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Nearly 100% Out-of-Africa in the past 100,000 years

Gene Expression
By Razib Khan
Apr 23, 2010 10:58 AMNov 19, 2019 8:34 PM


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Since I've been talking about the possibility of admixture with "archaics" (I'm starting to think the term is a bit too H. sapiens sapiens-centric, is the Neandertal genome turning out to have more ancestral alleles?) I thought I'd point to a paper out in PLoS ONE which reiterates the basic fact that the overwhelming genetic evidence today suggests a massive demographic expansion from an African population within the last 100,000 years. Study after study has supported this contention since the mid-1980s. The question is whether this is the exclusive component of modern human genetic ancestry, which is a somewhat more extreme scenario. In any case, the paper is Formulating a Historical and Demographic Model of Recent Human Evolution Based on Resequencing Data from Noncoding Regions:

Our results support a model in which modern humans left Africa through a single major dispersal event occurring ~60,000 years ago, corresponding to a drastic reduction of ~5 times the effective population size of the ancestral African population of ~13,800 individuals. Subsequently, the ancestors of modern Europeans and East Asians diverged much later, ~22,500 years ago, from the population of ancestral migrants. This late diversification of Eurasians after the African exodus points to the occurrence of a long maturation phase in which the ancestral Eurasian population was not yet diversified.

They took 213 individuals, a little over half from diverse African groups, and the other half split evenly between Europeans and East Asians, and sequenced 20 distinct noncoding autosomal regions of the genome. ~27 kilobases per person. The noncoding part is important because they are trying to look at neutral regions of the genome, not subject to natural selection (this is obviously an approximation, as there is some evidence that even noncoding regions may have some selective value). The variation is what you'd expect, Africans more varied than non-Africans, and the two Eurasian populations are distinct from each other, but less so than either is from the Africans. Lots of statistics ensue, and an "Approximate Bayesian Computation (ABC) analysis." I'll cut to the chase, the highest probability model is illustrated in panel A of figure 4. Expansion out of Africa ~60,000 years ago, major bottleneck, a ~40,000 year interregnum where there was a relatively unified Eurasian population genetically, and then a separation between East and West Eurasians ~20,000 years ago.

I'll stipulate that I haven't dug deep into the statistics, nor would I really comprehend all the details if I did spend a weekend on it. But I'm rather skeptical of the 40,000 year period of a common Eurasian population. Reading the text where they discuss this finding it seems clear that it was surprising to the authors, and I'm not sure how convinced they are about it either. It is interesting that the second most probable scenario, B, is a simultaneous expansion out of Africa by two different groups which lead to East and West Eurasians. That makes me a little less confident about the details on Eurasian demographic history overall than I'd already been. They do note that some Y chromosomal data imply that all Eurasian populations may have derived from a Central Asian group, and the settlement of Europe ~35,000 years ago may actually indicate population replacement (though it's pretty clear that many Central Asian groups have been recently heavily admixed with the incursion of Turks from Mongolia in historical time overlain upon a Iranian substrate, and some sequencing of ancient Cro-Magnon mtDNA shows that their haplgroup is still found in many Eurasian, and even New World, populations). Perhaps there is a more complicated story to be told about the replacement of early modern H. sapiens sapiens by later H. sapiens sapiens. I wouldn't discount it, but one analysis does not push me to consider this at all likely. Additionally, they obviously couldn't test the "two wave" model Out-of-Africa whereby there was a southern migration which skirted the Indian ocean along with a north wave which pushed into Central Asia; they didn't have any "southern" Eurasian samples. Also, I do want to make a note of the fact that they had a lot more parameters in their model than I'm mentioning, including migration between the two Eurasian groups. But let's jump to the conclusion and highlight a portion which is relevant to what I've been discussing on this weblog over the past few days. As I observe above they constructed scenarios with different parameters to see which fit the data best, and one of those parameters was interbreeding with older hominin groups in Eurasia. Here's what they say in the discussion:

For those historical and demographic parameters that have been previously studied, our co-estimations are in agreement with previous reports, highlighting the general accuracy of our estimates. For example, our estimation of the replacement rate of archaic hominids by modern humans, although indicating that the introgression of archaic material into the gene pool of modern humans has been minimal, did not rule out the presence of minor archaic admixture of other hominids in modern humans in agreement with previous observations...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.

Their models don't offer any plausible scenarios where more than 1% of the sequence which they analyzed was derived from populations which were not from the recent Out-of-Africa movement. But, they do specifically say that they lose power to ascertain whether there was admixture at levels below 1%. At some point in the medium term future when we have a fair amount of ancient DNA from Neandertals sequenced, as well as a lot of genomes of modern human beings, if we still don't find any evidence for alleles which have introgressed from other lineages which had long been separated, the time for hedging may be over. But at this point there's still some wiggle room. What I'm wondering though is how the University of New Mexico group found lots of evidence of introgressed lineages when other groups have not. Granted, they had 10 times as many individuals and more diverse populations, but presumably far less of the genome. If there was admixture which we could detect, in light of the nearly two decades of this sort of stuff, I assumed it would be cases of adaptive introgression. Here a very low level of admixture could still lead to the increase in frequency of a haplotype which bears the hallmarks of having been in a distinct population from H. sapiens sapiens for long periods of time (like haplogroup D for the microcephalin gene). In other words, I assumed that evidence of introgression would be a story of genetics & natural selection and not genomics & admixture. For instance, particular metabolism genes and the like which new Africa populations might have picked up just like they'd eventually develop their own adaptations from mutation or extant variation if they didn't admix. I guess 614 microsatellites may not count as genomics, but if adaptive introgression on a few select genes was how we'd detect interbreeding between native Eurasian groups and the Africans this not a way I'd assume you could find any evidence of that. Citation:

Laval G, Patin E, Barreiro LB, Quintana-Murci (201). Formulating a Historical and Demographic Model of Recent Human Evolution Based on Resequencing Data from Noncoding Regions PLoS One : 10.1371/journal.pone.0010284

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