The Journey of Man: A Genetic Odyssey (20 page)

Neanderthals were the first hominid ancestor to be discovered, at
that cave in the Neander Valley back in 1856. In spite of the initial reluctance to accept the fact of human evolution, within a few decades most people came to believe that Neanderthals were the ancestors of modern Europeans. The genetic studies of the 1980s, however, called into question this theory. If mitochondrial DNA told us that everyone had come out of Africa relatively recently, how could modern Europeans have evolved from a hominid like the Neanderthal, present in Europe from around 250,000 years ago? It was a contentious question, with anthropologists such as Milford Wolpoff of the University of Michigan insisting that the DNA evidence was wrong, and that Europeans were Neanderthal under the skin.

The only problem with inferring details about the past from data collected in the present is, as we saw in
Chapter 2
, that you need to make use of theories of how DNA sequences actually change over time. These theories, although supported by generations’ worth of genetic and evolutionary research, are still theories. Unfortunately, it’s impossible to go back in time and check the evidence in order to confirm whether our theoretical inferences are valid. Or is it? Can we study the DNA of our long-dead ancestors?

The field of ancient DNA research was pioneered in the 1980s by Svante Pääbo and his colleagues (including Allan Wilson, of mitochondrial Eve fame) in Berkeley and Munich. The impetus behind this work was to do the impossible – to go back in time by examining the DNA that existed in a long-dead individual. It was, in effect, an attempt to develop a genetic time machine that would allow us to answer questions about our ancestors directly. One of the first applications was in the analysis of DNA from Egyptian mummies, but soon people were trying it on fossils that were millions of years old. Michael Crichton’s novel
Jurassic Park
was based on the heady early days of the field, when it seemed that anything would be possible – even getting intact dinosaur DNA from bloodsucking insects embedded in amber!

While the claims for successful retrieval of DNA from sources that were tens of millions of years old eventually proved unfounded, usually resulting from minute amounts of contamination by modern DNA, it was sometimes possible to retrieve DNA from more recent samples, or those that had been preserved in ideal conditions for tens of thousands of years. The frozen bodies of mammoths and ancient alpine
travellers yielded analysable DNA, as did the dried remains from mummies and other desert-dwellers. Even then, the analysis was almost always limited to mitochondrial DNA, present in huge numbers of copies in every cell – making it more likely that one copy would have survived the Russian roulette of molecular degradation over the centuries. It was still extremely difficult to do this sort of analysis, though, because in most cases the molecules had completely disintegrated after death. This meant that negative results were far more common than positives – but the stories revealed by the tiny fraction of cases where DNA could be successfully extracted made the effort worthwhile. It was with this in mind that Pääbo’s group had developed reliable ways of evaluating and extracting DNA from ancient samples, and his laboratory represented the state of the art in the early 1990s – they were the undisputed experts in the field.

The scientific coup that led to my near-death experience in San Francisco actually began with the very first Neanderthal bones to be unearthed. Comprising the so-called type specimen – the one against which all the others were judged by palaeoanthropologists – these bones had sat in a museum in Bonn for nearly 140 years when the Munich group was approached to do the analysis on them. Pääbo jumped at the chance, and his graduate student Matthias Krings performed the DNA analysis as part of his PhD thesis work. In over a year of tedious trial-and-error work, Krings gradually managed to extract enough intact mitochondrial DNA to create a 105-base-pair sequence. What he saw when he pieced it together was extraordinary. Krings relates the first glimpse of the 40,000-year-old DNA:

I basically knew the sequence by heart … and I was certainly able to spot a substitution [DNA sequence change] when I saw one. After looking over the first sequence, I had something crawl down my spine. There were eight substitutions in a region which usually had – at most – three or four. I thought, ‘This is a very funny sequence.’

After painstakingly reproducing the result from a separate bone fragment, and duplicating the experiment in a laboratory on a different continent (to be certain that a contaminant in the Munich laboratory was not producing an experimental artefact), he accepted the validity
of the sequence. By repeating the procedure several times, he eventually managed to obtain 327 base pairs of mitochondrial DNA sequence from the remains – enough to generate a statistically significant estimate of its evolutionary divergence. The sequence was clearly not from modern human mtDNA, but it didn’t belong to an ape either. Rather, it came from a hominid that last shared a common ancestor with modern humans around 500,000 years ago. This date was consistent with what was predicted by palaeoanthropologists who had studied the dispersal of so-called ‘archaic humans’ from Africa into Europe, and it proved that Neanderthal was not the direct ancestor of modern humans. Rather, Neanderthals represented a local population of archaic hominids who were later replaced by modern
Homo sapiens
– with no detectable admixture. Of the thousands of human mitochondrial sequences that have been obtained from people all over the world, not one is anywhere near as divergent as Krings’ Neanderthal sequence. Neanderthals fall well outside the range of genetic variation found in the human species – and therefore they represent a
separate
species. This early result has been confirmed by two additional genetic studies of Neanderthal remains from different parts of Europe, showing that the Neanderthals were closely related to each other, but very distantly related to us. The genetic data is incontrovertible – modern Europeans trace their recent ancestry to Africa, in common with everyone else in the world.

Along with the study of 12,000 Asian Y-chromosomes discussed in the last chapter, the Neanderthal results placed the final nail in the coffin of multiregionalism. Our hominid relatives were clearly replaced by modern humans who spread out of Africa within the past 50,000 years. While there are still a few anthropologists who argue for a multiregional model of human evolution, most have accepted that there simply is no compelling evidence for it. The ghost of Carleton Coon has finally been laid to rest by modern molecular biology. But, you might be thinking, if the Neanderthals were replaced, who replaced them?

In the autumn of 1922 two teenaged boys entered a cave near Cabrerets, France (a two-hour drive north-east from Toulouse). Against the advice of their parish priest, with whom they had first entered the cave in 1920, they were intent on exploring it more fully. What they saw there was extraordinary. The paintings at Pech Merle (as the cave was christened) were later called the ‘Sistine Chapel’ of the region by Abbé Henri Breuil, the French expert on ancient cave art. His detailed research on dozens of French caves was to reveal a rich artistic tradition dating back over thirty millennia, giving a unique insight into the minds of Palaeolithic Europeans.

The images painted and drawn on the walls here and at other Upper Palaeolithic sites in Europe show clear evidence of conceptual, abstract thought – the earliest such evidence in the world. The extraordinarily detailed artwork at Chauvet cave has been dated to around 32,000 years ago, the oldest in France. Recently discovered drawings at Fumane cave, near Verona in northern Italy, may date from as early as 35,000 years ago, which would make them the oldest examples of cave art anywhere in the world. In all these locations, the complexity of the subjects, and the skill with which they are rendered, marks an abrupt transition from the past. In effect, they are detailed time capsules left by early Europeans – beautifully crafted snapshots of their lives, hidden away inside sealed caves until they were discovered in the nineteenth and twentieth centuries.

The inhabitants of these European caves were clearly talented artists, and their culture marks a distinct departure from that of the Neanderthals that preceded them. It marks the beginning of the Upper Palaeolithic in Europe, and broadcasts the arrival of fully modern humans on the scene. Along with the diverse tools they left, their art gives us a fleeting glimpse into the minds of the people who created it. But were these first European artists – the creators of Pech Merle, Chauvet and Fumane – the ancestors of western Europeans? And if so, why did they appear on the scene so suddenly, around 35,000 years ago? The genetic data gives us the clues we need to solve this puzzle.

We saw earlier that the most obvious location from which to enter
Europe, the Middle East, appears to have contributed little to the gene pool of modern Europeans. The Y-chromosome lineage defined solely by M89, which would have characterized the earliest Middle Eastern populations around 45,000 years ago, is simply not very common in western Europe. It is such a tiny hop across the Bosporus from the Middle East to Europe that we might ask why it took so long – perhaps 10,000 years – for modern humans to make a significant foray into western Europe. To solve this riddle of where the majority of Upper Palaeolithic Europeans came from – we need to examine the genetic markers in western Europe and ask which Eurasian lineage they could have come from, and when.

I said at the beginning of
Chapter 5
that my Y-chromosome is defined by a marker known as M173. It turns out that this marker is not unique to me – in fact, it is found at high frequency throughout western Europe. Intriguingly, the highest frequencies are found in the far west, in Spain and Ireland, where M173 is present in over 90 per cent of men. It is, then, the dominant marker in western Europe, since most men belong to the lineage that it defines. The high frequency tells us two things. First, that the vast majority of western Europeans share a single male ancestor at some point in the past. And second, that something happened to cause the other lineages to be lost.

The first thing most of us want to know when we hear that almost all western Europeans trace their family line back to one man is ‘when did he live?’ This is where our absolute dating methods come in. If we examine genetic variation – polymorphisms – on the M173 chromosomes, we can estimate how long it would have taken for our mutational clock to create it. But if all of the chromosomes are M173, how can we study variation? Surely they are all identical?

Fortunately for us, they are not. While all of them are very closely related, and thus share the M173 marker, there are other markers that help to distinguish them. Unlike the stable markers we have studied to define the order – or relative dates – of the Y-chromosome lineages, these other markers do not involve simple one-letter changes in the
genetic code. Rather, they exist because of a biochemical speech impediment. When we replicate our DNA, the double strands of the molecule open up and tiny machines known as polymerases actually do the hard work of assembling the complementary copy. Remember that if we know the sequence of one strand of the double-stranded DNA molecule, then we also know the other, because of the inviolable rules of molecular biology. A always pairs with T, and C always pairs with G. This works very well for more than 99 per cent of the genome, where the letters occur in a unique order and it is easy to tell how the pairing should work. Unfortunately, a small fraction of our genome is not so simple. It consists of what are known as tandem repeats – short sections of the same sequence, repeated several times in a row in the DNA strand. These often take the form of a couple of letters, such as CACACACACA …, but there can be three, four or more letters in the motif that is repeated. As you might expect, the polymerase can become confused when it encounters these parts of the genome. After all, if there are a dozen or more repeats, how can you tell where you are in the sequence – is it repeat number ten or eleven? So, in a reasonable number of cases (about one in every thousand), the polymerase makes a mistake when it is assembling the complementary strand, and adds or subtracts a repeat. If the original strand had twelve repeats, the copy may have eleven or thirteen – simply by chance, due to an error at the molecular level. It is a process that Luca Cavalli-Sforza has called genetic ‘stuttering’.

One in a thousand may not seem like a very common event, but it is when we are talking about the work of DNA copying. If that was the rate at which polymerases made single-letter copying mistakes, then we would introduce an average of over a million mistakes, or mutations, into our DNA every time it was copied. Since genetic copying takes place when we are having offspring, this means that each child would be born with over a million new mutations. Biology takes a dim view of this level of mutation, and it is likely that the child would die of a horrible inherited disease – if it were born at all. Thus, the usual rate at which new mutations appear is much more sedate, perhaps twenty or thirty per generation. This is around 100,000 times lower than the mutation rate we see for repeats, which means that new mutations in ‘regular’ sequences are much less common than those in
repeats. The repeats are on an evolutionary speedway, accumulating diversity at an extraordinary pace.

While this has very little effect on the health of the child, since repeats are usually found in regions of the genome that do not affect well-being, it does give us a tool for studying diversity. These repeats, known as microsatellites, are particularly valuable when we want to ask questions about variation on lineages where we do not have much single-letter variation – such as the M173 chromosomes. They give us a way to determine absolute dates that we can use to test our hypotheses about the timing of human migrations. The rate at which mutations occur is roughly constant, so the level of variation tells us how long they have been mutating. This tells us how old the chromosome is, because all of the chromosomes descend from a single chromosome at some point in the past. By definition, the level of variation at this point was zero, since there was only one copy.