Saturday, 4 February 2012

Encounters between modern humans and archaics in Africa


Broken Hill (Kabwe) skull. In Africa, very archaic hominins persisted into recent times.

Were archaic hominins still roaming over parts of Africa when farming villages began to form in the Middle East? I raised this question in my last post. But others are now raising it too:

The lesson is that Africa, a vast continent encompassing virtually all of our recent evolutionary ancestry, contains yet unknown degrees of diversity. At the same time that modern humans were emerging, they would have lived in landscapes alongside more archaic populations, possibly into very recent times. This implies also that at least some of the traces of archaic genetic markers still found in people today may have arisen as a result of intermixing of archaic and modern populations within Africa, rather than interbreeding of ‘pristine’ modern people with archaic populations only after leaving Africa. (Wells, 2012)


A new convert to this view is the paleontologist Chris Stringer, who only ten years ago was arguing that archaic hominins had long disappeared from Africa when modern humans began to spread into Europe and Asia. Today, the evidence cannot be easily ignored. There are too many skulls from western and southern Africa that look archaic and yet are surprisingly recent, like the Broken Hill cranium:

A relatively late date for the Broken Hill cranium suggests a long time span for the “rhodesiensis/heidelbergensis’’ group and warrants caution about inferring the presence of early modern humans from the presence of early Middle Stone Age artifacts (Stringer, 2011).


Other paleontologists, like Lily Malekfar, are similarly taking a second look at African cranial and skeletal remains that had previously been thought to be modern human:

Current research indicates that modern Homo sapiens originated in East Africa and then migrated across Africa as well as out of Africa, where they encountered archaic hominins. The Klasies River Main site (KRM) in South Africa is one location where there is evidence that modern and archaic Homo sapiens may have interacted. As Smith and other researchers have suggested, the KRM mandibular sample, in particular, exhibits significant size and morphological variability, which counters claims that the KRM specimens are fully modern.

[…] The results demonstrate that the KRM sample is markedly more variable than any of the comparative samples, which rejects the null hypothesis and is one possible indicator of an admixed sample at KRM.
(Malekfar, 2012)


So just what is the story about modern humans and archaic hominins in Africa? Since DNA rapidly degrades in tropical climates, we will probably never retrieve DNA from those archaic skulls. But there is archaic DNA in living Africans, as Hammer et al (2011) discovered, so we may be able to piece together parts of the archaic African genome. Modern DNA can also tell us about ancient population movements within Africa, including the “big bang” that gave rise to modern humans some 60,000 years ago:

African mtDNA has three main lineages — L1, L2 and L3 — which have an estimated coalescence date of 126,000–165,000 yr BP. The L1 lineage is the most ancient and is present in the San population from South Africa and the Biaka Pygmies from the Central African Republic, which are two of the most genetically divergent populations in Africa18. L2 and L3 diverged from L1 ~60,000–103,000 yr BP. The L2 lineage is present in Mbuti Pygmies from the Democratic Republic of the Congo and in west African Bantu-speaking populations. The L3 lineage is widely dispersed throughout east Africa but is rare elsewhere in sub-Saharan Africa. Phylogenetic analysis indicates that the L3 haplogroup is the precursor of non-African mtDNA haplotypes and that a subset of this lineage (L3a) travelled out of Africa in the ancestors of modern Eurasians ~60,000–80,000 yr BP. The L3a lineage also occurs at a high frequency in Ethiopian mtDNA40, which supports the proposal that modern humans migrated out of Africa through Ethiopia. (Tishkoff & Williams, 2002)


Watson et al. (1997) elaborate further on this “big bang”:

It seems reasonable to speculate that a behavioral innovation appeared some 60,000-80,000 years ago in a subpopulation of anatomically modern humans, containing the ancestors of L3 (and possibly also L2), who had previously been living with a Middle Paleolithic/Middle Stone Age technology—and that this small subpopulation subsequently expanded as a result.


There seems to have been a series of expansions, beginning around 80,000 years ago. The last expansion, dated to c. 60,000 BP and associated with subcluster L3a, was the one that spread modern humans out of Africa and to the rest of the world (Watson et al., 1997).

In summary, the evolutionary sequence can be described as follows:

1. Half a million years ago, all of Africa was inhabited by an archaic population similar to the Neanderthals in Europe and the Denisovans in Asia

2. Over time, these African hominins differentiated into two populations: (a) an evolutionarily conservative one in western and southern Africa; and (b) a more evolving one in eastern Africa.

3. Around 120,000 years ago, the eastern hominins expanded north into the Levant (Skhul-Qafzeh). They were now almost like modern humans. Their material culture was like that of the Neanderthals but their anatomy was almost modern, albeit with some archaic features.

4. Beginning around 80,000 years ago, a sub-population of the eastern hominins underwent a series of expansions. Then, around 60,000 years ago, a final "big bang" eclipsed the preceding ones and gave rise to true modern humans.

5. Within Africa, these modern humans initially expanded into territory inhabited by “almost moderns,” i.e., people more or less modern in appearance while still largely archaic in behavior and material culture, like the Skhul-Qafzeh hominins of the Levant. Archaic admixture thus entered the gene pool of modern sub-Saharan Africans and today represents about 13% of the total.

6. As modern humans pushed farther into western and southern Africa, they encountered much more archaic hominins, almost like Homo erectus. There was less admixture from those archaics, only 2% of the total.

References

Hammer, M.F., A.E. Woerner, F.L. Mendez, J.C. Watkins, and J.D. Wall. (2011). Genetic evidence for archaic admixture in Africa, Proceedings of the National Academy of Science (USA), 108, 15123-15128.

Labuda, D., E. Zietkiewicz, & V. Yotova. (2000). Archaic lineages in the history of modern humans, Genetics, 156, 799–808.

Malekfar, L. (2012).
An analysis of the Klasies River hominins using a hybrid model, American Journal of Physical Anthropology, Program of the 81st Annual Meeting of the American Association of Physical Anthropologists, p. 201.
http://physanth.org/annual-meeting/2012

Stringer, C. (2011). The chronological and evolutionary position of the Broken Hill cranium. American Journal of Physical Anthropology, 144(supp. 52), 287

Tishkoff, S.A., & S.M. Williams. (2002). Genetic analysis of African populations: human evolution and complex disease, Nature Reviews – Genetics, 3, 611-621.

Watson, E., P. Forster, M. Richards, and H-J. Bandelt. (1997). Mitochondrial footprints of human expansions in Africa, American Journal of Human Genetics, 61, 691-704. 0024024
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024024

Wells, S. (2012).
What made us human? Simon Wells reviews Chris Stringer’s ‘The origin of our species’, Red Mist, January 4
http://redmistreviews.com/?p=848

22 comments:

ogunsiron said...

I have been dreading (because I'm black myself) for a few years that something like this was bound to come out.

I've seen,observed people here and there among african and african derived populations whose facial structure just screamed archaic.

Their cranial volume notwithstanding, they looked like they had just stepped out of a documentary on homo erectus, homo habilis and the like (though it seems that the upper range of cranial volume for homo erectus overlapped with the lower range for modern humans).I had a hard time imagining natural selection sculpting such faces. What for ? I figured that maybe it was because of selection for brute masculinity that such primitive looking facial traits had ridden along. Admixture was pretty much ruled out until a few years ago so it wasn't even considered. Times have changed and it seems that there was admixture after all.

I'm at once very curious and afraid of what else is coming.

I'm curious to see if there is great variance in the archaic contribution to the genome of various populations of black africans. Who has more of it ? Who has little of it ?

PS : when I speak of primitive looking faces, unlike the author of Erectus Among Us, I'm not talking about the faces of the average black person.Those people I'm thinking of were rare but very striking looking.

Anonymous said...

Ogunsiron,

Can you find any pictures online of the type of "look" you are describing?

Peter,

Does it mean anything substantive that Africans may have 15% archaic admixture? I think I remember you saying before that the admixture events happened so far back that it's not possible to draw any inferences.

Sean said...

The estimates of archiac admixture in the gene pool are for the present day. Presuming that the archaic admixture was selected against is there an upper limit for the level that archaic admixture could have been at in the modern human gene pool ?

Anonymous said...

PS : when I speak of primitive looking faces, unlike the author of Erectus Among Us, I'm not talking about the faces of the average black person.Those people I'm thinking of were rare but very striking looking.

Do you mean someone like Patrick Ewing?

Anonymous said...

Their cranial volume notwithstanding

If you've ever been around large crowds of black people, their small heads are quite noticeable. The fact that they tend to have shaved heads exaggerates the effect. It's especially noticeable when there are whites and Asians around in the crowd as well. Asians tend to have large, bulbous, pumpkin heads and small, slight bodies so the contrast can be quite striking when you observe these crowds.

Anonymous said...

the author of Erectus Among Us

You're referring to the book Erectus Walks Amongst Us: The Evolution of Modern Humans by Richard D. Fuerle, available for free in its entirety here:

http://erectuswalksamongst.us/

Doesn't a lot of the recent science covered on blogs like this and elsewhere suggest that the books claims may not be as controversial as previously believed?

Insightful said...

I get the feeling that 'ogunsiron' (the first poster) may not be black at all but someone pretending

Difference Maker said...

I have seen Chinese looking like live, walking H. heidelbergensis reconstructions, complete with tiny forehead.

After seeing such a one, traces of common ancestry could be detected occasionally in certain other Chinese.

It was most disturbing, frankly.

Anonymous said...

I have seen Chinese looking like live, walking H. heidelbergensis reconstructions, complete with tiny forehead.

After seeing such a one, traces of common ancestry could be detected occasionally in certain other Chinese.

It was most disturbing, frankly.


Those are probably traces of Homo erectus pekinensis aka "Peking Man" who was discovered in Beijing. Heidelbergensis was found in Europe. The Chinese believe that Peking Man was an ancestor of the Chinese and I think multiregional theory supports that.

Peter Frost said...

Ogunsiron,

There seems to be more archaic admixture in western and southern Africa than in eastern Africa. According to Hammer et al., the highest levels of admixture are found in Pygmy and Khoisan populations.

Anon,

That's the big question. What does it mean? Or does it mean anything?

In theory, if the environment of natural selection remains unchanged, archaic admixture wouldn't really alter anything over the long term. Maladaptive alleles would be weeded out and replaced by adaptive ones. Over time, the admixture would only show up in "junk genes" of little or no selective value.

In fact, archaic admixture might be an asset. It could provide new alleles that are actually more adaptive. Evolution would thus speed up. This is the "cherry picking" theory of archaic admixture currently promoted by John Hawkes, Greg Cochran, and others.

But, on second thought, why would the environment of natural selection remain unchanged? This environment isn't just the physical environment (climate, vegetation, habitat, food sources). It's also the social, cultural, and behavioral environment. Wouldn't that component of the environment be altered by archaic admixture?

In other words, archaic admixture could have altered the way ancestral humans behaved, thereby creating a new behavioral environment, a new set of selection pressures, and a different evolutionary trajectory.

To be honest, the more I think about this question, the less clear it all seems to me. I'd appreciate hearing the thoughts of any readers out there.

Sean,

The estimates of archaic admixture come from genes that are of little or no selective value. The picture is probably different if we look at genes that are more vulnerable to natural selection.

Ben10 said...

' ...This environment isn't just the physical environment (climate, vegetation, habitat, food sources). It's also the social, cultural, and behavioral environment. Wouldn't that component of the environment be altered by archaic admixture?...'

I am sure it was. To answer that we would need to know the entire 'history' of each 3 billions basepairs of human genome, down to each of its ancestor's bearer. Weird things might have happen during the history of hominid's genetic. We will have to live long to know the answer. From my genetic classes I remember this story about a retrovirus transmitted to drosophila, making the female bearer unfertile with non-bearer males, but still able to reproduce with infected males.
Certainly the first hominid hybrids (always starting at 50%) were getting a load of things like retrotransposons and the like. These might have drifted, at least for while, the hominid population description out of a classical mendelien framework.
Chromosome segregation during meiosis is also a big question for hybrids. Persistance of archaic DNA might have occured because the archaic chromosomes were 'positively discriminated' during the meiosis.
Many other weirdnesses exists. PKD1, the gene responsible for autosomal dominant polycystic kidney disease, is present on the tip of chromosome 16. The PKD1 gene has been replicated several times, but only 'recently', during evolution. The pkd1 'pseudogenes' are presents only in big apes and human. Still, one would expect the replicated genes, if they are harmfull, to be eliminated, or at least silenced, after a dozen million years but that's not the case. Why?
Also, you were yourself mentioning that some commensal vaginal yeasts could possibly modify woman's behavior to their benefit. Who could have guessed that? That's a mother to daughter transmission that shows we are not just transmitting genes. And not forgeting the no-less weirdo case of the tasmanian wolves, who are so inbred they can transmit skin cancer to each other by simple contact without a rejection reaction, to the point they are now endangered. Again, who could have guessed that? Early hominids, hybrids or not, were certainly very inbred. Maybe they needed some hybridization to escape the decay of one of their doomed chromosome (for example, the human Y is predicted to decay in a few thousands years).

Last, I have seen the last 'planet of the apes' and not only it kind of convinces you that these apes were once more humans that they are now. They 'decided' to stop hominization and go back to the trees. But if that's the case, they might also have been able to introgress some DNA into erectus or australopithecus, and therefore to us. So, maybe we should look there too.

ogunsiron said...

Re: pictures
I haven't come recently come across any pictures of the type of people I have a mind, sorry.

Re : Patrick Ewing.
I find him pretty brutal but the folks I'm thinking off were weirder looking than that.

Re: Erectus walks among us :
The author was right in leaving admixture on the table all this time but I think that he pushes the idea too far. Ridiculously far. Doesn't he state that the andamanese descent directly from australopitecines or something like that? I may have read wrong.

Anonymous said...

Peter Frost wrote: "In fact, archaic admixture might be an asset."

Coloured pop. 4 539 790 http://en.wikipedia.org/wiki/Coloured

Anonymous said...

Ogunsiron, you do realize australian aborigines have the highest frequency of archaic features out of all modern humans (moreso than africans), yet under these models have less archaic ancestry than africans? (the same as other australo-melanesians, whom differ markedly in physical appearance overall.)

Sean said...

'4.'in the evolutionary sequence The eastern hominins evolved into modern humans. That was the biggest step of all and it happened by selection from the eastern hominins' own gene pool. The challenging unstable conditions in East Africa must have been the most important factor in bringing the eastern hominins' own, but previously unused, genetic variants into expression (Evolutionary capacitance) and selecting for modern humans' cooperative social and cultural transmission of useful information. It is difficult to believe that the part archaic would be able to keep up in a modern human social environment. On the other hand if they were very rare the grunting uncooperative part-archaic humans could be the rare hawk who does well among the doves, and the bigger brain alleles eventually went to fixation while the other retro alleles disappeared.

The modern humans who went north out of Africa got bigger brains. "They got the big brains from archaics they met up there'. Very well then; where did those archiacs acquire the alleles for their own big brains from? Presumably they evolved them under the selection pressure of environmental stress in the same way the African hominins evolved into humans in East Africa. The modern humans who went south, along the Indian Ocean, certainly didn't get big brains by introgression from the archaics they met along the way. Maybe their brains were wastefully big and they adaptively acquired smaller brains from the small brained southern archiacs.

Anonymous said...

Peter Frost wrote: "In fact, archaic admixture might be an asset."

For whom?

Anonymous said...

For whom?

See Patrick Ewing.

Sean said...

The earliest fully modern humans got a heavy deleterious load of archaic admixture because they had not evolved a suspicion of strange groups or individuals?

Eventually a specifically modern human form of group selection (requiring intolerance of outsiders migrating into a group) evolved in Africa in response to lethal competition between bands. The archaic admixture was weeded out in those conflicts between groups. As Samuel Bowles says humans became fully modern in cooperation and altuism though warfare. The group-selected-through-warfare modern humans in Africa who came into contact with archaics exterminated them I think.

Grey said...

I don't have enough knowledge to comment but...

High levels of archaic admixture makes me imagine a collection of sub-species existing concurrently (in their own environmental niche?) with none adaptable enough to displace the others from their niche - so less a progression of hominids from lower to higher functioning than a collection of more or less equally adapted branches.

(If the archaics were adapted to a particular niche then the archaic admixture might be the useful bits like high altitude adaptations?)

Then one of the branchs became more adaptable - either through some special spark or perhaps simply because their geographical location had a migration route to an empty and different environment which forced them to adapt to fill - and that newfound adaptability allowed them to backflow and displace the what then become archaic others.

The obvious prime candidate for a geographical migration explanation would be Ethiopia in east Africa close to Arabia.

So it's the out of Africa event itself that creates a more adaptable hominid.

Anonymous said...

There are various species of snub-nosed monkeys in southern China and northern SE Asia. Snub-nosed monkeys sort of resemble Asians. Is it possible that Asians evolved from them or are related to them?

Japanese macaques sort of resemble Europeans but Japan is so far from Europe.

Rev. Right said...

Current research indicates that modern Homo sapiens originated in East Africa and then migrated across Africa as well as out of Africa, where they encountered archaic hominins.

So, what current human population is the most 'pure' modern human? Ethiopians?

Anonymous said...

Ethiopians?


The genetic affinities of Ethiopians
http://blogs.discovermagazine.com/gnxp/2011/01/the-genetic-affinities-of-ethiopians/