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WHAT THE COMPLETE APE GENOME IS REVEALING ABOUT THE EARLIEST HUMANS
 
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Michael Marshall
May 15, 2025
New Scientist
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_ We now have full genome sequences for six species of apes, helping
us to pin down our last common ancestor – and potentially changing
how we think of the earliest hominins _

"Bonobo TZ", by phōs graphé (CC BY-NC 2.0)

 

_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 [[link removed]]._

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)
[[link removed]] consortium, a
group of geneticists led by Adam Phillippy
[[link removed]] at the
National Human Genome Research Institute and Karen Miga
[[link removed]] 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
[[link removed]],
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
[[link removed]].
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”
[[link removed]].
DNA varies from person to person, so it isn’t possible to obtain a
single definitive genome. Instead, the Human Pangenome Reference
Consortium [[link removed]] wants to obtain genomes
from dozens of people
[[link removed]] 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.

Read more: How our ancestors invented clothing and transformed it into
fashion
[[link removed]]

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
[[link removed]]: 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
[[link removed]], 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
[[link removed]].
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
[[link removed]]. 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
[[link removed]] database reckons humans
split from the ancestors of chimps and bonobos 6.4 million years ago
[[link removed]]. A 2021 analysis put it around 7.5 million
years ago [[link removed]], while cautious
authors offer ranges like 4 million to 8 million
[[link removed]] and 5.7 million to 10
million years ago [[link removed]].

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
[[link removed]].
As I’ve explained in previous instalments of Our Human Story, it’s
not clear whether it walked upright on two legs
[[link removed]] like
a hominin, or did something more ape-like
[[link removed]] 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_
[[link removed]].
The fossils are 6 million years old
[[link removed]],
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
[[link removed]].
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_
[[link removed]].
The fossils are 6 million years old
[[link removed]],
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
[[link removed]].
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_
[[link removed]].
The fossils are 6 million years old
[[link removed]],
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
[[link removed]].
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
[[link removed]] 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 [[link removed]] is the world’s
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