The Mysterious World of the Human Genome

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The Mysterious World of the Human Genome Page 24

by Frank Ryan


  The applications were taken up by other laboratories and extended to the woolly mammoth, cave bear, and coelacanth, as well as fossil plants. Meanwhile, Pääbo and his team addressed the single most exciting challenge that had faced his lab from the very beginning of this pioneering research: they would attempt the extraction of the genome of our long-lost human cousin, Neanderthal man. Time, perhaps, for us to take a brief look at what is known of our human evolutionary history.

  In his notebook, during the decades in which he gradually assembled his thoughts on how a new species might arise from an existing one, Charles Darwin sketched something resembling the branching pattern of a tree. This branching pattern has since then been amply confirmed by biological study, and the same pattern neatly fits with the Linnaean classification of life into species, genera, families, and so on—the disciplines biologists call “phylogenetics” and “taxonomy.” Humans are no exception to this; as recently as 70,000 years ago, some five different species of humans cohabited the Earth. All five had directly or indirectly descended from a single ancestral species known as Homo erectus. One of the five was our direct ancestors, “early modern humans”—or to give them their formal Linnaean classification, Homo sapiens. Both H. sapiens and the still-evolving H. erectus shared the planet with Neanderthal man, or Homo neanderthalensis, who inhabited large areas of Eurasia; the so-called “Hobbit,” or Homo floresiensis, who lived on the Asian island of Flores; and a mysterious species only recently mooted, called Denisovan Man, or Denisova hominins, who appears to have inhabited parts of Asia. All members of the human evolutionary tree that evolved after our divergence from the common human-chimpanzee ancestor are referred to as “hominins.” We need to distinguish this term from a second umbrella term, “hominids,” which includes all hominins as well as all modern and extinct Great Apes, including chimpanzees, gorillas, and orangutans.

  A good place to begin our exploration of this human evolutionary tree is with the common ancestor Homo erectus, who first evolved in Africa approximately 2 million years ago. An almost complete skull of an early individual was unearthed in Kenya, and an almost complete skeleton of a juvenile was discovered near to Lake Turkana, Kenya, by Richard Leakey's team. This juvenile skeleton was attributed to a boy who, judging by his five-foot-three stature and skeletal development, was initially thought to be 12 or 13 years of age. Later on his age had to be adjusted to eight years when scientists discovered the meticulous accuracy of counting the growth lines in teeth. This intrigued scientists since it suggested that childhood in Homo erectus was much shorter than that of human children today.

  Homo erectus individuals were as tall as modern humans, and they were even more robustly built. They controlled fire in hearths and manufactured stone tools of the “Acheulean” set, including beautifully sculptured hand axes and cleavers, which demanded the ability for mental imagery and planning and would have enabled them to kill and butcher animals. There is also some evidence that they may have cared for their weak and elderly. The skull of H. erectus was primitive in its features, with a heavy brow ridge, a low, flat vault, and protruding jaws, including a poorly developed chin. The brain volume was about twice the size of a chimpanzee's, at approximately 850ml, which compares to 1,300ml in an average male today. Homo erectus continued to evolve within Africa but, rather surprisingly, also migrated out of Africa at a very early stage in its evolution to populate the Eurasian landmass in the earliest-known hominin migration. Famous H. erectus fossils include skulls and jaws from Dmanisi in Georgia, dating to roughly 1.8 million years ago. Other fossil evidence finds H. erectus colonizing Asia close to a million years ago and the Middle East and Southern Europe about 730,000 years ago, where, as in Africa, the species continued to evolve bigger brains long after it had spawned the four descendant species, including our own. From this original dispersal, there are two schools of thought as to how modern humans might have come on the scene.

  The “multi-regional theory” pioneered by Milford H. Wolpoff suggests that subsequent human evolution of Homo erectus in regions such as Africa, Europe, Asia, and Australia gave rise to distinct local lineages, albeit with some mixing, through mating, between regional groups and perhaps with peoples migrating out of Africa. The “out of Africa” theory proposes that all currently living humans are descended from early modern human ancestors that evolved in Africa roughly 180,000 years ago, and who migrated, perhaps in a series of waves, out into the rest of the world. Until recently, these competing evolutionary theories were largely based on the fossil record and their associated paleoarcheology. As we have seen, the haplogroup genetic tracing tends by and large to favor the out-of-Africa scenario, but this leaves open the possibility of subsequent admixture of modern humans with other regionally distributed species of humans that had evolved from earlier migrations out of Africa, thus perhaps adding in a regional aspect to our evolution.

  Paleontologists had assumed that it was exceedingly unlikely that they would ever have the chance to study the genomes of these ancient cousin species, but now the picture was radically changed by Pääbo's spectacular breakthrough in genetic technology, with its pioneering of a whole new arm of genetic investigation—including a new name for it: paleogenetics.

  In interviews, Pääbo admits that his work in relation to paleontology was inspired by the desire to answer many questions. To begin with, was it possible to extract any DNA from such ancient fossils? Even if he managed to extract useful sequences, perhaps confined to mitochondrial DNA, what would this tell us about our human evolution? What if he could extract significant nuclear genomic sequences? Would this help to clarify the debate as to why the Neanderthals became extinct? Would it also answer important unknowns about our own species’ evolution? For example, would it help to clarify which of the competing hypotheses for our own human origins was correct?

  Many of the most interesting and provocative questions were directed at the Neanderthals. What do we really know about them? Were they the stupid cavemen of popular prejudice? In what landscape and ecology did they live? How did they survive in terms of food and shelter? What was their society like? Would they have understood love, family, friendship? How were they like us—and how did they differ? What possible catastrophe could have so befallen a people who had survived for a quarter of a million years in the Eurasian landscape only to become extinct within ten to fifteen thousand years of the arrival into Eurasia of modern humans?

  Neanderthals are so named because one of the early fossils was found in a cave in the valley of the Neander River in Germany. The “th” diphthong is pronounced “t,” in the German manner, so Neanderthal is pronounced “Neandertal.” The earliest features typical of Neanderthals first appear in the European fossil record about 400,000 years ago, which probably marks something close to their evolutionary origins. They are generally thought to have descended from an intermediary species, Homo heidelbergensis, which in turn descended from Homo erectus. Neanderthal fossils and tools are found widely throughout Europe and western Asia, as far east as southern Siberia, and as far south as the Middle East, before disappearing from the fossil record about 28,000 years ago, with the most recent remains found in a cave in Gibraltar. And although they are usually classed as a separate species from modern humans, evolutionary biologists regard them as our closest and most recent human cousins.

  What did they look like and how do they compare to us?

  On average, they appear to have been shorter and stockier than us, in particular having shorter legs and forearms. Their stature is thought to be an adaptation to living in a cold climate. Their skulls were long, more flattened on top than our own. They had much more prominent eyebrow ridges, and their noses were also much larger than we find in the average modern human—Stringer imagined that their noses must have been “remarkably prominent.” In some cases, the nasal bone jutted out nearly horizontally under the brows. Their front teeth were very large and often heavily worn, even when compared with those of their own ancestors, H. heide
lbergensis. Stringer and Gamble have queried if these facial appearances are an adaptation that came about because the Neanderthals may have used their incisor teeth as an extra appendage. Many adult Neanderthals display incisors worn down to mere stubs, suggesting they might have used them like a portable vice while working some material, perhaps, in the opinion of Shara Bailey at New York University, the processing of skins to make leather goods. Their cheeks were swept back on either side of the nose, giving the central part of the face a marked protuberance. The lower jaw followed this forward projection of the upper face and, like H. erectus, this resulted in the loss of a pointed chin. When compared to modern humans, Neanderthals also showed differences in their chest shape, the pelvic bones, and the limb bones, which tended to be thicker, with wider, stronger joints, all of which suggest that the Neanderthals were adapted to more powerful physical activities and stresses than was the case with early modern humans.

  Contrary to the unenlightened earlier interpretations, Neanderthals were neither stupid nor brutal. The Neanderthal brain is slightly bigger in volume than our modern human brain, even today. Casts of their brains taken from fossil skulls show that they had the same tendency to be right-handed. Intriguingly, their eye sockets were larger than ours, and the occipital lobes of their brains were also larger, suggesting that, perhaps, they had better night vision than us, which might have given them a survival advantage in their hunting lifestyle in the murky twilight of the cold northern climate, with its dark and dreary winters. Another intriguing difference was the time taken for childhood growth and maturation. As we saw with H. erectus, studies based on dental growth lines suggest that Neanderthal children may also have matured more quickly than modern human children.

  We need to avoid drawing derogatory inferences from such observations. For example, we should compare Neanderthal children's growth not to that of modern human children but to the fossils of early modern children, dating to the same time period as the Neanderthals under study. But if this proves to carry true, this shortened childhood might have important cultural implications since so much learning takes place during the extended period of development of our children.

  One of the more questionable theories to emerge in the past has been the suggestion that Neanderthals did not possess language. They must have had language, albeit it would very likely have been simpler than we humans possess today. They lived in hunter-gatherer bands of perhaps a dozen or two, very likely extended families. Although few Neanderthals appear to have lived beyond 40 years, there is some evidence that they possessed knowledge of herbal medicine, cared for their elderly, and looked after infirm individuals.

  We are currently in the middle of an extensive reappraisal of Neanderthal evolution and culture in which some paleontologists draw attention to the fact that the Neanderthals survived in Europe for roughly 250,000 years, despite very testing climatic conditions, colonizing a vast geographic territory. And now, as the first breakthroughs in genetics became available, we find that they were not swarthy and covered with black hair, as in the early drawings and models, but more likely fair-skinned, as we might have better imagined a species long adapted for survival in the cold northern climates of Europe. Still, the die-hards insisted that Neanderthals lacked the one key feature that lay at the very core of our advanced civilization: they lacked the higher cognitive function that enabled complex language and symbolic thinking, the quintessentially human cognitive breakthroughs that enabled symbolic art and subtleties of reasoning that came with language.

  In 2001, a human gene was identified by Oxford University geneticists Simon Fisher and Anthony Monaco, now known as FOXP2, which is important in our ability to articulate language. Mutations of the gene gave rise to difficulty with muscle control in the vocal cords, tongue, and lips that were needed to speak. This made scientists wonder if this particular gene was a key acquisition exclusive to modern humans and responsible for our evolution of language.

  However, a single gene is unlikely to code for our ability to speak. The evolution of speech and language involved complex changes in the structures of the human voice box, or larynx, the throat, and the mobility of the human tongue and lips, all of which would also have required long-term and complex modification of the areas of the brain that control thought, sensation, movement, and the coordination of these various body parts. We know that speech is dependent on the development of specific regions of the brain, such as Broca's area, which would hardly have evolved over the 200,000 years of our separation from Neanderthals. From study of feral children, we know that so closely is this “speech module” linked to culture that if a child is not exposed to picking up language from parents and those teaching him or her up to around the age of seven, they never develop proper speech. Remarkably, the late neurobiologist and avian scientist, Peter Marler, discovered that something similar applies to the song of birds.

  Socially there is some evidence that the Neanderthal hunter-gatherer bands were smaller in number than those of early modern humans, and they appear to have been less mobile and possibly less connected with other population groups. Their tools were adapted from local resources where the early moderns appeared to trade, and move, more widely. At first anthropologists believed they did not produce original art, in terms of cave painting or personal ornaments, such as necklaces and sculptured items. But a modern reappraisal suggests that the Neanderthals were more inventive than previously assumed. They made use of string some 90,000 years ago. The presence of Neanderthal tools on Mediterranean islands confirmed that they knew how to cross the sea in some kind of craft. Where the appearance of complex tools and shell or bead body adornment in Neanderthal settlements were thought to have been copied from arriving early moderns, a collection of sophisticated bone tools, known as lissoirs, were discovered at two sites in southwest France that were dated to between 45,000 and 51,000 years ago, which, if true, is several thousand years before early moderns arrived there. Some anthropologists still proposed that, on the weight of evidence, Neanderthals lacked the higher mental evolution implicit in symbolism, pointing to the beautifully illustrated cave paintings of France, Spain, and much further afield in Australia; but others have cautioned that the wonderful cave paintings were not produced by early modern humans at the time of the Neanderthals, but painted some 20–30,000 years after the Neanderthals had disappeared—plenty of time for a subsequent cultural evolution.

  In 2010, a group of scientists from many different university centers published a paper on the symbolic use of marine shells and mineral pigments by Iberian Neanderthals. Their paper, headed by João Zilhão, reported the discovery of two Neanderthal-associated Middle Paleolithic sites; one, a large cave near to the Mediterranean, and another, a rock shelter by the Mula River, both in present-day Spain and dated to roughly 50,000 years ago. Here the investigators discovered pigment-stained marine shells that had been deliberately perforated to allow them to be strung together into some kind of decorated adornment. They also discovered lumps of yellow and red colorants and residues preserved inside a Spondylus shell, together with many other tools and artifacts. The symbolic use of perforated and pigmented shells, used for necklaces, contradicted previous cultural assumptions. It suggested that Neanderthals may have had a similar ability for symbolic thought to early modern humans—they might even have taught our arriving early moderns a thing or two about the sophisticated manufacture and use of bone tools.

  As part of this reappraisal, some paleoanthropologists are coming round to a new perspective on the Neanderthals, arguing that they were little different in their cultural evolution from early moderns at the time they first emerged from Africa. For example, two American experts, P. Villa and W. Roebroeks, suggest that much of the earlier prejudice had resulted from a false comparison between Neanderthals, based on dig sites dating from the early to middle Stone Age, and modern humans from much more recent times. Others argue that even if modern humans were more advanced in their culture than Neanderthals, this does not neces
sarily reflect superiority in genetic or intellectual potential, but the sort of differences in culture seen in our modern human history, brought about by the development and transmission of ideas.

  However, none of this debate reveals why the Neanderthals vanished off the global map, facing us with the mystery of their disappearance. Were they exterminated in the same way that some native populations were exterminated by arriving European colonists? Were they wiped out by diseases carried into Eurasia by moderns arriving out of tropical Africa? Were they simply out-competed through the cultural superiority of the arriving modern humans? These questions had dogged paleoanthropologists for a century and a half. Svante Pääbo's new discipline of paleogenetics was about to suggest a completely different explanation for the extinction of the Neanderthals.

  Early in our analysis of the human remains from Lagar Velho, we proposed that the child's skeleton presented evidence of prior blending of local Neanderthal and arriving early modern human populations in western Iberia. Our interpretation has been widely accepted as both interesting and reasonable, being rejected a priori only by those who are intellectually immune to the idea of Neanderthal–modern human productive interbreeding.

 

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