and a type of gibbon called a siamang.

As you read that list, you are moving further away from humans – while chimps and bonobos are our closest living relatives, gorillas are more distant, and orangutans and gibbons further still. This is reflected in their locations; chimps, bonobos and gorillas live in Africa – the continent where humans originated – but orangutans and gibbons are found in tropical Asia.

The new genomes are virtually complete, with between 99.2 and 99.9 per cent of the sequence read. Previously, 10-15 per cent of each ape genome was unavailable. The researchers estimate their error rate at less than 1 letter in 2.7 million.

These new genomes will be studied for years to come – assuming Donald Trump doesn’t gut the relevant research funding – but a few things stood out straightaway.

First, the researchers found regions of the apes’ genomes that have been under strong selection; that is, evolution has been pushing them to change in some way. Across all six species, they found 143 candidates for “hard selective sweeps”, meaning evolution had strongly favoured one version of the sequence over another. There were another 86 possible “partial” selective sweeps, where the evolutionary pressure was weaker but still detectable.

Much of this was new. “Approximately half of the hard selective sweeps (74 out of 143) and more than 80% of the partial selective sweeps (70 out of 86) were previously unknown,” the team wrote. Intriguingly, 43 of these regions overlapped with known selective sweeps in humans. What happened there? Did evolution push apes and humans to change in the same ways? Or were we sent in different directions by the different pressures we experienced?

As with the human genome, the researchers were able to find a lot of large-scale shifts in the ape genomes, like inversions and duplications. For instance, there were 1140 inversions larger than 10,000 letters, of which 522 were new to science. Likewise, each ape species has hundreds of segmental duplications, some of which contain multiple genes.

Such massive changes can affect the course of evolution. For instance, if a long sequence gets copied, one of the copies is free to mutate and evolve because the original is serving its initial purpose – potentially leading to new traits and abilities.

This should change our way of thinking about how apes and humans evolved to be so different, the researchers say. Based on previous genomes, it’s been stated that humans and chimps share 99 per cent of their DNA. Consequently, geneticists concluded that a lot of the changes have been in the way genes are regulated: which ones are turned on and off in which parts of the body at which times.

The thing is, that 99 per cent figure isn’t quite right. It’s true if you look at individual sequences letter by letter, but previous genomes couldn’t resolve all those large-scale duplications and inversions. Yet those large-scale changes have probably been a big factor in ape evolution.

Our origins

Finally, let’s bring this full circle and get back to the last common ancestor that we share with the apes. Armed with their new complete ape genomes, the researchers estimated when the various groups diverged. They can do this by looking at how different the genomes of the various species are: the more different the genome, the more distantly related the species and the further back in time was their last common ancestor.

The team estimated the dates of three key splits. The ancestors of African apes split from those of orangutans, they say, 18.2 to 19.6 million years ago. Then, among the African apes, the ancestors of gorillas split from the ancestors of chimps and bonobos 10.6 to 10.9 million years ago. Finally, the last common ancestor of humans, chimps and bonobos lived between 5.5 and 6.3 million years ago.

Now, this is not a shocker on the face of it. It compares reasonably well with existing estimates. The TimeTree database reckons humans split from the ancestors of chimps and bonobos 6.4 million years ago. A 2021 analysis put it around 7.5 million years ago, while cautious authors offer ranges like 4 million to 8 million and 5.7 million to 10 million years ago.

However, it does raise questions about some key fossils. Because the date is based on such complete genomes, it ought to be more reliable than previous estimates, which creates an interesting conflict.

The oldest purported hominin is Sahelanthropus tchadensis, known from one location in Chad and dated to 7 million years ago. Because we don’t have a complete skeleton, Sahelanthropus’s status has been in dispute for 20 years. As I’ve explained in previous instalments of Our Human Story, it’s not clear whether it walked upright on two legs like a hominin, or did something more ape-like such as knuckle-walking.

Here’s the thing. If Sahelanthropus really is 7 million years old, and the ape genome is revealing that our ancestors didn’t split from those of chimps and bonobos until 5.5 million years ago, then Sahelanthropus can’t be a hominin. There were no hominins at that time; it must have been an ape.

A similar problem might bedevil the next-oldest hominin, Orrorin tugenensis. The fossils are 6 million years old, right in the middle of the window for the last common ancestor. Again, if we take the dates at face value, this suggests Orrorin is either an extremely early hominin, or it’s something very close to the long-sought last common ancestor. This would be odd, because Orrorin seems to have walked upright.

You might have noticed that I put caveats on all those statements. That’s because there is some wiggle room with the date of the last common ancestor. Even if we accept the new ape genomes as definitive, to work out the timing of the ape-human split, we have to know roughly how many generations there have been since the last common ancestor. That means we need to know how old apes generally are when they reproduce. We know this reasonably well for modern apes, because we can watch them in the wild, but not for extinct ones.

Because of this uncertainty, it would be going way too far to say that Sahelanthropus is out of the hominin family based on these new ape genomes. That’s not at all how this works.

What it does show, I think, is that we could learn a lot from these new ape genomes once everyone gets stuck into them.

Here’s the thing. If Sahelanthropus really is 7 million years old, and the ape genome is revealing that our ancestors didn’t split from those of chimps and bonobos until 5.5 million years ago, then Sahelanthropus can’t be a hominin. There were no hominins at that time; it must have been an ape.

A similar problem might bedevil the next-oldest hominin, Orrorin tugenensis. The fossils are 6 million years old, right in the middle of the window for the last common ancestor. Again, if we take the dates at face value, this suggests Orrorin is either an extremely early hominin, or it’s something very close to the long-sought last common ancestor. This would be odd, because Orrorin seems to have walked upright.

You might have noticed that I put caveats on all those statements. That’s because there is some wiggle room with the date of the last common ancestor. Even if we accept the new ape genomes as definitive, to work out the timing of the ape-human split, we have to know roughly how many generations there have been since the last common ancestor. That means we need to know how old apes generally are when they reproduce. We know this reasonably well for modern apes, because we can watch them in the wild, but not for extinct ones.

Because of this uncertainty, it would be going way too far to say that Sahelanthropus is out of the hominin family based on these new ape genomes. That’s not at all how this works.

What it does show, I think, is that we could learn a lot from these new ape genomes once everyone gets stuck into them.

Here’s the thing. If Sahelanthropus really is 7 million years old, and the ape genome is revealing that our ancestors didn’t split from those of chimps and bonobos until 5.5 million years ago, then Sahelanthropus can’t be a hominin. There were no hominins at that time; it must have been an ape.

A similar problem might bedevil the next-oldest hominin, Orrorin tugenensis. The fossils are 6 million years old, right in the middle of the window for the last common ancestor. Again, if we take the dates at face value, this suggests Orrorin is either an extremely early hominin, or it’s something very close to the long-sought last common ancestor. This would be odd, because Orrorin seems to have walked upright.

You might have noticed that I put caveats on all those statements. That’s because there is some wiggle room with the date of the last common ancestor. Even if we accept the new ape genomes as definitive, to work out the timing of the ape-human split, we have to know roughly how many generations there have been since the last common ancestor. That means we need to know how old apes generally are when they reproduce. We know this reasonably well for modern apes, because we can watch them in the wild, but not for extinct ones.

Because of this uncertainty, it would be going way too far to say that Sahelanthropus is out of the hominin family based on these new ape genomes. That’s not at all how this works.

What it does show, I think, is that we could learn a lot from these new ape genomes once everyone gets stuck into them.

Michael Marshall is a science writer focused on life sciences, health and the environment. He has a BA and MPhil in experimental psychology from the University of Cambridge and an MSc in science communication from Imperial College London. He has worked as a staff journalist at New Scientist and the BBC. Since 2017, he has been a freelance writer, published by outlets including BBC Future, National Geographic, Nature, New Scientist, The Observer and The Telegraph.

New Scientist is the world’s most popular weekly science and technology publication. Our website, app and print editions cover international news from a scientific standpoint, and ask the big-picture questions about life, the universe and what it means to be human. If someone in the world has a good idea, you will read about it in New Scientist.

Since the magazine was founded in 1956 for “all those interested in scientific discovery and its social consequences”, it has expanded to include newsletters, videos, podcasts, courses and live events in the UK, US and Australia, including New Scientist Live, the world’s greatest festival of science. New Scientist is based in London and New York, with operations elsewhere in the UK, the US and Australia.