The Mysterious World of the Human Genome

by Frank Ryan

  Crucial to understanding this stage in our history is the archeological exploration of the timing of the first evolutionary emergence of early modern humans, a topic we touched upon in the previous chapter. And from there it is equally crucial to establish a reliable framework, in date and geography, of the movements of these pioneering ancestors during their migration, or migrations, out of Africa. This has proved extremely challenging for archeologists, in part because of the paucity of archeological evidence discovered to date and because most such sites are situated in warmer areas of Africa, Europe, and Asia, where preservation of organic remains tends to be poor and therefore not easily dated. But this is now changing; windows of opportunity are opening up through new scientific techniques of dating and the genetic extraction from animal bones and human fossils, as well as through a broadening of geographic horizons. On May 1, 2014, I traveled to Oxford to interview Katerina Douka, of the Oxford Radiocarbon Accelerator Unit, in the hope of getting to know more about these interesting developments.

  Dr. Douka was born in Greece; after graduating from the University in Athens with a basic degree in archeology and archeological sciences she went to Oxford to study for a masters degree and, ultimately, a PhD. Her topic was the dispersal of modern humans out of Africa and into Europe, and within this broad theme, her primary interest was radiocarbon dating. It was one of her published papers that introduced me to Libby's concept of the great wilderness of prehistory, and her interest in radiocarbon dating was one of the keys that might open the lock onto this wilderness. I asked her if she had become interested in archeology at school—or if perhaps a member of her family had stirred her curiosity.

  “No. If you come from Greece you are a little bit overwhelmed with archeology because it is everywhere. I'm just interested in the past, whether it is two hundred years ago or two hundred thousand years ago.”

  Perhaps, I ventured, it was people who really interested her?

  “Yes—the past and its relation to people.”

  The theme of Dr. Douka's PhD thesis was: “The dispersal of modern humans out of Africa and into Europe—from a radiocarbon-dating perspective.”

  In 2006, Sir Paul Mellars produced what is now a famous paper in which he described how modern humans were likely to have entered Europe. If Mellars is right, a series of breakthroughs in technology took place in Africa roughly 60,000 to 80,000 years ago. Powerful evidence for this was found in layers of the Blombos Cave in South Africa, which dated to roughly 75,000 to 55,000 years ago. The advances included new patterns of fine stone blade technology, scrapers for working skins and hides, tools for the shaping of bone and wood, bone points for the tips of throwing spears and sharply pointed awls, and carefully shaped artifacts for throwing spears and even, conceivably, the first arrows. These were found in the same sediments as perforated shells used for personal ornament, the earliest such items ever found, as well as large quantities of imported red ocher, including pieces incised with geometric ornamentation. All of this was accompanied by evidence of large-scale exchange and distribution over distances. Equally significant was the evidence, gathered by other scientists, of an accompanying rapid population growth in the ancestral African population between 60,000 and 80,000 years ago.

  These specific African tools and cultural ornamentation show a striking resemblance to what was appearing in archeological sites throughout the Middle East, Europe, and Asia, taken as evidence for the migration of modern humans out of Africa and into these landscapes roughly 45,000 to 50,000 years ago. It was, of course, this very expansion of the ancestors of modern humans into Eurasia that had been the focus of Katerina Douka's PhD, and it has further extended to her present field of scientific interest.

  One of her recent scientific papers, which bore the title “Exploring ‘the Great Wilderness of Prehistory,’” described how the transition from a Neanderthal-dominated western Eurasia to a continent in which modern humans were now the sole inhabitants marked one of the biggest transformations ever witnessed in this vast region. I was aware that some scientists believed that there had been at least two major migrations of early modern humans out of Africa: one about 120,000 years ago, related to some hominin fossil discoveries in the Skhul and Qafzeh cave sites, then in Palestine, and another migration, dated to roughly 45,000 to 39,000 years ago, linked to a famous rock shelter site in Lebanon, known as the Ksar Akil that was also associated with hominin fossils. The latter site was widely regarded as a key staging post in the most important migration, starting in or passing through the Near East. To this end, Katerina Douka led a team that set out to apply modern radiocarbon dating to the human settlements at Ksar Akil.

  I asked her about Libby's intriguing phrase: the wilderness of prehistory. What had he meant by it? Did he mean that prehistory in itself was a wilderness in the sense that there was very little known about it?

  “Libby is one of the greatest, if not the greatest, figure in radiocarbon dating. He developed the ideas that led to carbon dating while working as a physicist on the Manhattan Project, and for these ideas he later received the Nobel Prize in Chemistry.”

  Radiocarbon dating is based on the known rate of decay of the carbon isotope carbon–14. Basically, the atmosphere contains different isotopes of carbon in the form of carbon dioxide, which include the main stable isotope, C–12, as well as the unstable isotope, C–14, which are present in roughly constant proportions. These isotopes are taken up by plants and micro-organisms, from where they enter the living bodies of other life-forms. Once an organism dies, there is no possibility of replenishing the carbon isotopes, and from that moment the ratio of C–14 to C–12 will progressively fall over time as the unstable isotope decays to the stable one. Measurement of the ratio of these isotopes is the basis of radiocarbon dating, which has revolutionized the dating of Paleolithic archeology sites. This, I presumed, was Libby's contribution to exploring the wilderness.

  “That's right. If we look at scientific papers pre-1960, there is no absolute dating. People are talking about a few thousand years, or tens of thousands, or hundreds of thousands, but there was no way of quantifying this as far as time was concerned.”

  “How far back can you accurately go with radiocarbon dating?”

  “Fifty thousand years.”

  “But there's a big chunk of time before that?”

  “That's our actual limitation. But in fact we are lucky because the upper limit of this method allows us to calibrate the last years of the Neanderthals and their interaction with modern humans in Europe and more broadly Eurasia. For previous epochs we need to use other methods, such as thermoluminescence, which can take us back 200,000 or 300,000, maybe even half a million years.”

  I was interested to know more of the work she did for her PhD.

  The idea, as Douka explained, was to focus on the Mediterranean rim and try to trace migrations deep into Europe. There were two broad possibilities: one route was likely to have followed the Mediterranean coastline; the other would most likely have headed northwest, along the Danube River corridor. For many years, people had assumed that the likely crossroads from Africa to Eurasia had been through the Near East, but the evidence, and dating, for such a crossroads was scanty. Perhaps it was time that Paleolithic archeologists examined this again?

  “For me,” Douka laughed, “it was great timing. I had just started my PhD and I was interested in following up Mellars's ideas. So the idea was to date shell beads from around the Mediterranean to see if we could date modern human expansion. Traditionally Neanderthals are not thought to have used ornaments in the same way—or essentially not manufactured shell beads anyway. Ksar Akil was one of the first sites I looked at.”

  I was keen to know more about the potential of such a simple and common resource as seashells. “Do you find these shell beads very frequently in modern human sites dating from this period?”

  “Yes you do—especially around the Mediterranean. They are not rare findings, but they have exciting potential. And whe
n you do find them, they are often in great numbers. We're talking about hundreds.”

  “When you say around the Mediterranean—in what sort of places?”

  “Lebanon, southern Turkey, southern Greece, Italy, and all along the French and Spanish coasts extending also into the north of Spain.”

  “What sorts of shells are we talking about?”

  “Essentially they are small, about 1 to 2 centimeters diameter and perforated with a stone tool.”

  “Too small to be considered food?”

  “These are not food residue. These people were very selective in what species they gathered. Most likely they collected the shells directly from the beach as empty shells, but only freshly dead. They then pierced the shells—this is how we know that they were used as beads, whether as jewelry or decoration for clothing…So the idea for my research was to go back to the sites, go back to the original collections, and date this material, which amounted to several hundred shell beads.”

  Carbon dating can make use of many different materials, including soft tissues, such as skin and derived leather, bone, charcoal, seeds—anything that exchanges carbon with its environment. Douka has made a special study of sea shells as a reliable source, which she applied to a new appraisal of the Ksar Akil site in Lebanon, working in association with colleagues, including Professors Robert E. M. Hedges and Thomas F. G. Higham from the Oxford Radiocarbon Accelerator Unit, Dr. Christopher H. Bergman from Cincinnati, and Dr. Frank P. Wesselingh from Leiden in the Netherlands.

  There were considerable problems that needed to be overcome, though. A major handicap was the fact that human fossil remains from the region had been scanty even in the original excavations, and much of this had been lost over the decades since. Excavation of Ksar Akil had begun as long ago as 1937 by a group of American Jesuits, and it had extended, in phases, and with different experts conducting the excavations, until 1975. The work over this period of time had revealed more than 30 stratigraphic layers some 23 meters deep. The earliest excavation had discovered the skeleton fossil playfully named “Egbert.” The fossil is now lost and so it is only known through photographs and casts made at the time. When these casts were examined at the British Museum, by Bergman and Stringer, they suggested that the skull, which is small and delicately built, is likely to be that of a girl aged between seven and nine years. A second human fossil, that of a more primitive-looking upper jaw with a single canine tooth, was playfully named Ethelruda—perhaps after an Anglo-Saxon female saint. This was initially thought to be the jaw of a Neanderthal but is now considered very likely to be that of a modern human. While Egbert remains lost, Ethelruda was rediscovered in the Archaeological Museum of Lebanon but appeared to lack collagen, the usual source of carbon in such fossils that enables radiocarbon dating, so an alternative indicator was needed. Douka switched her attention to sea shells. As it happened, the molluscan collection from Ksar Akil was one of the largest ever discovered at a Paleolithic site, containing approximately 2,000 specimens, the majority of which showed evidence of human modification such as perforation for ornament or the presence of ocher pigments applied to them.

  These shells had also been lost back in the 1960s, but in 2006 Douka and her colleagues traced them to the Netherlands. They were then able to locate the levels layer by layer, from the levels they knew were associated with Neanderthals to those associated with modern humans. The shells from these layers could now be transported to the Oxford laboratory for preparation and testing. Recent research into ways of excluding contamination when dating shell carbonates now proved useful in the preparation and grinding down of a small piece of each shell into a fine dust that she could use to radiocarbon date the site and, by inference, its associated human fossils.

  “What dates did you find?”

  “From the shell beads we got a radiocarbon dating for the earliest modern human layers at around 37,000 radiocarbon years, which converts to about 42,000 calendar years.” This allowed Douka to use a probability mathematical calculation, known as Bayesian modeling, to date the skull of Egbert to between 40,800 and 39,200 years old and the jaw of Ethelruda to between 42,400 and 41,700 years old.

  This established time frame had additional implications; it put the arrival of modern humans into the Levant somewhat later than had been previously assumed. There was evidence elsewhere that the big migration out of Africa dated to several thousand years earlier than this. So Douka's findings suggested new possibilities. The main migration route might have been elsewhere, perhaps direct east from northeast Africa through Arabia and Central Asia, later curling toward the Near East. “We needed to cast the net more widely to include other places and migration routes in the historic human dispersal out of Africa.”

  Whether Ksar Akil had been on the crossroads, or whether the migration had arrived at Ksar Akil a few thousand years later, the site remains a very important source of information, bringing together hominin fossils with evidence of the prevailing culture. I had more questions to ask before moving further afield.

  “What were these people like? What was their society like? What did they eat? What sort of clothes did they wear?”

  “From Ksar Akil, and other sites along the Mediterranean, we know that these people were hunter-gatherers with a very varied diet. Throughout the year they were hunting large animals, such as deer, whatever was available. But they also ate a wide variety of different foods, including a wide array of plants, nuts, and fruits. We are still working on this, but we think they may have been collecting shellfish when other dietary resources were sparse, probably in late winter or early spring.” In terms of population size, Douka thought we were probably looking at groups of about 80 people living in relatively close proximity.

  But there was something else that puzzled me. While accepting that Ksar Akil was linked to the main movement of modern humans out of Africa and into Eurasia, I recalled that there was supposed to have been an earlier migration, judging from other evidence in the Near East. What, I wondered, had happened to that earlier migration? Why didn't they populate Eurasia? I knew, of course, that in Eurasia there had been a major problem with recurrent Ice Age pulsations, starting about 2,580,000 years ago and extending to the current interglacial period. These big freezes must have played havoc with human habitation and movements in Eurasia, in particular with a freeze called Riss, which lasted from 180,000 to 130,000 years ago, and one called the Würm, which lasted from 70,000 to roughly 10,000 years ago. Might this suggest that climate amelioration, beginning soon after the end of the Riss glaciation, had encouraged that earlier human migration out of Africa? But what then happened to that purported earlier migration?

  Some of the best evidence for an earlier modern human migration out of Africa comes from the two fossil sites Es Skhul and Qafzeh. Es Skhul is a cave on the slopes of Mount Carmel, and Qafzeh is a rock shelter in Lower Galilee. These two sites have proved rich in early hominin fossils, which have been tentatively dated at between 80,000 and 120,000 years old using techniques suitable for this level of antiquity, known as electron spin resonance and thermoluminescence. In particular, the fossils include a number of well-preserved skulls of male and female individuals and of a variety of ages. These skulls show a mix of archaic and modern features, with heavy brow ridges and a projecting lower face similar to the Neanderthals, but the brain case and upper skull is more the shape associated with modern-day humans.

  The mixture of features is so striking that at first these were interpreted as evidence for a partial evolution from Neanderthals to modern humans, but then obvious Neanderthal remains were discovered in the nearby Kebara cave that were dated to a much later period, roughly 61,000 to 48,000 years ago, disproving any such idea. Some anthropologists now proposed that the Es Skhul and Qafzeh hominins represent an early exodus of modern humans from Africa, around 125,000 years ago, so that the robust features represented a more archaic H. sapiens that would in time evolve to what we see today. If so, perhaps the Skhul/Qafzeh people may have
represented a true earlier out-of-Africa migration that simply stopped in the Near East. In other words, a migration that came to a dead end here, with no contribution to the people of Eurasia.

  “Yes,” Douka mused, “we know there was an Ice Age coming. Perhaps in Eurasia at that earlier time, the Neanderthal population was at its peak. Perhaps they were holding strong. But then again it is very difficult to know why—it might just have been an effect of relative population sizes. Again, the earlier migration might not have become completely extinct…”

  A set of teeth discovered in the nearby Tabun Cave in 2005 was thought to show Neanderthal features. These teeth were tentatively dated to around 90,000 years ago. This, together with the discovery of more Neanderthal remains, again tentatively dated to 120,000 years ago, suggests that Neanderthals and modern humans might have made contact in the Near East at this time. This introduced the possibility that what we are seeing at Skhul/Qafzeh is a sexual crossing between the two species, giving rise to a hybrid people who were part modern human and part Neanderthal.

  Dr. Douka shrugged: “This is something we are trying to look at. We know very little about any earlier migration from fossil evidence. I think a lot of weight is put into the Near East when it might not be the most likely place we should be looking at. But we now have a major five-year project under way that is looking at all the possibilities from Eastern Europe all the way to Central Asia, including Siberia.”

  As we shall see in a subsequent chapter, some remarkable new genetic evidence is becoming available from the fossil remains of early humans, including Neanderthals, which is likely to revolutionize paleoanthropology. It will clearly help when more archaic genomes from the fossil record can be added to the genetic picture, since these will not only allow genomic study for haplogroups but will also allow calibration of genomic dating with fossil-dating methods such as carbon–14, electron spin resonance, and thermoluminescence. In time, this will shed more light on the timing and migrations of our ancestors, whether they actually went north through the Levant or east through Arabia—or even directly across the Mediterranean Sea from North Africa. Some scientists are persuasively arguing that future study should include more of the extraordinary variation found in the human genome. The spread of endogenous retroviruses, such as HERV-106, HERV-113, and HERV-115, and the genetic and epigenetic regulatory regions of the genome, including those all-important non-coding RNAs, will also help to pin down movements and dates more accurately. I think we should be prepared for the true record to prove complex, with allowance for population advances and retreats, with mixing of different populations, and in particular with the problems of a harrowing Ice Age causing major upheavals in large swathes of the Eurasian landmass.