The Journey of Man: A Genetic Odyssey

by Spencer Wells

  Rebecca Cann, as part of her PhD work in Wilson’s laboratory, began to study the pattern of mtDNA variation in humans from around the world. The Berkeley group went to great lengths to collect samples of human placentas (an abundant source of mtDNA) from many different populations – Europeans, New Guineans, Native Americans and so on. The goal was to assess the pattern of variation for the entire human species, with the aim of inferring something about human origins. What they found was extraordinary.

  Cann and her colleagues published their initial study of human mitochondrial diversity in 1987. It was the first time that human DNA polymorphism data had been analysed using parsimony methods to infer a common ancestor and estimate a date. In the abstract to the paper they state the main finding clearly and succinctly: ‘All these mitochondrial DNAs stem from one woman who is postulated to have lived about 200,000 years ago, probably in Africa.’ The discovery was big news, and this woman became known in the tabloids as Mitochondrial Eve – the mother of us all. In a rather surprising twist, though, she wasn’t the only Eve in the garden – only the luckiest.

  The analysis performed by Cann and her colleagues involved asking how the mtDNA sequences were related to each other. In their paper they assumed that if two mtDNA sequences shared a sequence variant at a polymorphic site (say, a C at a position where the sequences had either a C or a T), then they shared a common ancestor. By building up a network of the mtDNA sequences – 147 in all – they were able to infer the relationships between the individuals who had donated the samples. It was a tedious process, and involved a significant amount of time analysing the data on a computer. What their results showed were that the greatest divergence between mtDNA sequences was actually found among the Africans – showing that they had been diverging for longer. In other words, Africans are the oldest group on the planet – meaning that our species had originated there.

  Figure 2 Proof that modern humans originated in Africa – the deepest split in the genealogy of mtDNA (‘Eve’) is between mtDNA sequences from Africans, showing that they have been accumulating evolutionary changes for longer.

  One of the features of the parsimony analysis used by Cann, Stoneking and Wilson to analyse their mtDNA sequence data is that it inevitably leads back to a single common ancestor at some point in the past. For any region of the genome that does not recombine – in this case, the mitochondrion – we can define a single ancestral mitochondrion from which all present-day mitochondria are descended. It is like looking at an expanding circle of ripples in a pond and inferring where the stone must have dropped – in the dead centre of the circle. The evolving mtDNA sequences, accumulating polymorphisms as they are passed from mother to daughter, are the expanding waves, and the ancestor is the point where the stone entered the water. By applying Zuckerkandl and Pauling’s methods of analysis, we can ‘see’ the single ancestor that lived thousands of years ago, and which has mutated over time to produce all of the diverse forms that exist today. Furthermore, if we know the rate at which mutations occur, and we know how many polymorphisms there are by taking a sample of human diversity from around the globe, then we can calculate how many years have elapsed from the point when the stone dropped – in other words, to the ancestor from whom all of the mutated descendants must have descended.

  Crucially, though, the fact that a single ancestor gave rise to all of the diversity present today does not mean that this was the only person alive at the time – only that the descendant lineages of the other people alive at the same time died out. Imagine a Provencal village in the eighteenth century, with ten families living there. Each has its own special recipe for bouillabaisse, but it can only be passed on orally from mother to daughter. If the family has only sons, then the recipe is lost. Over time, we gradually reduce the number of starting recipes, because some families aren’t lucky enough to have had girls. By the time we reach the present century we are left with only one surviving recipe – la bouillabaisse profonde. Why did this one survive? By chance – the other families simply didn’t have girls at some point in the past, and their recipes blew away with the mistral. Looking at the village today, we might be a little disappointed at its lack of culinary diversity. How can they all eat the same fish soup?

  Of course, in the real world, no one transmits a recipe from one generation to the next without modifying it slightly to fit her own tastes. An extra clove of garlic here, a bit more thyme there, and voilà! – a bespoke variation on the matrimoine. Over time, these variations on a theme will produce their own diversity in the soup bowls – but the recipe extinction continues none the less. If we look at the bespoke village today we see a remarkable diversity of recipes – but they can still be traced back to a single common ancestor in the eighteenth century, thanks to Ock the Knife. This is the secret of Mitochondrial Eve.

  The results from the 1987 study by Cann and her colleagues were followed up by a more detailed analysis a few years later, and both studies pointed out two important facts: that human mitochondrial diversity had been generated within the past 200,000 years, and that the stone had dropped in Africa. So, in a very short period of time – at least in evolutionary terms – humans had spread out of Africa to populate the rest of the world. There were some technical objections to the statistical analysis in the papers, but more extensive recent studies of mitochondrial DNA have confirmed and extended the conclusions of the original analysis. We all have an African great-great … grandmother who lived approximately 150,000 years ago.

  Darwin, in his 1871 book on human evolution The Descent of Man, and Selection in Relation to Sex, had noted that ‘in each great region of the world the living mammals are closely related to the extinct species of the same region. It is therefore probable that Africa was formerly inhabited by extinct apes closely allied to the gorilla and chimpanzee; and as these two species are now man’s nearest allies, it is somewhat more probable that our early progenitors lived on the African continent than elsewhere.’ In some ways this statement is incredibly far-sighted, since most nineteenth-century Europeans would have placed Adam and Eve in Europe or Asia. In other ways it is rather trivial, since apes originated in Africa around 23 million years ago, so if we go back far enough we are eventually bound to encounter our ancestors in this continent. The key is to give a date – and this is why the genetic results were so revolutionary.

  Anthropologists such as Carleton Coon had argued for the origin of human races through a process of separate speciation events from ape-like ancestors in many parts of the world. This hypothesis became known as multiregionalism, and it persists in some anthropological circles even today. The basic idea is that ancient hominid, or humanlike, species migrated out of Africa over the course of the past couple of million years or so, establishing themselves in east Asia very early on, and then evolving in situ into modern-day humans – in the process creating the races identified by Coon. To understand why this theory was so widely accepted, we need to leave aside DNA for a while and rummage around in some old bones.

  Dutch courage

  Linnaeus named our species Homo sapiens, Latin for ‘wise man’, because of our uniquely well-developed intellect. Since the nineteenth century, however, it has been known that other hominid species existed in the past. In 1856, for instance, a skull was discovered in the Neander Valley of western Germany. In pre-Darwinian Europe the bones were originally thought to be the remains of a malformed modern human, but it was later found to be a widespread and distinct species of ancestral hominid, christened Neanderthal Man after the site of its discovery. This was the first scientific recognition of a human ancestor, and provided concrete evidence that the hominid lineage has evolved over time. By the end of the nineteenth century the race was well and truly on to find other ‘missing links’ between humans and apes. And in 1890 a doctor working for the Dutch East India company in Java hit the jackpot.

  Eugène Dubois was obsessed with human evolution, and his medical appointment in the Far East was actually part of an elaborate p
lan to bring him closer to what he saw as the cradle of humanity. Born in 1858 in Eijsden, Holland, Dubois specialized in anatomy at medical school. By 1881, he had been appointed as an assistant at the University of Amsterdam, but he found academic life to be too confining and hierarchical. So, in 1887, he packed up his worldly belongings and convinced his wife to set off with him on a quest to find hominid remains.

  Dubois believed that humans were most closely related to gibbons, a species of ape only found in the Indo-Malaysian archipelago. This was because of their skull morphology (lack of a massive, bony crest on the top and a flatter face than that found in other apes) and the fact that they sometimes walked erect on their hind legs – both reasonable enough pieces of evidence, he thought, to look for the missing link in south-east Asia. His first excavations in Sumatra yielded only the relatively recent remains of modern humans, orang-utans and gibbons, but when he turned his attention to Java his luck changed.

  In 1890 Dubois was sifting through fossils recovered from a river-bank at Trinil, in central Java, when he found a rather odd skullcap. To him it looked like the remains of an extinct chimpanzee known as Anthropopithecus, although without benefit of a good anatomical collection for comparison (he was in a colonial outpost, after all) it was difficult to be certain. The following year, however, a femur recovered from the same location threw the specimen into a whole new light. The leg bone was clearly not from a climbing chimpanzee, but rather from a species that walked upright. His calculations of the cranial capacity, or brain size, of the new find, in combination with its upright stance, led him to make a bold leap of faith. He named the new species Pithecanthropus erectus, Latin for ‘erect ape-man’. This was the missing link everyone had been searching for.

  The main objection to Dubois’ discovery – battled out in public debates and carefully worded publications over the next decade – was that there was very little evidence that the skull and femur (and a tooth that was later found at the site) had actually come from the same individual. They were excavated at different times, and the relationship between the soil layers from which they had been recovered was unknown. Later finds of Pithecanthropus did reveal the Trinil femur to be anomalous, and it seems likely that it actually belongs to a more modern human. The tooth may well be that of an ape. Despite this, and despite Dubois’ incorrect assertion that the remains proved that modern humans had originated in south-east Asia from gibbon-like ancestors, the discovery of the Trinil skullcap was a watershed event in anthropology. The Javanese ape-man was clearly a long-extinct human ancestor – one with a cranial capacity much lower than our own, but still far above the range seen in apes. Although he got it wrong in so many ways, Dubois had got it right where it counted.

  The competition to find other hominid remains intensified in the early twentieth century, with the lion’s share of the activity focused on east Asia and Africa. The discovery of Pithecanthropus-like fossils in the 1920s and 30s at Zhoukoudian, China, showed that Dubois’ ape-man had been widespread in Asia. The uniting of the Zhoukoudian Sinanthropus (‘Peking man’) with Pithecanthropus (‘Java man’) in the 1950s provided the first clear evidence for a widespread, extinct species of hominid: Homo erectus. Bus the most amazing finds were to come from Africa, starting with the work of Raymond Dart in the 1920s.

  In 1922 Dart was appointed Professor of Anatomy at the University of the Witwatersrand in South Africa. This must have come as a bit of a blow to the academically high-flying Australian (who was previously based in Britain), since ‘Wits’ at that time was a scientific backwater. Nonetheless, he set about building the foundation of an academic Department of Anatomy in the newly created university, which involved the establishment of a collection of anatomical specimens. He urged his students to send him material, and after one of them found a fossil baboon skull from a quarry at Taung, near Johannesburg, Dart felt that he was on to something interesting.

  Up to this point, most fossilized human remains had come from Europe and Asia: Neanderthal, Peking Man, Java Man – all were found outside Africa. In 1921, however, a Neanderthal-like skull was unearthed in Northern Rhodesia (now Zambia), proving that Africa had an ancient hominid pedigree as well. Dart was well aware of this when he contacted the owner of the Taung quarry to send him additional samples of material. What he found in the first crates to arrive in the summer of 1924 was, to his great delight, the oldest human fossil yet discovered.

  As he painstakingly picked off the compressed rubbish accumulated over aeons in the Taung cave, Dart revealed an ape-like face staring back at him. Its small size and intact milk teeth immediately gave it away as a child’s skull, and Dart’s estimate of its cranial capacity revealed it to be well within the normal range found in modern apes – around 500 cubic centimetres. What was odd about the find was the size of the canine teeth – much smaller than those of apes – and the location of the foramen magnum, which serves as a conduit for the spinal column in its connection to the brain: it was orientated downward in the fossil, like modern humans, rather than backward, as is the case in apes. To Dart, both of these features indicated that the Taung baby, as it became known, was no ordinary simian. In a 1925 paper he asserted that the skull represented the remains of a new species, which he called Australopithecus africanus (‘African southern ape’), that walked upright and used tools. In Dart’s own words, the Southern Ape was ‘one of the most significant finds ever made in the history of anthropology’. It was the first clear evidence for a missing link between apes and humans in Africa, and it set off a tidal wave of human-origins research that was to culminate a few decades later in universal acceptance for the African origin of humanity. However, most of this work was to focus on a region a few thousand miles away, in eastern Africa.

  The African Rift Valley is part of a massive line of intense geological upheaval formed by the action of great tectonic plates that make up the earth’s crust. Roughly 2,000 miles long, it stretches from Eritrea in the north to Mozambique in the south, and is most recognizable by the series of lakes along its length – Turkana, Victoria, Tanganyika and Malawi, among others. This longitudinal gash has been a cauldron of activity over the past 20 million years, with volcanoes, lakes, mountains and rivers coming and going at a brisk pace. For this reason, the accumulated layers of millions of years – soil, volcanic ash, lake sediments – are constantly being tossed about and exposed. When this happens in east Africa, interesting things often turn up – all you have to do is look for them.

  Louis Leakey had grown up in Kenya. The son of English missionaries, and raised in a Kikuyu village, he had spent his life looking for fossil remains in the valleys and riverbeds of the Rift. In 1959 at Olduvai, in northern Tanzania, his search was to pay off. It was nearing the end of the field season and, with research funds running on empty, Louis and his wife Mary were preparing to return to Nairobi. On the way back to camp one evening Mary stumbled upon a skull exposed by a recent rockslide. After painstakingly excavating the fossil over the next three weeks, the Leakeys returned to their laboratory at the Kenyan National Museum. The detailed analysis of the remains revealed it to be an Australopithecus, the first to be found in east Africa. But the shocker came when the layer of sediment surrounding the skull was dated using the newly developed technique of isotopic analysis, which calculates age based on the rate of radioactive decay. The skull had been buried 1.75 million years ago. This nearly doubled the length of time that most scientists had allowed for human evolution. Yet here was a missing link, midway between apes and humans, dating from that time. The scientific world was amazed – and encouraged. The massive boost in funding that the Leakeys and their colleagues received in the wake of the Olduvai discovery enabled them to find many more Australopithecines in the Rift over the subsequent thirty years.

  The discovery of the Southern Ape Man in east Africa pointed the way towards modern humans, but it was only when unequivocal members of our own genus, Homo, were discovered there in the 1960s and 70s that the African origin hypothesis be
came widely accepted. The earliest Homo erectus fossils yet discovered date from around 1.8 million years ago, and they were found in east Africa (the African variant of Homo erectus is sometimes given the name Homo ergaster). Recent discoveries in the medieval city of Dmanisi, in the former Soviet Republic of Georgia, show that they left Africa soon thereafter – perhaps reaching east Asia within 100,000 years. From this we can infer that all Homo erectus around the world last shared a common ancestor in Africa nearly 2 million years ago. But according to the Berkeley mitochondrial data, Eve lived in Africa less than 200,000 years ago. How can we reconcile the two results?

  It’s all about timing

  Let’s step back for a moment and consider the case objectively. The evidence for an African Genesis of Homo erectus is circumstantial – we see evolutionary ‘missing links’ in Africa, either uniquely or first. These include an unbroken chain of ancestral hominids stretching back more than 5 million years to the recently discovered chimpanzee-like apes Ardipithecus. But is this evidence sufficient to conclude that Africa was also the birthplace of our species? Perhaps, but fossils can be misleading. Imagine finding a perfectly preserved Neanderthal skeleton in south-western France, dated accurately to 40,000 years ago, and one of Australopithecus, in Africa, dated to 2 million years before. Of these two extinct hominids, separated in time by millions of years and in place by thousands of miles, which is actually more likely to be a direct ancestor of modern Europeans? Oddly enough, it is not the obvious choice. As we’ll see later in the book, modern Europeans are almost certainly not the descendants of Neanderthals (despite what you may think of your colleague in the office next door), while the Southern Ape is, surprisingly, more likely to be our direct ancestor. Stones and bones inform our knowledge of the past, but they cannot tell us about our genealogy – only genes can do this.