by Frank Ryan
We should maintain a prudent caution here—for reasons that will become clear a little later. For the moment, let us celebrate our common matrilineal ancestor with a visit to meet her in her hunter-gatherer community, and look at how she has been linked to the entire world.
We can reasonably assume that she would have appeared little different to the other women in her small, close-knit community. Some believe that she would have resembled the San people, who, until very recently, still followed a hunter-gatherer existence in southern Africa, with the men spearing fish in the shallows or hunting land animals for meat and the women digging for roots or foraging along the shoreline for shellfish. We know that she had the gift of language, with all of the social potential that conveys. We also know that she might have painted her skin or clothing with patterns in ocher. We can hazard a guess at what might have been her clothing—perhaps a covering skirt from the waist down made from plant fibers or animal hides. A study by the University of Florida found evidence that humans may have begun to wear clothes as early as 170,000 years ago. She is also likely to have decorated her neck, wrists, or clothing with beads of small, similarly sized sea shells, which were brightly colored with natural pigments. We can also pretty much assume that the older females taught the children and younger adult females what to do, in foraging through forest and seashore and in the bearing and caring for children.
Mitochondrial Eve was not the ultimate great-grandmother of all humanity. She would have been one of many females alive and reproductively active at the time she acquired the founder haplogroup. All of these other reproductive women would have been just as likely to contribute to the species gene pool, but she was the only one whose mitochondrial genome found its way into all modern humans. Let me explain how this is likely to have arisen.
Let us say that there are ten reproductively active women in a single hunter-gatherer group. Only one of these—Eve—has the founder mutation, or small cluster of mutations, in her mitochondrial genome. Perhaps eight of the women are reproductively successful, giving rise to two or three surviving offspring per woman. Eve, for example, might have given birth to two surviving daughters and a son. All three will inherit her mitochondrial genome, but her son will not pass it on—males do not contribute to the mitochondrial lineage. Other women in the same group may, through chance, have had no daughters, so they will not have contributed to the mitochondrial lineage. In subsequent generations the same actions of chance will continue to operate. Generation after generation, for some 140,000 to 200,000 years, Eve's descendants must have given birth to a daughter in every generation for this to result in an unbroken matrilineal lineage over the vast time period to the present day.
So now we understand how really it was a game of chance that resulted in mitochondrial Eve drawing the winning ticket. But this does not mean that those other mothers—and fathers for that matter—have not contributed to us all genetically. We have already seen how, using simple mathematics, we share very many common ancestors who will have contributed to other aspects of our genome.
Mitochondrial Eve would have almost certainly lived in Africa, although where in Africa is uncertain; perhaps somewhere in the region of modern-day Tanzania. Eve's founder mitochondrial haplogroup is the “macrohaplogroup” L, and it probably did originate somewhere between 120,000 to 200,000 years ago. Current thinking suggests that her matrilineal line first spread out over the remainder of Africa, the original L haplogroup evolving to regional subgroups L0 and L1 to L6. Although we tend to imagine these ancestral populations radiating out from East Africa into the Middle East, and from there radiating west to Europe and northeast and southeast to Asia, Australasia, and the Americas, in fact the genetic evidence suggests a complex admixture and movement with waves of advance and return. After this, perhaps, a new migration, starting about 60,000 years ago, saw the mitochondrial haplogroup L3 first diversify into haplogroups M and N in East Africa before crossing into the Arabian Peninsula, from where it spread and diversified, perhaps through a coastal migration, into Asia, Eurasia, Europe, and the New World. This would imply that all the mitochondrial lineages outside of Africa descended from the M and N lineages.
These basal M and N lineages have now been traced along the southern Asian shoreline. A combination of archeological and genetic evidence has also revealed that as the expansion and migration progressed over thousands of years, these M and N subgroups acquired further defining sub-subgroups, as the populations moved and the lineages split into smaller and smaller branches. For example, if we screen modern populations, we can infer that those with mitochondrial haplogroups H, I, J, N1b, T, U, V, and W are of European origin; those with A, B, C, and D are of Asian and New World origins and those with G, Y, and Z are predominantly associated with western Asia.
It is in the nature of scientists to be skeptical, and the scientist in me asks the question: Are we being overly simplistic in assuming that this sequence of mitochondrial haplogroups extrapolates to actual population movements and present human diversity?
Two geneticists, Brigitte Pakendorf and Mark Stoneking (the latter one of the original Wilson group at Berkeley), have warned us that the studying of mitochondrial haplogroups has limitations when it is extrapolated to explain major population movements. They don't deny that it is a useful tool, but they advocate expanding the searches to the analysis of the entire mitochondrial genome and further, to a much wider genetic analysis. A very obvious next step would be to extend the genetic analysis to the patrilineal ancestry. So where in all this historic exploration is the genetic evidence for the ancestral Adam?
Just as the mitochondrial inheritance passes entirely through the maternal genetic lineage, we assume that the Y-chromosome nuclear inheritance passes entirely through the paternal genetic lineage. This is based on the Y chromosome having no corresponding partner to recombine with during the formation of the sperm cells, so it is subjected to no mixing of chromosomal elements from both parents during the formation of the germ cells. In fact, this is not completely true. Some 5 percent of the Y can and does recombine with a corresponding part of the X chromosome during germ cell formation. But geneticists get around this by focusing on the 95 percent that is invariably passed from father to son. This is called the “male specific region” of the Y chromosome, or “MSRY.”
Acronyms—brrrh!
Perhaps, like me, you have an instinctive aversion to acronyms? Alas, we need to get the hang of yet another two that geneticists are fond of flinging into the heated air of debate when it comes to matrilineal and patrilineal lineages—namely LCA and MRCA, which in fact denote exactly the same thing: the “last common ancestor” and the “most recent common ancestor.”
Brrrh—and brrrh again!
In contrast to the mitochondrial genome, which comprises roughly 16,000 base pairs, the Y chromosome comprises 60 million. This means that the study of Y-chromosome mutations, those Snips and haplotypes and haplogroups, is more complex than that of mitochondrial mutations. But the consolation is that since they focus on two different genomes, with different evolutionary and genetic origins and thus different mutational rates and properties, the sum effect of combining the two adds significantly to the accuracy of all those archeogenetic calculations.
For a start, studies of Y-chromosome haplogroups also point to Africa as the place where modern humans evolved. But in this case it suggests either eastern or southern Africa as the place where “Adam,” the earliest detectable common male ancestor, or “Y-MRCA,” was born.
A basal haplogroup lineage, conveniently labeled Haplogroup A, is more frequently found in males from Africa than anywhere else in the world. Adam's arrival on the scene was variously estimated as 188,000 years ago—or 270,000 or 306,000 or 142,000 or 338,000 years ago. Some of this disagreement may have come about from different ways of calculating the so-called “molecular clock,” but it may also have resulted from problems with the genetic analysis of very long DNA sequences. More recently, a study by G. David Pozni
k and colleagues in 69 males from nine very different populations, and one by Paolo Francalacci and colleagues from 1,204 Sardinian males, arrived at estimates of the Y-MRCA, the mean of which tallied a little more closely with the purported age of our common maternal ancestor. These offered a range of from 120,000 to 300,000 years ago.
Y-chromosome Adam clearly did not inhabit an African Eden at the same time as mitochondrial Eve. Nevertheless, through such genetic studies the evidence that modern humans originated in Africa gathered momentum. But where we might have looked for helpful confirmation from the fossil record over the same key period of 100,000 to 300,000 years, this proved somewhat elusive. Chris Stringer, at the Natural History Museum in London, drew attention to this prevailing lack of paleoanthropological information in an article in the journal Nature in 2003. But he was pleased to draw attention to two reports in the same issue of the magazine, which described three fossilized skulls from close to the village of Herto in Ethiopia that were, in his opinion, some of the most significant paleontological discoveries of early Homo sapiens to date.
The skulls, which included two adults and one juvenile, were almost complete, and their antiquity, at about 160,000 years old, tallied remarkably well with the genetic dating. They were associated with stone tools of the so-called Acheulean, or Middle Stone Age, types. The paleontologists also found evidence that the heads of the adults and juvenile had been removed from the bodies after death, with the lower jaws deliberately disarticulated and the skulls systematically defleshed. While this could have been associated with cannibalism, which is sometimes found in human fossils, there were additional “more decorative” cut marks, incised by a very sharp and fine blade, that suggested an alternative explanation. These, combined with the polishing of some of the rounded surfaces of the skull, suggested formal mortuary practices followed by cultural or ritualistic treatment. The patterns of the marks were similar to what is seen in the skulls of some much more recent New Guinea crania, which were known to play a role in ritual mortuary practices.
This paleoanthropological evidence, combined with the historic evidence stored within our human DNA, is providing powerful corroborative evidence for the origins of modern humans in Africa. Yet further mysteries need to be resolved. When did our distant African ancestors move out to populate the rest of the world? Did they do so in a single historic migration? Or, given human migratory behavior in more historic times, together with the major climatic variability produced by the comings and goings of Ice Ages and natural calamities such as volcanic eruptions, is it more likely that there was a series of ebbs and flows, like smaller wavelets overlapping two or more major waves of migrations over time?
The Wilson study mentioned above, and many subsequent studies of human genetic diversity, highlight what may be a related puzzle. If we compare our human genetic diversity to, say, that of our evolutionary cousin, the chimpanzee, we discover significantly less genetic diversity in the human genome. This is particularly noticeable if we compare the important genetic region known as the major histocompatibility complex, or MHC, which, as we saw earlier, determines immunological and biological self and plays a vital role in our immunological reaction to invading infectious organisms, such as viruses and bacteria. This loss of diversity is a significant finding. It suggests that at some time in our evolutionary history—and some geneticists believe that it was a time very close to the origins of early moderns as a species, or perhaps close to the timing of the spread of the species out of Africa—that the ancestral human population was subjected to a near-extinction event. This created a genetic bottleneck that reduced the founder population to less than 10,000 individuals, and some even think it may have been as few as 1,000. What possible disaster could have brought about such a shocking cull?
One suggestion was the explosion of a volcano called Mount Toba on the island of Sumatra, which is believed to have erupted 70,000 years ago. But if this distant catastrophe was capable of slate-wiping populations extending from east Asia to Africa, it would have wiped out the human population closer to the epicenter. The survival of populations in India, as shown by primitive stone tool assemblages in layers above the ash, brings this into question. Moreover, the distinguished paleontologist Sir Paul Mellars, at the University of Cambridge, has produced convincing evidence that modern humans are more likely to have reached Asia through a coastal migration at least 10,000 years after the volcanic explosion, which would cast additional doubts on Mount Toba being the causative catastrophe. There is, however, another contender; one that brings us back to the endogenous retroviruses that account for roughly 9 percent of our human DNA.
We recall that these endogenous viruses entered the prehuman and human germ line during retroviral epidemics. The most recent of the genomic viral invaders are called the HERV-Ks, a group that first invaded the ancestral primate genome somewhere around 30 million years ago. The evolutionary virologist Luis P. Villarreal, based at the University of California at Irvine, believes that the arrival, and explosive colonization, of the primate genome by HERV-Ks was a watershed event in primate and subsequent human evolution. It coincided with the switching off of an earlier viral colonization of the human genome by DNA-based viruses or so-called “transposons.” Most of the HERV-Ks are present, in the same chromosomal distributions, in all of us, many now having entered into useful holobiontic function with the rest of the genome. At least ten subgroups of the HERV-Ks invaded the human germ line after our separation from chimpanzees, so these HERV-Ks are exclusive to the human genome. Four of these are believed to have entered the human genome during the last million years, including HERV-K106, HERV-K113, HERV-K115, and HERV-K116. Based on the molecular clock—in this case we are applying it to DNA mutations in the regulatory regions of the viruses, known as long terminal repeats, or LTRs—HERV-K115 inserted into human chromosome 8 roughly a million years ago, while HERV-K113 inserted into chromosome 19 roughly 800,000 years ago. HERV-K116, which inserted into chromosome 1, and HERV-K106, which inserted into chromosome 3, have no mutations in their LTR regions. This suggests that their insertions, and the relevant exogenous retroviral epidemics, were much more recent than HERV-K115 and HERV-K113.
In 2011, Jha and colleagues reported the research outcome of six different groups of American genetic and evolutionary scientists who combined forces to examine the distribution of HERV-K106 in 51 Americans of diverse ethnic origins. This allowed them to separate the test populations into four different haplogroups. They concluded from the haplogroup evidence that HERV-K106 inserted into the human genome roughly 91,000 to 154,000 years ago. This must have resulted from a retroviral epidemic affecting the human population at the same time. Yet unlike HERV-K115 and HERV-K113, HERV-K106 was found to be universally present in the genomes of their test subjects, suggesting it was ferociously infectious. Judging from the patterns of the two prevailing retroviral pandemics, HIV-1 in humans and the koala pandemic in Australia, exogenous retroviruses are extremely efficient in their spread as emerging infections within a geographically contiguous species. And we know how they behave in relation to their new hosts. Think of AIDS in a virgin human population with no knowledge of epidemiology and no therapy; for its endogenous version to be universal, the exogenous K106 is likely to have swept through all of the human population that contributed to the descendant people who populate the Earth today. And the date of virus insertion appears to coincide fairly well with the approximate dates drawn from both the mitochondrial and the more recent Y-chromosome calibrations, as well as the fossil discoveries from Middle Awash in Ethiopia. In time, study of ancient human genomes, including a careful examination of the endogenous viral components, may help to answer whether or not HERV-106 was the culprit for the human culling that produced the apparent genetic bottleneck.
Putting aside such speculations, the weight of evidence is pointing strongly to modern humans having originated in Africa at a date roughly about 150,000 years ago. But this also leaves us with a new set of questions. When did mode
rn humans migrate from Africa to populate the rest of the world? Was there just a single major migration, or was there more than one? We know that our ancestors encountered other, so-called “archaic” human species when they entered Europe and Asia, so what happened when they met up with them?
…in the second stage we had to go into the great wilderness of prehistory to see whether there were elements of internal consistency which would lead one to believe that the method was sound or not.
WILLIAM F. LIBBY
History fascinates us because it tells us how we, and the society in which we live, came to be. For most of us, this tends to be a distinctly parochial fascination, the town or county in which we live or, in the widest sense, the country or continent we feel that we belong to. This is altogether natural since it is the world we are familiar with. But there is a deeper history, older by far than national or even continental boundaries—one that takes us back to a time when life was simpler and yet more challenging. There were no schools, no employers and employees, no farms, no herded animals with their supplies of milk and ready meat, no shops with their implicit exchange in the form of money, and above all no metal tools—no machines. This lost world is what Libby, the pioneer of radiocarbon dating, refers to as the “great wilderness of prehistory.” It is a deeply fascinating world, and one that we know very little about. It is also a world that constituted an extremely important phase in our human history, one that goes beyond national, ethnic, and indeed all divisional boundaries because it is a world that every single human being on Earth living today has in common. We are all descendants of these early modern humans, and thus we have a common interest in how these ancestors came to evolve in Africa, and how, out of Africa, they came to colonize the rest of the planet.