Out of Africa: mend it, don't end it!

By Razib Khan | December 27, 2010 11:51 pm

Dilettante human genetics blogger Dienekes Pontikos has a post up with a somewhat oblique title, Is multi-regional evolution dead? I say oblique because a straightforward title would be “Multi-regionalism lives!” He posted a chart from a 2008 paper which outlines various models of human origins, and their relationship to molecular data at the time. I have also posted the chart, but with a little creative editing on the “assimilation” scenario to reflect the possible Neandertal and Denisovan admixture events. Of these models the “candelabra” can be rejected as highly implausible. It posits very deep roots in a given region for distinct human populations. Unless you accept some sort of hominin population structure in Africa which were maintained by distinctive migrations out of Africa then the “replacement” model can be discarded (since the classic replacement model did not posit ancient African population structure being of any relevance outside of Africa you’d have to salvage it with a modification in light of new results).

So the two primary disputants are a resurrected multi-regional model, and the assimilation model. But these two are really endpoints on a spectrum of models. What you need to do is vary the number of discrete populations and the rate of migration between the populations over time. The beauty of the replacement model was its parsimony: as far as recent human origins were concerned past gene flow via migration was a relatively academic concern. It was an exceedingly simple narrative framework. Consider this first episode of a 2009 British documentary, The Incredible Human Journey:

In the first episode, Roberts introduces the notion that genetic analysis suggests that all modern humans are descended from Africans. She visits the site of the Omo remains in Ethiopia, which are the earliest known anatomically modern humans, and visits the San people of Namibia to demonstrate the hunter-gatherer lifestyle. In South Africa, she visits Pinnacle Point, to see the cave in which very early humans lived. She then explains that genetics suggests that all non-Africans may descend from a single, small group of Africans who left the continent tens of thousands of years ago. She explores various theories as to the route they took. She describes the Jebel Qafzeh remains in Israel as a likely dead end of a traverse across Suez, and sees a route across the Red Sea and the around the Arabian coast as the likelier route for modern human ancestors, especially given the lower sea levels in the past.

A neat and tidy story. But reality is getting a lot less tidy & neat. Personally, the assimilation model as we understand it now seems to be the most plausible model. It remains more parsimonious than the alternatives: ancient population structure and complex patterns of gene flow and hybridization. But parsimony has misled us toward undo confidence in the recent past, so we should not weight this as strongly at this point. Where would we be without ancient DNA extraction? Some researchers have long claimed a more complex model than Out of Africa, but as long we relied in inferences from extant populations theses result were ignored or dismissed (notably, ancient DNA extraction is also unsettling our understanding of the very recent human past).

There is though the pattern of greater African genetic diversity. Dienekes observes that a recent paper reports that some Indian populations may be more diverse genetically than HapMap Africans. I’m not too keen on overturning a generation of consensus yet in regards to this question based on one deeply sequenced region on one chromosome comparing some Indian tribal groups to two HapMap African populations (Yoruba, and a Kenyan Bantu group). So I accept the pattern of greater diversity until further research brings it more into doubt. Now the question is to explain the pattern. The most plausible explanation would naturally be the one outlined above in the 2009 documentary: non-Africans are the descendants by and large of a small number of Africans who left ~100,000 years B.P. They went through a population bottleneck which reduced genetic diversity sharply. Their genetic variance was a subset of that of Africans (with some admixture from other human lineages outside of Africa, as it now happens).

But, there are other possibilities. One option sounds rather bizarre to me on first blush:

With respect to the reduced genetic diversity, one idea is that it is the result of genetic drift following a bottleneck in a small African population. But, the data can just as well be explained by species-wide selection which culled genetic variation.

Presumably selection would operate outside of Africa and homogenize non-Africans through a series of sweeps. Remember that selection and stochastic population events can sometimes be hard to differentiate, because both expunge variation from long swaths of the genome, resulting in long linkage disequilibrium blocks. This seems rather incredible as a proposition to me. Could selection operate all across Eurasia in such a fashion? From what I can tell in relation to more recent signatures of natural selection that does not tend to occur. The pattern for skin color for example is convergent phenotypes through different genetic architectures. How could gene flow tie together ancient human lineages and not H. sapiens sapiens? On the other hand, this could be an explanation for the consistent and taxon wide pattern of encephalization (though I believe this occurred in Africa as well).

A second alternative would be that Africa’s greater genetic diversity is simply a function of a much longer term effective population. In this model the climatic fluctuations of the Pleistocene periodically reduced non-African population to such an extent that these groups became a very minor proportion of the total census size of humans, and were so were swamped out by gene flow with the more numerous African humans. It seems to me that an extreme case of this model really verges into the same territory as the assimilation model. So I see this as more of a difference of degree than kind.

Dienekes points to Y chromosomal markers which suggest “back-migration” to Africa. I don’t totally discount this, but looking at the enormous diversity in groups like the Bushmen, I don’t think we can attribute that to back-migration from Eurasia. It is notable that the Bushmen are basal to the rest of humanity, including the Yoruba + (Eurasicans + Australasians). Also, the genetic divergence between the Denisovan/Neandertal clade and modern humans is only ~33% greater than between Bushmen and Papuans. Speaking of differences of degree, that is becoming more and more the case when it comes to the so-called “dead ends” of human evolution and ourselves.

Finally, there’s the issue of non-neo-African admixture. Reich et al. give a figure of ~7.5% in Melanesians, and ~2.5% in Eurasicans. It is valid I think to point out that though others have offered figures in the literature before only with the reference sequences of ancient DNA are these widely accepted values. Perhaps they would be revised upward with other sequences. But two cautions:

- There are only so many hominins to go around. Australia and the New World were only settled by modern humans. So how many were there running around in Eurasia? I think perhaps there may have been something different in South Asia, but that’s just a very uninformed guess.

- On the margin it seems clear that the autosomal DNA has enough fudge that interpretation meant that the archaic admixture signal could be dismissed. But the upper bound can’t be that high, or the Fst values would be more extreme than they currently are. Modern humans do seem to share a great deal of “shallow” common ancestry.

At the end of the day I am going to put my money on the assimilationist model because I believe in diminishing marginal returns. The Out of Africa replacement model was maximalist. Some tweaking on the margin is not very surprising, at least in hindsight, but more baroque forms of multi-regionalism have far too many moving parts. Newtonian mechanics may have been superseded in some domains by Einstein’s theories and Quantum Mechanics, but for many purposes it does very well at predicting phenomena and modeling the world. I have full expectation of further refinements in the assimilation model, but I would bet that the age of revolutions is over for a long time. Then again, my confidence is modest at best. This is no time for certitudes.

Note: A illustration of models:

CATEGORIZED UNDER: Culture, Genetics, Genomics, Uncategorized
  • bioIgnoramus

    Not a time for certitudes, perhaps, but certainly a time for writing kinder, warmer material about our dear kin.
    http://www.dailymail.co.uk/sciencetech/article-1341983/How-Neanderthal-cuisine-far-sophisticated-thought.html

  • bob sykes

    What is the difference between Eurasians and Eurasicans? Does the latter include Amerindians?

  • http://www.kinshipstudies.org German Dziebel

    “Dienekes observes that a recent paper reports that some Indian populations may be more diverse genetically than HapMap Africans. I’m not too keen on overturning a generation of consensus yet in regards to this question based on one deeply sequenced region on one chromosome comparing some Indian tribal groups to two HapMap African populations (Yoruba, and a Kenyan Bantu group). So I accept the pattern of greater diversity until further research brings it more into doubt.”

    Razib, this “consensus” has always been driven by academic politics to some extent. The paper that Dienekes references didn’t mention the 1991 Ward et al. paper (followed by a couple of other ones) that showed that a single Amerindian tribe sported nucleotide diversity tantamount to some 60% of diversity found in urban Tokyo. It exceeded the diversity found in African hunter-gatherers (!Kung in the sample) despite the Amerindian tribe having a lower demographic population size. Tribal diversities are lower than African continental ones (or urban ones) but the continental and urban values are inflated by agricultural/pastoral and industrial admixture, hence they should be weeded out from the comparisons attempting to cast light on Pleistocene state of affairs.

    See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC52581/

    Rick Ward, James Neel and other scholars always emphasized, in contradistinction with the out-of-African theorists, that tribal genetics in the Americas aren’t compatible with the bottleneck hypothesis. See http://onlinelibrary.wiley.com/doi/10.1002/ajpa.1330860405/abstract.

    This hasn’t changed since the early 1990s (see Fig, 4 in http://rspb.royalsocietypublishing.org/content/early/2009/10/05/rspb.2009.1473.full).

    There’s a difference between an academic consensus and “packaged academic goods.” There’s a whole host of studies and data that contradict the out-of-Africa model. They just haven’t been packaged into a media-worthy theory. I did it with the “out-of-America” theory. The out-of-Africa model is based on a highly selective set of studies and facts but they are well packaged into a media-worthy story. The Xin et al. paper is just not part of the out-of-Africa brand of studies.

  • http://washparkprophet.blogspot.com ohwilleke

    I come to the same conclusion as Razib, but the question “Could selection operate all across Eurasia in such a fashion? ” does have some plausible answers.

    The most plausible one, it seems to me, is that the Neolithic led to deadly illnesses that wiped out pre-existing diversity of non-food producers. Post-Columbian America and post-European Australia was headed on the path, and had Europeans been bent on bringing out the extinction of Native Americans and Aborginines respectively, they certainly could have done so. Perhaps early Neolithics did not pull back as the Europeans did once their dominance in population was unquestionable.

  • http://www.kinshipstudies.org German Dziebel

    “But, the data can just as well be explained by species-wide selection which culled genetic variation.”

    This is exactly where linguistics comes in handy. Languages are not subject to natural selection, hence if selection operated on the human genome, languages would show a radically different pattern of differentiation from genes. This is exactly what we see in the distribution of the levels of linguistic diversity. Africa and Europe are low in linguistic diversity, while the New World, parts of Asia and Melanesia are very diverse linguistically. This indicates that natural selection has pruned genetic diversity in Asia, Melanesia and the Americas, while it didn’t affect Africa. Or, as human populations expanded, they experienced a relaxation of selective constraints. Africa reaped all the benefits of this increasing heterozygosity as populations moved from “eastern” regions into Europe and Africa.

  • http://3lbmonkeybrain.blogspot.com/ Mike Keesey

    “On the other hand, this could be an explanation for the consistent and taxon wide pattern of encephalization”

    Isn’t encephalization a general primate trend, though? E.g., chimpanzees are brainier than Ardipithecus ramidus, Australopithecus boisei is brainier than Australopithecus africanus, etc.

  • dan

    also, how confident are you about the “400,000 year old tooth” found recently? proceed with great caution?

  • http://www.kinshipstudies.org German Dziebel

    “Dienekes points to Y chromosomal markers which suggest “back-migration” to Africa. I don’t totally discount this, but looking at the enormous diversity in groups like the Bushmen, I don’t think we can attribute that to back-migration from Eurasia.”

    Dienekes is talking about hg E, which is very widely spread in Africa and accounts for the majority of African Y chromosomes but it is not the hg A and B found in Bushmen and Pygmies at high frequencies. A back migration is still perfectly fine. hg E is characterized by the unique YAP+ marker (YAP- is the ancestral state), which is not found on such older lineages as Sub-Saharan A and B and extra-African F and C. The big question is why the sharing of YAP- between A, B, C and F didn’t lead to the primary phylogenetic split between A and B vs. C and F in the existing phylogenies?

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    german, i’ll check your cites in the new year when i have more time. i appreciate you linking to them.

  • Andrew Lancaster

    The big question is why the sharing of YAP- between A, B, C and F didn’t lead to the primary phylogenetic split between A and B vs. C and F in the existing phylogenies?

    Maybe I am not understanding the point but I do not see why this is a big question. The YAP mutation happened along the branch coming to modern D and E haplogroups. C and F share other mutations which D and E do not have. And indeed A and B are not really literally “old” clades, but modern clades deep rooting clades which also have their own unique mutations.

  • http://www.kinshipstudies.org German Dziebel

    @Razib

    “german, i’ll check your cites in the new year when i have more time. i appreciate you linking to them.”

    I’ll e-mail you another paper by Neel published in Brazil in Portuguese: Estrutura populacional de amerindios e algumas interpretacoes sobre evolucao humana. You can’t download it. It’s the first critique of out-of-Africa from the point of view of tribal microdifferentiation. Just in case you care to whip your Latin back into shape.

    @Andrew Lancaster

    A, B, C and F share YAP-. D and E are YAP+. A, B, C, and F should share a node in the phylogeny followed by the DE node, no? Whatever mutations E shares with A and B must be homoplastic.

  • http://www.kinshipstudies.org German Dziebel

    @Andrew Lancaster

    Sorry for a disjointed response. What I’m trying to say is that AB and CF are equally deep rooting but possessing their own slew of mutations. A and B are African-specific, C and F are not found in Africa. D and E form a “swing” clade shared between Africa (and Europe) and Asia. (Notably, it’s not found in the Americas meaning that the New World was peopled much earlier than we think.) DE seems to be closer to the CF pole than to the AB pole, hence hg E is likely to represent a back-migration into Africa (some 45-40K YBP). This leaves us with AB in Sub-Saharan Africa and C(pre-DE)F in Asia immediately prior to the back migration, with no out of Africa “trail” whatsoever. If hg E back-migrated into Africa, and this accounts for the majority of extant African lineages, then it’s possible that the YAP- chromosomes in Africa also back-migrated into Africa. As I pointed out on Dienekes (http://dienekes.blogspot.com/2010/12/is-multi-regional-evolution-dead.html), chimp and human Y chromosomes are too divergent to justify using matches between A and chimp sequences as a solid indication of common descent and not homoplasy.

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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