The Incredible Human Journey (39 page)

I met up with Ed Green, one of the geneticists hard at work on the Neanderthal Genome Project. Ed had brought along some casts
of the original fossils from which DNA had been extracted.

‘How do you go about trying to extract DNA from these fossils?’ I asked Ed.

‘Well, the first thing is to find the fossil that has ancient DNA that can be extracted. Then the way it’s done is to simply
to take a dentist’s drill, drill a bit, get some bone powder, and then use a standard extraction method where you bind DNA
to silica beads.

‘Then the really fun part begins – trying to sequence this DNA, and see what is there. Is this DNA from the individual that
owned this bone originally? Or DNA from bugs that have crawled into the bone since then?’

‘And presumably there’s quite a lot of modern human DNA knocking around as well – from the archaeologists who excavated them,’
I suggested. Ed agreed. He was very keen to encourage archaeologists to excavate fossils in a ‘sterile’ way today, but there were many
bones that had been discovered decades ago, and handled by scores of archaeologists and curators.

The team had looked at more than seventy Neanderthal fossil bones, and tested them first to see if they were
likely
to contain any usable DNA by checking the condition of other organic molecules: amino acids. Six of the specimens had good
levels of these protein building blocks, so there was a good(ish) chance that some DNA might be in them as well. They went
on to extract DNA, but, always aware that this genetic material could come from modern people, they checked for contamination
before going any further.

A sample from a fragment of Neanderthal bone from Vindija Cave in Croatia looked particularly promising. ‘Luckily for us,
this shard of bone was not interesting enough morphologically to have been handled and looked at a lot – so this guy is nearly
free from contamination by modern humans,’ said Ed.

So the geneticists chose to try out DNA sequencing procedure on the extract from the Vindija fossil. This technology is advancing
at an astonishing rate. Inside insignificant looking white boxes in genetics labs there are small trays holding hundreds
of wells of DNA fragments. And the genetic material they are dealing with is
very
fragmentary: over time, long stretches of DNA that start off with millions of base pairs become broken and broken again into
short sections of just a few hundred or tens of base pairs each. So the process involved sequencing those fragments and then
virtually sticking them back together. New technology meant that many different fragments could be sequenced at the same time.
‘The throughput for DNA sequencing is hundreds of times more than it was just three or four years ago,’ Ed told me.

He explained the sequencing method in a very visual way (considering you can’t actually open up the box and watch it in action).
In each well, there were many copies of one strand of DNA, and the machine worked out the sequence by ‘asking’ each strand
what nucleotide base (A, C, T or G) was next. It did this by flowing a solution over the wells containing each base in turn.
If the ‘next’ base was T, the solutions of A, C and G would flow over uneventfully. When the solution containing T was introduced,
enzymes would grab the base and at the same time emit a flash of light. This is called ‘pyrosequencing’. ‘Every flow, you’ve
got different wells lighting up, like a firework display,’ said Ed. Every time a nucleotide solution passed through, some
of the wells would answer ‘yes’ by emitting a flash. The machine cycled on and on, until all the strands in all the wells
had been sequenced. This technique can read segments of 100–200 nucleotides in length: perfect when you’re looking at tiny
fragments of an ancient genome.

Many of the sequences had turned out to be bacterial, but that’s exactly what the geneticists expected. But comparing the
sequenced fragments with human, chimpanzee and mouse genomes, a good percentage of them looked primate. Then came the work
of assembling those sequenced fragments into longer pieces. Eventually, if they managed to extract enough fragments, the geneticists
would be able to sequence the entire Neanderthal genome.
⁶

Analysis of Neanderthal DNA should be able to cast light on many areas of enquiry, not only the question of hybridisation.
By comparing the differences between Neanderthal and modern human DNA, the geneticists can estimate the time of the ‘split’
between the lineages. At the moment, in Leipzig, that’s looking as though it happened some time around 516,000 years ago.
This is older than the split suggested by fossils, at about 400,000 years ago – but that’s unsurprising. The genetic split
would have happened in a population that was still ‘together’.

This is ground-breaking science, so it’s not surprising that there are still problems that need to be ironed out. And probably
the most tricky one is that problem of contamination with modern DNA, which could skew results. Pääbo’s Leipzig lab isn’t
the only place where Neanderthal genome sequencing is going on. A team led by Edward Rubin, in California, are also at it
– and they published their first chunk of Neanderthal sequence in the same week as Pääbo’s team. But they came up with different
results and a different – even earlier – prediction for the divergence of Neanderthals and modern humans, of around 706,000
years ago.
⁷
So it seems that, even with all that careful screening, some contamination may have crept in, explaining the earlier dates
coming out of the Leipzig lab.
⁸
With each lab acting as a check on the other, though, the scientists hope that they will be able to overcome these teething
problems.
⁹
The Californian dates may seem very early indeed, but it’s important to remember that this is the predicted date of divergence
of the mtDNA lineages, not of the actual populations. Based on this genetic data, Rubin’s team estimated that the population
split happened about 370,000 years ago, which is quite a good match with the fossil data.

Another potential application for ancient DNA is in identifying bone fragments that are too small to characterise on the basis
of size and shape. In fact, this has already been applied to fossils from at least two sites. A child skeleton from Teshik Tash in Uzbekistan
has often been held up as the most easterly example of a Neanderthal, but some have disputed its credentials. Even further
east, bones and teeth from Okladnikov Cave in Siberia, found alongside Mousterian tools, were too broken up for it to be decided
if they were modern human or Neanderthal. Genetics to the rescue, then. Scientists working in labs in Leipzig and in Lyons
independently extracted and analysed the mtDNA from the bones from both sites. The results showed that the Teshik Tash child
had Neanderthal mtDNA, and so did two of the bone fragments from Okladnikov.
¹⁰
This study was very significant: it hugely extended the known range of Neanderthals to the east, right into Central Asia.
Maybe they even got to Mongolia and China. Genetic analysis is clearly an exciting addition to the toolkit of the Palaeolithic
archaeologist.

There is also exciting potential for finding out – at some point in the distant future, when we know a lot more about the
functions of genes in us and other animals – more about Neanderthal biology.
⁶
But even now we know that at least some Neanderthals possessed a version of a gene that probably gave them red hair. The
gene in question is
melanocortin 1
receptor
(or ‘mc1r’). In modern humans today, mutations that impair the function of this receptor gene produce red hair and pale skin.
A team of geneticists managed to extract DNA – including part of the mc1r gene, from two Neanderthal fossils, one from Spain
and another from Italy. Both fossils contained a mutated version of the mc1r gene, different from any of the variants seen in modern humans. To see
what effect this gene would have, scientists inserted it into cells in the lab and found that it had a partial loss of function
– like the other variations in the mc1r gene that produce red hair in humans today.
¹¹
It is important to note that this is a
different
mutation from that in modern human redheads. It doesn’t imply any genetic mixing between Neanderthals and modern humans, and it certainly doesn’t suggest that the redheads
among us are Neanderthals!

Another particular gene that has been identified in Neanderthals is FOXP2. This is a gene that has two specific differences
in humans compared with other living primates. People missing out on those human-specific changes to FOXP2 have problems in
both producing and understanding speech. Analysis of FOXP2 in living people suggested that it appeared and swept through the
human population about 200,000 years ago, which seemed to fit quite well with the appearance of modern humans in Africa. It
suggests that ‘modern’ language and symbolic behaviour are uniquely human attributes, with a biological basis. Eric Trinkaus
took issue with this interpretation. He argued that there was evidence for symbolic behaviour in the Neanderthal archaeological
record, with intentional burial, for instance. And he found it hard to imagine how complex subsistence strategies would have
appeared – from around 800,000 years ago – without complex social communication. And yet the ‘human’ version of FOXP2 was
initially estimated to have arisen well after the split between modern human and Neanderthal lineages.
¹²
But a recent DNA study of two Spanish Neanderthal fossils showed that they both carried the ‘human’ form of FOXP2.13 For Trinkaus,
this showed that the ‘much maligned Neanderthals’ had a degree of human behaviour that was reflected in the archaeological
record but that he felt had often been played down. But how can we explain the same version of FOXP2 existing in both modern humans and Neanderthals? Either it is much older
than the earlier studies suggested, and was present in the ancestors of modern humans and Neanderthals, or it has passed from
one population to the other by gene flow. The latter seems very unlikely as no other genetic studies to date had produced
any evidence of gene flow.
¹³

But what about the ambitious Neanderthal Genome Project? Was there any evidence for hybridisation emerging from the nuclear
DNA? The key to looking for evidence of hybridisation was to concentrate on genes or other bits of chromosomes that are specific
to modern Europeans (and this is a tall order as most genetic differences are shared between populations across the globe
rather than being specific to one area), keeping an eye out for these sequences in the Neanderthal genome. If any European-specific DNA sequences were found in Neanderthals, this would strongly imply that there had been some sharing of genes between Neanderthals
and modern humans in Europe.

When I visited the Max Planck Institute in the early summer of 2008 Ed told me that they had managed to sequence about 5 per
cent of the Neanderthal genome. I asked him a difficult question, considering that the Neanderthal Genome Project was still
such a long way from completion: ‘If chimpanzees are about 1.3 per cent different from us, in terms of the sequence of DNA,
do you have a feeling for how different the Neanderthal genome is going to be from ours?’

‘Yes, we do,’ he replied. ‘It’s looking about ten times closer than the chimpanzee. But Neanderthals are so closely related
to us, it’s hard to speak in terms of percent differences. It really depends on which Neanderthal and which human you’re talking
about.’

‘And have you seen any suggestion at all of hybridisation with modern humans?’ I asked.

‘No. There’s no evidence to date of any hybridisation between modern humans and Neanderthals,’ he replied. ‘But by the end
of the summer we should have 65 per cent of the Neanderthal genome, so we’ll be able to give a much more definitive answer
then.’

This question of what happened when modern humans walked into Neanderthal territory was fascinating. I asked Ed what he would
have done if he’d met one of our cousins.

‘If I came face to face with a Neanderthal, the first thing I would do is ask for a DNA sample,’ said Ed, ever the scientist.

So far, then, Neanderthal genetics has shed light on how far this ancient species ranged across Europe and Asia, has shown
that they possessed the same ‘language gene’ as modern humans (although it must be stressed that the development of language
cannot be linked to just one gene), and that some of them had red hair. And, bearing in mind that there was still a lot of
genome left to sequence, there was no evidence – yet – for any mixing between Neanderthals and modern humans in Europe. (Nearly
a year after I visited Leipzig, Svante Pääbo announced the completion of the first draft of the Neanderthal genome – 63 per
cent of it, over three billion bases – at the annual meeting of the American Association for the Advancement of Science in
Chicago. There was still no sign of interbreeding with modern humans.)
¹⁴

But it’s also important to remember that the conclusions from genetic studies like this can never rule out
any
hybridisation. Perhaps it’s just that Neanderthal lineages have not survived to the present day, and maybe some Neanderthals
had modern human genes – just not the ones whose genomes were being sequenced.

Does this make the whole endeavour futile? Far from it. If there is no evidence of mixing, then we can at least say that hybridisation
didn’t happen at a level that we could consider to be significant, and so it cannot explain the apparent disappearance of
Neanderthals from the fossil and archaeological record: they cannot have been absorbed and assimilated into ‘modern’ populations.

Thus far, all the genetic studies suggest that any hybridisation was, at the most, insignificant. And, actually, when you
take a closer look at when and where Neanderthals and modern humans were living in Ice Age Europe, this makes some sense.
There are only two areas where the dates for modern humans and Neanderthals actually coincide: in southern France and in south-west
Iberia, in the period between 25,000 and 35,000 years ago.
¹⁵
Even then, they could have missed each other by hundreds or thousands of years, so the opportunities for inter-species sex
would have been extremely few and far between anyway. So it’s not really surprising that no ‘Neanderthal’ genes have been
found in the modern gene pool – or vice versa.