The puzzle of Neanderthal admixture

Skhul V – one of the Skhul-Qafzeh hominins. Were they the middleman between Neanderthal genes and the modern human genome?

When I initially published my last post, I pooh-poohed the rumors about the reconstructed Neanderthal genome. How could modern humans have Neanderthal DNA when no such admixture appeared in previous analyses of mtDNA, dentition, and noncoding DNA? Any Neanderthal admixture would have to be less than 1%.

I then logged on to Razib Khan’s site. The news had just broken: modern humans outside Africa are 1 to 4% Neanderthal. I hurriedly rewrote my post and spent the rest of the day eating crow.

In retrospect, I now realize I had put too much faith in the existing data. I had also ignored the warning signs. The HBD community correctly decoded the silence that had fallen over Pääbo’s research team, as well as a remark made by Linda Vigilant.

Despite the crow-phagia, this is good news. It means the end to a long and bitter conflict between proponents of two models of human origins: ‘Out of Africa’ versus multiregionalism. Anthropologists may still disagree, but the room for disagreement has greatly shrunk from what it was only a week ago. We can now move on.

The winning model is a weak version of Out of Africa. Modern humans are largely descended from a series of population expansions that began around 80,000 years ago somewhere in eastern Africa and culminated c. 60,000 BP in a ‘big bang’ that would create 96-99% of the gene pool outside Africa. The remaining 1-4% came from archaic Europeans and Asians, i.e., Neanderthals in Europe and West Asia, and other hominins elsewhere (Almas in Siberia? Hobbits in southeast Asia?). This admixture seems to have occurred in two stages: an early one in the Middle East, when modern humans began spreading out of Africa, and a later one, when modern humans began to spread from Asia to Oceania (Dalton, 2010). Curiously, the admixture looks Neanderthal in both cases.

Did this admixture contribute anything useful? We still don’t know. Some academics had identified the new variant of the microcephalin gene as being probably of Neanderthal origin, but this variant is absent from the reconstructed Neanderthal genome. To date, Pääbo’s team is of the opinion that “the Neanderthal DNA does not seem to have played a great role in human evolution” (Wade, 2010).

Surprisingly, the same level of Neanderthal admixture was found in a French subject, a Chinese subject, and a Papuan subject. This seems to suggest that Neanderthal admixture happened when modern humans began spreading out of Africa, probably in southwest Asia. But why was there no further admixture in Europe, where the two populations co-existed much longer? If there had been, we would see more Neanderthal admixture in present-day Europeans, but we don’t.

There are several possible explanations:

1. Noise in the data obscures the higher level of Neanderthal admixture in present-day Europeans. The picture should become clearer once we have sequenced 100% of the Neanderthal genome, and not the current 60% (Richard Green in an interview on CBC).

2. Early modern Europeans were replaced by Middle Eastern immigrants when farming replaced hunting and gathering (Green et al., 2010).

3. In Europe, early modern humans greatly outnumbered the Neanderthals. Subsequent admixture thus had little effect (Green et al., 2010).

4. In East Asia and Oceania, ‘Neanderthal admixture’ is actually a proxy for something else. These regions had non-Neanderthal archaic populations that were probably more closely related to the Neanderthals than to modern humans. If so, ‘Neanderthal admixture’ in these regions may correspond, more or less, to admixture with other archaic humans (my idea).

5. Neanderthal genes entered modern Eurasian populations indirectly, via an intermediate Middle Eastern population that already had Neanderthal admixture (because of prolonged contact) while being fairly close to modern humans in appearance and behavior. Modern humans may thus have more readily intermixed with them but not with Neanderthals in Europe. The latter were so different in appearance and behavior that admixture would have been minimal (my idea).

I’m inclined toward the last two explanations. Explanation #4 would explain why the later admixture in Asia/Oceania seems to have been as ‘Neanderthal’ as the early admixture in the Middle East. Unfortunately, to test this explanation, we must first reconstruct the genome of archaic humans from the Asia/Oceania transition zone. This will be difficult, if not impossible, given the accelerated degradation of DNA in the tropics.

Explanation #5 is also tempting. Not long before modern humans began spreading out of Africa, the Middle East was home to a population with both modern human and Neanderthal characteristics, as attested by remains from Skhul and Qafzeh in northern Israel. These hominins first appeared in the Levant some 120,000 years ago, perhaps as part of an earlier out-of-Africa expansion into south Asia. Their technology was Mousterian and Neanderthal-like, but their anatomy was relatively modern with some archaic features (Kidder et al., 1992; Pearson, 1998). These “almost-moderns” existed on the periphery of a range centered on the African continent. Only a bit farther north were the Neanderthals of Europe and West Asia.

When the climate cooled during the Early Pleniglacial (70,000-55,000 BP), the southern limit of the Neanderthal range shifted accordingly. Neanderthals then occupied the Levant until the arrival of modern humans some 50,000 years ago (Grun & Stringer, 1991; Schwarcz et al., 1989; Valladas et al., 1987).

What happened to the Skhul-Qafzeh hominins? They probably moved farther south, perhaps to the Hejaz. Such a location would have been athwart the main line of expansion of modern humans as they spread out of Africa. Unfortunately, despite many interesting sites, there has been no dating so far of early human occupation in Saudi Arabia (Petraglia & Alsharekh, 2003).

References

Dalton, R. (2010). Neanderthals may have interbred with humans. Genetic data points to ancient liaisons between species. Naturenews, April 20.
http://www.nature.com/news/2010/100420/full/news.2010.194.html

Green, R.E., J. Krause, A.W. Briggs, T. Maricic, U. Stenzel, M. Kircher, et al. (2010). A draft sequence of the Neandertal genome, Science, 328, 710-722.
http://www.sciencemag.org/cgi/reprint/328/5979/710.pdf

Grun, R., and C.B. Stringer. (1991). Electron spin resonance dating and the evolution of modern humans, Archaeometry, 33, 153-199.

Kidder, J.H., R.L. Jantz, and F.H. Smith. (1992). Defining modern humans: A multivariate approach, in G. Bräuer and F.H. Smith (eds.) Continuity or Replacement. Controversies in Homo Sapiens Evolution, pp. 157-177, Rotterdam: A.A. Balkema.

Pearson, O.M. (1998). Postcranial Morphology and the Origin of Modern Humans, Ph.D. dissertation, State University of New York at Stony Brook, Ann Arbor: University Microfilms International.

Petraglia, M.D. and A. Alsharekh. (2003). The middle palaeolithic of Arabia: implications for modern human origins, behaviour and dispersals, Antiquity Journal, 77, 671–684.
http://repository.ksu.edu.sa/jspui/handle/123456789/5520

Schwarcz, H.P., B. Blackwell, P. Goldberg, and A.E. Marks. (1979). Uranium series dating of travertine from archaeological sites, Nahal Zin, Israel, Nature, 277, 558-560.

Valladas, H., J.L. Joron, G. Valladas, B. Arensburg, O. Bar-Yosef, A. Belfer-Cohen, P. Goldberg, H. Laville, L. Meignen, Y. Rak, E. Tchernov, A.M. Tillier, and B. Vandermeersch. (1987). Thermoluminescence dates for the Neanderthal burial site at Kebara in Israel, Nature, 330, 159-160.

Wade, N. (2010). Signs of Neanderthals mating with humans, New York Times, May 7, 2010.http://www.nytimes.com/2010/05/07/science/07neanderthal.html (read)

Ask the rhino

Linda Vigilant – Was she in on the Big Secret? Was the rhino?

The HBD blogosphere has been rife with speculation about the reconstruction of the Neanderthal genome. John Hawks, Razib Khan, and Steve Sailer felt that something big was in the offing. Above all, this something would resurrect the multiregional model of human origins.

Much of the stir centered on a recent study by Sarah Joyce that showed a higher-than-expected amount of variability in the microsatellite DNA of modern humans. Since this DNA is unaffected by natural selection, the unexplained variability must have come from an outside source, i.e., Neanderthals and other archaic humans.

Then there was this comment:

Linda Vigilant, an anthropologist at the Planck Institute, found Joyce's talk a convincing answer to "subtle deviations" noticed in genetic variation in the Pacific region.

"This information is really helpful," says Vigilant. "And it's cool." (Dalton, 2010)

Linda Vigilant works at the Planck Institute, where a team headed by Svante Pääbo is reconstructing the Neanderthal genome. Perhaps she was privy to something big that Pääbo had discovered but was waiting to disclose.

Now the hand-wringing is over. This morning, it's been revealed that modern Europeans and Asians are 1-4% Neanderthal. Does this mean the multiregional model has been vindicated?

First, let’s be clear about what we mean by the multiregional model. Originally, it meant that Homo sapiens evolved out of earlier, more archaic humans at different times and at different places. Modern Europeans are thus primarily descended from Neanderthals, East Asians from Peking Man, and so on.

That version is now dead as a dodo. No one accepts it anymore. If we look at mtDNA or dental traits, the Neanderthals are no closer to modern Europeans than they are to modern Africans or modern East Asians (Krings et al., 1999; Ovchinnikov et al., 2000; Tyrrell & Chamberlain, 1998). In addition Joyce’s findings were not corroborated by Laval et al. (2010), who failed to find evidence of admixture in the noncoding DNA of modern Europeans and modern East Asians. The latest findings have backtracked a bit on this consensus, but not a lot.

So the current multiregional model is a weak version of the original. The idea now is that sporadic admixture brought potentially valuable Neanderthal alleles into our gene pool. Natural selection then caused the alleles to spread and multiply among modern humans. There could thus have been considerable Neanderthal introgression into our gene pool at certain loci, despite very low levels of admixture (Hawks & Cochran, 2006; Hawks et al., 2007). Laval et al. (2010) concede this point in their recent study:

However, it is important to emphasize that our inferences are based on non-coding neutral regions of the genome and that adaptive introgression from archaic to modern humans may have occurred to a greater extent. Indeed, in contrast to neutral alleles, adaptive variants may attain high frequencies by natural selection after minimal genetic introgression. Future studies comparing coding-sequence variation in modern humans and extinct hominids (e.g. Neanderthals) should help to answer this question. (Laval et al., 2010).

What do I think? This ‘minimal multiregionalism’ suffers from two arguments that seem to me weak:

1. Microbes do it. Why not humans?

Different strains of bacteria regularly swap genes, thus allowing new and better variants to leapfrog from one strain to another. Such ‘lateral gene transfer’ is a powerful engine of evolutionary change because it spares different species the trouble of having to reinvent the wheel.

But what works in simple organisms or for simple traits does not necessarily work elsewhere. Yes, if the gene works more or less independently, you can plug it into another genome and get the same result, like the pigment gene that aphids have somehow taken from fungi. But this kind of ‘plug and play’ is harder to pull off with complex traits in complex organisms, like humans. A particular gene might work like fresh sliced bread in one species … and like burnt toast in another.

But perhaps some adaptive solutions are still essentially the same in different complex organisms, like Neanderthals and modern humans. This point is made by Greg Cochran:

Selection often stalls out (in the medium term) because genetic variety has been exhausted, but an injection of archaic genes would have facilitated adaptive change. Moreover, some of those archaic alleles must have been useful ( i.e. had a fitness edge), since archaic humans in Eurasia had had a long time to adapt to their non-African ecology. (Khan, 2010)

Cochran and Hawks seem to be particularly interested in alleles relating to brain function, like the microcephalin allele that they had earlier attributed to gene transfer (Hawks & Cochran, 2006; Hawks et al., 2007). The Neanderthal microcephalin gene has since been reconstructed and … it does not have that allele (Hawks, 2009).

Yet Cochran and Hawks remain undeterred. One reason why they don’t see the weaknesses in their hypothesis is their unwillingness to spell it out in detail. Why won’t they? Well, ask the rhino.

As I understand it, their hypothesis is that Eurasian populations are relatively smart because their ancestors received special brain alleles from the Neanderthal gene pool. If I’m right in my understanding, they’re probably wrong in theirs. Modern humans adapted to temperate and arctic Eurasian environments in ways that were unique and unparalleled. Neanderthal brainpower had nothing to do with it. Although the Neanderthals apparently borrowed cultural and technological adaptations from modern humans, there is no evidence of any borrowing in the other direction. In fact, these archaic humans seem to have had very little to offer our ancestors:

Despite the apparent advances over their predecessors, Neanderthal technological complexity falls at the low end of the scale for recent hunter-gatherers. Both in terms of the number of types and component parts of individual implements, the complexity of Neanderthal tools and weapons is significantly lower than that of hunter-gatherers in northern latitudes (and more typical of modern groups in temperate or equatorial regions). Technological complexity in colder environments seems to reflect the need for greater foraging efficiency in settings where many resources are available only for limited periods of time. More specifically, the Neanderthals seem to have lacked untended facilities (e.g., traps and snares) and devices for food storage, which are common technological strategies for coping with resource fluctuations and high mobility requirements among hunter-gatherers in high latitudes. (Hoffecker, 2002, p. 135)

2. If Europeans were part-Neanderthal, they’d have native rights

This is an interesting argument: “If we Europeans are even a little bit Neanderthal, no one could deny our special claim to the European continent. People like Gordon Brown and Ségolène Royal would stop saying we’re no more indigenous than newly arrived immigrants.”

I have two responses. First, modern humans have inhabited Europe for some 35,000 years. If that length of residency doesn’t confer native rights, then no one anywhere has any—certainly not the Amerindians or the Inuit, who have been in the Americas for less than 15,000 years.

Which brings me to my second point. The currently dominant ideology—global capitalism—denies the very notion of native rights. It doesn’t matter whether your people have inhabited their land for 35,000 years or 35 million years. That’s just history, and we’ve come to the End of History. From now on, we’re all just individuals interacting in a global marketplace.

Eventually, this ideology will fall victim to its own contradictions. A market economy can exist with minimal state supervision only in a relatively homogeneous ‘high trust’ society. Liquidate that social environment, and you liquidate the economic environment that comes with it. At ‘best’, you’ll get a kind of totalitarian capitalism where everyone is deemed to be a potential thief or terrorist. At ‘worst’, the system will collapse, as communism did in Eastern Europe.

Of course, we shouldn’t wait passively for globalism to self-destruct. As thinking individuals with foresight, we should actively take part in the process. But such activism must start with an honest understanding of the world we live in. The lies of the current system cannot be fought with counter-lies. Europeans will not become more indigenous to their continent because they are found to have a few Neanderthal alleles here and there. They’re already indigenous, and that’s that.

Well, maybe the rhino can tell us more.

References

Dalton, R. (2010). Neanderthals may have interbred with humans. Genetic data points to ancient liaisons between species. Naturenews, April 20.
http://www.nature.com/news/2010/100420/full/news.2010.194.html

Hawks, J. (2010). Multiregional evolution lives! John Hawks Weblog, April 21, 2010.

http://johnhawks.net/weblog/reviews/evolution/introgression/joyce-dalton-interbreeding-2010.html

Hawks, J. (2009). The Neandertal genome FAQ, February 2009 edition, John Hawks Weblog, February 17, 2009.
http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/neandertal-genome-faq-2-2009.html

Hawks J., Cochran G., Harpending H.C., Lahn BT. (2007). A genetic legacy from archaic Homo. Trends Genet doi:10.1016/j.tig.2007.10.003

Hawks J., Cochran G. (2006). Dynamics of adaptive introgression from archaic to modern humans. PaleoAnthropology, 2006, 101-115. Open access

Hoffecker, J.F. (2002). Desolate Landscapes. Ice-Age Settlement in Eastern Europe. New Brunswick: Rutgers University Press.

Khan, R. (2010). Neandertal genomics paper coming? Discover magazine, April 27, 2010.
http://blogs.discovermagazine.com/gnxp/2010/04/neandertal-genomics-paper-coming/

Krings, M., Geisert, H., Schmitz, R.W., Krainitzki, H., & Pääbo, S. (1999). DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen. Proceedings of the National Academy of Sciences USA, 96, 5581-5585.

Laval, G., E. Patin, L.B. Barreiro, and L-Quintana-Murci. (2010). Formulating a historical and demographic model of recent human evolution based on resequencing data from noncoding regions, PloS ONE 5(4) : e10284

Ovchinnikov, I.V., Götherström, A., Romanova, G.P., Kharitonov, V.M., Lidén, K., & Goodwin, W. (2000). Molecular analysis of Neanderthal DNA from the Northern Caucasus. Nature, 404, 490-493.

Sailer, S. (2010). The Neanderthal within. Steve Sailer’s iSteve Blog, May 2, 2010.
http://isteve.blogspot.com/2010/05/neanderthal-within.html

Tyrrell, A.J. & Chamberlain, A.T. (1998). Non-metric trait evidence for modern human affinities and the distinctiveness of Neanderthals. Journal of Human Evolution, 34, 549-554.

Cheap shots and collateral damage

Ségolène Royal and supporters

A University of New Mexico research team has announced that the human gene pool seems to have admixture from an outside source, most likely from the Neanderthals and other archaic humans. This conclusion was based on analysis of variation in microsatellite DNA from European, Asian, and Oceanic populations. Since microsatellite DNA is thought to be of neutral selective value, any variation must be due to the slow gradual accumulation of new mutations or admixture from outside our gene pool.

The researchers pinpointed two admixture events:

Using projected rates of genetic mutation and data from the fossil record, the researchers suggest that the interbreeding happened about 60,000 years ago in the eastern Mediterranean and, more recently, about 45,000 years ago in eastern Asia. (Dalton, 2010)

This analysis suffers from several problems. For one thing, it is based on rough estimates, i.e., the length of time that modern humans have existed outside Africa and the speed at which new mutations accumulate in microsatellite DNA. There is also the dubious assumption that this DNA is never affected by natural selection.

Nonetheless, this announcement has delighted anthropologists like John Hawks, Greg Cochran, and Alan Templeton who have long argued against the ‘Out of Africa’ model of human origins. As multiregionalists, they used to argue that modern humans evolved out of earlier archaic populations in Africa, Europe, and Asia. Thus, modern Europeans would primarily be descended from Neanderthals, Modern Asians from Peking man, and so on.

Today, the multiregional model is no longer accepted, and its proponents are now backing a compromise. Modern Europeans, for instance, would largely descend from the wave of humans that spread out of Africa 60,000 to 40,000 years ago, but they would still have some admixture from Neanderthals in their gene pool.

Will this debate ever be settled? Yes, and very soon. That’s the good news. In a few months, the reconstruction of the Neanderthal genome will be published. By comparing it with the genome of modern Europeans, we should find out whether any genes flowed from one to the other. Preliminary comparisons have already been done and to date have found … nothing.

Now the bad news. The triumph of the ‘Out of Africa’ model will be heavily politicized. Although I support this model, I feel nothing but shame for the cheap shots that many other adherents have made. A common one has been to cast multiregionalists as ‘racists.’

This name-calling appears in a New York Times article that presents multiregionalists as “inheritors of a culturally infected biology” and its opponents as “supporting our better inclinations.” In an interview, paleontologist Chris Stringer clearly enjoyed being on the side of the angels, while snidely accusing the other side of racism. He recalled an encounter with Carleton Coon in a Harvard washroom where the aged professor referred to one of his critics as ''that . . . Jew Weiner.''

What irks me about this anecdote is not that it is unverifiable (washroom conversations are not published and Coon has long been dead), but simply its irrelevance. Suppose it could be shown that Carleton Coon had regularly sodomized his grad students. Or would microwave live kittens. Or had bad breath. What would that prove or disprove about the multiregional model? Nothing. This is ad hominem at its sleaziest.

In the same interview, Stringer went on to say that our species is so young that differences among humans can only be skin-deep:

Since so little time has passed since they [modern humans] decamped from Africa, dispersing to the far regions of the world -- 100,000 years being a mere paleontological moment -- ''only slight differences, if any, in intellect and innate behavior are likely to have evolved between modern human populations.'' We are ''all Africans under our skin.''

Uh, 100,000 years is not a mere paleontological moment. A population can undergo significant physical and genetic change in as little as eight generations. In fact, many animal species go back only to the last ice age (25,000-10,000 BP). Evolutionary change is due primarily to the intensity of natural selection and only secondarily to the passage of time. Indeed, the faster such change has occurred, the more important it must be, since it is being driven by intense natural selection and not by adaptively neutral processes like genetic drift or founder effects.

I can forgive journalists for not knowing the above. I find it harder to forgive Chris Stringer, who is fully aware of how fast natural selection can operate. There is no point in winning a debate if you inflict a lot of collateral damage in the process.

Clearly, there has been collateral damage. The catch phrase “We are all Africans” has taken on a life of its own, with almost 100,000 Google hits. In the last French election, Ségolène Royal cited the latest findings in paleontology when she proclaimed, “Nous sommes tous des Africains!” This cute expression is even appearing in high school textbooks.

And we’ll probably see it in newspaper headlines when the Neanderthal genome is finally published.

References

Dalton, R. (2010). Neanderthals may have interbred with humans. Genetic data points to ancient liaisons between species. Naturenews, April 20.
http://www.nature.com/news/2010/100420/full/news.2010.194.html

Hawks, J. (2010). Multiregional evolution lives! John Hawks Weblog, April 21
http://johnhawks.net/weblog/reviews/evolution/introgression/joyce-dalton-interbreeding-2010.html

Richards, R.J. (1997). Neanderthals need not apply, New York Times, August 17, 1997.
http://www.nytimes.com/books/97/08/17/reviews/970817.17richart.html

Are we part-Neanderthal?

How did archaic humans evolve into the different populations of Homo sapiens we see today? The answer has long divided anthropologists. Some opt for the ‘out-of-Africa’ model; others for the multiregional model.

According to the out-of-Africa model, we all descend from a small group that existed some 100,000 to 80,000 years ago somewhere in eastern Africa. This group had an advantage over other humans, perhaps a superior ability to construct mental models in all four dimensions (Dubreuil, 2008; Klein & Edgar, 2002). They thus grew in numbers and progressively replaced their more archaic rivals, first in Africa and then elsewhere after 60,000-40,000 BP. Extinction was thus the common fate of all archaic humans throughout Europe and Asia, be they Neanderthals, Neanderthaloids, or mysterious Hobbits.

This claim is disputed by the multiregional model, which asserts that archaic Europeans and Asians did not die out. In fact, they went on to provide most of the gene pool of present-day Europeans and Asians. Modern humans thus have regional differences that can be traced to longstanding continental differences among earlier hominids. These continental groups evolved in parallel from the archaic evolutionary grade to the modern one, with gene flow gradually spreading advantageous alleles from one group to another.

The multiregional model no longer has many supporters, at least not in its pure form. With the recovery of DNA from Neanderthal remains, it has become clear that any genetic continuity with modern humans must be minor at best. There is nonetheless some support for a hybrid model, i.e., our current gene pool largely comes from a population that expanded out of Africa, but with significant admixtures from archaic Europeans and Asians. This view finds backing in a recent paper by Wall et al. (2009).

Wall and colleagues compared genetic polymorphisms in subjects of European, West African (Yoruba), and East Asian descent. They first looked for gene loci whose alleles show multiple mutational differences—a sign that the polymorphism either is very old or has undergone some kind of diversifying selection (i.e., a balanced polymorphism). Among these loci, they next looked for those that lay close to other polymorphic loci whose alleles likewise show multiple mutational differences. The authors reasoned that the more the apparently ancient alleles clustered by continental origin (West African, European, or East Asian), the greater the likelihood that these alleles had entered the gene pool from local archaic groups that modern humans had encountered while spreading out of Africa.

And the results? Wall and colleagues found significant archaic admixture: 14% in Europeans and 1.5% in East Asians. Curiously, no estimate was made for the West African subjects. The authors simply state: “Interestingly, we also find evidence for ancient admixture in the Yoruba.”

Well, how much? I’d like to know because there is another estimate based on a different methodology. When Watson et al. (1997) studied mtDNA lineages in sub-Saharan Africans, 87% of the lineages seemed to originate in a series of population expansions that began some 80,000 years ago. One cluster of lineages, dated to c. 60,000 BP, defines almost all non-African humans. The remaining 13% look much older and seem to be “the relics of a less dramatic and more ancient expansion event across Africa.”

As for archaic admixture outside Africa, Wall and colleagues (like John Hawks) point to the Neanderthals and other local hominids. The admixture must have been specific to Europe and then East Asia because the European and East Asian subjects had different sets of apparently archaic alleles.

In contrast, Dienekes argues that the admixture occurred before modern humans began to spread out of Africa. The archaic alleles then persisted to varying degrees in the small founder groups that ‘budded off’ from the parent African population:

Thus, the expanding African population that eventually spilled over into Eurasia, would indeed be quite inbred and homogeneous, but its gene pool would also contain traces of the smaller, less successful African populations it had absorbed. Because of their low frequency, these traces would be more susceptible to extinction in the series of bottlenecks that led to Europeans on one side and East Asians on the other, with different sets of archaic genes preserved in either region.

I lean more to Dienekes’ explanation. If Europeans and East Asians have different archaic alleles because of separate admixture, their ancestors must have parted company before encountering the Neanderthals not long after leaving Africa (c. 40,000 BP). Yet this seems counterintuitive because the genetic distance between Europeans and East Asians (and hence their time of separation) is much less than that between Africans and non-Africans.

There is in fact a convergence of genetic, linguistic, and archeological evidence for a late split between ancestral Europeans and ancestral East Asians. A Y-chromosome study indicates that all North Eurasian peoples descend from a common ancestral population dated to about 15,000 BP (Stepanov & Puzyrev, 2000; see also Armour et al., 1996; Santos et al., 1999; Zerjal et al., 1997). The language families of northern Eurasia, particularly Uralic and Yukaghir and more generally Uralic-Yukaghir, Eskimo-Aleut, Chukotko-Kamchatkan and Altaic, share deep structural affinities that point to a common origin and not simply to word borrowing (Cavalli-Sforza, 1994, pp. 97-99; Fortescue, 1998; Rogers, 1986). Archeological evidence (characteristic lithic technology, grave goods with red ocher and sites with small shallow basins) also suggests a common cultural tradition throughout Europe and Siberia 20,000 to 15,000 years ago (Goebel, 1999; Haynes, 1980; Haynes, 1982). Finally, dental and cranial remains from southern Siberia (23,000-20,000 BP) indicate strong affinities with Upper Paleolithic Europeans (Alexeyev & Gokhman, 1994; Goebel, 1999).

Rogers (1986) places the European/East Asian split at the glacial maximum (20,000-15,000 BP). At that time, advancing glaciers and swollen glacial lakes created a barrier along the present-day Ob, thereby dividing a nomadic Eurasian population that hunted reindeer and other herbivores within a steppe-tundra belt stretching from Western Europe to Beringia.

A word of caution

Finally, a word of caution. Like any statistical analysis, the Wall et al. approach will yield a certain number of false positives. Many loci are highly polymorphic because selection has favored allele diversity, such as with balanced polymorphisms, and not because they are very old. And some will lie close on the genome to other balanced polymorphisms that likewise look older than they really are. And the alleles of these adjoining loci will often cluster by continental origin because they face different selection pressures in sub-Saharan Africans, Europeans, and East Asians—or just because of pure chance.

These false positives may also be more frequent among Europeans than among East Asians. If ancestral East Asians had budded off from an older European population, they would have taken less genetic diversity with them. They should have proportionately fewer polymorphisms and less diverse ones.

In conclusion, the jury is still out on this one. We won’t have a definite answer until we can match these continentally specific alleles with identical alleles on the Neanderthal genome now being reconstructed.

References

Alexeyev, V.P., & Gokhman, I.I. (1994). Skeletal remains of infants from a burial on the Mal'ta Upper Paleolithic site. Homo, 45, 119‑126.

Armour, J.A.L., Anttinen, T., May, C.A., Vega, E.E., Sajantila, A., Kidd, J.R., Kidd, K.K., Bertranpetit, J., Paabo, S., & Jeffreys, A.J. (1996). Minisatellite diversity supports a recent African origin for modern humans. Nature Genetics, 13, 154‑160.

Cavalli-Sforza, L.L., Menozzi, P. & Piazza, A. (1994). The History and Geography of Human Genes. Princeton: Princeton University Press.

Dienekes. (2009). Archaic admixture in modern humans? Dienekes’ Anthropology Blog.

Dubreuil, B. (2008). What do modern behaviors in Homo sapiens imply for the evolution of language? http://african.cyberlogic.net/bdubreuil/pdf/Evolang2008.pdf

Fortescue, M.D. (1998). Language Relations across Bering Strait. Reappraising the Archaeological and Linguistic Evidence. Cassell: London.

Goebel, T. (1999). Pleistocene human colonization of Siberia and peopling of the Americas: An ecological approach. Evolutionary Anthropology, 8, 208‑227.

Hawks, J. (2009). A new study of genetic introgression and human ancestry. John Hawks Weblog.

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