New Scientist - USA (2022-04-09)

9 April 2022 | New Scientist | 9

THE genomes of more than
600 plants, animals and fungi
that went extinct tens or even
hundreds of millions of years ago,
leaving no physical trace on Earth,
have been partially reconstructed
by rewinding the evolutionary
history of their living descendants.
This has given us the best pictures
so far of the genomes of various
distant ancestors of humans,
from the ancestor of monkeys
and apes all the way back to the
ancestor of the first amphibians
and of all vertebrates.
Almost all that we know about
past life comes from fossils. As
important as they are, most fossil
species aren’t the direct ancestors
of the organisms alive today. For
instance, almost all dinosaurs
died out, with just one branch
surviving in the form of birds.
“It’s not easy to connect a fossil to
modern species, because you don’t
know where it is in the tree of life,”
says Hugues Roest Crollius at the
École Normale Supérieure in Paris.
Unlike fossils, however, the
genomes of living creatures give
us a direct link to their ancestors,
he says. Genomes are a record of
evolutionary history going back to
the dawn of life. And by comparing
the genomes of two or more
related species, it is possible to

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Elephants, bats, lemurs

and frogs are just some of

the organisms analysed

Ancestral genomes could help

efforts to resurrect species such

as the woolly mammoth.

Several groups hope to create

animals that resemble extinct

species by sequencing the DNA in

preserved samples, then editing

the genome of a close living

relative to make it a good match

for the extinct species.

The problem with this approach,

says Thomas Gilbert at the

University of Copenhagen in

Denmark, is that ancient DNA

breaks into lots of little pieces. The

only way to reassemble them is to

use the genome of a living relative

as a guide. But both the extinct and

living species will have changed

since splitting from their common

ancestor, so the reassembled

ancient genome will have some

key parts missing.

In a 2020 study, Gilbert and

his colleagues showed that

reconstructing the genome of a

common ancestor and using that as

a guide can improve the accuracy

of reassembled ancient genomes.

“If you halve the evolutionary

divergence by reconstructing the

ancestor, it can improve the amount

of data you can reconstruct from

your crappy ancient DNA, as you

are mapping to a reference that

is closer,” says Gilbert.

Could we bring back extinct species?

effectively rewind those historical

changes to work out the genome

of a shared ancestor.

Biologists have been doing this

ever since the genomes of different

species started to become available.

In 2017, for instance, Denis Larkin

at the Royal Veterinary College,

University of London, and his

colleagues used a computer

algorithm to partially reconstruct

the genomes of seven ancestors

of humans, including the ancestor

of a group called Boreoeutheria

that contains most placental

mammals, and which lived

around 95 million years ago.

Since then, the genomes of

thousands more species have been

sequenced. This means ancestral

genomes can be reconstructed

more accurately, but it also poses

a challenge in terms of the amount

of processing power required. So

Roest Crollius and his colleagues

have developed a streamlined

algorithm that works out which

genes an ancestor had and the

order in which they were arranged

along chromosomes.

Because more genomes are

available and the algorithm is so

fast, Roest Crollius’s team has been

able to reconstruct hundreds of

ancestral genomes. They include

the 45-million-year-old ancestor

more accurately and with greater

resolution, and also it goes further

back in time,” says Roest Crollius.

Many other ancestral genomes

have never been reconstructed

before. These include the ancestor

of lemurs, bushbabies and lorises,

and the ancestor of bats.

With even more genomes and

processing power, it may become

possible to work out the genetic

code of ancestral genes. But

reconstructing the sequence

of the non-coding DNA between

genes isn’t feasible, says Roest

Crollius, as it changes too fast.

“Nobody will be able to go back

very far in time reconstructing

entire genomes,” he says.

In most species, much of this

non-coding DNA is junk, consisting

of thousands of mutated copies

of genetic parasites known as

transposons. But some non-coding

DNA helps regulate gene activities

and plays an important role in

evolution – and without this

regulatory DNA, it will be

impossible to resurrect extinct

species, says Roest Crollius. ❚

of monkeys and apes including us,

the 50-million-year-old ancestor

of grasses and the 102-million-

year-old ancestor of placental

mammals including elephants.

The team even reconstructed

the ancestor of all vertebrates

and of all tetrapods (amphibians

and their descendants), but

these ancient genomes are

incomplete and fragmentary

(bioRxiv, doi.org/hpdk).

The researchers say their

reconstructions closely match

previous ones where they exist,

but are more complete. “Our

approach does reconstructions

Michael Le Page

Genomes of extinct species revealed

by massive analysis of living organisms