Thursday, May 28, 2009

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.


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?

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.

Haynes, C.V. (1982).Were Clovis progenitors in Beringia? In Paleoecology of Beringia, D.M. Hopkins (Ed.). New York: Academic Press, pp. 383‑398.

Haynes, C.V. (1980). The Clovis culture. Canadian Journal of Anthropology, 1, 115‑121.

Rogers, R.A. (1986). Language, human subspeciation, and Ice Age barriers in Northern Siberia. Canadian Journal of Anthropology, 5, 11‑22.

Santos, F.R., Pandya, A., Tyler‑Smith, C., Pena, S.D.J., Schanfield, M., Leonard, W.R., Osipova, L., Crawford, M.H., & Mitchell, R.J. (1999). The Central Siberian origin for Native American Y chromosomes. American Journal of Human Genetics, 64, 619‑628.

Stepanov, V.A., & Puzyrev, V.P. (2000). Evolution of Y‑chromosome haplotypes in populations of North Eurasia. American Journal of Human Genetics, 67, 220.

Wall JD, Lohmueller KE, and Plagnol V. (2009). Detecting ancient admixture and estimating demographic parameters in multiple human populations. Molecular Biology and Evolution (early online)

Watson, E., P. Forster, M. Richards, & H-J. Bandelt. (1997). Mitochondrial footprints of human expansions in Africa. American Journal of Human Genetics, 61, 691-704.

Zerjal, T., Dashnyam, B., Pandya, A., Kayser, M., Roewer, L., Santos, F.R., Scheifenhövel, W., Fretwell, N., Jobling, M.A., Harihara, S., Shimizu, K., Semjidmaa, D., Sajantila, A., Salo, P., Crawford, M.H., Ginter, E.K., Evgrafov, O.V., & Tyler‑Smith, C. (1997). Genetic relationships of Asians and Northern Europeans, revealed by Y‑chromosomal DNA analysis. American Journal of Human Genetics, 60, 1174‑1183.


RG said...

1) Can you briefly explain the "ancient admixture" thing. Is it the same thing as comparing with "ancient polymorphisms" that can be obtained by sequencing fossil DNA (neanderthal genome is on its way I believe),
or is it just by estimating the age of the polymorphism, derived from the mutation rate for this polymorphism ?

2) I've read the Dieneke's blog when he discuss the apparent presence of 800 000 years old markers in pygmee's genome. I am not shocked by the idea of early homo sapiens in Africa interbreeding somehow with late erectus or other archaic humans. After all, 200 000 years ago, early sapiens were just beginning to diverge from other archaic humans, and if we expect that they were in relatively small numbers, it might not have been a big deal for them. But 40 000 years ago in Europe ? that's 160 000 years after the first sapiens diverged from archaic human in Africa. So genetically, interbreeding must not have been so easy, even if H. Erectus genome was 99.98% identical to ours.
I would therefore expect more archaic marquers in african populations than in europeans.

Peter Frost said...


Wall et al. didn't look at the Neanderthal genome. They reasoned that a polymorphism is archaic if it meets three criteria: (1) its alleles show multiple differences; (2) it is near another polymorphism with alleles that likewise show multiple differences; and (3) the two polymorphisms show similar patterns of geographic variation.

The more I think about this methodology, the more it strikes me as being flawed. If the two adjacent polymorphisms are balanced polymorphisms, their alleles will very likely show (a) multiple differences and (b) similar patterns of geographic variation. Why wouldn't they?

I also suspect that Wall et al. did attempt an admixture estimate for the African sample, but then threw it out because it was far too high. If so, this is unfortunate because we could have estimated the proportion of 'false positives' by comparing their admixture estimate with the earlier one I mention in my post.

I agree with your second point. Archaic admixture should be higher in sub-Saharan Africans in part because the two groups were more similar there than in Europe and Asia and in part because they probably co-existed for a longer period of time.

Tod said...

The more I find out the more I think the ideas of Marcellin Boule, (artists impression), were more accurate than almost everything that followed.

"In part, where Neanderthals were placed on the human evolutionary tree was largely influenced by how their anatomy and behavior were viewed. Boule, for instance, who studied the Neanderthal remains from La Chapelle-aux-Saints (fig.3) and La Ferassie, described Neanderthals ... as... too apish to be ancestoral to modern humans. Boule sought to distance modern humans from what he saw as brutish beings, arguing forcefully that the Neanderthals had been annihilated by the more “elegant…inventive” Homo sapiens,"

How Neanderthals met a grisly fate: devoured by humans.

RG said...

Accurate portrait ?
who knows anymore. Not me.
20-15 years ago, Neanderthals were portrayed as beasts covered with fur, then they had a period of rehabilitation and until very recently, they were depicted as almost as advanced as modern sapiens, with clothes and language. But recently the picture started to deteriorate again, they were not able to speak after all, were canibalous, not able of symbolic thoughts and achieved only by copying the modern sapiens. They became again the stocky beasts possibly covered with fur that we knew.
Maybe one day we'll be lucky and find depictions or statues of them in a cave.

In this web site
The last picture from "illustrator Jay Matternes, from the October issue of Science 81" looks more european than the recently published "first modern european".
These first modern humans could have interbred with this guy, but not with the australopithecus-like guy depicted in your picture Tod.

Tod said...

The boosting of Neanderthals goes back to the 40's

"Neanderthals on Trial" (PBS 2002).

"[...]after WWII, the tide turned.

In the era of civil rights(?), a new generation of anthropologists rejected racial type casting as a way of understanding human variation, and some began to question whether Neanderthals were really all that different.

They were also wary of judging the capabilities of people based on their physical features.

Attention turned from Neanderthal anatomy to behavior [...]
Recast as Stone Age flower people, Neanderthals were welcomed back in the family as direct, European ancestors just a few evolutionary steps away from becoming modern humans.

MILFORD WOLPOFF: I will say that no matter how different human beings are, when human populations come into contact, they may trade, they may fight, they may ignore each other, or they may merge, but the one thing they always do is interbreed."

(MILFORD WOLPOFF trained John Hawkes I believe)

Peter Frost said...


I suspect that the Neanderthals looked very ape-like. I also suspect that relic groups persisted until modern times in high mountainous areas of central Asia. Throughout that area, the oral tradition often refers to large 'mountain apes' who were as big as humans. I don't think they were macaques.

Once the Neanderthal genome is reconstructed, we may have a better idea as to how they looked. Unfortunately, we don't know how most genes work.

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