New Scientist - USA (2020-09-12)

12 September 2020 | New Scientist | 41

two species share, the more likely they are

to be closely related. Proteins are suitable

for this sort of evolutionary analysis because

animals typically produce equivalent versions

of the same proteins – collagen, keratin,

haemoglobin and so on – and because the

sequence of amino acids within these

proteins can differ slightly between species.

This means that if you extract large chunks

of particular proteins from extinct hominins

and read their amino acid sequences, you

can use that to work out how they relate to

one another, and to living humans.

There are some caveats. Although the

human body contains tens of thousands

of distinct proteins, surprisingly few of these

are found in the tissues that readily become

fossilised. Teeth are a good example. Tooth

enamel preserves ancient proteins very well,

but even in a living human it contains just

10 or so different proteins, says Frido Welker,

also at the University of Copenhagen. Each

protein is generally 50 to 2000 amino acids

long, so even if all the proteins found in

enamel – the “enamel proteome” – are

recovered from a fossil tooth, there might be

a combined sequence of about 20,000 amino

acids at most. For comparison, a complete

ancient human genome contains a genetic

sequence billions of base pairs long. The

question then is: do ancient proteomes

contain enough information to build a

reliable evolutionary tree?

Recent work suggests they do. Over the

past five years, this approach has been used

to construct evolutionary trees for various

ancient mammals. A 2019 analysis of

sloths, for instance, looked so different

to conventional evolutionary trees for

this group of animals that it was viewed

suspiciously by some people in the field. But

in a second study, geneticists independently

analysed sloth relations using a tried-and-

trusted DNA analysis and it gave essentially

the same result as the protein study.

The field of palaeoproteomics, as it is

known, has now moved into the realm

of primates. Last year, Welker and Enrico

Cappellini, also at the University of

Copenhagen, led an analysis of an ancient

enamel proteome taken from the largest

of extinct apes, Gigantopithecus. The

information it contained suggested that the

ancient primate, which lived in South-East

Asia until about 300,000 years ago, was

BE

NC

E^ V

IOL

A,^ M

AX

PL

AN

CK

IN

ST

ITU

TE

FO

R^ E

VO

LU

TIO

NA

RY

AN

TH

RO

PO

LO

GY

Denisova cave in Siberia, where

archaeologists discovered an

entirely new group of humans

“ We are missing

vital genetic

information from

most of human

evolutionary

history”

analysis of DNA from living people and
samples from a handful of ancient humans
who lived in cooler parts of Eurasia within
the past 50,000 years. We could learn a
lot more by analysing even older genetic
material, but DNA tends to fall apart over
such time spans. That means we are missing
vital genetic information from most of
human evolutionary history, which arguably
began around the time that H. erectus
evolved and began spreading across Africa
and Eurasia. Furthermore, DNA is completely
silent on our earlier, more ape-like hominin
ancestors that lived in Africa between about
7 million and 2 million years ago.
This is where proteins can help. Large
and complex molecules, they are built
from smaller components, amino acids, that
occur in sequences according to instructions
encoded in genes, so they contain the same
sort of information as DNA. We have known
for 65 years that proteins, or at least bits
of them, might survive in the fossil record.
The problem was that studying them was
always too fiddly and difficult.
Things changed at the beginning of the
21st century with the development of new
techniques. They involved adding electrically
charged ions to the ancient and fragile
protein fragments, which means the
molecules can be run through a machine
called a mass spectrometer to quickly
identify their amino acid sequence. Ancient
protein research took a huge leap forward.
“Anyone can do this,” says Collins.
And they have every reason to. Analysing
fragments of protein in this way can offer
insights into ancient human behaviour,
including what sort of foods people ate
and even clues about their sex lives (see
“Extracting insights into ancient lives”,
page 43). Extract larger chunks of ancient
protein, however, and you might be able
to work out where our strange cousins
belong in the hominin family tree.
Biologists build evolutionary trees by
examining similarities and differences
between species, whether in terms of their
physical appearance or their molecular
make-up. By and large, the more similarities

RO

BE

RT

CL

AR

K/N

AT

ION

AL

GE

OG

RA

PH

IC^ C

RE

AT

IVE

>