Lone Survivors (29 page)

Of course population movements, particularly in the last millennium, have translocated many lineages far from their places of origin, and a large industry has grown up to help people trace their ancient ancestry through mtDNA. This has proved controversial because your mtDNA ancestry is only a small part of your total genetic ancestry, but along with Y-chromosome DNA for males, mtDNA is very easy to sample, sequence, and track. Yet even when it is tracked back successfully, the results are only as good as the comparative data that are used to “relocate” people (or at least those small bits of their DNA) to their original homelands, and many parts of the world, including Africa, are still poorly sampled for DNA. We do know that African mtDNA contains the most ancient lineages and the greatest diversity for modern humans, consistent with Africa being both our place of origin and the region with the largest ancient population size, which was thus able to conserve that diversity.

Mitochondrial DNA has been widely used to gauge ancient population sizes, though estimates of these from genetic data are fraught with difficulties, one of which is that calculations generally provide an
effective population size
—in essence, the size of the breeding population. For mtDNA, this is the estimated size of the pool of “mothers,” while the actual population size (including breeding males and individuals either too young or too old to be involved in breeding) would obviously be much larger. However, many estimates of ancient population size, whether from mtDNA, Y-DNA, X-DNA, or other autosomal DNA, are startlingly low when we consider the billions of humans on Earth today. The long-term effective size of the ancestral population for modern humans might have been only about 10,000 breeding individuals, while the effective size of the female population, judged from surviving mtDNA, is sometimes estimated at less than 5,000!

If such numbers are a true reflection of the original population size in Africa, humans were present only in numbers comparable to those of gorillas and chimpanzees, species that inhabit relatively small parts of the African continent today. Our ancestors cannot have been widespread across the continent, let alone spread far outside of it, but were probably concentrated in pockets, and those pockets would have been vulnerable to extinction. Using three complete human genomes, the geneticists Chad Huff, Lynn Jorde, and their colleagues made comparisons that reached even deeper back in time to suggest that human population numbers a million years ago (the time of
Homo erectus
) were somewhat larger, closer to 20,000 breeding individuals, but even this size could hardly have spread across a continent as large as Africa.

Mitochondrial DNA can also be used to track population growth, and some studies suggest that while haplogroups L0 and L1 grew steadily in their early history, L2 expanded only quite recently, while L3 grew rapidly about 70,000 years ago. In mtDNA terms, as we have seen, the latter group was ancestral to lineages M and N found outside of Africa, so that expansion might well have spilled over into western Asia and hence to the rest of the world.

MtDNA has been used to calibrate events in human evolution, as we saw from the original calculation of Eve's antiquity of about 200,000 years, and from the estimate of the expansion of haplogroup L3 at about 70,000 years, but as with population size estimates such calculations are reliant on several assumptions and can only be approximate. For example, most calibrations are based on the assumption that we split from our closest living relatives, chimpanzees, about 6 million years ago. The number of substitutions in our mtDNA compared with that of chimpanzees is then compared with the number of substitutions determined for other events, such as our split from Neanderthals or our exit from Africa. The ratio of substitutions found is then converted into a “date,” along a 6-million-year time scale. However, when substitution rates are determined in very recently diverged human mtDNA, such as in historic populations on islands, or family studies where there are unusual mitochondrial diseases, the rates are much faster than the rate found when comparing our mtDNA with that of chimps. Scientists have argued that “purifying selection” removes many disadvantageous mtDNA mutations through time, thus explaining the rate discrepancy between the short-term and long-term evolutionary events. But when we attempt to calibrate relatively recent events in human evolution, such as the date for Eve or our exit from Africa, should the slow (long-term) rate be used, as it most often is, or should a faster rate be applied?

I recently collaborated with the geneticists Phillip Endicott, Simon Ho, and Mait Metspalu to compare two existing calibrations for recent human evolution with newly calculated substitution rates that are not based on the ancient and somewhat uncertain 6-million-year separation time for chimps and humans. The new rates gave younger estimated ages for recent events in human evolution, but ones consistent with the latest fossil and archaeological data for the exit from Africa and for our arrival in Asia, Australia, Europe, and the Americas. “African Eve” would have lived about 135,000 rather than 200,000 years ago, the exit from Africa would have taken place about 55,000 years ago, and the arrival in the Americas at about 14,000 years ago. If they are correct, these new and younger dates for human mtDNA evolution necessitate rethinking the mtDNA time scale for several key events in our evolutionary history, implying a younger date for our divergence from Neanderthals, a separation of many millennia between the first modern human fossils in Africa and Eve, and they also cast doubt on ideas of an early exit from Africa toward China and Australia. I will return to these issues shortly, but it certainly seems that geneticists need to reconsider their reliance on the human–chimp divergence to calibrate much more recent events in human evolution.

Compared with mtDNA, the Y-chromosome—the source of data on male history—has been slower to make an impact on the reconstruction of modern human origins than its female-tracking mitochondrial equivalent. One of the major reasons for this is that the Y is actually rather small and boring in terms of its genes and DNA compared with other more enlightening parts of our genome. It is predominantly made up of less informative junk DNA, and only small parts of its genetic material are ever exchanged with the X-chromosome. Nevertheless, it has now been completely sequenced, and increasing refinements in analysis have meant that even this recalcitrant chromosome has yielded important data on recent human history.

The most recent detailed comparisons of the human and chimp Y-chromosomes by Jennifer Hughes and David Page showed that these two are surprisingly different, with the human Y retaining many more coding regions. Because it is inherited through males only, there is a theoretical “Adam” to represent the last common ancestor of all modern Y-chromosomes, and as with mtDNA there is so far no evidence of a more ancient surviving variant of Y that could have been inherited from archaic people like the Neanderthals. Until recently “Adam” was estimated to have lived about 80,000 years ago, much later than “Eve,” with the initial and deepest two branches of the Y evolutionary tree widespread in Africa, one common from Bushman to Sudanese populations, the other in central African “pygmy” tribes. But new analyses by the geneticist Fulvio Cruciani and colleagues have instead placed the common ancestor at about 142,000 years ago, most likely (based on present distributions) in central or northwestern Africa. As with mtDNA, populations outside of Africa have lower diversity, this time with a slightly younger common male ancestor some 40,000 years old. Y is also useful in tracking unusual demographic events involving males in recent human history, such as the dominance of one Y-chromosome type across much of central Asia with an antiquity of about 1,000 years—perhaps the legacy of Genghis Khan's habit of impregnating large numbers of women in conquered populations, as well as the historically documented reproductive success of his known male descendants.

The use of autosomal DNA to study human population relationships has a long history, at least in terms of the study of the geographic distribution of its products such as blood groups, proteins, and enzymes. In the 1970s attempts were made to reconstruct the genetic history of humans by combining data on the frequency of many different genetic markers in populations from across the world. However, these often gave conflicting signals, sometimes relating the populations of Europe and Asia together, and sometimes indicating a closer relationship between Africa and Europe. One exception was the pioneering use of a genetic distance technique by the geneticists Masatoshi Nei and Arun Roychoudhury that allowed them to calculate that modern humans were closely related to each other but that Europeans and Asians had diverged about 55,000 years ago, while their ancestors had diverged from Africans about 115,000 years ago.

These estimates look crude now, and no one would suggest that these were real evolutionary “splits,” but the inferred relationships were in line with those determined by mtDNA and several other analyses a decade later. The arrival of techniques that used enzymes to chop the DNA into studiable segments (
Restriction Fragment Length Polymorphisms
) led to examination of the gene for betaglobin (which makes up part of our blood's hemoglobin) in 1986, and to early support for the concept of an African origin and a subsequent Out of Africa dispersal. Since then, hundreds of studies of autosomal DNA have shown the same pattern: African populations have the greatest diversity, and people outside of Africa are essentially a subset of that variation. In one of the largest recent investigations of over 1,000 genetic markers in 113 African populations, it was shown that they could be classified into fourteen groups, closely matching known cultural and language affiliations. Populations such as central African “pygmies,” hunter-gatherers such as the Sandawe and Hadza of Tanzania, and the Khoisan of southern Africa shared ancestors about 40,000 years ago. What was also interesting was that the latter three populations all speak “click” languages, suggesting that this could have been an ancient shared aspect of their languages.

While autosomal DNA studies have repeatedly confirmed the low diversity of most gene systems in non-Africans, they have also thrown an intriguing light on the pattern of dispersal of modern humans from their ancestral homeland. Just as non-African DNA variation can be seen as a subset of African variation and was originally sampled from it, so, as modern humans dispersed, that pattern seems to have repeated itself over and over again. The front line of expanding moderns from Africa was evidently small in number, and thus these pioneer groups radiating out from southwest Asia themselves only represented a small part of their parent population, with consequent lower DNA diversity. As a relic of that process today, DNA diversity steadily declines with overland distance from Africa, reaching its lowest points in faraway regions such as Arctic Europe, the Americas, Polynesia, and Australasia—and a matching pattern can even be found in the DNA history of
Helicobacter pylori,
a bacterium that infects most of us and can cause peptic ulcers!

Just as intriguingly, this pattern of decreasing diversity from Africa can be picked up in the measurements of skulls of populations from different parts of the world, suggesting that most of the regional differences between crania that are utilized by forensic programs were generated by drift rather than natural selection. I say
most
because there is evidence that certain populations like the Siberian Buryats and Greenland Eskimo underwent head and face shape selection under the impact of extreme cold—being large-headed and flat-faced seems to be advantageous under such conditions. But they represent exceptions to the general rule. Such decreasing diversity in both genes and morphology provides a challenge to the assimilationist idea that the expanding moderns mixed everywhere with remaining populations of archaics such as the Neanderthals and descendants of
Homo erectus
in the Far East. If that were so, we would expect to see repeated reversals of the decline in diversity where such different kinds of humans had significant input into modern human variation, and this has not been observed so far—with one very important exception. The geneticist Jeffrey Long and his colleagues recently reported a hot spot of increased diversity in the southeast Asian islands of Melanesia, and this was a clue to significant local complications in the Out of Africa dispersal, as we will see shortly.

One of the most difficult aspects for some people to accept, if we evolved very recently in Africa, is why we all look so different. As I said more than twenty years ago, “we are all Africans under the skin,” and yet what lies in and on the skin seems to distinguish us from each other so markedly. Humans come in many different sizes, shapes, and colors and differ in the form of their eyes, hair, nose, and lips. These “racial” or, better, regional or geographic differences are immediately apparent, and thus some people assume they must be highly significant genetically. Yet if we had a recent African origin, these differences must have evolved after we became the modern human species and started to spread out from our place of origin. Thus we evolved our shared species-specific features—our high and rounded skull, small brow ridges, small retracted faces, chins, and so on—first in Africa. Then, on that shared modern template, the regional features were superimposed. But what led to those additions? Here there are several different ideas, and two in particular stand out: climatic adaptation through natural selection, and sexual (in humans, also cultural) selection. Surprisingly, despite Darwin's (and Wallace's) emphasis on natural selection as the predominant agent of evolutionary change, when Darwin came to publish
The Descent of Man
in 1871, it was the second part of the title—
and Selection in Relation to Sex
—that dominated his thoughts on the evolution of “racial” characters in humans.